Starting phenix.real_space_refine
on Tue Mar  3 21:51:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vjz_21221/03_2026/6vjz_21221.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vjz_21221/03_2026/6vjz_21221.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2026/6vjz_21221.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2026/6vjz_21221.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2026/6vjz_21221.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vjz_21221/03_2026/6vjz_21221.cif"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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      43      5.16       5
     C    5875      2.51       5
     N    1477      2.21       5
     O    1601      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8996
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1355
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 1355
          Classifications: {'peptide': 165}
          Link IDs: {'PTRANS': 5, 'TRANS': 159}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 280, 2343
          Classifications: {'peptide': 280}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 275}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 4923
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 4923
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 20, 'TRANS': 582}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 375
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 375
          Classifications: {'peptide': 45}
          Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 40}
  Time building chain proxies: 1.89, per 1000 atoms: 0.21
  Number of scatterers: 8996
  At special positions: 0
  Unit cell: (103.95, 101.25, 151.2, 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      43     16.00
     O    1601      8.00
     N    1477      7.00
     C    5875      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 0.69
  Conformation dependent library (CDL) restraints added in 328.4 milliseconds
  

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 0 sheets defined
      81.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'C' and resid 13 through 32
    Processing helix  chain 'C' and resid 36 through 41
      removed outlier: 3.969A  pdb=" N   VAL C  40 " --> pdb=" O   ASP C  36 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   VAL C  41 " --> pdb=" O   PRO C  37 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 36 through 41'
    Processing helix  chain 'C' and resid 43 through 51
    Processing helix  chain 'C' and resid 52 through 62
      removed outlier: 3.752A  pdb=" N   LEU C  56 " --> pdb=" O   GLN C  52 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 86
    Processing helix  chain 'C' and resid 90 through 113
    Processing helix  chain 'C' and resid 117 through 134
      removed outlier: 3.692A  pdb=" N   LEU C 121 " --> pdb=" O   SER C 117 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 151 through 166
      removed outlier: 4.099A  pdb=" N   ILE C 155 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 170 through 192
      Proline residue:  C 178  - end of helix
    Processing helix  chain 'B' and resid 3 through 31
    Processing helix  chain 'B' and resid 34 through 43
    Processing helix  chain 'B' and resid 44 through 72
    Processing helix  chain 'B' and resid 75 through 98
      Proline residue:  B  87  - end of helix
    Processing helix  chain 'B' and resid 99 through 100
      No H-bonds generated for 'chain 'B' and resid 99 through 100'
    Processing helix  chain 'B' and resid 101 through 104
    Processing helix  chain 'B' and resid 105 through 135
    Processing helix  chain 'B' and resid 143 through 175
    Processing helix  chain 'B' and resid 179 through 220
      removed outlier: 3.888A  pdb=" N   THR B 183 " --> pdb=" O   ASP B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 294
      removed outlier: 3.652A  pdb=" N   TYR B 270 " --> pdb=" O   GLY B 266 " (cutoff:3.500A)
      Proline residue:  B 292  - end of helix
    Processing helix  chain 'B' and resid 297 through 324
    Processing helix  chain 'A' and resid 27 through 35
    Processing helix  chain 'A' and resid 42 through 47
      removed outlier: 3.643A  pdb=" N   GLU A  46 " --> pdb=" O   ASP A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 80
    Processing helix  chain 'A' and resid 83 through 100
      removed outlier: 3.610A  pdb=" N   PHE A 100 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 116
    Processing helix  chain 'A' and resid 123 through 139
      removed outlier: 3.655A  pdb=" N   ALA A 127 " --> pdb=" O   ASN A 123 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   HIS A 128 " --> pdb=" O   MET A 124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 156
    Processing helix  chain 'A' and resid 170 through 185
      removed outlier: 3.720A  pdb=" N   GLY A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 199
    Processing helix  chain 'A' and resid 206 through 223
      removed outlier: 3.902A  pdb=" N   SER A 210 " --> pdb=" O   ASN A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 226 through 232
    Processing helix  chain 'A' and resid 315 through 331
      removed outlier: 4.230A  pdb=" N   ILE A 319 " --> pdb=" O   SER A 315 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE A 320 " --> pdb=" O   GLU A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
      removed outlier: 4.025A  pdb=" N   ALA A 343 " --> pdb=" O   ASN A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 361
    Processing helix  chain 'A' and resid 364 through 383
      removed outlier: 3.842A  pdb=" N   TYR A 368 " --> pdb=" O   LEU A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 407
      removed outlier: 4.088A  pdb=" N   ARG A 407 " --> pdb=" O   GLU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 426
    Processing helix  chain 'A' and resid 429 through 442
      removed outlier: 3.907A  pdb=" N   ALA A 433 " --> pdb=" O   ASN A 429 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   LYS A 442 " --> pdb=" O   MET A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 461
    Processing helix  chain 'A' and resid 462 through 465
      removed outlier: 3.693A  pdb=" N   LYS A 465 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 462 through 465'
    Processing helix  chain 'A' and resid 468 through 480
    Processing helix  chain 'A' and resid 481 through 495
      removed outlier: 3.866A  pdb=" N   ILE A 485 " --> pdb=" O   PHE A 481 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   TYR A 486 " --> pdb=" O   ILE A 482 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 501 through 517
      removed outlier: 3.687A  pdb=" N   THR A 505 " --> pdb=" O   SER A 501 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   GLU A 517 " --> pdb=" O   VAL A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 533
      removed outlier: 4.074A  pdb=" N   THR A 526 " --> pdb=" O   PRO A 522 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ASN A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 548
      removed outlier: 3.937A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 563
    Processing helix  chain 'A' and resid 576 through 594
      removed outlier: 3.661A  pdb=" N   GLY A 594 " --> pdb=" O   ALA A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 597 through 610
      removed outlier: 3.506A  pdb=" N   VAL A 601 " --> pdb=" O   ASP A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 614 through 624
    Processing helix  chain 'A' and resid 627 through 640
      removed outlier: 3.608A  pdb=" N   HIS A 640 " --> pdb=" O   TYR A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 662
    Processing helix  chain 'A' and resid 665 through 686
      removed outlier: 3.779A  pdb=" N   THR A 686 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 746 through 753
    Processing helix  chain 'D' and resid 763 through 777
      removed outlier: 3.579A  pdb=" N   VAL D 777 " --> pdb=" O   VAL D 773 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 781 through 789
      removed outlier: 4.274A  pdb=" N   ASP D 788 " --> pdb=" O   LYS D 784 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ASP D 789 " --> pdb=" O   GLU D 785 " (cutoff:3.500A)

    633 hydrogen bonds defined for protein.
    1890 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: 1.31

  Time building geometry restraints manager: 0.97 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2775
        1.34 -     1.46: 2192
        1.46 -     1.58: 4177
        1.58 -     1.70: 0
        1.70 -     1.81: 77
  Bond restraints: 9221
  Sorted by residual:
  bond pdb=" N   HIS B 101 "
       pdb=" CA  HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.14e-02 7.69e+03 7.54e+00
  bond pdb=" C   ALA A 521 "
       pdb=" N   PRO A 522 "
    ideal  model  delta    sigma   weight residual
    1.337  1.305  0.033 1.24e-02 6.50e+03 6.88e+00
  bond pdb=" CE1 HIS B 101 "
       pdb=" NE2 HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.321  1.339 -0.018 1.00e-02 1.00e+04 3.14e+00
  bond pdb=" C   HIS B 101 "
       pdb=" O   HIS B 101 "
    ideal  model  delta    sigma   weight residual
    1.234  1.250 -0.016 1.07e-02 8.73e+03 2.29e+00
  bond pdb=" CB  VAL A 658 "
       pdb=" CG1 VAL A 658 "
    ideal  model  delta    sigma   weight residual
    1.521  1.476  0.045 3.30e-02 9.18e+02 1.83e+00
  ... (remaining 9216 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.87: 11989
        1.87 -     3.74: 435
        3.74 -     5.61: 52
        5.61 -     7.48: 10
        7.48 -     9.34: 5
  Bond angle restraints: 12491
  Sorted by residual:
  angle pdb=" N   GLY C  64 "
        pdb=" CA  GLY C  64 "
        pdb=" C   GLY C  64 "
      ideal   model   delta    sigma   weight residual
     114.16  104.82    9.34 2.00e+00 2.50e-01 2.18e+01
  angle pdb=" C   PRO D 757 "
        pdb=" N   ASP D 758 "
        pdb=" CA  ASP D 758 "
      ideal   model   delta    sigma   weight residual
     121.70  129.64   -7.94 1.80e+00 3.09e-01 1.95e+01
  angle pdb=" CA  TYR B 104 "
        pdb=" C   TYR B 104 "
        pdb=" N   PHE B 105 "
      ideal   model   delta    sigma   weight residual
     114.59  120.13   -5.54 1.48e+00 4.57e-01 1.40e+01
  angle pdb=" C   TYR B 104 "
        pdb=" N   PHE B 105 "
        pdb=" CA  PHE B 105 "
      ideal   model   delta    sigma   weight residual
     122.42  116.63    5.79 1.55e+00 4.16e-01 1.40e+01
  angle pdb=" N   GLY A 253 "
        pdb=" CA  GLY A 253 "
        pdb=" C   GLY A 253 "
      ideal   model   delta    sigma   weight residual
     112.48  116.81   -4.33 1.21e+00 6.83e-01 1.28e+01
  ... (remaining 12486 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.75: 4806
       16.75 -    33.51: 518
       33.51 -    50.26: 93
       50.26 -    67.02: 18
       67.02 -    83.77: 12
  Dihedral angle restraints: 5447
    sinusoidal: 2189
      harmonic: 3258
  Sorted by residual:
  dihedral pdb=" CA  TYR C  63 "
           pdb=" C   TYR C  63 "
           pdb=" N   GLY C  64 "
           pdb=" CA  GLY C  64 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.24  -28.76     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" CA  ASN A 516 "
           pdb=" C   ASN A 516 "
           pdb=" N   GLU A 517 "
           pdb=" CA  GLU A 517 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.94   26.06     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  SER A 245 "
           pdb=" C   SER A 245 "
           pdb=" N   ASP A 246 "
           pdb=" CA  ASP A 246 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.07   25.93     0      5.00e+00 4.00e-02 2.69e+01
  ... (remaining 5444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1199
       0.065 -    0.131: 179
       0.131 -    0.196: 9
       0.196 -    0.262: 0
       0.262 -    0.327: 1
  Chirality restraints: 1388
  Sorted by residual:
  chirality pdb=" CA  LEU A 252 "
            pdb=" N   LEU A 252 "
            pdb=" C   LEU A 252 "
            pdb=" CB  LEU A 252 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CB  VAL D 777 "
            pdb=" CA  VAL D 777 "
            pdb=" CG1 VAL D 777 "
            pdb=" CG2 VAL D 777 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.85e-01
  chirality pdb=" CA  THR D 778 "
            pdb=" N   THR D 778 "
            pdb=" C   THR D 778 "
            pdb=" CB  THR D 778 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.34    0.18 2.00e-01 2.50e+01 8.52e-01
  ... (remaining 1385 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 100 "   -0.013 2.00e-02 2.50e+03   2.69e-02 7.23e+00
        pdb=" C   PHE B 100 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE B 100 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   HIS B 101 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D 758 "   -0.039 5.00e-02 4.00e+02   5.88e-02 5.53e+00
        pdb=" N   PRO D 759 "    0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO D 759 "   -0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO D 759 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP B 305 "   -0.008 2.00e-02 2.50e+03   1.69e-02 2.84e+00
        pdb=" C   TRP B 305 "    0.029 2.00e-02 2.50e+03
        pdb=" O   TRP B 305 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ASP B 306 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1090
        2.74 -     3.28: 10487
        3.28 -     3.82: 14944
        3.82 -     4.36: 17123
        4.36 -     4.90: 26922
  Nonbonded interactions: 70566
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 107 "
            pdb=" OG  SER A 110 "
     model   vdw
     2.195 3.040
  nonbonded pdb=" O   GLU A 463 "
            pdb=" NZ  LYS A 465 "
     model   vdw
     2.204 3.120
  nonbonded pdb=" O   PHE B  95 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O   GLN B 312 "
            pdb=" OG1 THR B 315 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   LEU B 118 "
            pdb=" ND1 HIS B 122 "
     model   vdw
     2.223 3.120
  ... (remaining 70561 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:             0.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.330
  Find NCS groups from input model:        0.040
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
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      :  0.006   0.058   9221  Z= 0.321
  Angle     :  0.832   9.345  12491  Z= 0.485
  Chirality :  0.046   0.327   1388
  Planarity :  0.005   0.059   1546
  Dihedral  : 14.502  83.769   3343
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 21.68
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  6.15 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  9.56 %
    Favored  : 90.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.21 (0.21), residues: 1073
  helix: -1.58 (0.15), residues: 826
  sheet:  None (None), residues: 0
  loop : -3.48 (0.31), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  85 
 TYR   0.028   0.002   TYR B  18 
 PHE   0.019   0.002   PHE A  59 
 TRP   0.023   0.002   TRP A 541 
 HIS   0.005   0.002   HIS B 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00633 ( 9221)
  covalent geometry    : angle       0.83227 (12491)
  hydrogen bonds       : bond        0.13437 (  633)
  hydrogen bonds       : angle       6.41496 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 315
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.8540 (t60) cc_final: 0.7984 (t60)
REVERT: C   80 HIS cc_start: 0.8596 (m90) cc_final: 0.7780 (m90)
REVERT: C  108 MET cc_start: 0.8411 (mmp) cc_final: 0.8193 (mmm)
REVERT: C  171 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7750 (mm-30)
REVERT: C  176 PHE cc_start: 0.8060 (p90) cc_final: 0.7729 (p90)
REVERT: C  177 MET cc_start: 0.8564 (tmm) cc_final: 0.8223 (tmm)
REVERT: C  184 TYR cc_start: 0.8408 (t80) cc_final: 0.8118 (t80)
REVERT: B    5 ASN cc_start: 0.7504 (p0) cc_final: 0.6466 (t0)
REVERT: B    9 GLN cc_start: 0.8546 (mt0) cc_final: 0.8254 (mt0)
REVERT: B   61 LEU cc_start: 0.9519 (mt) cc_final: 0.9127 (tt)
REVERT: B   88 PHE cc_start: 0.8664 (m-80) cc_final: 0.8404 (m-80)
REVERT: B   92 ASN cc_start: 0.8623 (m-40) cc_final: 0.7918 (m-40)
REVERT: B   95 PHE cc_start: 0.8335 (t80) cc_final: 0.7989 (t80)
REVERT: B  106 PHE cc_start: 0.8303 (m-80) cc_final: 0.7603 (p90)
REVERT: B  114 LEU cc_start: 0.9257 (tp) cc_final: 0.8857 (tp)
REVERT: B  119 LYS cc_start: 0.9493 (mtmt) cc_final: 0.8877 (mtmm)
REVERT: B  121 PHE cc_start: 0.8439 (m-80) cc_final: 0.8167 (m-80)
REVERT: B  163 GLN cc_start: 0.8677 (tt0) cc_final: 0.7983 (tp-100)
REVERT: B  186 TYR cc_start: 0.8752 (m-10) cc_final: 0.8539 (m-80)
REVERT: B  193 PHE cc_start: 0.8487 (m-80) cc_final: 0.8237 (m-80)
REVERT: B  195 MET cc_start: 0.8267 (mtp) cc_final: 0.7949 (ttt)
REVERT: B  271 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8677 (mt-10)
REVERT: B  289 MET cc_start: 0.7057 (ttm) cc_final: 0.6817 (ttm)
REVERT: B  319 LYS cc_start: 0.8967 (mttm) cc_final: 0.8678 (mttm)
REVERT: A   49 MET cc_start: 0.7862 (mmm) cc_final: 0.6973 (ppp)
REVERT: A  119 ASN cc_start: 0.8981 (m-40) cc_final: 0.8460 (t0)
REVERT: A  219 GLU cc_start: 0.8970 (tp30) cc_final: 0.8663 (mm-30)
REVERT: A  327 LEU cc_start: 0.9184 (tp) cc_final: 0.8980 (tt)
REVERT: A  520 MET cc_start: 0.8619 (mmm) cc_final: 0.8289 (mmm)
REVERT: A  577 ASP cc_start: 0.9119 (p0) cc_final: 0.8881 (t70)
  outliers start: 1
  outliers final: 1
  residues processed: 316
  average time/residue: 0.0947
  time to fit residues: 41.1272
Evaluate side-chains
  228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 227
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.6980
   chunk 106 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
B 189 GLN
B 202 ASN
B 206 GLN
B 210 ASN
A  86 GLN
A 101 ASN
A 117 GLN
A 135 ASN
A 202 ASN
A 336 GLN
A 429 ASN
A 479 ASN
A 564 GLN
A 593 GLN
A 661 HIS
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.112329 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.083246 restraints weight = 28908.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.085421 restraints weight = 17947.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.086876 restraints weight = 12931.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.087809 restraints weight = 10315.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.088485 restraints weight = 8853.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9221  Z= 0.159
  Angle     :  0.651  11.504  12491  Z= 0.347
  Chirality :  0.041   0.140   1388
  Planarity :  0.005   0.062   1546
  Dihedral  :  5.122  27.685   1204
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.51 %
    Allowed  :  4.78 %
    Favored  : 94.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.24), residues: 1073
  helix:  0.41 (0.17), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.77 (0.36), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  92 
 TYR   0.021   0.002   TYR C  44 
 PHE   0.049   0.002   PHE B 152 
 TRP   0.037   0.002   TRP B 123 
 HIS   0.006   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 ( 9221)
  covalent geometry    : angle       0.65139 (12491)
  hydrogen bonds       : bond        0.04838 (  633)
  hydrogen bonds       : angle       4.60378 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  303 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 298
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.8145 (t60) cc_final: 0.7829 (t60)
REVERT: C   45 ASP cc_start: 0.8015 (p0) cc_final: 0.7562 (p0)
REVERT: C   80 HIS cc_start: 0.8767 (m90) cc_final: 0.8209 (m90)
REVERT: C   81 LEU cc_start: 0.9434 (mt) cc_final: 0.8922 (mt)
REVERT: C   85 GLU cc_start: 0.8682 (tp30) cc_final: 0.7889 (pt0)
REVERT: C   96 TRP cc_start: 0.4861 (m-10) cc_final: 0.4439 (m-10)
REVERT: C   99 PHE cc_start: 0.8684 (m-80) cc_final: 0.8422 (m-10)
REVERT: C  171 GLU cc_start: 0.7289 (mt-10) cc_final: 0.6440 (mt-10)
REVERT: C  176 PHE cc_start: 0.7929 (p90) cc_final: 0.7619 (p90)
REVERT: C  177 MET cc_start: 0.8769 (tmm) cc_final: 0.8509 (tmm)
REVERT: C  184 TYR cc_start: 0.8678 (t80) cc_final: 0.8359 (t80)
REVERT: B    5 ASN cc_start: 0.7008 (p0) cc_final: 0.6517 (t0)
REVERT: B   37 GLN cc_start: 0.9213 (tt0) cc_final: 0.8743 (tm-30)
REVERT: B   61 LEU cc_start: 0.9408 (mt) cc_final: 0.9159 (tt)
REVERT: B   64 GLN cc_start: 0.9175 (tm-30) cc_final: 0.8963 (tm-30)
REVERT: B   85 ARG cc_start: 0.9246 (mtt180) cc_final: 0.8923 (mtt-85)
REVERT: B   88 PHE cc_start: 0.8759 (m-80) cc_final: 0.8469 (t80)
REVERT: B   92 ASN cc_start: 0.8621 (m-40) cc_final: 0.8401 (m-40)
REVERT: B   95 PHE cc_start: 0.8750 (t80) cc_final: 0.8481 (t80)
REVERT: B  106 PHE cc_start: 0.8183 (m-80) cc_final: 0.7397 (p90)
REVERT: B  118 LEU cc_start: 0.9498 (mm) cc_final: 0.9209 (mm)
REVERT: B  119 LYS cc_start: 0.9627 (mtmt) cc_final: 0.9211 (mtmm)
REVERT: B  121 PHE cc_start: 0.8787 (m-80) cc_final: 0.8212 (m-80)
REVERT: B  122 HIS cc_start: 0.8519 (m90) cc_final: 0.8316 (m90)
REVERT: B  152 PHE cc_start: 0.7747 (m-80) cc_final: 0.7464 (m-80)
REVERT: B  163 GLN cc_start: 0.8767 (tt0) cc_final: 0.8003 (tp-100)
REVERT: B  175 ASN cc_start: 0.8324 (m-40) cc_final: 0.7680 (p0)
REVERT: B  186 TYR cc_start: 0.8994 (m-10) cc_final: 0.8732 (m-80)
REVERT: B  191 MET cc_start: 0.9110 (tmm) cc_final: 0.8851 (tmm)
REVERT: B  193 PHE cc_start: 0.8987 (m-80) cc_final: 0.8668 (m-80)
REVERT: B  274 ILE cc_start: 0.9394 (mt) cc_final: 0.9114 (tt)
REVERT: B  286 HIS cc_start: 0.8126 (m-70) cc_final: 0.7712 (m-70)
REVERT: A   49 MET cc_start: 0.7795 (mmm) cc_final: 0.6866 (ppp)
REVERT: A  119 ASN cc_start: 0.8912 (m-40) cc_final: 0.8528 (t0)
REVERT: A  327 LEU cc_start: 0.9248 (tp) cc_final: 0.8829 (pp)
REVERT: A  388 LYS cc_start: 0.9041 (mmmm) cc_final: 0.8600 (mmtm)
REVERT: A  402 LEU cc_start: 0.9394 (tt) cc_final: 0.9080 (tt)
REVERT: A  438 MET cc_start: 0.9073 (mmp) cc_final: 0.8566 (mmm)
REVERT: A  472 LEU cc_start: 0.9449 (mt) cc_final: 0.9105 (mm)
REVERT: A  473 MET cc_start: 0.8048 (mmm) cc_final: 0.7697 (mmm)
REVERT: A  474 GLU cc_start: 0.9270 (pt0) cc_final: 0.9069 (pt0)
REVERT: A  481 PHE cc_start: 0.8054 (t80) cc_final: 0.7459 (t80)
REVERT: A  520 MET cc_start: 0.8656 (mmm) cc_final: 0.8285 (mmm)
REVERT: A  577 ASP cc_start: 0.9177 (p0) cc_final: 0.8574 (t70)
  outliers start: 5
  outliers final: 1
  residues processed: 300
  average time/residue: 0.0824
  time to fit residues: 35.1581
Evaluate side-chains
  236 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 235
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 85 optimal weight:    0.0030
   chunk 89 optimal weight:    5.9990
   chunk 82 optimal weight:    0.4980
   chunk 60 optimal weight:    0.7980
   chunk 98 optimal weight:    0.5980
   chunk 10 optimal weight:   10.0000
   chunk 4 optimal weight:   10.0000
   chunk 59 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 91 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   overall best weight:    0.5390

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

Flipped N/Q/H residues before XYZ refinement:
C 113 GLN
** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 210 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 GLN
A 360 ASN
A 663 HIS
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.115637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.086910 restraints weight = 28409.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.089263 restraints weight = 17529.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.090858 restraints weight = 12536.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.091946 restraints weight = 9872.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.092437 restraints weight = 8322.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9221  Z= 0.120
  Angle     :  0.593   9.933  12491  Z= 0.307
  Chirality :  0.038   0.136   1388
  Planarity :  0.004   0.058   1546
  Dihedral  :  4.633  23.183   1204
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.27 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.25), residues: 1073
  helix:  1.54 (0.17), residues: 825
  sheet:  None (None), residues: 0
  loop : -2.51 (0.36), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  33 
 TYR   0.019   0.001   TYR C  44 
 PHE   0.028   0.001   PHE B 152 
 TRP   0.013   0.001   TRP C  68 
 HIS   0.005   0.001   HIS A 661 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9221)
  covalent geometry    : angle       0.59323 (12491)
  hydrogen bonds       : bond        0.04128 (  633)
  hydrogen bonds       : angle       4.11081 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 312
  time to evaluate  : 0.240 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.8004 (t60) cc_final: 0.7638 (t60)
REVERT: C   45 ASP cc_start: 0.7994 (p0) cc_final: 0.7056 (p0)
REVERT: C   80 HIS cc_start: 0.8596 (m90) cc_final: 0.7995 (m90)
REVERT: C   81 LEU cc_start: 0.9318 (mt) cc_final: 0.8394 (pp)
REVERT: C   85 GLU cc_start: 0.8763 (tp30) cc_final: 0.7775 (pt0)
REVERT: C   91 ARG cc_start: 0.6162 (mtt90) cc_final: 0.4019 (ptm160)
REVERT: C   99 PHE cc_start: 0.8587 (m-80) cc_final: 0.8292 (m-10)
REVERT: C  176 PHE cc_start: 0.7993 (p90) cc_final: 0.7636 (p90)
REVERT: C  177 MET cc_start: 0.8815 (tmm) cc_final: 0.8581 (tmm)
REVERT: C  184 TYR cc_start: 0.8706 (t80) cc_final: 0.8406 (t80)
REVERT: B    5 ASN cc_start: 0.6940 (p0) cc_final: 0.5332 (t0)
REVERT: B    9 GLN cc_start: 0.8559 (mt0) cc_final: 0.7873 (mt0)
REVERT: B   37 GLN cc_start: 0.9157 (tt0) cc_final: 0.8655 (tm-30)
REVERT: B   85 ARG cc_start: 0.8909 (mtt180) cc_final: 0.8594 (mtt90)
REVERT: B   88 PHE cc_start: 0.8841 (m-80) cc_final: 0.8440 (t80)
REVERT: B   95 PHE cc_start: 0.8707 (t80) cc_final: 0.8495 (t80)
REVERT: B  106 PHE cc_start: 0.8222 (m-80) cc_final: 0.7505 (p90)
REVERT: B  114 LEU cc_start: 0.9365 (tp) cc_final: 0.8742 (tp)
REVERT: B  115 LEU cc_start: 0.9473 (tp) cc_final: 0.9259 (tp)
REVERT: B  118 LEU cc_start: 0.9453 (mm) cc_final: 0.9175 (mm)
REVERT: B  119 LYS cc_start: 0.9584 (mtmt) cc_final: 0.9119 (mtmm)
REVERT: B  121 PHE cc_start: 0.8780 (m-80) cc_final: 0.8475 (m-80)
REVERT: B  152 PHE cc_start: 0.7400 (m-80) cc_final: 0.7170 (m-80)
REVERT: B  163 GLN cc_start: 0.8676 (tt0) cc_final: 0.7958 (tp-100)
REVERT: B  164 ILE cc_start: 0.9142 (mt) cc_final: 0.8842 (mm)
REVERT: B  175 ASN cc_start: 0.8408 (m-40) cc_final: 0.7906 (p0)
REVERT: B  191 MET cc_start: 0.8960 (tmm) cc_final: 0.8735 (tmm)
REVERT: B  193 PHE cc_start: 0.8966 (m-80) cc_final: 0.8691 (m-80)
REVERT: B  274 ILE cc_start: 0.9375 (mt) cc_final: 0.8967 (tt)
REVERT: B  319 LYS cc_start: 0.8424 (mmpt) cc_final: 0.8217 (mttm)
REVERT: A   69 ASN cc_start: 0.9149 (m110) cc_final: 0.8771 (t0)
REVERT: A  119 ASN cc_start: 0.8817 (m-40) cc_final: 0.8478 (t0)
REVERT: A  124 MET cc_start: 0.8812 (tpp) cc_final: 0.8546 (tpp)
REVERT: A  191 GLN cc_start: 0.9546 (tt0) cc_final: 0.9329 (tm-30)
REVERT: A  219 GLU cc_start: 0.8836 (mm-30) cc_final: 0.8489 (mm-30)
REVERT: A  327 LEU cc_start: 0.9190 (tp) cc_final: 0.8780 (pp)
REVERT: A  374 GLN cc_start: 0.9225 (mt0) cc_final: 0.8995 (mt0)
REVERT: A  388 LYS cc_start: 0.8960 (mmmm) cc_final: 0.8583 (mmtm)
REVERT: A  437 TYR cc_start: 0.9044 (m-10) cc_final: 0.8768 (m-80)
REVERT: A  438 MET cc_start: 0.8894 (mmp) cc_final: 0.8529 (mmm)
REVERT: A  447 ASN cc_start: 0.8186 (p0) cc_final: 0.7978 (p0)
REVERT: A  472 LEU cc_start: 0.9377 (mt) cc_final: 0.8894 (mm)
REVERT: A  473 MET cc_start: 0.8070 (mmm) cc_final: 0.7707 (mmm)
REVERT: A  479 ASN cc_start: 0.8614 (m110) cc_final: 0.8078 (m-40)
REVERT: A  481 PHE cc_start: 0.7926 (t80) cc_final: 0.7198 (t80)
REVERT: A  520 MET cc_start: 0.8395 (mmm) cc_final: 0.8030 (mmm)
REVERT: A  552 GLU cc_start: 0.8689 (pp20) cc_final: 0.8383 (pp20)
REVERT: A  577 ASP cc_start: 0.9184 (p0) cc_final: 0.8652 (t70)
REVERT: A  675 LYS cc_start: 0.8634 (tttt) cc_final: 0.8118 (tptm)
REVERT: D  775 PHE cc_start: 0.8367 (t80) cc_final: 0.8149 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 312
  average time/residue: 0.0805
  time to fit residues: 35.7646
Evaluate side-chains
  238 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 56 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 97 optimal weight:    0.9980
   chunk 65 optimal weight:    0.3980
   chunk 64 optimal weight:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   chunk 86 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
** C 180 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 ASN
B 286 HIS
A 336 GLN
A 595 ASN
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.114738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.086305 restraints weight = 28554.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.088621 restraints weight = 17015.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.090240 restraints weight = 11924.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.091238 restraints weight = 9307.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.092011 restraints weight = 7864.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9221  Z= 0.131
  Angle     :  0.598  10.547  12491  Z= 0.313
  Chirality :  0.039   0.129   1388
  Planarity :  0.004   0.057   1546
  Dihedral  :  4.563  22.775   1204
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.25), residues: 1073
  helix:  1.69 (0.17), residues: 833
  sheet:  None (None), residues: 0
  loop : -2.41 (0.38), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  33 
 TYR   0.013   0.001   TYR A 619 
 PHE   0.023   0.001   PHE B 152 
 TRP   0.015   0.001   TRP A 541 
 HIS   0.007   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 9221)
  covalent geometry    : angle       0.59799 (12491)
  hydrogen bonds       : bond        0.04105 (  633)
  hydrogen bonds       : angle       4.08212 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 295
  time to evaluate  : 0.344 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.7953 (t60) cc_final: 0.7677 (t60)
REVERT: C   45 ASP cc_start: 0.7718 (p0) cc_final: 0.7172 (p0)
REVERT: C   80 HIS cc_start: 0.8631 (m90) cc_final: 0.8222 (m90)
REVERT: C   81 LEU cc_start: 0.9298 (mt) cc_final: 0.8798 (mt)
REVERT: C   85 GLU cc_start: 0.8779 (tp30) cc_final: 0.7779 (pt0)
REVERT: C   91 ARG cc_start: 0.5914 (mtt90) cc_final: 0.3963 (ptm160)
REVERT: C   96 TRP cc_start: 0.4683 (m-10) cc_final: 0.4358 (m-10)
REVERT: C   99 PHE cc_start: 0.8615 (m-80) cc_final: 0.8309 (m-10)
REVERT: C  108 MET cc_start: 0.8469 (mmp) cc_final: 0.8036 (ttp)
REVERT: C  176 PHE cc_start: 0.7930 (p90) cc_final: 0.7418 (p90)
REVERT: C  177 MET cc_start: 0.8862 (tmm) cc_final: 0.8641 (tmm)
REVERT: B    5 ASN cc_start: 0.7023 (p0) cc_final: 0.5536 (t0)
REVERT: B    9 GLN cc_start: 0.8648 (mt0) cc_final: 0.8195 (mt0)
REVERT: B   37 GLN cc_start: 0.9179 (tt0) cc_final: 0.8708 (tm-30)
REVERT: B   79 HIS cc_start: 0.8239 (m90) cc_final: 0.7943 (m90)
REVERT: B   88 PHE cc_start: 0.8873 (m-80) cc_final: 0.8375 (t80)
REVERT: B  106 PHE cc_start: 0.8259 (m-80) cc_final: 0.7552 (p90)
REVERT: B  114 LEU cc_start: 0.9433 (tp) cc_final: 0.8925 (tp)
REVERT: B  118 LEU cc_start: 0.9609 (mm) cc_final: 0.9249 (mm)
REVERT: B  119 LYS cc_start: 0.9635 (mtmt) cc_final: 0.9263 (mtmm)
REVERT: B  121 PHE cc_start: 0.8763 (m-80) cc_final: 0.8296 (m-80)
REVERT: B  152 PHE cc_start: 0.7365 (m-80) cc_final: 0.7018 (m-80)
REVERT: B  163 GLN cc_start: 0.8647 (tt0) cc_final: 0.8117 (tp-100)
REVERT: B  175 ASN cc_start: 0.8426 (m-40) cc_final: 0.7955 (p0)
REVERT: B  191 MET cc_start: 0.9022 (tmm) cc_final: 0.8787 (tmm)
REVERT: B  193 PHE cc_start: 0.8995 (m-80) cc_final: 0.8779 (m-80)
REVERT: B  206 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8795 (tm-30)
REVERT: B  269 MET cc_start: 0.8515 (tmm) cc_final: 0.8315 (tmm)
REVERT: A   69 ASN cc_start: 0.9165 (m110) cc_final: 0.8819 (t0)
REVERT: A  109 LEU cc_start: 0.9387 (tp) cc_final: 0.9046 (tp)
REVERT: A  119 ASN cc_start: 0.8880 (m-40) cc_final: 0.8489 (t0)
REVERT: A  176 LEU cc_start: 0.9102 (mm) cc_final: 0.8800 (pp)
REVERT: A  219 GLU cc_start: 0.8850 (mm-30) cc_final: 0.8461 (mm-30)
REVERT: A  327 LEU cc_start: 0.9228 (tp) cc_final: 0.8817 (pp)
REVERT: A  388 LYS cc_start: 0.8875 (mmmm) cc_final: 0.8481 (mmtm)
REVERT: A  402 LEU cc_start: 0.9411 (tt) cc_final: 0.9161 (tt)
REVERT: A  434 ILE cc_start: 0.9435 (mt) cc_final: 0.9222 (mt)
REVERT: A  472 LEU cc_start: 0.9379 (mt) cc_final: 0.8977 (mt)
REVERT: A  473 MET cc_start: 0.8380 (mmm) cc_final: 0.7948 (mmm)
REVERT: A  481 PHE cc_start: 0.7790 (t80) cc_final: 0.7115 (t80)
REVERT: A  520 MET cc_start: 0.8413 (mmm) cc_final: 0.8198 (mmm)
REVERT: A  577 ASP cc_start: 0.9212 (p0) cc_final: 0.8670 (t70)
REVERT: A  675 LYS cc_start: 0.8600 (tttt) cc_final: 0.8090 (tptm)
REVERT: D  775 PHE cc_start: 0.8484 (t80) cc_final: 0.8194 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 295
  average time/residue: 0.0764
  time to fit residues: 32.8298
Evaluate side-chains
  234 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    7.9990
   chunk 61 optimal weight:    6.9990
   chunk 34 optimal weight:    5.9990
   chunk 5 optimal weight:   20.0000
   chunk 83 optimal weight:    5.9990
   chunk 94 optimal weight:    0.9990
   chunk 11 optimal weight:    5.9990
   chunk 54 optimal weight:    9.9990
   chunk 53 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   overall best weight:    2.7388

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

Flipped N/Q/H residues before XYZ refinement:
C 180 HIS
B 286 HIS
A 336 GLN
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.112393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.083967 restraints weight = 29017.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.086270 restraints weight = 17326.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.087769 restraints weight = 12216.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.088789 restraints weight = 9603.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.089477 restraints weight = 8127.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.4443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9221  Z= 0.164
  Angle     :  0.622   9.897  12491  Z= 0.328
  Chirality :  0.041   0.135   1388
  Planarity :  0.004   0.056   1546
  Dihedral  :  4.629  23.136   1204
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.85 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.22 (0.25), residues: 1073
  helix:  1.66 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -2.33 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  33 
 TYR   0.014   0.001   TYR A 612 
 PHE   0.019   0.001   PHE A 607 
 TRP   0.033   0.001   TRP A 541 
 HIS   0.008   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 ( 9221)
  covalent geometry    : angle       0.62238 (12491)
  hydrogen bonds       : bond        0.04157 (  633)
  hydrogen bonds       : angle       4.11561 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  283 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 283
  time to evaluate  : 0.343 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.7870 (t60) cc_final: 0.7587 (t60)
REVERT: C   45 ASP cc_start: 0.7891 (p0) cc_final: 0.7310 (p0)
REVERT: C   80 HIS cc_start: 0.8698 (m90) cc_final: 0.8240 (m90)
REVERT: C   81 LEU cc_start: 0.9299 (mt) cc_final: 0.8857 (mt)
REVERT: C   85 GLU cc_start: 0.8918 (tp30) cc_final: 0.7906 (pt0)
REVERT: C   91 ARG cc_start: 0.5943 (mtt90) cc_final: 0.3854 (ptm160)
REVERT: C   99 PHE cc_start: 0.8530 (m-80) cc_final: 0.8199 (m-10)
REVERT: C  176 PHE cc_start: 0.8007 (p90) cc_final: 0.7435 (p90)
REVERT: C  177 MET cc_start: 0.8905 (tmm) cc_final: 0.8626 (tmm)
REVERT: B    5 ASN cc_start: 0.6904 (p0) cc_final: 0.5207 (t0)
REVERT: B    9 GLN cc_start: 0.8690 (mt0) cc_final: 0.8125 (mt0)
REVERT: B   37 GLN cc_start: 0.9195 (tt0) cc_final: 0.8770 (tm-30)
REVERT: B   79 HIS cc_start: 0.8383 (m90) cc_final: 0.8062 (m90)
REVERT: B   88 PHE cc_start: 0.8910 (m-80) cc_final: 0.8376 (t80)
REVERT: B  106 PHE cc_start: 0.8287 (m-80) cc_final: 0.7493 (p90)
REVERT: B  114 LEU cc_start: 0.9439 (tp) cc_final: 0.8888 (tp)
REVERT: B  118 LEU cc_start: 0.9590 (mm) cc_final: 0.9355 (mm)
REVERT: B  119 LYS cc_start: 0.9652 (mtmt) cc_final: 0.9206 (mtmm)
REVERT: B  121 PHE cc_start: 0.8820 (m-80) cc_final: 0.8349 (m-80)
REVERT: B  152 PHE cc_start: 0.7351 (m-80) cc_final: 0.6979 (m-80)
REVERT: B  163 GLN cc_start: 0.8599 (tt0) cc_final: 0.8121 (tp-100)
REVERT: B  193 PHE cc_start: 0.9103 (m-80) cc_final: 0.8769 (m-80)
REVERT: B  206 GLN cc_start: 0.9113 (tm-30) cc_final: 0.8859 (tm-30)
REVERT: B  274 ILE cc_start: 0.9378 (mt) cc_final: 0.9126 (mt)
REVERT: A   69 ASN cc_start: 0.9172 (m110) cc_final: 0.8843 (t0)
REVERT: A  119 ASN cc_start: 0.8964 (m-40) cc_final: 0.8523 (t0)
REVERT: A  152 MET cc_start: 0.8758 (tpt) cc_final: 0.8217 (tpt)
REVERT: A  176 LEU cc_start: 0.9131 (mm) cc_final: 0.8863 (pp)
REVERT: A  219 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8445 (mm-30)
REVERT: A  327 LEU cc_start: 0.9289 (tp) cc_final: 0.8848 (pp)
REVERT: A  388 LYS cc_start: 0.8892 (mmmm) cc_final: 0.8498 (mmtm)
REVERT: A  402 LEU cc_start: 0.9455 (tt) cc_final: 0.9203 (tt)
REVERT: A  438 MET cc_start: 0.8882 (mmp) cc_final: 0.8659 (mmm)
REVERT: A  472 LEU cc_start: 0.9395 (mt) cc_final: 0.9182 (mm)
REVERT: A  473 MET cc_start: 0.8498 (mmm) cc_final: 0.8021 (mmm)
REVERT: A  481 PHE cc_start: 0.8194 (t80) cc_final: 0.7426 (t80)
REVERT: A  520 MET cc_start: 0.8562 (mmm) cc_final: 0.8308 (mmm)
REVERT: A  541 TRP cc_start: 0.8952 (t60) cc_final: 0.8694 (t60)
REVERT: A  552 GLU cc_start: 0.8921 (pp20) cc_final: 0.8601 (pp20)
REVERT: A  577 ASP cc_start: 0.9255 (p0) cc_final: 0.8650 (t70)
REVERT: A  675 LYS cc_start: 0.8605 (tttt) cc_final: 0.8078 (tptm)
REVERT: D  775 PHE cc_start: 0.8483 (t80) cc_final: 0.8110 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 283
  average time/residue: 0.0749
  time to fit residues: 31.0274
Evaluate side-chains
  228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 52 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 1 optimal weight:    7.9990
   chunk 71 optimal weight:    6.9990
   chunk 87 optimal weight:    0.7980
   chunk 4 optimal weight:    8.9990
   chunk 75 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 24 optimal weight:    4.9990
   chunk 10 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
C  73 ASN
** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  47 ASN
B 286 HIS
A 336 GLN
A 479 ASN
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.110735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.081909 restraints weight = 29191.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.084129 restraints weight = 17485.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.085593 restraints weight = 12405.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.086534 restraints weight = 9822.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.087217 restraints weight = 8392.239|
|-----------------------------------------------------------------------------|
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7934
moved from start:          0.4562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9221  Z= 0.204
  Angle     :  0.675   9.450  12491  Z= 0.357
  Chirality :  0.042   0.148   1388
  Planarity :  0.004   0.059   1546
  Dihedral  :  4.840  23.915   1204
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 12.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.25), residues: 1073
  helix:  1.47 (0.17), residues: 832
  sheet:  None (None), residues: 0
  loop : -2.32 (0.38), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  33 
 TYR   0.036   0.002   TYR C  44 
 PHE   0.018   0.002   PHE A 607 
 TRP   0.028   0.002   TRP A 541 
 HIS   0.009   0.002   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 ( 9221)
  covalent geometry    : angle       0.67480 (12491)
  hydrogen bonds       : bond        0.04358 (  633)
  hydrogen bonds       : angle       4.32220 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.7964 (t60) cc_final: 0.7674 (t60)
REVERT: C   45 ASP cc_start: 0.7888 (p0) cc_final: 0.7215 (p0)
REVERT: C   80 HIS cc_start: 0.8698 (m90) cc_final: 0.8227 (m90)
REVERT: C   81 LEU cc_start: 0.9338 (mt) cc_final: 0.8901 (mt)
REVERT: C   85 GLU cc_start: 0.8945 (tp30) cc_final: 0.7870 (pt0)
REVERT: C   91 ARG cc_start: 0.5957 (mtt90) cc_final: 0.3805 (ptm160)
REVERT: C   96 TRP cc_start: 0.4700 (m-10) cc_final: 0.4369 (m-10)
REVERT: C   99 PHE cc_start: 0.8534 (m-80) cc_final: 0.8175 (m-10)
REVERT: C  176 PHE cc_start: 0.8310 (p90) cc_final: 0.7870 (p90)
REVERT: C  177 MET cc_start: 0.8906 (tmm) cc_final: 0.8576 (tmm)
REVERT: C  184 TYR cc_start: 0.8725 (t80) cc_final: 0.8505 (t80)
REVERT: B    5 ASN cc_start: 0.6853 (p0) cc_final: 0.5119 (t0)
REVERT: B    9 GLN cc_start: 0.8670 (mt0) cc_final: 0.8117 (mt0)
REVERT: B   37 GLN cc_start: 0.9191 (tt0) cc_final: 0.8761 (tm-30)
REVERT: B   79 HIS cc_start: 0.8620 (m90) cc_final: 0.8341 (m90)
REVERT: B   80 GLU cc_start: 0.9324 (pt0) cc_final: 0.8982 (pp20)
REVERT: B   84 GLU cc_start: 0.9117 (pt0) cc_final: 0.8399 (pt0)
REVERT: B   88 PHE cc_start: 0.8924 (m-80) cc_final: 0.8375 (t80)
REVERT: B  106 PHE cc_start: 0.8325 (m-80) cc_final: 0.7453 (p90)
REVERT: B  114 LEU cc_start: 0.9426 (tp) cc_final: 0.8847 (tp)
REVERT: B  118 LEU cc_start: 0.9582 (mm) cc_final: 0.9362 (mm)
REVERT: B  119 LYS cc_start: 0.9587 (mtmt) cc_final: 0.9193 (mtmm)
REVERT: B  121 PHE cc_start: 0.8879 (m-80) cc_final: 0.8416 (m-80)
REVERT: B  122 HIS cc_start: 0.8796 (m90) cc_final: 0.8502 (m90)
REVERT: B  163 GLN cc_start: 0.8678 (tt0) cc_final: 0.8141 (tp-100)
REVERT: B  193 PHE cc_start: 0.9134 (m-80) cc_final: 0.8775 (m-80)
REVERT: B  206 GLN cc_start: 0.9122 (tm-30) cc_final: 0.8873 (tm-30)
REVERT: A   69 ASN cc_start: 0.9236 (m110) cc_final: 0.8852 (t0)
REVERT: A  119 ASN cc_start: 0.9042 (m-40) cc_final: 0.8589 (t0)
REVERT: A  176 LEU cc_start: 0.9129 (mm) cc_final: 0.8874 (pp)
REVERT: A  219 GLU cc_start: 0.8913 (mm-30) cc_final: 0.8487 (mm-30)
REVERT: A  327 LEU cc_start: 0.9303 (tp) cc_final: 0.9035 (tt)
REVERT: A  336 GLN cc_start: 0.9041 (tt0) cc_final: 0.8836 (tt0)
REVERT: A  388 LYS cc_start: 0.8917 (mmmm) cc_final: 0.8532 (mmtm)
REVERT: A  438 MET cc_start: 0.8925 (mmp) cc_final: 0.8697 (mmm)
REVERT: A  473 MET cc_start: 0.8509 (mmm) cc_final: 0.8056 (mmm)
REVERT: A  481 PHE cc_start: 0.8154 (t80) cc_final: 0.7438 (t80)
REVERT: A  520 MET cc_start: 0.8571 (mmm) cc_final: 0.8288 (mmm)
REVERT: A  577 ASP cc_start: 0.9256 (p0) cc_final: 0.8636 (t70)
REVERT: A  675 LYS cc_start: 0.8373 (tttt) cc_final: 0.7696 (tptm)
REVERT: D  775 PHE cc_start: 0.8520 (t80) cc_final: 0.8158 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.0795
  time to fit residues: 30.9466
Evaluate side-chains
  235 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 2 optimal weight:   20.0000
   chunk 28 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 79 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   chunk 54 optimal weight:    8.9990
   chunk 1 optimal weight:    8.9990
   chunk 72 optimal weight:    7.9990
   chunk 21 optimal weight:    0.7980
   chunk 76 optimal weight:    3.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
C 134 ASN
B 286 HIS
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.112066 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.084011 restraints weight = 28319.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.086169 restraints weight = 17239.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.087611 restraints weight = 12324.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.088586 restraints weight = 9760.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.089187 restraints weight = 8300.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.4840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9221  Z= 0.159
  Angle     :  0.640  10.664  12491  Z= 0.336
  Chirality :  0.041   0.149   1388
  Planarity :  0.004   0.058   1546
  Dihedral  :  4.756  23.131   1204
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.14 (0.25), residues: 1073
  helix:  1.59 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -2.30 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  33 
 TYR   0.030   0.002   TYR C  44 
 PHE   0.019   0.001   PHE A 607 
 TRP   0.023   0.001   TRP A 541 
 HIS   0.008   0.001   HIS A 640 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9221)
  covalent geometry    : angle       0.64015 (12491)
  hydrogen bonds       : bond        0.04104 (  633)
  hydrogen bonds       : angle       4.24372 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  277 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 277
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.8116 (t60) cc_final: 0.7802 (t60)
REVERT: C   45 ASP cc_start: 0.7869 (p0) cc_final: 0.7209 (p0)
REVERT: C   80 HIS cc_start: 0.8673 (m90) cc_final: 0.8278 (m90)
REVERT: C   81 LEU cc_start: 0.9325 (mt) cc_final: 0.8511 (pp)
REVERT: C   85 GLU cc_start: 0.8871 (tp30) cc_final: 0.7882 (pt0)
REVERT: C   91 ARG cc_start: 0.5998 (mtt90) cc_final: 0.3802 (ptm160)
REVERT: C   96 TRP cc_start: 0.4916 (m-10) cc_final: 0.4490 (m-10)
REVERT: C   99 PHE cc_start: 0.8535 (m-80) cc_final: 0.8154 (m-10)
REVERT: C  176 PHE cc_start: 0.8260 (p90) cc_final: 0.7770 (p90)
REVERT: C  177 MET cc_start: 0.8836 (tmm) cc_final: 0.8432 (tmm)
REVERT: C  184 TYR cc_start: 0.8728 (t80) cc_final: 0.8499 (t80)
REVERT: B    5 ASN cc_start: 0.6947 (p0) cc_final: 0.5058 (t0)
REVERT: B    9 GLN cc_start: 0.8628 (mt0) cc_final: 0.8097 (mt0)
REVERT: B   37 GLN cc_start: 0.9281 (tt0) cc_final: 0.8808 (tm-30)
REVERT: B   64 GLN cc_start: 0.9237 (tm-30) cc_final: 0.8989 (tm-30)
REVERT: B   79 HIS cc_start: 0.8608 (m90) cc_final: 0.8290 (m90)
REVERT: B   80 GLU cc_start: 0.9269 (pt0) cc_final: 0.8853 (pp20)
REVERT: B   84 GLU cc_start: 0.9039 (pt0) cc_final: 0.8334 (pt0)
REVERT: B   88 PHE cc_start: 0.8861 (m-80) cc_final: 0.8341 (t80)
REVERT: B  106 PHE cc_start: 0.8278 (m-80) cc_final: 0.7408 (p90)
REVERT: B  119 LYS cc_start: 0.9555 (mtmt) cc_final: 0.9053 (mtmm)
REVERT: B  121 PHE cc_start: 0.8883 (m-80) cc_final: 0.8475 (m-80)
REVERT: B  152 PHE cc_start: 0.7264 (m-80) cc_final: 0.6743 (m-80)
REVERT: B  163 GLN cc_start: 0.8567 (tt0) cc_final: 0.8047 (tp-100)
REVERT: B  175 ASN cc_start: 0.8684 (m-40) cc_final: 0.8246 (p0)
REVERT: B  193 PHE cc_start: 0.9071 (m-80) cc_final: 0.8746 (m-80)
REVERT: B  206 GLN cc_start: 0.9039 (tm-30) cc_final: 0.8756 (tm-30)
REVERT: B  298 MET cc_start: 0.9082 (tmm) cc_final: 0.8846 (tmm)
REVERT: A   69 ASN cc_start: 0.9204 (m110) cc_final: 0.8806 (t0)
REVERT: A  119 ASN cc_start: 0.8938 (m-40) cc_final: 0.8543 (t0)
REVERT: A  176 LEU cc_start: 0.9094 (mm) cc_final: 0.8854 (pp)
REVERT: A  216 ASP cc_start: 0.8407 (t0) cc_final: 0.8083 (t0)
REVERT: A  219 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8396 (mm-30)
REVERT: A  336 GLN cc_start: 0.8999 (tt0) cc_final: 0.8682 (tt0)
REVERT: A  374 GLN cc_start: 0.9079 (mt0) cc_final: 0.8441 (mm-40)
REVERT: A  388 LYS cc_start: 0.8927 (mmmm) cc_final: 0.8561 (mmtm)
REVERT: A  406 ARG cc_start: 0.9042 (mmm-85) cc_final: 0.8774 (mmm-85)
REVERT: A  472 LEU cc_start: 0.9481 (mm) cc_final: 0.9066 (mm)
REVERT: A  473 MET cc_start: 0.8407 (mmm) cc_final: 0.7949 (mmm)
REVERT: A  481 PHE cc_start: 0.8140 (t80) cc_final: 0.7581 (t80)
REVERT: A  577 ASP cc_start: 0.9217 (p0) cc_final: 0.8587 (t70)
REVERT: D  787 LEU cc_start: 0.8919 (pp) cc_final: 0.8695 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 277
  average time/residue: 0.0726
  time to fit residues: 29.5184
Evaluate side-chains
  238 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 238
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 43 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 1 optimal weight:    9.9990
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   chunk 100 optimal weight:    5.9990
   chunk 63 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 41 optimal weight:    5.9990
   overall best weight:    3.3388

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

Flipped N/Q/H residues before XYZ refinement:
** C 175 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 HIS
A 336 GLN
A 595 ASN
A 633 ASN
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.110887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.082208 restraints weight = 28774.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.084407 restraints weight = 17433.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.085858 restraints weight = 12458.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.086785 restraints weight = 9873.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.087474 restraints weight = 8454.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4878

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   9221  Z= 0.190
  Angle     :  0.678  10.301  12491  Z= 0.356
  Chirality :  0.042   0.167   1388
  Planarity :  0.004   0.058   1546
  Dihedral  :  4.807  23.435   1204
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 12.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.02 (0.25), residues: 1073
  helix:  1.50 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -2.35 (0.38), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  33 
 TYR   0.027   0.002   TYR C  44 
 PHE   0.043   0.002   PHE B 152 
 TRP   0.022   0.001   TRP A 541 
 HIS   0.007   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 9221)
  covalent geometry    : angle       0.67765 (12491)
  hydrogen bonds       : bond        0.04334 (  633)
  hydrogen bonds       : angle       4.37187 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 270
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.8040 (t60) cc_final: 0.7789 (t60)
REVERT: C   45 ASP cc_start: 0.7773 (p0) cc_final: 0.7320 (p0)
REVERT: C   80 HIS cc_start: 0.8697 (m90) cc_final: 0.8224 (m90)
REVERT: C   81 LEU cc_start: 0.9343 (mt) cc_final: 0.8907 (mt)
REVERT: C   85 GLU cc_start: 0.8835 (tp30) cc_final: 0.7849 (pt0)
REVERT: C   91 ARG cc_start: 0.6032 (mtt90) cc_final: 0.3849 (ptm160)
REVERT: C   96 TRP cc_start: 0.5163 (m-10) cc_final: 0.4747 (m-10)
REVERT: C   99 PHE cc_start: 0.8557 (m-80) cc_final: 0.8181 (m-10)
REVERT: C  104 ILE cc_start: 0.8776 (tp) cc_final: 0.8455 (pt)
REVERT: C  176 PHE cc_start: 0.8319 (p90) cc_final: 0.7932 (p90)
REVERT: C  177 MET cc_start: 0.8847 (tmm) cc_final: 0.8438 (tmm)
REVERT: B    5 ASN cc_start: 0.7012 (p0) cc_final: 0.5041 (t0)
REVERT: B    9 GLN cc_start: 0.8635 (mt0) cc_final: 0.8114 (mt0)
REVERT: B   37 GLN cc_start: 0.9217 (tt0) cc_final: 0.8752 (tm-30)
REVERT: B   79 HIS cc_start: 0.8602 (m90) cc_final: 0.8266 (m90)
REVERT: B   80 GLU cc_start: 0.9295 (pt0) cc_final: 0.8886 (pp20)
REVERT: B   88 PHE cc_start: 0.8880 (m-80) cc_final: 0.8351 (t80)
REVERT: B  106 PHE cc_start: 0.8423 (m-80) cc_final: 0.7570 (p90)
REVERT: B  114 LEU cc_start: 0.9443 (tp) cc_final: 0.9000 (tp)
REVERT: B  115 LEU cc_start: 0.9700 (tp) cc_final: 0.9438 (tp)
REVERT: B  118 LEU cc_start: 0.9549 (mm) cc_final: 0.9292 (mm)
REVERT: B  119 LYS cc_start: 0.9561 (mtmt) cc_final: 0.8988 (mtmm)
REVERT: B  121 PHE cc_start: 0.8899 (m-80) cc_final: 0.8500 (m-80)
REVERT: B  122 HIS cc_start: 0.8731 (m90) cc_final: 0.8508 (m90)
REVERT: B  152 PHE cc_start: 0.7279 (m-80) cc_final: 0.6970 (m-80)
REVERT: B  163 GLN cc_start: 0.8606 (tt0) cc_final: 0.8061 (tp-100)
REVERT: B  175 ASN cc_start: 0.8632 (m-40) cc_final: 0.8267 (p0)
REVERT: B  193 PHE cc_start: 0.9085 (m-80) cc_final: 0.8728 (m-80)
REVERT: B  206 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8763 (tm-30)
REVERT: B  322 ARG cc_start: 0.8499 (tpt90) cc_final: 0.8248 (ttp80)
REVERT: A   69 ASN cc_start: 0.9222 (m110) cc_final: 0.8814 (t0)
REVERT: A  119 ASN cc_start: 0.8960 (m-40) cc_final: 0.8613 (t0)
REVERT: A  219 GLU cc_start: 0.8851 (mm-30) cc_final: 0.8434 (mm-30)
REVERT: A  388 LYS cc_start: 0.8947 (mmmm) cc_final: 0.8586 (mmtm)
REVERT: A  402 LEU cc_start: 0.9395 (tt) cc_final: 0.9188 (tt)
REVERT: A  406 ARG cc_start: 0.9054 (mmm-85) cc_final: 0.8781 (mmm-85)
REVERT: A  437 TYR cc_start: 0.9053 (m-10) cc_final: 0.8774 (m-80)
REVERT: A  438 MET cc_start: 0.8878 (mmp) cc_final: 0.8661 (mmm)
REVERT: A  472 LEU cc_start: 0.9504 (mm) cc_final: 0.9092 (mm)
REVERT: A  473 MET cc_start: 0.8405 (mmm) cc_final: 0.7993 (mmm)
REVERT: A  481 PHE cc_start: 0.8188 (t80) cc_final: 0.7655 (t80)
REVERT: A  520 MET cc_start: 0.8326 (mmm) cc_final: 0.7990 (mmm)
REVERT: A  577 ASP cc_start: 0.9181 (p0) cc_final: 0.8724 (t70)
REVERT: D  787 LEU cc_start: 0.8888 (pp) cc_final: 0.8652 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 270
  average time/residue: 0.0760
  time to fit residues: 29.8614
Evaluate side-chains
  228 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 55 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0970
   chunk 59 optimal weight:    0.8980
   overall best weight:    1.9982

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

Flipped N/Q/H residues before XYZ refinement:
** B  79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 286 HIS
A 336 GLN
A 595 ASN
A 633 ASN
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.112724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.083729 restraints weight = 28674.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.086022 restraints weight = 17218.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.087531 restraints weight = 12228.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.088540 restraints weight = 9643.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.089167 restraints weight = 8199.599|
|-----------------------------------------------------------------------------|
r_work (final): 0.3279
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.5146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   9221  Z= 0.142
  Angle     :  0.652  10.285  12491  Z= 0.336
  Chirality :  0.041   0.185   1388
  Planarity :  0.004   0.059   1546
  Dihedral  :  4.672  22.640   1204
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.26), residues: 1073
  helix:  1.69 (0.17), residues: 834
  sheet:  None (None), residues: 0
  loop : -2.29 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  33 
 TYR   0.019   0.001   TYR B 186 
 PHE   0.041   0.001   PHE B 152 
 TRP   0.018   0.001   TRP A 541 
 HIS   0.007   0.001   HIS B 286 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 9221)
  covalent geometry    : angle       0.65171 (12491)
  hydrogen bonds       : bond        0.04102 (  633)
  hydrogen bonds       : angle       4.18903 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 278
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.7994 (t60) cc_final: 0.7753 (t60)
REVERT: C   80 HIS cc_start: 0.8690 (m90) cc_final: 0.8210 (m90)
REVERT: C   81 LEU cc_start: 0.9319 (mt) cc_final: 0.8468 (pp)
REVERT: C   85 GLU cc_start: 0.8799 (tp30) cc_final: 0.7813 (pt0)
REVERT: C   91 ARG cc_start: 0.5979 (mtt90) cc_final: 0.3829 (ptm160)
REVERT: C   99 PHE cc_start: 0.8553 (m-80) cc_final: 0.8174 (m-10)
REVERT: C  104 ILE cc_start: 0.8827 (tp) cc_final: 0.8489 (pt)
REVERT: C  176 PHE cc_start: 0.8322 (p90) cc_final: 0.7916 (p90)
REVERT: C  177 MET cc_start: 0.8836 (tmm) cc_final: 0.8405 (tmm)
REVERT: B    5 ASN cc_start: 0.6962 (p0) cc_final: 0.5012 (t0)
REVERT: B    9 GLN cc_start: 0.8627 (mt0) cc_final: 0.8078 (mt0)
REVERT: B   37 GLN cc_start: 0.9265 (tt0) cc_final: 0.8789 (tm-30)
REVERT: B   79 HIS cc_start: 0.8538 (m90) cc_final: 0.8275 (m90)
REVERT: B   80 GLU cc_start: 0.9284 (pt0) cc_final: 0.8843 (pp20)
REVERT: B   84 GLU cc_start: 0.8968 (pt0) cc_final: 0.8281 (pt0)
REVERT: B   88 PHE cc_start: 0.8879 (m-80) cc_final: 0.8324 (t80)
REVERT: B   92 ASN cc_start: 0.8929 (m-40) cc_final: 0.8716 (m-40)
REVERT: B  106 PHE cc_start: 0.8339 (m-80) cc_final: 0.7571 (p90)
REVERT: B  114 LEU cc_start: 0.9401 (tp) cc_final: 0.8873 (tp)
REVERT: B  115 LEU cc_start: 0.9689 (tp) cc_final: 0.9459 (tp)
REVERT: B  118 LEU cc_start: 0.9557 (mm) cc_final: 0.9308 (mm)
REVERT: B  119 LYS cc_start: 0.9522 (mtmt) cc_final: 0.9032 (mtmm)
REVERT: B  121 PHE cc_start: 0.8814 (m-80) cc_final: 0.8422 (m-80)
REVERT: B  152 PHE cc_start: 0.7107 (m-80) cc_final: 0.6764 (m-80)
REVERT: B  163 GLN cc_start: 0.8526 (tt0) cc_final: 0.7985 (tp-100)
REVERT: B  175 ASN cc_start: 0.8618 (m-40) cc_final: 0.8355 (p0)
REVERT: B  193 PHE cc_start: 0.9045 (m-80) cc_final: 0.8710 (m-80)
REVERT: B  206 GLN cc_start: 0.9006 (tm-30) cc_final: 0.8671 (tm-30)
REVERT: B  269 MET cc_start: 0.8510 (ttp) cc_final: 0.8050 (tmm)
REVERT: B  312 GLN cc_start: 0.7022 (mp10) cc_final: 0.6185 (mp10)
REVERT: A   69 ASN cc_start: 0.9179 (m110) cc_final: 0.8782 (t0)
REVERT: A  119 ASN cc_start: 0.8966 (m-40) cc_final: 0.8602 (t0)
REVERT: A  216 ASP cc_start: 0.8471 (t0) cc_final: 0.8135 (t0)
REVERT: A  219 GLU cc_start: 0.8811 (mm-30) cc_final: 0.8365 (mm-30)
REVERT: A  336 GLN cc_start: 0.8969 (tt0) cc_final: 0.8733 (tt0)
REVERT: A  374 GLN cc_start: 0.9095 (mt0) cc_final: 0.8453 (mm-40)
REVERT: A  388 LYS cc_start: 0.8974 (mmmm) cc_final: 0.8609 (mmtm)
REVERT: A  402 LEU cc_start: 0.9368 (tt) cc_final: 0.9139 (tt)
REVERT: A  406 ARG cc_start: 0.9059 (mmm-85) cc_final: 0.8744 (mmm-85)
REVERT: A  472 LEU cc_start: 0.9489 (mm) cc_final: 0.9148 (mm)
REVERT: A  473 MET cc_start: 0.8420 (mmm) cc_final: 0.7998 (mmm)
REVERT: A  481 PHE cc_start: 0.8184 (t80) cc_final: 0.7582 (t80)
REVERT: A  552 GLU cc_start: 0.8934 (pp20) cc_final: 0.8670 (pp20)
REVERT: A  577 ASP cc_start: 0.9228 (p0) cc_final: 0.8599 (t70)
REVERT: D  787 LEU cc_start: 0.8906 (pp) cc_final: 0.8677 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 278
  average time/residue: 0.0728
  time to fit residues: 29.7777
Evaluate side-chains
  223 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 223
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 84 optimal weight:    0.8980
   chunk 51 optimal weight:   10.0000
   chunk 86 optimal weight:    0.0030
   chunk 107 optimal weight:    0.9990
   chunk 6 optimal weight:    9.9990
   chunk 96 optimal weight:    0.9980
   chunk 106 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 99 optimal weight:    0.0970
   chunk 68 optimal weight:    7.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 ASN
A 633 ASN
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.115899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.087229 restraints weight = 28276.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.089585 restraints weight = 17071.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.091199 restraints weight = 12120.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.092165 restraints weight = 9500.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.092884 restraints weight = 8141.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047   9221  Z= 0.123
  Angle     :  0.643  10.091  12491  Z= 0.327
  Chirality :  0.040   0.188   1388
  Planarity :  0.004   0.060   1546
  Dihedral  :  4.415  20.524   1204
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.51 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.62 (0.26), residues: 1073
  helix:  2.00 (0.18), residues: 828
  sheet:  None (None), residues: 0
  loop : -2.30 (0.39), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  33 
 TYR   0.018   0.001   TYR B 186 
 PHE   0.038   0.001   PHE B 152 
 TRP   0.012   0.001   TRP A 541 
 HIS   0.003   0.001   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 9221)
  covalent geometry    : angle       0.64302 (12491)
  hydrogen bonds       : bond        0.03830 (  633)
  hydrogen bonds       : angle       4.06883 ( 1890)

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

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

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2146 Ramachandran restraints generated.
    1073 Oldfield, 0 Emsley, 1073 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  289 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 288
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   19 TRP cc_start: 0.8099 (t60) cc_final: 0.7889 (t60)
REVERT: C   80 HIS cc_start: 0.8685 (m90) cc_final: 0.8262 (m90)
REVERT: C   81 LEU cc_start: 0.9276 (mt) cc_final: 0.8359 (pp)
REVERT: C   85 GLU cc_start: 0.8781 (tp30) cc_final: 0.7861 (pt0)
REVERT: C   91 ARG cc_start: 0.5475 (mtt90) cc_final: 0.3717 (ptm160)
REVERT: C   99 PHE cc_start: 0.8510 (m-80) cc_final: 0.8109 (m-10)
REVERT: C  104 ILE cc_start: 0.8881 (tp) cc_final: 0.8571 (pt)
REVERT: C  112 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7464 (tm-30)
REVERT: C  176 PHE cc_start: 0.8257 (p90) cc_final: 0.7800 (p90)
REVERT: C  177 MET cc_start: 0.8795 (tmm) cc_final: 0.8352 (tmm)
REVERT: B    5 ASN cc_start: 0.6947 (p0) cc_final: 0.4947 (t0)
REVERT: B    9 GLN cc_start: 0.8619 (mt0) cc_final: 0.8073 (mt0)
REVERT: B   37 GLN cc_start: 0.9220 (tt0) cc_final: 0.8823 (tm-30)
REVERT: B   61 LEU cc_start: 0.9567 (mt) cc_final: 0.9339 (tt)
REVERT: B   79 HIS cc_start: 0.8497 (m90) cc_final: 0.8015 (m-70)
REVERT: B   80 GLU cc_start: 0.9276 (pt0) cc_final: 0.8819 (pp20)
REVERT: B   88 PHE cc_start: 0.8879 (m-80) cc_final: 0.8317 (t80)
REVERT: B   93 THR cc_start: 0.9548 (p) cc_final: 0.9270 (p)
REVERT: B  106 PHE cc_start: 0.8288 (m-80) cc_final: 0.7608 (p90)
REVERT: B  114 LEU cc_start: 0.9361 (tp) cc_final: 0.8816 (tp)
REVERT: B  115 LEU cc_start: 0.9667 (tp) cc_final: 0.9465 (tp)
REVERT: B  118 LEU cc_start: 0.9476 (mm) cc_final: 0.9202 (mm)
REVERT: B  119 LYS cc_start: 0.9466 (mtmt) cc_final: 0.8997 (mtmm)
REVERT: B  121 PHE cc_start: 0.8726 (m-80) cc_final: 0.8341 (m-80)
REVERT: B  152 PHE cc_start: 0.6766 (m-80) cc_final: 0.6308 (m-80)
REVERT: B  163 GLN cc_start: 0.8561 (tt0) cc_final: 0.8073 (tp-100)
REVERT: B  175 ASN cc_start: 0.8662 (m-40) cc_final: 0.8414 (p0)
REVERT: B  193 PHE cc_start: 0.8892 (m-80) cc_final: 0.8607 (m-80)
REVERT: B  206 GLN cc_start: 0.8905 (tm-30) cc_final: 0.8686 (tm-30)
REVERT: B  298 MET cc_start: 0.9166 (tmm) cc_final: 0.8919 (tmm)
REVERT: B  306 ASP cc_start: 0.8170 (m-30) cc_final: 0.7746 (m-30)
REVERT: A   69 ASN cc_start: 0.9030 (m110) cc_final: 0.8698 (t0)
REVERT: A  186 ASN cc_start: 0.7970 (OUTLIER) cc_final: 0.7251 (t0)
REVERT: A  219 GLU cc_start: 0.8666 (mm-30) cc_final: 0.8369 (mm-30)
REVERT: A  336 GLN cc_start: 0.8937 (tt0) cc_final: 0.8567 (tt0)
REVERT: A  374 GLN cc_start: 0.8945 (mt0) cc_final: 0.8287 (mm-40)
REVERT: A  388 LYS cc_start: 0.8971 (mmmm) cc_final: 0.8631 (mmtm)
REVERT: A  406 ARG cc_start: 0.8951 (mmm-85) cc_final: 0.8746 (mmm-85)
REVERT: A  472 LEU cc_start: 0.9443 (mm) cc_final: 0.9060 (mm)
REVERT: A  473 MET cc_start: 0.8256 (mmm) cc_final: 0.7913 (mmm)
REVERT: A  481 PHE cc_start: 0.7944 (t80) cc_final: 0.7244 (t80)
REVERT: A  520 MET cc_start: 0.8057 (mmm) cc_final: 0.7779 (mmm)
REVERT: A  577 ASP cc_start: 0.9135 (p0) cc_final: 0.8407 (t70)
REVERT: A  619 TYR cc_start: 0.9053 (m-80) cc_final: 0.8759 (m-80)
REVERT: D  786 LYS cc_start: 0.9412 (tmmt) cc_final: 0.9163 (tmmt)
  outliers start: 1
  outliers final: 0
  residues processed: 289
  average time/residue: 0.0733
  time to fit residues: 30.7128
Evaluate side-chains
  238 residues out of total 984 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 237
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 6 optimal weight:    9.9990
   chunk 41 optimal weight:    7.9990
   chunk 60 optimal weight:    0.0270
   chunk 49 optimal weight:    5.9990
   chunk 94 optimal weight:    0.3980
   chunk 67 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 3 optimal weight:   10.0000
   chunk 56 optimal weight:    0.4980
   overall best weight:    0.4238

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

Flipped N/Q/H residues before XYZ refinement:
B  47 ASN
** A  86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 336 GLN
A 633 ASN
** D 745 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.116428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.087776 restraints weight = 27858.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090176 restraints weight = 16869.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.091733 restraints weight = 11971.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.092762 restraints weight = 9463.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.093415 restraints weight = 8051.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7815
moved from start:          0.5774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   9221  Z= 0.128
  Angle     :  0.662  10.071  12491  Z= 0.334
  Chirality :  0.040   0.190   1388
  Planarity :  0.004   0.056   1546
  Dihedral  :  4.322  20.767   1204
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.20 %
    Favored  : 99.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.61 (0.26), residues: 1073
  helix:  1.99 (0.18), residues: 829
  sheet:  None (None), residues: 0
  loop : -2.32 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  33 
 TYR   0.024   0.001   TYR C  44 
 PHE   0.035   0.001   PHE B 152 
 TRP   0.039   0.001   TRP A 541 
 HIS   0.003   0.000   HIS A 122 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9221)
  covalent geometry    : angle       0.66220 (12491)
  hydrogen bonds       : bond        0.03731 (  633)
  hydrogen bonds       : angle       4.07484 ( 1890)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1599.79 seconds
wall clock time: 28 minutes 17.46 seconds (1697.46 seconds total)