Starting phenix.real_space_refine
on Tue Mar 11 18:00:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7dqa_30816/03_2025/7dqa_30816.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7dqa_30816/03_2025/7dqa_30816.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2025/7dqa_30816.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2025/7dqa_30816.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2025/7dqa_30816.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7dqa_30816/03_2025/7dqa_30816.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      37      5.16       5
     Cl      1      4.86       5
     C    4151      2.51       5
     N    1070      2.21       5
     O    1316      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6576
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4877
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
      Conformer: "B"
        Number of residues, atoms: 597, 4870
          Classifications: {'peptide': 597}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 569}
          bond proxies already assigned to first conformer: 4998
    Chain: "C"
      Number of atoms: 1547
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 194, 1541
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
      Conformer: "B"
        Number of residues, atoms: 194, 1541
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 10, 'TRANS': 183}
          bond proxies already assigned to first conformer: 1577
    Chain: "A"
      Number of atoms: 58
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 58
          Unusual residues: {' CL': 1, ' ZN': 1, 'NAG': 4}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 71
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 71, 71
          Classifications: {'water': 71}
          Link IDs: {None: 70}
    Chain: "C"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 9
          Classifications: {'water': 9}
          Link IDs: {None: 8}
  Time building chain proxies: 7.79, per 1000 atoms: 1.18
  Number of scatterers: 6576
  At special positions: 0
  Unit cell: (101.362, 96.3937, 102.356, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Cl      1     17.00
     S      37     16.00
     O    1316      8.00
     N    1070      7.00
     C    4151      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 133 " - pdb=" SG  CYS A 141 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 344 " - pdb=" SG  CYS A 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 530 " - pdb=" SG  CYS A 542 " distance=2.02
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 903 " - " ASN A 546 "
      " NAG A 904 " - " ASN A  90 "
      " NAG A 905 " - " ASN A 322 "
      " NAG A 906 " - " ASN A  53 "
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 901 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 374 "
        pdb="ZN    ZN A 901 " - pdb=" NE2 HIS A 378 "


  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      37 helices and 6 sheets defined
      56.9% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 53
      removed outlier: 3.847A  pdb=" N   HIS A  34 " --> pdb=" O   ASP A  30 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   ASP A  38 " --> pdb=" O   HIS A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 55 through 81
    Processing helix  chain 'A' and resid 82 through 83
      No H-bonds generated for 'chain 'A' and resid 82 through 83'
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.749A  pdb=" N   GLU A  87 " --> pdb=" O   PRO A  84 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ILE A  88 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 84 through 88'
    Processing helix  chain 'A' and resid 90 through 102
    Processing helix  chain 'A' and resid 103 through 108
    Processing helix  chain 'A' and resid 109 through 129
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 157 through 193
      removed outlier: 4.612A  pdb=" N   LYS A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   GLN A 175 " --> pdb=" O   GLU A 171 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A 176 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      Proline residue:  A 178  - end of helix
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 220 through 252
      Proline residue:  A 235  - end of helix
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 278 through 283
    Processing helix  chain 'A' and resid 293 through 300
      removed outlier: 3.601A  pdb=" N   GLN A 300 " --> pdb=" O   ALA A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 319
      removed outlier: 3.703A  pdb=" N   VAL A 318 " --> pdb=" O   PHE A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 365 through 385
      removed outlier: 3.722A  pdb=" N   HIS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 393
    Processing helix  chain 'A' and resid 399 through 413
      removed outlier: 3.772A  pdb=" N   ALA A 403 " --> pdb=" O   GLY A 399 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   MET A 408 " --> pdb=" O   VAL A 404 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   SER A 409 " --> pdb=" O   GLY A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 421
    Processing helix  chain 'A' and resid 431 through 447
    Processing helix  chain 'A' and resid 449 through 465
    Processing helix  chain 'A' and resid 469 through 471
      No H-bonds generated for 'chain 'A' and resid 469 through 471'
    Processing helix  chain 'A' and resid 472 through 484
      removed outlier: 3.725A  pdb=" N   GLU A 479 " --> pdb=" O   LYS A 475 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ARG A 482 " --> pdb=" O   TRP A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 503
      removed outlier: 3.870A  pdb=" N   LEU A 503 " --> pdb=" O   ASP A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 508
    Processing helix  chain 'A' and resid 513 through 533
    Processing helix  chain 'A' and resid 547 through 559
      removed outlier: 4.131A  pdb=" N   MET A 557 " --> pdb=" O   LYS A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 564
      removed outlier: 3.757A  pdb=" N   SER A 563 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   GLU A 564 " --> pdb=" O   GLY A 561 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 560 through 564'
    Processing helix  chain 'A' and resid 565 through 575
    Processing helix  chain 'A' and resid 581 through 588
    Processing helix  chain 'A' and resid 588 through 599
    Processing helix  chain 'C' and resid 337 through 344
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'C' and resid 385 through 390
      removed outlier: 4.034A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU C 390 " --> pdb=" O   LEU C 387 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 410
    Processing helix  chain 'C' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 132 through 133
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
      removed outlier: 6.153A  pdb=" N   LEU A 262 " --> pdb=" O   VAL A 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 350
    Processing sheet with id=AA4, first strand: chain 'C' and resid 354 through 358
    Processing sheet with id=AA5, first strand: chain 'C' and resid 452 through 453
    Processing sheet with id=AA6, first strand: chain 'C' and resid 473 through 474

    319 hydrogen bonds defined for protein.
    905 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.83 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2085
        1.35 -     1.47: 1808
        1.47 -     1.60: 2726
        1.60 -     1.72: 0
        1.72 -     1.85: 58
  Bond restraints: 6677
  Sorted by residual:
  bond pdb=" N   CYS A 498 "
       pdb=" CA  CYS A 498 "
    ideal  model  delta    sigma   weight residual
    1.460  1.428  0.031 1.50e-02 4.44e+03 4.37e+00
  bond pdb=" C1  NAG A 905 "
       pdb=" O5  NAG A 905 "
    ideal  model  delta    sigma   weight residual
    1.406  1.447 -0.041 2.00e-02 2.50e+03 4.26e+00
  bond pdb=" CB  VAL A 581 "
       pdb=" CG1 VAL A 581 "
    ideal  model  delta    sigma   weight residual
    1.521  1.455  0.066 3.30e-02 9.18e+02 4.01e+00
  bond pdb=" C1  NAG A 906 "
       pdb=" O5  NAG A 906 "
    ideal  model  delta    sigma   weight residual
    1.406  1.438 -0.032 2.00e-02 2.50e+03 2.63e+00
  bond pdb=" CB  TRP A 566 "
       pdb=" CG  TRP A 566 "
    ideal  model  delta    sigma   weight residual
    1.498  1.451  0.047 3.10e-02 1.04e+03 2.27e+00
  ... (remaining 6672 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.78: 8944
        2.78 -     5.57: 120
        5.57 -     8.35: 12
        8.35 -    11.13: 2
       11.13 -    13.91: 1
  Bond angle restraints: 9079
  Sorted by residual:
  angle pdb=" CA  CYS A 141 "
        pdb=" CB  CYS A 141 "
        pdb=" SG  CYS A 141 "
      ideal   model   delta    sigma   weight residual
     114.40  123.74   -9.34 2.30e+00 1.89e-01 1.65e+01
  angle pdb=" C   VAL A 581 "
        pdb=" CA  VAL A 581 "
        pdb=" CB  VAL A 581 "
      ideal   model   delta    sigma   weight residual
     111.85  106.72    5.13 1.27e+00 6.20e-01 1.63e+01
  angle pdb=" CA  LEU A  73 "
        pdb=" CB  LEU A  73 "
        pdb=" CG  LEU A  73 "
      ideal   model   delta    sigma   weight residual
     116.30  130.21  -13.91 3.50e+00 8.16e-02 1.58e+01
  angle pdb=" N   CYS A 498 "
        pdb=" CA  CYS A 498 "
        pdb=" C   CYS A 498 "
      ideal   model   delta    sigma   weight residual
     110.06  104.49    5.57 1.43e+00 4.89e-01 1.52e+01
  angle pdb=" C   PHE C 497 "
        pdb=" N   GLN C 498 "
        pdb=" CA  GLN C 498 "
      ideal   model   delta    sigma   weight residual
     122.48  116.77    5.71 1.62e+00 3.81e-01 1.24e+01
  ... (remaining 9074 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 3452
       17.91 -    35.83: 402
       35.83 -    53.74: 116
       53.74 -    71.65: 28
       71.65 -    89.56: 11
  Dihedral angle restraints: 4009
    sinusoidal: 1679
      harmonic: 2330
  Sorted by residual:
  dihedral pdb=" CA  CYS A 141 "
           pdb=" C   CYS A 141 "
           pdb=" N   LEU A 142 "
           pdb=" CA  LEU A 142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.75  -27.25     0      5.00e+00 4.00e-02 2.97e+01
  dihedral pdb=" CA  LEU C 390 "
           pdb=" C   LEU C 390 "
           pdb=" N   CYS C 391 "
           pdb=" CA  CYS C 391 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.18  -25.82     0      5.00e+00 4.00e-02 2.67e+01
  dihedral pdb=" CA  VAL C 524 "
           pdb=" C   VAL C 524 "
           pdb=" N   CYS C 525 "
           pdb=" CA  CYS C 525 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.00  -25.00     0      5.00e+00 4.00e-02 2.50e+01
  ... (remaining 4006 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 679
       0.052 -    0.104: 244
       0.104 -    0.156: 38
       0.156 -    0.209: 1
       0.209 -    0.261: 2
  Chirality restraints: 964
  Sorted by residual:
  chirality pdb=" C1  NAG A 905 "
            pdb=" ND2 ASN A 322 "
            pdb=" C2  NAG A 905 "
            pdb=" O5  NAG A 905 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.14   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" C1  NAG A 906 "
            pdb=" ND2 ASN A  53 "
            pdb=" C2  NAG A 906 "
            pdb=" O5  NAG A 906 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.62    0.22 2.00e-01 2.50e+01 1.17e+00
  chirality pdb=" CA  CYS C 432 "
            pdb=" N   CYS C 432 "
            pdb=" C   CYS C 432 "
            pdb=" CB  CYS C 432 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.95e-01
  ... (remaining 961 not shown)

  Planarity restraints: 1178
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 498 "   -0.043 5.00e-02 4.00e+02   6.52e-02 6.80e+00
        pdb=" N   PRO C 499 "    0.113 5.00e-02 4.00e+02
        pdb=" CA  PRO C 499 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 499 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS A 234 "    0.029 5.00e-02 4.00e+02   4.45e-02 3.16e+00
        pdb=" N   PRO A 235 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A 235 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A 235 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  CYS A 498 "   -0.008 2.00e-02 2.50e+03   1.68e-02 2.82e+00
        pdb=" C   CYS A 498 "    0.029 2.00e-02 2.50e+03
        pdb=" O   CYS A 498 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 499 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1175 not shown)

  Histogram of nonbonded interaction distances:
        1.92 -     2.51: 102
        2.51 -     3.11: 5149
        3.11 -     3.71: 10900
        3.71 -     4.30: 15977
        4.30 -     4.90: 25314
  Nonbonded interactions: 57442
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 402 "
            pdb="ZN    ZN A 901 "
     model   vdw
     1.918 2.230
  nonbonded pdb=" O   PHE A 327 "
            pdb=" OG  SER A 331 "
     model   vdw
     2.007 3.040
  nonbonded pdb=" OH  TYR A 183 "
            pdb=" OD1 ASP A 509 "
     model   vdw
     2.043 3.040
  nonbonded pdb=" O   HOH A1022 "
            pdb=" O   HOH A1034 "
     model   vdw
     2.069 3.040
  nonbonded pdb=" O   HOH A1011 "
            pdb=" O   HOH A1052 "
     model   vdw
     2.100 3.040
  ... (remaining 57437 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.470
  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:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     24.980
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.040
  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:14.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6740
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      :  0.007   0.066   6677  Z= 0.485
  Angle     :  0.863  13.914   9079  Z= 0.492
  Chirality :  0.051   0.261    964
  Planarity :  0.005   0.065   1173
  Dihedral  : 17.506  89.563   2494
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 18.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  6.03 %
    Allowed  : 19.80 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.29 (0.24), residues: 789
  helix: -2.34 (0.19), residues: 393
  sheet: -1.53 (0.62), residues: 58
  loop : -1.91 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  48 
 HIS   0.006   0.002   HIS A  34 
 PHE   0.016   0.003   PHE A 285 
 TYR   0.021   0.002   TYR C 495 
 ARG   0.008   0.001   ARG C 357 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 147
  time to evaluate  : 0.666 
Fit side-chains
REVERT: A   23 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6902 (mm-30)
REVERT: A   30 ASP cc_start: 0.6792 (OUTLIER) cc_final: 0.6469 (t0)
REVERT: A   62 MET cc_start: 0.7554 (ttt) cc_final: 0.7204 (ttp)
REVERT: A   68 LYS cc_start: 0.6424 (mtpp) cc_final: 0.6189 (tttm)
REVERT: A   73 LEU cc_start: 0.5589 (OUTLIER) cc_final: 0.4740 (mt)
REVERT: A  131 LYS cc_start: 0.7440 (ptpp) cc_final: 0.7196 (ptmm)
REVERT: A  136 ASP cc_start: 0.3336 (OUTLIER) cc_final: 0.2870 (p0)
REVERT: A  146 PRO cc_start: 0.6097 (Cg_endo) cc_final: 0.5814 (Cg_exo)
REVERT: A  151 ILE cc_start: 0.6579 (mt) cc_final: 0.5640 (mp)
REVERT: A  159 ASN cc_start: 0.6007 (m-40) cc_final: 0.5716 (m110)
REVERT: A  249 MET cc_start: 0.5732 (ptt) cc_final: 0.5487 (ttp)
REVERT: A  313 LYS cc_start: 0.6775 (ttmt) cc_final: 0.6532 (mtpp)
REVERT: A  314 PHE cc_start: 0.7063 (t80) cc_final: 0.6496 (t80)
REVERT: A  341 LYS cc_start: 0.6040 (tptt) cc_final: 0.5729 (tttm)
REVERT: A  368 ASP cc_start: 0.7211 (t0) cc_final: 0.6560 (m-30)
REVERT: A  401 HIS cc_start: 0.8637 (OUTLIER) cc_final: 0.8186 (m-70)
REVERT: A  429 GLN cc_start: 0.5970 (OUTLIER) cc_final: 0.5184 (tm-30)
REVERT: A  540 HIS cc_start: 0.7053 (p-80) cc_final: 0.6777 (p90)
REVERT: A  600 LYS cc_start: 0.6515 (mtmt) cc_final: 0.6286 (mtmm)
REVERT: C  356 LYS cc_start: 0.6965 (mptt) cc_final: 0.6707 (mtpp)
REVERT: C  459 SER cc_start: 0.6597 (OUTLIER) cc_final: 0.6086 (p)
REVERT: C  467 ASP cc_start: 0.5688 (t0) cc_final: 0.5427 (t0)
REVERT: C  516 GLU cc_start: 0.5748 (OUTLIER) cc_final: 0.4887 (pp20)
  outliers start: 40
  outliers final: 6
  residues processed: 183
  average time/residue: 1.0204
  time to fit residues: 197.8538
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 ASP
Chi-restraints excluded: chain A residue   73 LEU
Chi-restraints excluded: chain A residue  124 SER
Chi-restraints excluded: chain A residue  136 ASP
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  401 HIS
Chi-restraints excluded: chain A residue  411 SER
Chi-restraints excluded: chain A residue  429 GLN
Chi-restraints excluded: chain A residue  449 THR
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain C residue  459 SER
Chi-restraints excluded: chain C residue  516 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.2980
   chunk 39 optimal weight:    0.7980
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 102 GLN
A 117 ASN
A 194 ASN
A 239 HIS
A 325 GLN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 442 GLN
A 531 GLN
A 535 HIS
A 580 ASN
C 388 ASN
C 450 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.180706 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151928 restraints weight = 17659.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3741 rms_B_bonded: 3.71
r_work: 0.3473 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3452
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3452 r_free = 0.3452    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3452
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   6677  Z= 0.229
  Angle     :  0.662   8.242   9079  Z= 0.347
  Chirality :  0.044   0.183    964
  Planarity :  0.005   0.041   1173
  Dihedral  :  7.922  60.507    989
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 25.25 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.27), residues: 789
  helix: -0.46 (0.23), residues: 399
  sheet: -1.34 (0.70), residues: 47
  loop : -0.88 (0.32), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.008   0.001   HIS A 374 
 PHE   0.018   0.002   PHE A 588 
 TYR   0.016   0.002   TYR A 385 
 ARG   0.008   0.001   ARG A 219 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 110
  time to evaluate  : 0.673 
Fit side-chains
REVERT: A   23 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7530 (mm-30)
REVERT: A  151 ILE cc_start: 0.6642 (mt) cc_final: 0.6379 (mp)
REVERT: A  249 MET cc_start: 0.5525 (ptt) cc_final: 0.5225 (ttp)
REVERT: A  341 LYS cc_start: 0.6388 (tptt) cc_final: 0.6070 (tttm)
REVERT: A  408 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7328 (mmt)
REVERT: A  597 ASP cc_start: 0.6288 (t0) cc_final: 0.6057 (t70)
REVERT: C  356 LYS cc_start: 0.7363 (mptt) cc_final: 0.7010 (mtpp)
REVERT: C  467 ASP cc_start: 0.5959 (t0) cc_final: 0.5658 (t0)
  outliers start: 21
  outliers final: 4
  residues processed: 124
  average time/residue: 1.0848
  time to fit residues: 142.3270
Evaluate side-chains
  93 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 0.685 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  463 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 36 optimal weight:    0.5980
   chunk 43 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   chunk 77 optimal weight:   30.0000
   chunk 47 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 76 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 194 ASN
A 210 ASN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.180711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.150339 restraints weight = 13970.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3718 rms_B_bonded: 2.68
r_work: 0.3532 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.3532
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3514
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3514 r_free = 0.3514    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3514 r_free = 0.3514    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3514
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7235
moved from start:          0.3130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6677  Z= 0.202
  Angle     :  0.613  10.317   9079  Z= 0.319
  Chirality :  0.044   0.200    964
  Planarity :  0.004   0.036   1173
  Dihedral  :  5.479  36.559    968
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 25.54 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.29), residues: 789
  helix:  0.35 (0.25), residues: 401
  sheet: -1.10 (0.67), residues: 48
  loop : -0.37 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 165 
 HIS   0.013   0.001   HIS A 540 
 PHE   0.013   0.002   PHE A 588 
 TYR   0.017   0.001   TYR A 521 
 ARG   0.004   0.001   ARG C 357 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.749 
Fit side-chains
REVERT: A  151 ILE cc_start: 0.6634 (mt) cc_final: 0.6334 (mp)
REVERT: A  171 GLU cc_start: 0.7322 (OUTLIER) cc_final: 0.6773 (mp0)
REVERT: A  297 MET cc_start: 0.6787 (mtm) cc_final: 0.6043 (mtp)
REVERT: A  300 GLN cc_start: 0.6283 (mt0) cc_final: 0.5799 (tt0)
REVERT: A  341 LYS cc_start: 0.6411 (tptt) cc_final: 0.6081 (tttm)
REVERT: A  408 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7301 (mmt)
REVERT: C  356 LYS cc_start: 0.7297 (mptt) cc_final: 0.7088 (tttp)
REVERT: C  446 GLU cc_start: 0.5750 (OUTLIER) cc_final: 0.5290 (mm-30)
REVERT: C  467 ASP cc_start: 0.5795 (t0) cc_final: 0.5381 (t0)
REVERT: C  468 ILE cc_start: 0.6998 (OUTLIER) cc_final: 0.6770 (mm)
  outliers start: 17
  outliers final: 4
  residues processed: 103
  average time/residue: 1.1287
  time to fit residues: 123.2809
Evaluate side-chains
  89 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.706 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  408 MET
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  446 GLU
Chi-restraints excluded: chain C residue  468 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 27 optimal weight:    6.9990
   chunk 31 optimal weight:    0.1980
   chunk 16 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 36 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 19 optimal weight:    0.7980
   chunk 60 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 121 ASN
A 194 ASN
A 210 ASN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
C 474 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.182365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152490 restraints weight = 11113.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3755 rms_B_bonded: 1.90
r_work: 0.3592 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3487 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3462
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3462 r_free = 0.3462    target_work(ls_wunit_k1) = 0.128         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3462
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6677  Z= 0.182
  Angle     :  0.575  11.559   9079  Z= 0.298
  Chirality :  0.042   0.183    964
  Planarity :  0.004   0.034   1173
  Dihedral  :  4.886  35.889    968
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 25.25 %
    Favored  : 71.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.29), residues: 789
  helix:  0.73 (0.25), residues: 400
  sheet: -0.68 (0.70), residues: 46
  loop : -0.21 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.011   0.001   PHE A 315 
 TYR   0.018   0.001   TYR A 521 
 ARG   0.004   0.001   ARG C 357 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.702 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 GLN cc_start: 0.6326 (mp10) cc_final: 0.5991 (mp10)
REVERT: A  114 LYS cc_start: 0.7795 (ptmm) cc_final: 0.7062 (pttp)
REVERT: A  171 GLU cc_start: 0.7376 (OUTLIER) cc_final: 0.6414 (mp0)
REVERT: A  300 GLN cc_start: 0.6374 (mt0) cc_final: 0.5922 (tt0)
REVERT: A  341 LYS cc_start: 0.6467 (tptt) cc_final: 0.6092 (tttm)
REVERT: C  356 LYS cc_start: 0.7349 (mptt) cc_final: 0.7126 (tttp)
REVERT: C  418 ILE cc_start: 0.7467 (mp) cc_final: 0.7141 (mp)
REVERT: C  446 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5437 (mm-30)
REVERT: C  467 ASP cc_start: 0.5911 (t0) cc_final: 0.5410 (t0)
REVERT: C  468 ILE cc_start: 0.6978 (OUTLIER) cc_final: 0.6708 (mm)
  outliers start: 20
  outliers final: 8
  residues processed: 112
  average time/residue: 1.1360
  time to fit residues: 134.5972
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue  142 LEU
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  446 GLU
Chi-restraints excluded: chain C residue  468 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   chunk 44 optimal weight:    4.9990
   chunk 74 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    6.9990
   chunk 66 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
A 121 ASN
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
A 535 HIS
C 474 GLN
** C 498 GLN ** 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 = 0.4031 r_free = 0.4031 target = 0.177246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.146797 restraints weight = 17730.576|
|-----------------------------------------------------------------------------|
r_work (start): 0.3683 rms_B_bonded: 3.31
r_work: 0.3410 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3398
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3398 r_free = 0.3398    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3397 r_free = 0.3397    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3397
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7364
moved from start:          0.3709

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6677  Z= 0.252
  Angle     :  0.648  10.341   9079  Z= 0.333
  Chirality :  0.045   0.167    964
  Planarity :  0.004   0.032   1173
  Dihedral  :  5.145  35.525    968
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 25.39 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.29), residues: 789
  helix:  0.57 (0.25), residues: 403
  sheet: -0.21 (0.78), residues: 47
  loop : -0.32 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 594 
 HIS   0.006   0.001   HIS A 195 
 PHE   0.019   0.002   PHE A 285 
 TYR   0.022   0.002   TYR A 521 
 ARG   0.004   0.001   ARG A 192 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A  121 ASN cc_start: 0.7935 (m-40) cc_final: 0.7263 (t0)
REVERT: A  146 PRO cc_start: 0.7409 (Cg_endo) cc_final: 0.6894 (Cg_exo)
REVERT: A  151 ILE cc_start: 0.7140 (mt) cc_final: 0.6931 (tt)
REVERT: A  171 GLU cc_start: 0.7486 (OUTLIER) cc_final: 0.6482 (mp0)
REVERT: A  249 MET cc_start: 0.5839 (mtp) cc_final: 0.5471 (ttp)
REVERT: A  300 GLN cc_start: 0.6419 (mt0) cc_final: 0.5983 (tt0)
REVERT: A  341 LYS cc_start: 0.6525 (tptt) cc_final: 0.6146 (tttm)
REVERT: C  356 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7280 (tttp)
  outliers start: 18
  outliers final: 8
  residues processed: 102
  average time/residue: 1.0915
  time to fit residues: 118.2358
Evaluate side-chains
  92 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain C residue  356 LYS
Chi-restraints excluded: chain C residue  443 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 65 optimal weight:    8.9990
   chunk 57 optimal weight:    0.7980
   chunk 12 optimal weight:    9.9990
   chunk 77 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 40 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 34 optimal weight:    0.3980
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
A 535 HIS
** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.182127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.152407 restraints weight = 13425.822|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 2.81
r_work: 0.3525 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3513
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3513 r_free = 0.3513    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3513
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7251
moved from start:          0.3975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6677  Z= 0.205
  Angle     :  0.608   8.830   9079  Z= 0.311
  Chirality :  0.043   0.144    964
  Planarity :  0.004   0.033   1173
  Dihedral  :  4.918  35.792    968
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 26.54 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.29), residues: 789
  helix:  0.76 (0.25), residues: 400
  sheet: -0.29 (0.78), residues: 46
  loop : -0.26 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.021   0.002   PHE C 486 
 TYR   0.021   0.002   TYR A 521 
 ARG   0.003   0.001   ARG C 357 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.714 
Fit side-chains
   revert: symmetry clash
REVERT: A   82 MET cc_start: 0.6029 (mmt) cc_final: 0.5506 (tpp)
REVERT: A  146 PRO cc_start: 0.7444 (Cg_endo) cc_final: 0.6931 (Cg_exo)
REVERT: A  163 TRP cc_start: 0.7444 (t60) cc_final: 0.7167 (t60)
REVERT: A  171 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6341 (mp0)
REVERT: A  249 MET cc_start: 0.5617 (mtp) cc_final: 0.5266 (ttp)
REVERT: A  300 GLN cc_start: 0.6368 (mt0) cc_final: 0.5941 (tt0)
REVERT: A  341 LYS cc_start: 0.6433 (tptt) cc_final: 0.6079 (tttm)
REVERT: A  470 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7735 (ttpt)
REVERT: C  467 ASP cc_start: 0.6179 (t0) cc_final: 0.5786 (t0)
  outliers start: 12
  outliers final: 7
  residues processed: 100
  average time/residue: 1.1108
  time to fit residues: 117.6049
Evaluate side-chains
  91 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  443 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 51 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 38 optimal weight:    1.9990
   chunk 22 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 61 optimal weight:    5.9990
   chunk 71 optimal weight:    0.0570
   chunk 64 optimal weight:    3.9990
   chunk 14 optimal weight:    5.9990
   chunk 40 optimal weight:    3.9990
   overall best weight:    1.8104

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

Flipped N/Q/H residues before XYZ refinement:
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
** A 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
C 474 GLN
** C 498 GLN ** 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 = 0.4018 r_free = 0.4018 target = 0.175647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.145458 restraints weight = 11791.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3670 rms_B_bonded: 2.04
r_work: 0.3490 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3367 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3357
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3357 r_free = 0.3357    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3357
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7409
moved from start:          0.4110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   6677  Z= 0.281
  Angle     :  0.671   8.806   9079  Z= 0.343
  Chirality :  0.045   0.141    964
  Planarity :  0.004   0.032   1173
  Dihedral  :  5.147  35.651    968
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 10.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 26.11 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.29), residues: 789
  helix:  0.55 (0.25), residues: 403
  sheet: -0.05 (0.84), residues: 45
  loop : -0.38 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.022   0.002   PHE A 285 
 TYR   0.023   0.002   TYR A 521 
 ARG   0.004   0.001   ARG C 509 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   37 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6736 (tp30)
REVERT: A   82 MET cc_start: 0.6230 (mmt) cc_final: 0.5869 (mmp)
REVERT: A  146 PRO cc_start: 0.7797 (Cg_endo) cc_final: 0.7207 (Cg_exo)
REVERT: A  159 ASN cc_start: 0.7359 (t0) cc_final: 0.6917 (t0)
REVERT: A  163 TRP cc_start: 0.7649 (t60) cc_final: 0.7334 (t60)
REVERT: A  171 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.6610 (mp0)
REVERT: A  249 MET cc_start: 0.5928 (mtp) cc_final: 0.5481 (ttp)
REVERT: A  300 GLN cc_start: 0.6552 (mt0) cc_final: 0.6023 (tt0)
REVERT: A  341 LYS cc_start: 0.6588 (tptt) cc_final: 0.6266 (tttm)
REVERT: A  474 MET cc_start: 0.8100 (mmp) cc_final: 0.7436 (mmp)
  outliers start: 18
  outliers final: 9
  residues processed: 103
  average time/residue: 1.1965
  time to fit residues: 130.2019
Evaluate side-chains
  94 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue   52 THR
Chi-restraints excluded: chain A residue   92 THR
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain A residue  591 LEU
Chi-restraints excluded: chain C residue  443 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 55 optimal weight:    0.0970
   chunk 75 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 GLN
A 535 HIS
** C 498 GLN ** 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 = 0.4069 r_free = 0.4069 target = 0.180679 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.150189 restraints weight = 15106.873|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.93
r_work: 0.3523 rms_B_bonded: 3.21 restraints_weight: 0.5000
r_work (final): 0.3523
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3511
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3511 r_free = 0.3511    target_work(ls_wunit_k1) = 0.132         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3511
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7261
moved from start:          0.4334

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6677  Z= 0.190
  Angle     :  0.610   8.247   9079  Z= 0.313
  Chirality :  0.043   0.135    964
  Planarity :  0.004   0.033   1173
  Dihedral  :  4.865  35.620    968
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 10.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.87 %
    Allowed  : 27.69 %
    Favored  : 70.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.25 (0.29), residues: 789
  helix:  0.72 (0.25), residues: 406
  sheet: -0.09 (0.82), residues: 45
  loop : -0.36 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 594 
 HIS   0.006   0.001   HIS A 540 
 PHE   0.019   0.002   PHE C 486 
 TYR   0.022   0.002   TYR A 521 
 ARG   0.003   0.001   ARG A 482 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.656 
Fit side-chains
REVERT: A  146 PRO cc_start: 0.7668 (Cg_endo) cc_final: 0.7066 (Cg_exo)
REVERT: A  159 ASN cc_start: 0.7405 (t0) cc_final: 0.6971 (t0)
REVERT: A  171 GLU cc_start: 0.7328 (OUTLIER) cc_final: 0.6342 (mp0)
REVERT: A  249 MET cc_start: 0.5584 (mtp) cc_final: 0.5134 (ttp)
REVERT: A  300 GLN cc_start: 0.6607 (mt0) cc_final: 0.6048 (tt0)
REVERT: A  341 LYS cc_start: 0.6444 (tptt) cc_final: 0.6162 (tttm)
REVERT: A  474 MET cc_start: 0.7857 (mmp) cc_final: 0.7251 (mmp)
REVERT: C  467 ASP cc_start: 0.6057 (t0) cc_final: 0.5767 (t0)
REVERT: C  474 GLN cc_start: 0.5548 (tt0) cc_final: 0.4747 (tp-100)
  outliers start: 11
  outliers final: 6
  residues processed: 94
  average time/residue: 1.2043
  time to fit residues: 119.6559
Evaluate side-chains
  87 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 80
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain C residue  443 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 28 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 50 optimal weight:    1.9990
   chunk 36 optimal weight:    4.9990
   chunk 30 optimal weight:    0.0770
   chunk 2 optimal weight:    0.7980
   chunk 27 optimal weight:    0.7980
   chunk 71 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 70 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 535 HIS
** C 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.181982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.151622 restraints weight = 17056.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3715 rms_B_bonded: 4.00
r_work: 0.3490 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.3490
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3472
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3472 r_free = 0.3472    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3472
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7285
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6677  Z= 0.187
  Angle     :  0.603   8.638   9079  Z= 0.309
  Chirality :  0.042   0.136    964
  Planarity :  0.004   0.033   1173
  Dihedral  :  4.720  35.453    968
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 10.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 27.83 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.33 (0.29), residues: 789
  helix:  0.80 (0.25), residues: 409
  sheet: -0.10 (0.83), residues: 45
  loop : -0.35 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.013   0.001   PHE A 588 
 TYR   0.027   0.001   TYR C 351 
 ARG   0.004   0.001   ARG A 482 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 0.709 
Fit side-chains
REVERT: A  114 LYS cc_start: 0.7666 (ptmm) cc_final: 0.6875 (pttp)
REVERT: A  146 PRO cc_start: 0.7443 (Cg_endo) cc_final: 0.6967 (Cg_exo)
REVERT: A  159 ASN cc_start: 0.7619 (t0) cc_final: 0.7158 (t0)
REVERT: A  171 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6393 (mp0)
REVERT: A  249 MET cc_start: 0.5594 (mtp) cc_final: 0.5212 (ttp)
REVERT: A  300 GLN cc_start: 0.6578 (mt0) cc_final: 0.5996 (tt0)
REVERT: A  341 LYS cc_start: 0.6490 (tptt) cc_final: 0.6125 (tttm)
REVERT: A  470 LYS cc_start: 0.7779 (mtpp) cc_final: 0.7480 (ttmm)
REVERT: A  474 MET cc_start: 0.7901 (mmp) cc_final: 0.7333 (mmp)
REVERT: C  351 TYR cc_start: 0.7529 (p90) cc_final: 0.7065 (p90)
REVERT: C  406 GLU cc_start: 0.8107 (mt-10) cc_final: 0.7663 (tt0)
REVERT: C  467 ASP cc_start: 0.6113 (t0) cc_final: 0.5807 (t0)
REVERT: C  474 GLN cc_start: 0.5583 (tt0) cc_final: 0.4810 (tp-100)
REVERT: C  487 ASN cc_start: 0.5793 (OUTLIER) cc_final: 0.5330 (t0)
  outliers start: 8
  outliers final: 6
  residues processed: 95
  average time/residue: 1.2422
  time to fit residues: 124.2064
Evaluate side-chains
  88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 80
  time to evaluate  : 0.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain C residue  443 SER
Chi-restraints excluded: chain C residue  487 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 65 optimal weight:    8.9990
   chunk 33 optimal weight:    0.6980
   chunk 9 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 53 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 210 ASN
A 531 GLN
A 535 HIS
** C 498 GLN ** 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 = 0.4061 r_free = 0.4061 target = 0.180146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.149506 restraints weight = 14774.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 3.24
r_work: 0.3496 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3488
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3488 r_free = 0.3488    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3488
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7291
moved from start:          0.4523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6677  Z= 0.218
  Angle     :  0.620   8.675   9079  Z= 0.317
  Chirality :  0.043   0.137    964
  Planarity :  0.004   0.031   1173
  Dihedral  :  4.822  34.926    968
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 27.12 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.29), residues: 789
  helix:  0.79 (0.25), residues: 403
  sheet: -0.00 (0.83), residues: 45
  loop : -0.31 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.002   TRP A 594 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.016   0.002   PHE A 588 
 TYR   0.028   0.002   TYR C 351 
 ARG   0.005   0.001   ARG A 482 

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

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

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1578 Ramachandran restraints generated.
    789 Oldfield, 0 Emsley, 789 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.654 
Fit side-chains
REVERT: A   37 GLU cc_start: 0.6816 (OUTLIER) cc_final: 0.6588 (tp30)
REVERT: A  114 LYS cc_start: 0.7672 (ptmm) cc_final: 0.6885 (pttp)
REVERT: A  146 PRO cc_start: 0.7522 (Cg_endo) cc_final: 0.7050 (Cg_exo)
REVERT: A  159 ASN cc_start: 0.7428 (t0) cc_final: 0.6953 (t0)
REVERT: A  171 GLU cc_start: 0.7414 (OUTLIER) cc_final: 0.6382 (mp0)
REVERT: A  249 MET cc_start: 0.5609 (mtp) cc_final: 0.5245 (ttp)
REVERT: A  300 GLN cc_start: 0.6547 (mt0) cc_final: 0.5998 (tt0)
REVERT: A  341 LYS cc_start: 0.6481 (tptt) cc_final: 0.6147 (tttm)
REVERT: A  470 LYS cc_start: 0.7820 (mtpp) cc_final: 0.7513 (ttmm)
REVERT: A  474 MET cc_start: 0.7947 (mmp) cc_final: 0.7359 (mmp)
REVERT: C  351 TYR cc_start: 0.7541 (p90) cc_final: 0.7062 (p90)
REVERT: C  406 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7695 (tt0)
REVERT: C  467 ASP cc_start: 0.6228 (t0) cc_final: 0.5931 (t0)
REVERT: C  474 GLN cc_start: 0.5701 (tt0) cc_final: 0.4948 (tp-100)
  outliers start: 13
  outliers final: 7
  residues processed: 93
  average time/residue: 1.2501
  time to fit residues: 122.6560
Evaluate side-chains
  88 residues out of total 693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.714 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 THR
Chi-restraints excluded: chain A residue   37 GLU
Chi-restraints excluded: chain A residue   42 GLN
Chi-restraints excluded: chain A residue  171 GLU
Chi-restraints excluded: chain A residue  280 SER
Chi-restraints excluded: chain A residue  463 VAL
Chi-restraints excluded: chain A residue  475 LYS
Chi-restraints excluded: chain A residue  491 VAL
Chi-restraints excluded: chain C residue  443 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 49 optimal weight:    0.0570
   chunk 20 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0970
   chunk 71 optimal weight:    0.6980
   chunk 57 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   chunk 16 optimal weight:    0.2980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.3696

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

Flipped N/Q/H residues before XYZ refinement:
** A  42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 194 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.185276 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.155980 restraints weight = 11153.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 1.98
r_work: 0.3634 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3521 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3521
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3498
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3498 r_free = 0.3498    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3498
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7252
moved from start:          0.4770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6677  Z= 0.165
  Angle     :  0.583   8.888   9079  Z= 0.298
  Chirality :  0.042   0.136    964
  Planarity :  0.004   0.033   1173
  Dihedral  :  4.532  33.899    968
  Min Nonbonded Distance : 2.062

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 27.69 %
    Favored  : 70.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.70 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.30), residues: 789
  helix:  0.95 (0.26), residues: 406
  sheet: -0.06 (0.83), residues: 45
  loop : -0.18 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 594 
 HIS   0.005   0.001   HIS A 540 
 PHE   0.011   0.001   PHE A 588 
 TYR   0.026   0.001   TYR C 351 
 ARG   0.003   0.000   ARG A 482 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5554.26 seconds
wall clock time: 95 minutes 35.87 seconds (5735.87 seconds total)