Starting phenix.real_space_refine
on Mon Jul 28 13:12:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sea_40408/07_2025/8sea_40408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sea_40408/07_2025/8sea_40408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sea_40408/07_2025/8sea_40408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sea_40408/07_2025/8sea_40408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sea_40408/07_2025/8sea_40408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sea_40408/07_2025/8sea_40408.cif"
  }
  resolution = 3.4
  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=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      37      5.16       5
     C    6490      2.51       5
     N    1792      2.21       5
     O    1888      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10208
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 992, 7712
          Classifications: {'peptide': 992}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 65, 'TRANS': 926}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 4, 'TRANS': 74}
    Chain: "C"
      Number of atoms: 1243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1243
          Classifications: {'peptide': 152}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133}
    Chain: "D"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 603
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'GLY%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Unusual residues: {'AMP%rna2p': 1}
          Classifications: {'RNA_mixed': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 6.79, per 1000 atoms: 0.67
  Number of scatterers: 10208
  At special positions: 0
  Unit cell: (91.652, 104.983, 117.481, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     P       1     15.00
     O    1888      8.00
     N    1792      7.00
     C    6490      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.39
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2426

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 13 sheets defined
      44.9% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.52
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 32
      removed outlier: 4.059A  pdb=" N   ARG A  29 " --> pdb=" O   PRO A  25 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN A  31 " --> pdb=" O   MET A  27 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 55
    Processing helix  chain 'A' and resid 69 through 74
      removed outlier: 3.527A  pdb=" N   ALA A  74 " --> pdb=" O   ASP A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 99
      removed outlier: 4.077A  pdb=" N   GLU A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LEU A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 119
    Processing helix  chain 'A' and resid 128 through 142
    Processing helix  chain 'A' and resid 197 through 203
      removed outlier: 4.031A  pdb=" N   HIS A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 221
      removed outlier: 3.517A  pdb=" N   ASN A 221 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 221'
    Processing helix  chain 'A' and resid 266 through 273
      removed outlier: 4.330A  pdb=" N   LEU A 272 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLN A 273 " --> pdb=" O   THR A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 305
    Processing helix  chain 'A' and resid 312 through 326
    Processing helix  chain 'A' and resid 327 through 331
    Processing helix  chain 'A' and resid 342 through 352
    Processing helix  chain 'A' and resid 357 through 378
    Processing helix  chain 'A' and resid 392 through 395
    Processing helix  chain 'A' and resid 404 through 409
    Processing helix  chain 'A' and resid 415 through 423
      removed outlier: 4.640A  pdb=" N   VAL A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 433
    Processing helix  chain 'A' and resid 442 through 455
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 4.128A  pdb=" N   VAL A 488 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 504
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.951A  pdb=" N   GLU A 521 " --> pdb=" O   PRO A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 532
      removed outlier: 3.522A  pdb=" N   VAL A 532 " --> pdb=" O   PHE A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 556
      removed outlier: 3.554A  pdb=" N   ARG A 545 " --> pdb=" O   SER A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 593
      removed outlier: 4.306A  pdb=" N   ASP A 593 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 607 through 631
      removed outlier: 3.870A  pdb=" N   LEU A 625 " --> pdb=" O   GLU A 621 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 627 " --> pdb=" O   PHE A 623 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU A 628 " --> pdb=" O   ARG A 624 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 637
      removed outlier: 3.554A  pdb=" N   HIS A 637 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 651
      removed outlier: 4.000A  pdb=" N   THR A 648 " --> pdb=" O   ASP A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 657
    Processing helix  chain 'A' and resid 672 through 681
    Processing helix  chain 'A' and resid 681 through 692
    Processing helix  chain 'A' and resid 721 through 740
      removed outlier: 3.518A  pdb=" N   LEU A 725 " --> pdb=" O   GLN A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 757
    Processing helix  chain 'A' and resid 761 through 765
      removed outlier: 4.070A  pdb=" N   MET A 765 " --> pdb=" O   PRO A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 800
      removed outlier: 3.914A  pdb=" N   GLN A 786 " --> pdb=" O   PHE A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 832
    Processing helix  chain 'A' and resid 838 through 845
      removed outlier: 3.557A  pdb=" N   SER A 842 " --> pdb=" O   ASN A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 873
    Processing helix  chain 'A' and resid 877 through 881
    Processing helix  chain 'A' and resid 927 through 940
    Processing helix  chain 'A' and resid 959 through 967
    Processing helix  chain 'A' and resid 970 through 980
    Processing helix  chain 'B' and resid 103 through 116
      removed outlier: 3.511A  pdb=" N   LEU B 107 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 17
      removed outlier: 3.701A  pdb=" N   LYS C  16 " --> pdb=" O   GLU C  12 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LYS C  17 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 47
      No H-bonds generated for 'chain 'C' and resid 45 through 47'
    Processing helix  chain 'C' and resid 100 through 114
      removed outlier: 3.873A  pdb=" N   VAL C 104 " --> pdb=" O   LYS C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 132
    Processing helix  chain 'C' and resid 132 through 148
    Processing helix  chain 'D' and resid 103 through 116
      removed outlier: 3.726A  pdb=" N   LEU D 107 " --> pdb=" O   THR D 103 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLN D 110 " --> pdb=" O   HIS D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 122
    Processing helix  chain 'D' and resid 136 through 141
      removed outlier: 4.430A  pdb=" N   TYR D 140 " --> pdb=" O   PRO D 136 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106
      removed outlier: 6.301A  pdb=" N   VAL A  35 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   HIS A  62 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   VAL A  37 " --> pdb=" O   HIS A  62 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 121 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 155 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106
      removed outlier: 6.301A  pdb=" N   VAL A  35 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   HIS A  62 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   VAL A  37 " --> pdb=" O   HIS A  62 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 121 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168
    Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179
      removed outlier: 4.492A  pdb=" N   LEU A 208 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 184
      removed outlier: 3.739A  pdb=" N   LEU A 236 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 214 through 216
    Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512
      removed outlier: 6.083A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU A 437 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   VAL A 535 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   ALA A 562 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ALA A 537 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 559 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 906
    Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 919
      removed outlier: 6.502A  pdb=" N   LEU A 917 " --> pdb=" O   HIS A1009 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   GLU A1011 " --> pdb=" O   LEU A 917 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   VAL A 919 " --> pdb=" O   GLU A1011 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU A 946 " --> pdb=" O   LEU A 953 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 98
      removed outlier: 9.051A  pdb=" N   VAL B 148 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU B  85 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   MET B 150 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ARG B  87 " --> pdb=" O   MET B 150 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   LEU B 152 " --> pdb=" O   ARG B  87 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 26
      removed outlier: 6.029A  pdb=" N   ASN C  24 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU C  38 " --> pdb=" O   ASN C  24 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 26
      removed outlier: 6.029A  pdb=" N   ASN C  24 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU C  38 " --> pdb=" O   ASN C  24 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL C 149 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 124 through 126
      removed outlier: 3.508A  pdb=" N   THR D 125 " --> pdb=" O   PHE D 149 " (cutoff:3.500A)

    455 hydrogen bonds defined for protein.
    1281 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: 3.44

  Time building geometry restraints manager: 2.86 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3420
        1.34 -     1.46: 1327
        1.46 -     1.57: 5653
        1.57 -     1.69: 4
        1.69 -     1.81: 56
  Bond restraints: 10460
  Sorted by residual:
  bond pdb=" C1' AMP B1101 "
       pdb=" O4' AMP B1101 "
    ideal  model  delta    sigma   weight residual
    1.426  1.624 -0.198 2.00e-02 2.50e+03 9.77e+01
  bond pdb=" C1' AMP B1101 "
       pdb=" C2' AMP B1101 "
    ideal  model  delta    sigma   weight residual
    1.524  1.366  0.158 2.00e-02 2.50e+03 6.22e+01
  bond pdb=" C6  AMP B1101 "
       pdb=" N6  AMP B1101 "
    ideal  model  delta    sigma   weight residual
    1.355  1.497 -0.142 2.00e-02 2.50e+03 5.08e+01
  bond pdb=" C4' AMP B1101 "
       pdb=" O4' AMP B1101 "
    ideal  model  delta    sigma   weight residual
    1.426  1.295  0.131 2.00e-02 2.50e+03 4.30e+01
  bond pdb=" C4  AMP B1101 "
       pdb=" C5  AMP B1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.374  0.116 2.00e-02 2.50e+03 3.36e+01
  ... (remaining 10455 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 14204
        3.59 -     7.19: 32
        7.19 -    10.78: 2
       10.78 -    14.37: 3
       14.37 -    17.96: 1
  Bond angle restraints: 14242
  Sorted by residual:
  angle pdb=" C2' AMP B1101 "
        pdb=" C1' AMP B1101 "
        pdb=" N9  AMP B1101 "
      ideal   model   delta    sigma   weight residual
     109.47  127.43  -17.96 3.00e+00 1.11e-01 3.59e+01
  angle pdb=" N9  AMP B1101 "
        pdb=" C1' AMP B1101 "
        pdb=" O4' AMP B1101 "
      ideal   model   delta    sigma   weight residual
     109.47   95.38   14.09 3.00e+00 1.11e-01 2.21e+01
  angle pdb=" O2P AMP B1101 "
        pdb=" P   AMP B1101 "
        pdb=" O3P AMP B1101 "
      ideal   model   delta    sigma   weight residual
     119.90  106.37   13.53 3.00e+00 1.11e-01 2.03e+01
  angle pdb=" O1P AMP B1101 "
        pdb=" P   AMP B1101 "
        pdb=" O2P AMP B1101 "
      ideal   model   delta    sigma   weight residual
     119.60  107.51   12.09 3.00e+00 1.11e-01 1.62e+01
  angle pdb=" O1P AMP B1101 "
        pdb=" P   AMP B1101 "
        pdb=" O3P AMP B1101 "
      ideal   model   delta    sigma   weight residual
     119.90  110.37    9.53 3.00e+00 1.11e-01 1.01e+01
  ... (remaining 14237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.84: 5681
       13.84 -    27.68: 436
       27.68 -    41.52: 141
       41.52 -    55.36: 27
       55.36 -    69.21: 14
  Dihedral angle restraints: 6299
    sinusoidal: 2548
      harmonic: 3751
  Sorted by residual:
  dihedral pdb=" N   PHE A 211 "
           pdb=" CA  PHE A 211 "
           pdb=" CB  PHE A 211 "
           pdb=" CG  PHE A 211 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   -0.14  -59.86     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  ARG A 895 "
           pdb=" CB  ARG A 895 "
           pdb=" CG  ARG A 895 "
           pdb=" CD  ARG A 895 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.15   58.15     3      1.50e+01 4.44e-03 9.46e+00
  dihedral pdb=" N   GLU A  46 "
           pdb=" CA  GLU A  46 "
           pdb=" CB  GLU A  46 "
           pdb=" CG  GLU A  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -117.64   57.64     3      1.50e+01 4.44e-03 9.45e+00
  ... (remaining 6296 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1033
       0.030 -    0.061: 398
       0.061 -    0.091: 91
       0.091 -    0.122: 62
       0.122 -    0.152: 7
  Chirality restraints: 1591
  Sorted by residual:
  chirality pdb=" C3' AMP B1101 "
            pdb=" C2' AMP B1101 "
            pdb=" C4' AMP B1101 "
            pdb=" O3' AMP B1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.66    0.15 2.00e-01 2.50e+01 5.81e-01
  chirality pdb=" CA  GLN A 385 "
            pdb=" N   GLN A 385 "
            pdb=" C   GLN A 385 "
            pdb=" CB  GLN A 385 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.06e-01
  chirality pdb=" CA  ILE A 834 "
            pdb=" N   ILE A 834 "
            pdb=" C   ILE A 834 "
            pdb=" CB  ILE A 834 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 5.00e-01
  ... (remaining 1588 not shown)

  Planarity restraints: 1867
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS C  76 "    0.022 5.00e-02 4.00e+02   3.37e-02 1.81e+00
        pdb=" N   PRO C  77 "   -0.058 5.00e-02 4.00e+02
        pdb=" CA  PRO C  77 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO C  77 "    0.019 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 876 "   -0.018 5.00e-02 4.00e+02   2.67e-02 1.14e+00
        pdb=" N   PRO A 877 "    0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO A 877 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 877 "   -0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 759 "   -0.017 5.00e-02 4.00e+02   2.59e-02 1.07e+00
        pdb=" N   PRO A 760 "    0.045 5.00e-02 4.00e+02
        pdb=" CA  PRO A 760 "   -0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO A 760 "   -0.014 5.00e-02 4.00e+02
  ... (remaining 1864 not shown)

  Histogram of nonbonded interaction distances:
        1.27 -     2.00: 2
        2.00 -     2.72: 415
        2.72 -     3.45: 14994
        3.45 -     4.17: 23096
        4.17 -     4.90: 42039
  Nonbonded interactions: 80546
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C 121 "
            pdb=" OXT GLY D 157 "
     model   vdw
     1.270 3.120
  nonbonded pdb=" NZ  LYS C 121 "
            pdb=" C   GLY D 157 "
     model   vdw
     1.332 3.350
  nonbonded pdb=" O   GLY A  39 "
            pdb=" OG1 THR A 125 "
     model   vdw
     2.213 3.040
  nonbonded pdb=" O   ASN A 695 "
            pdb=" OG  SER A 706 "
     model   vdw
     2.219 3.040
  nonbonded pdb=" OE2 GLU A 592 "
            pdb=" NH1 ARG B 155 "
     model   vdw
     2.233 3.120
  ... (remaining 80541 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 82 through 157)
  selection = chain 'D'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             28.990
  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:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.200
  Find NCS groups from input model:        0.130
  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:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.198  10461  Z= 0.234
  Angle     :  0.578  17.964  14242  Z= 0.258
  Chirality :  0.038   0.152   1591
  Planarity :  0.004   0.034   1867
  Dihedral  : 11.764  69.205   3873
  Min Nonbonded Distance : 1.270

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  7.08 %
    Favored  : 89.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 (0.24), residues: 1291
  helix:  1.74 (0.24), residues: 476
  sheet: -1.21 (0.38), residues: 185
  loop : -0.12 (0.26), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 948 
 PHE   0.007   0.001   PHE A 146 
 TYR   0.011   0.001   TYR A 603 
 ARG   0.002   0.000   ARG A  87 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17714 (  436)
  hydrogen bonds       : angle       6.52220 ( 1281)
  covalent geometry    : bond        0.00456 (10460)
  covalent geometry    : angle       0.57751 (14242)
  Misc. bond           : bond        0.08419 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 1.151 
Fit side-chains
REVERT: A  244 PHE cc_start: 0.5585 (OUTLIER) cc_final: 0.4391 (m-80)
REVERT: A  272 LEU cc_start: 0.8684 (mt) cc_final: 0.8304 (mm)
REVERT: A  282 GLN cc_start: 0.8504 (tt0) cc_final: 0.8097 (tp40)
REVERT: A  325 ASP cc_start: 0.8016 (t0) cc_final: 0.7807 (t0)
REVERT: A  643 MET cc_start: 0.0794 (mmm) cc_final: 0.0458 (mmm)
REVERT: A  710 GLN cc_start: 0.2452 (OUTLIER) cc_final: 0.1485 (pp30)
REVERT: A  715 LEU cc_start: 0.6883 (tt) cc_final: 0.6603 (tt)
REVERT: A  738 MET cc_start: 0.6749 (mtp) cc_final: 0.6539 (mtp)
REVERT: A  791 ASN cc_start: 0.7878 (m-40) cc_final: 0.7541 (m-40)
REVERT: B  114 LEU cc_start: 0.8305 (OUTLIER) cc_final: 0.8027 (mp)
REVERT: B  140 TYR cc_start: 0.8531 (m-10) cc_final: 0.8260 (m-10)
REVERT: C   21 TYR cc_start: 0.8274 (p90) cc_final: 0.7656 (p90)
REVERT: C   47 HIS cc_start: 0.7016 (OUTLIER) cc_final: 0.6331 (p90)
REVERT: C   67 MET cc_start: 0.7942 (mtt) cc_final: 0.7707 (mtp)
REVERT: C   76 HIS cc_start: 0.8354 (t70) cc_final: 0.7837 (t-90)
REVERT: C   81 GLU cc_start: 0.8014 (tt0) cc_final: 0.7205 (pt0)
REVERT: C  114 ARG cc_start: 0.7093 (tmm160) cc_final: 0.6758 (tmt170)
  outliers start: 33
  outliers final: 15
  residues processed: 171
  average time/residue: 0.2334
  time to fit residues: 56.6976
Evaluate side-chains
  132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  710 GLN
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  117 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 74 optimal weight:   30.0000
   chunk 116 optimal weight:    2.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A  31 GLN
A  41 GLN
A 385 GLN
A 476 ASN
A 522 HIS
A 631 ASN
A 981 GLN
B 102 GLN
B 110 GLN
C  43 GLN
C 103 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.181313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.120937 restraints weight = 13787.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3530 rms_B_bonded: 3.45
r_work: 0.3287 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
moved from start:          0.1028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10461  Z= 0.140
  Angle     :  0.584   6.958  14242  Z= 0.282
  Chirality :  0.040   0.149   1591
  Planarity :  0.004   0.038   1867
  Dihedral  :  6.378  55.434   1441
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  9.81 %
    Favored  : 86.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 (0.24), residues: 1291
  helix:  1.64 (0.23), residues: 498
  sheet: -0.98 (0.39), residues: 185
  loop : -0.20 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 614 
 HIS   0.003   0.001   HIS A 610 
 PHE   0.010   0.001   PHE A 146 
 TYR   0.014   0.001   TYR D  96 
 ARG   0.007   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04350 (  436)
  hydrogen bonds       : angle       5.07492 ( 1281)
  covalent geometry    : bond        0.00323 (10460)
  covalent geometry    : angle       0.58437 (14242)
  Misc. bond           : bond        0.00178 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 1.072 
Fit side-chains
   revert: symmetry clash
REVERT: A  170 ASP cc_start: 0.8227 (OUTLIER) cc_final: 0.8009 (p0)
REVERT: A  244 PHE cc_start: 0.5748 (OUTLIER) cc_final: 0.4496 (m-80)
REVERT: A  282 GLN cc_start: 0.8547 (tt0) cc_final: 0.8295 (tp40)
REVERT: A  540 ASP cc_start: 0.8609 (p0) cc_final: 0.8394 (p0)
REVERT: A  715 LEU cc_start: 0.7062 (tt) cc_final: 0.6785 (tt)
REVERT: A  791 ASN cc_start: 0.7826 (m-40) cc_final: 0.7473 (m-40)
REVERT: B  114 LEU cc_start: 0.8160 (OUTLIER) cc_final: 0.7905 (mp)
REVERT: B  143 LYS cc_start: 0.8914 (tppp) cc_final: 0.8706 (tppt)
REVERT: B  151 ASN cc_start: 0.9342 (m110) cc_final: 0.9039 (m110)
REVERT: C    5 MET cc_start: 0.8600 (tpp) cc_final: 0.8154 (mmm)
REVERT: C   21 TYR cc_start: 0.8129 (p90) cc_final: 0.7490 (p90)
REVERT: C   47 HIS cc_start: 0.7105 (OUTLIER) cc_final: 0.6429 (p90)
REVERT: C   80 ASP cc_start: 0.8103 (m-30) cc_final: 0.7895 (m-30)
REVERT: C  114 ARG cc_start: 0.7421 (tmm160) cc_final: 0.6179 (tmm160)
  outliers start: 36
  outliers final: 18
  residues processed: 150
  average time/residue: 0.2778
  time to fit residues: 58.6938
Evaluate side-chains
  133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 111
  time to evaluate  : 2.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 99 optimal weight:    7.9990
   chunk 71 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 48 optimal weight:    0.0070
   chunk 51 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 100 optimal weight:    1.9990
   overall best weight:    1.1202

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

Flipped N/Q/H residues before XYZ refinement:
A 981 GLN
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN
D 151 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.179863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.120722 restraints weight = 13998.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 3.33
r_work: 0.3269 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10461  Z= 0.161
  Angle     :  0.593   7.004  14242  Z= 0.284
  Chirality :  0.040   0.151   1591
  Planarity :  0.004   0.045   1867
  Dihedral  :  6.195  56.300   1435
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 11.44 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.46 (0.24), residues: 1291
  helix:  1.62 (0.23), residues: 494
  sheet: -1.04 (0.38), residues: 185
  loop : -0.26 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 966 
 PHE   0.011   0.001   PHE A 146 
 TYR   0.014   0.002   TYR D  96 
 ARG   0.007   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04033 (  436)
  hydrogen bonds       : angle       4.82716 ( 1281)
  covalent geometry    : bond        0.00384 (10460)
  covalent geometry    : angle       0.59346 (14242)
  Misc. bond           : bond        0.00101 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 118
  time to evaluate  : 1.269 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6047 (OUTLIER) cc_final: 0.5586 (t80)
REVERT: A  282 GLN cc_start: 0.8605 (tt0) cc_final: 0.8340 (tp40)
REVERT: A  540 ASP cc_start: 0.8659 (p0) cc_final: 0.8380 (p0)
REVERT: A  715 LEU cc_start: 0.7050 (tt) cc_final: 0.6733 (tt)
REVERT: A  791 ASN cc_start: 0.7851 (m-40) cc_final: 0.7527 (m-40)
REVERT: B  114 LEU cc_start: 0.8185 (OUTLIER) cc_final: 0.7914 (mp)
REVERT: B  139 GLU cc_start: 0.7805 (tp30) cc_final: 0.7529 (tp30)
REVERT: B  151 ASN cc_start: 0.9344 (m110) cc_final: 0.9060 (m110)
REVERT: C   21 TYR cc_start: 0.8127 (p90) cc_final: 0.7451 (p90)
REVERT: C   47 HIS cc_start: 0.7151 (OUTLIER) cc_final: 0.6496 (p90)
REVERT: C   80 ASP cc_start: 0.8127 (m-30) cc_final: 0.7863 (m-30)
REVERT: C  114 ARG cc_start: 0.7515 (tmm160) cc_final: 0.7181 (tmm160)
  outliers start: 37
  outliers final: 22
  residues processed: 145
  average time/residue: 0.2775
  time to fit residues: 58.4647
Evaluate side-chains
  133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 108
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 74 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0670
   chunk 3 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 113 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 100 optimal weight:    7.9990
   chunk 87 optimal weight:    0.5980
   chunk 8 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.8322

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

Flipped N/Q/H residues before XYZ refinement:
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.180764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.118024 restraints weight = 13831.951|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 3.11
r_work: 0.3284 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3284
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.1429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10461  Z= 0.133
  Angle     :  0.580   8.877  14242  Z= 0.275
  Chirality :  0.040   0.273   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  6.057  59.236   1433
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 12.44 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.49 (0.24), residues: 1291
  helix:  1.67 (0.23), residues: 493
  sheet: -1.04 (0.37), residues: 185
  loop : -0.28 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 614 
 HIS   0.002   0.001   HIS A 264 
 PHE   0.011   0.001   PHE A 146 
 TYR   0.019   0.001   TYR A 735 
 ARG   0.007   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03626 (  436)
  hydrogen bonds       : angle       4.63918 ( 1281)
  covalent geometry    : bond        0.00312 (10460)
  covalent geometry    : angle       0.58041 (14242)
  Misc. bond           : bond        0.00085 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6106 (OUTLIER) cc_final: 0.5601 (t80)
REVERT: A  282 GLN cc_start: 0.8582 (tt0) cc_final: 0.8323 (tp40)
REVERT: A  540 ASP cc_start: 0.8650 (p0) cc_final: 0.8341 (p0)
REVERT: A  715 LEU cc_start: 0.7074 (tt) cc_final: 0.6700 (tt)
REVERT: A  765 MET cc_start: 0.0369 (tpt) cc_final: 0.0068 (tpt)
REVERT: A  791 ASN cc_start: 0.7847 (m-40) cc_final: 0.7496 (m-40)
REVERT: A  973 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8222 (pp20)
REVERT: B  114 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7951 (mp)
REVERT: B  151 ASN cc_start: 0.9337 (m110) cc_final: 0.9045 (m110)
REVERT: C   21 TYR cc_start: 0.8147 (p90) cc_final: 0.7541 (p90)
REVERT: C   47 HIS cc_start: 0.7146 (OUTLIER) cc_final: 0.6386 (p-80)
REVERT: C   80 ASP cc_start: 0.8088 (m-30) cc_final: 0.7858 (m-30)
REVERT: C   81 GLU cc_start: 0.8340 (tt0) cc_final: 0.7589 (pt0)
REVERT: C  114 ARG cc_start: 0.7532 (tmm160) cc_final: 0.7114 (tmt170)
REVERT: C  118 ARG cc_start: 0.9094 (mmp80) cc_final: 0.8862 (mmp80)
  outliers start: 34
  outliers final: 21
  residues processed: 142
  average time/residue: 0.2496
  time to fit residues: 51.7347
Evaluate side-chains
  135 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 110
  time to evaluate  : 1.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  827 LEU
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  973 GLU
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 118 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 101 optimal weight:    0.5980
   chunk 46 optimal weight:    0.3980
   chunk 47 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.180770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.117858 restraints weight = 13854.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3483 rms_B_bonded: 3.17
r_work: 0.3288 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  10461  Z= 0.119
  Angle     :  0.560   6.182  14242  Z= 0.265
  Chirality :  0.040   0.212   1591
  Planarity :  0.004   0.040   1867
  Dihedral  :  5.956  57.981   1433
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 12.99 %
    Favored  : 83.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.53 (0.24), residues: 1291
  helix:  1.71 (0.23), residues: 494
  sheet: -1.05 (0.37), residues: 185
  loop : -0.24 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 614 
 HIS   0.002   0.000   HIS A 264 
 PHE   0.010   0.001   PHE A 119 
 TYR   0.012   0.001   TYR A 735 
 ARG   0.008   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03434 (  436)
  hydrogen bonds       : angle       4.53725 ( 1281)
  covalent geometry    : bond        0.00277 (10460)
  covalent geometry    : angle       0.55954 (14242)
  Misc. bond           : bond        0.00075 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 117
  time to evaluate  : 1.126 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6104 (OUTLIER) cc_final: 0.5598 (t80)
REVERT: A  282 GLN cc_start: 0.8551 (tt0) cc_final: 0.8288 (tp40)
REVERT: A  715 LEU cc_start: 0.7044 (tt) cc_final: 0.6606 (tt)
REVERT: A  765 MET cc_start: 0.0231 (tpt) cc_final: -0.0018 (tpt)
REVERT: A  791 ASN cc_start: 0.7908 (m-40) cc_final: 0.7575 (m-40)
REVERT: A  973 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8274 (pp20)
REVERT: B  114 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7940 (mp)
REVERT: B  139 GLU cc_start: 0.7712 (tp30) cc_final: 0.7476 (tp30)
REVERT: B  151 ASN cc_start: 0.9334 (m110) cc_final: 0.9051 (m110)
REVERT: C   21 TYR cc_start: 0.8176 (p90) cc_final: 0.7447 (p90)
REVERT: C   47 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6340 (p-80)
REVERT: C   80 ASP cc_start: 0.8080 (m-30) cc_final: 0.7819 (m-30)
REVERT: C   81 GLU cc_start: 0.8321 (tt0) cc_final: 0.7562 (pt0)
REVERT: C  114 ARG cc_start: 0.7556 (tmm160) cc_final: 0.7141 (tmt170)
REVERT: D  125 THR cc_start: 0.1513 (OUTLIER) cc_final: 0.1190 (p)
  outliers start: 37
  outliers final: 24
  residues processed: 145
  average time/residue: 0.2202
  time to fit residues: 46.3139
Evaluate side-chains
  140 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 1.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  827 LEU
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  973 GLU
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 16 optimal weight:    7.9990
   chunk 127 optimal weight:    0.9990
   chunk 80 optimal weight:    6.9990
   chunk 95 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 91 optimal weight:    0.6980
   chunk 118 optimal weight:    3.9990
   chunk 74 optimal weight:    0.0040
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.6394

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

Flipped N/Q/H residues before XYZ refinement:
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.180304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.118065 restraints weight = 13770.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 3.35
r_work: 0.3275 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.3275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10461  Z= 0.116
  Angle     :  0.562   7.854  14242  Z= 0.266
  Chirality :  0.040   0.184   1591
  Planarity :  0.004   0.047   1867
  Dihedral  :  5.622  55.507   1429
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.26 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.57 (0.24), residues: 1291
  helix:  1.75 (0.23), residues: 493
  sheet: -1.02 (0.37), residues: 185
  loop : -0.23 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 614 
 HIS   0.002   0.000   HIS A 264 
 PHE   0.010   0.001   PHE A 146 
 TYR   0.011   0.001   TYR B 140 
 ARG   0.008   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03304 (  436)
  hydrogen bonds       : angle       4.44013 ( 1281)
  covalent geometry    : bond        0.00270 (10460)
  covalent geometry    : angle       0.56219 (14242)
  Misc. bond           : bond        0.00075 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 117
  time to evaluate  : 1.385 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6098 (OUTLIER) cc_final: 0.5628 (t80)
REVERT: A  282 GLN cc_start: 0.8573 (tt0) cc_final: 0.8304 (tp40)
REVERT: A  381 MET cc_start: 0.8229 (tpt) cc_final: 0.7967 (tpt)
REVERT: A  715 LEU cc_start: 0.6969 (tt) cc_final: 0.6562 (tt)
REVERT: A  765 MET cc_start: 0.0238 (tpt) cc_final: 0.0022 (tpt)
REVERT: A  791 ASN cc_start: 0.7884 (m-40) cc_final: 0.7539 (m-40)
REVERT: A  973 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8272 (pp20)
REVERT: B  114 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7945 (mp)
REVERT: B  139 GLU cc_start: 0.7726 (tp30) cc_final: 0.7521 (tp30)
REVERT: B  151 ASN cc_start: 0.9327 (m110) cc_final: 0.9044 (m110)
REVERT: C   21 TYR cc_start: 0.8170 (p90) cc_final: 0.7450 (p90)
REVERT: C   47 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6318 (p-80)
REVERT: C   80 ASP cc_start: 0.8043 (m-30) cc_final: 0.7772 (m-30)
REVERT: C   81 GLU cc_start: 0.8327 (tt0) cc_final: 0.7580 (pt0)
REVERT: C  114 ARG cc_start: 0.7612 (tmm160) cc_final: 0.7182 (tmt170)
REVERT: D  125 THR cc_start: 0.1524 (OUTLIER) cc_final: 0.1145 (p)
  outliers start: 40
  outliers final: 27
  residues processed: 146
  average time/residue: 0.2861
  time to fit residues: 61.7352
Evaluate side-chains
  140 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 108
  time to evaluate  : 1.713 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  973 GLU
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 109 optimal weight:    1.9990
   chunk 57 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0030
   chunk 123 optimal weight:    0.6980
   chunk 78 optimal weight:    7.9990
   chunk 0 optimal weight:   10.0000
   chunk 87 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 31 optimal weight:    8.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.2994

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

Flipped N/Q/H residues before XYZ refinement:
A 617 HIS
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.178687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.119309 restraints weight = 14003.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 3.38
r_work: 0.3253 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.1778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10461  Z= 0.176
  Angle     :  0.596   7.400  14242  Z= 0.285
  Chirality :  0.041   0.169   1591
  Planarity :  0.004   0.040   1867
  Dihedral  :  5.611  52.525   1426
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 13.90 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.24), residues: 1291
  helix:  1.61 (0.23), residues: 492
  sheet: -1.14 (0.37), residues: 185
  loop : -0.27 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 264 
 PHE   0.018   0.001   PHE D 126 
 TYR   0.011   0.001   TYR A 735 
 ARG   0.006   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03740 (  436)
  hydrogen bonds       : angle       4.54335 ( 1281)
  covalent geometry    : bond        0.00425 (10460)
  covalent geometry    : angle       0.59580 (14242)
  Misc. bond           : bond        0.00087 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 111
  time to evaluate  : 1.476 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6172 (OUTLIER) cc_final: 0.5757 (t80)
REVERT: A  282 GLN cc_start: 0.8623 (tt0) cc_final: 0.8331 (tp40)
REVERT: A  381 MET cc_start: 0.8228 (tpt) cc_final: 0.7900 (tpt)
REVERT: A  580 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.8168 (pm20)
REVERT: A  715 LEU cc_start: 0.7065 (tt) cc_final: 0.6637 (tt)
REVERT: A  765 MET cc_start: 0.0235 (tpt) cc_final: 0.0025 (tpt)
REVERT: A  791 ASN cc_start: 0.7902 (m-40) cc_final: 0.7561 (m-40)
REVERT: A  973 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8316 (pp20)
REVERT: B   88 ASN cc_start: 0.8250 (t0) cc_final: 0.7865 (t0)
REVERT: B  114 LEU cc_start: 0.8270 (OUTLIER) cc_final: 0.7933 (mp)
REVERT: B  151 ASN cc_start: 0.9329 (m110) cc_final: 0.9030 (m110)
REVERT: C   80 ASP cc_start: 0.8094 (m-30) cc_final: 0.7812 (m-30)
REVERT: C   81 GLU cc_start: 0.8365 (tt0) cc_final: 0.7622 (pt0)
REVERT: C  114 ARG cc_start: 0.7669 (tmm160) cc_final: 0.7223 (tmt170)
REVERT: C  118 ARG cc_start: 0.9077 (mmp80) cc_final: 0.8529 (mmp80)
REVERT: D  125 THR cc_start: 0.1438 (OUTLIER) cc_final: 0.1077 (p)
  outliers start: 45
  outliers final: 30
  residues processed: 144
  average time/residue: 0.2810
  time to fit residues: 60.0733
Evaluate side-chains
  143 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 108
  time to evaluate  : 1.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  580 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue  973 GLU
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 92 optimal weight:    0.6980
   chunk 95 optimal weight:    0.7980
   chunk 89 optimal weight:    0.7980
   chunk 98 optimal weight:    0.4980
   chunk 79 optimal weight:    9.9990
   chunk 119 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 126 optimal weight:    6.9990
   chunk 38 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.180373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.120444 restraints weight = 13883.527|
|-----------------------------------------------------------------------------|
r_work (start): 0.3520 rms_B_bonded: 3.25
r_work: 0.3280 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10461  Z= 0.120
  Angle     :  0.573   6.916  14242  Z= 0.272
  Chirality :  0.040   0.236   1591
  Planarity :  0.004   0.040   1867
  Dihedral  :  5.535  52.068   1426
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.99 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.24), residues: 1291
  helix:  1.71 (0.23), residues: 493
  sheet: -1.09 (0.37), residues: 185
  loop : -0.25 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 817 
 PHE   0.015   0.001   PHE D 126 
 TYR   0.025   0.001   TYR C  21 
 ARG   0.008   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03333 (  436)
  hydrogen bonds       : angle       4.40062 ( 1281)
  covalent geometry    : bond        0.00281 (10460)
  covalent geometry    : angle       0.57312 (14242)
  Misc. bond           : bond        0.00073 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 110
  time to evaluate  : 1.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6133 (OUTLIER) cc_final: 0.5759 (t80)
REVERT: A  282 GLN cc_start: 0.8558 (tt0) cc_final: 0.8300 (tp40)
REVERT: A  381 MET cc_start: 0.8232 (tpt) cc_final: 0.7940 (tpt)
REVERT: A  715 LEU cc_start: 0.6980 (tt) cc_final: 0.6548 (tt)
REVERT: A  765 MET cc_start: 0.0441 (tpt) cc_final: 0.0229 (tpt)
REVERT: A  791 ASN cc_start: 0.7878 (m-40) cc_final: 0.7551 (m-40)
REVERT: A  973 GLU cc_start: 0.8537 (OUTLIER) cc_final: 0.8291 (pp20)
REVERT: B  114 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7891 (mp)
REVERT: B  151 ASN cc_start: 0.9319 (m110) cc_final: 0.9044 (m110)
REVERT: C    5 MET cc_start: 0.8564 (tpp) cc_final: 0.8136 (mmm)
REVERT: C   80 ASP cc_start: 0.8064 (m-30) cc_final: 0.7752 (m-30)
REVERT: C   81 GLU cc_start: 0.8343 (tt0) cc_final: 0.7601 (pt0)
REVERT: C  114 ARG cc_start: 0.7614 (tmm160) cc_final: 0.7169 (tmt170)
REVERT: D  125 THR cc_start: 0.1365 (OUTLIER) cc_final: 0.1018 (p)
  outliers start: 37
  outliers final: 29
  residues processed: 139
  average time/residue: 0.2628
  time to fit residues: 53.4288
Evaluate side-chains
  140 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 107
  time to evaluate  : 1.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue  973 GLU
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 73 optimal weight:    4.9990
   chunk 77 optimal weight:    9.9990
   chunk 9 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 95 optimal weight:    2.9990
   chunk 57 optimal weight:    0.0170
   overall best weight:    0.7220

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

Flipped N/Q/H residues before XYZ refinement:
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.180126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.121289 restraints weight = 13866.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 3.27
r_work: 0.3285 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10461  Z= 0.123
  Angle     :  0.583   9.742  14242  Z= 0.274
  Chirality :  0.040   0.339   1591
  Planarity :  0.004   0.043   1867
  Dihedral  :  5.511  52.265   1426
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 14.99 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.58 (0.24), residues: 1291
  helix:  1.79 (0.23), residues: 487
  sheet: -1.08 (0.37), residues: 185
  loop : -0.20 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 817 
 PHE   0.015   0.001   PHE D 126 
 TYR   0.026   0.001   TYR C  21 
 ARG   0.009   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03283 (  436)
  hydrogen bonds       : angle       4.35972 ( 1281)
  covalent geometry    : bond        0.00291 (10460)
  covalent geometry    : angle       0.58315 (14242)
  Misc. bond           : bond        0.00055 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 109
  time to evaluate  : 1.216 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6147 (OUTLIER) cc_final: 0.5800 (t80)
REVERT: A  282 GLN cc_start: 0.8536 (tt0) cc_final: 0.8289 (tp40)
REVERT: A  381 MET cc_start: 0.8226 (tpt) cc_final: 0.7939 (tpt)
REVERT: A  436 LEU cc_start: 0.9134 (OUTLIER) cc_final: 0.8823 (tp)
REVERT: A  580 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.8211 (pm20)
REVERT: A  715 LEU cc_start: 0.6935 (tt) cc_final: 0.6560 (tt)
REVERT: A  765 MET cc_start: 0.0460 (tpt) cc_final: 0.0247 (tpt)
REVERT: A  791 ASN cc_start: 0.7881 (m-40) cc_final: 0.7537 (m-40)
REVERT: A  973 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8296 (pp20)
REVERT: B  114 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.7842 (mp)
REVERT: B  151 ASN cc_start: 0.9319 (m110) cc_final: 0.9038 (m110)
REVERT: C    5 MET cc_start: 0.8573 (tpp) cc_final: 0.8140 (mmm)
REVERT: C   80 ASP cc_start: 0.8094 (m-30) cc_final: 0.7762 (m-30)
REVERT: C   81 GLU cc_start: 0.8344 (tt0) cc_final: 0.7602 (pt0)
REVERT: C  114 ARG cc_start: 0.7622 (tmm160) cc_final: 0.6736 (tmt170)
REVERT: C  118 ARG cc_start: 0.9007 (mmp80) cc_final: 0.8409 (mmp80)
REVERT: D  125 THR cc_start: 0.1342 (OUTLIER) cc_final: 0.1001 (p)
  outliers start: 37
  outliers final: 30
  residues processed: 139
  average time/residue: 0.2298
  time to fit residues: 45.9680
Evaluate side-chains
  142 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 106
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  436 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  580 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue  973 GLU
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 111 optimal weight:    0.9980
   chunk 79 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 100 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    9.9990
   chunk 87 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0030
   chunk 74 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   overall best weight:    0.8992

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

Flipped N/Q/H residues before XYZ refinement:
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.180093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.121145 restraints weight = 13802.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3529 rms_B_bonded: 3.30
r_work: 0.3273 rms_B_bonded: 3.31 restraints_weight: 0.5000
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10461  Z= 0.139
  Angle     :  0.593  10.540  14242  Z= 0.279
  Chirality :  0.041   0.399   1591
  Planarity :  0.004   0.046   1867
  Dihedral  :  5.559  58.804   1426
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 15.26 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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 (0.24), residues: 1291
  helix:  1.75 (0.23), residues: 487
  sheet: -1.13 (0.37), residues: 185
  loop : -0.21 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 817 
 PHE   0.014   0.001   PHE D 126 
 TYR   0.026   0.001   TYR C  21 
 ARG   0.010   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03370 (  436)
  hydrogen bonds       : angle       4.36928 ( 1281)
  covalent geometry    : bond        0.00331 (10460)
  covalent geometry    : angle       0.59300 (14242)
  Misc. bond           : bond        0.00060 (    1)

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 111
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6141 (OUTLIER) cc_final: 0.5817 (t80)
REVERT: A  282 GLN cc_start: 0.8570 (tt0) cc_final: 0.8316 (tp40)
REVERT: A  381 MET cc_start: 0.8244 (tpt) cc_final: 0.7962 (tpt)
REVERT: A  580 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.8213 (pm20)
REVERT: A  715 LEU cc_start: 0.6922 (tt) cc_final: 0.6556 (tt)
REVERT: A  791 ASN cc_start: 0.7878 (m-40) cc_final: 0.7248 (t0)
REVERT: A  973 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8312 (pp20)
REVERT: B  115 GLU cc_start: 0.6420 (mm-30) cc_final: 0.6161 (mm-30)
REVERT: B  151 ASN cc_start: 0.9327 (m110) cc_final: 0.9047 (m110)
REVERT: C    5 MET cc_start: 0.8552 (tpp) cc_final: 0.8114 (mmm)
REVERT: C   80 ASP cc_start: 0.8139 (m-30) cc_final: 0.7809 (m-30)
REVERT: C   81 GLU cc_start: 0.8352 (tt0) cc_final: 0.7598 (pt0)
REVERT: C  114 ARG cc_start: 0.7604 (tmm160) cc_final: 0.6746 (tmt170)
REVERT: C  118 ARG cc_start: 0.9006 (mmp80) cc_final: 0.8360 (mmp80)
REVERT: D  125 THR cc_start: 0.1326 (OUTLIER) cc_final: 0.0998 (p)
  outliers start: 37
  outliers final: 30
  residues processed: 139
  average time/residue: 0.2131
  time to fit residues: 42.7275
Evaluate side-chains
  142 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 108
  time to evaluate  : 1.048 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  573 VAL
Chi-restraints excluded: chain A residue  580 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue  973 GLU
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Chi-restraints excluded: chain D residue  125 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 118 optimal weight:    0.9990
   chunk 124 optimal weight:    5.9990
   chunk 119 optimal weight:    0.9980
   chunk 115 optimal weight:    0.0980
   chunk 8 optimal weight:    1.9990
   chunk 80 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 113 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 617 HIS
** A 631 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.180422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.120531 restraints weight = 13808.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 3.29
r_work: 0.3282 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.1990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10461  Z= 0.128
  Angle     :  0.590  10.352  14242  Z= 0.277
  Chirality :  0.041   0.402   1591
  Planarity :  0.004   0.040   1867
  Dihedral  :  5.378  53.022   1424
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.44 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    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:  0.58 (0.24), residues: 1291
  helix:  1.78 (0.23), residues: 487
  sheet: -1.13 (0.37), residues: 185
  loop : -0.19 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 817 
 PHE   0.014   0.001   PHE D 126 
 TYR   0.022   0.001   TYR C  21 
 ARG   0.011   0.000   ARG C  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03269 (  436)
  hydrogen bonds       : angle       4.32575 ( 1281)
  covalent geometry    : bond        0.00305 (10460)
  covalent geometry    : angle       0.59018 (14242)
  Misc. bond           : bond        0.00057 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5526.99 seconds
wall clock time: 100 minutes 27.36 seconds (6027.36 seconds total)