Starting phenix.real_space_refine
on Sat Aug 23 06:49:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sea_40408/08_2025/8sea_40408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sea_40408/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2025/8sea_40408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2025/8sea_40408.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2025/8sea_40408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sea_40408/08_2025/8sea_40408.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 2.16, per 1000 atoms: 0.21
  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: 1.02
  Conformation dependent library (CDL) restraints added in 349.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  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: 0.43
  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: 2.05

  Time building geometry restraints manager: 1.33 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:             4.400
  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:             0.020
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.110
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.310
-------------------------------------------------------------------------------
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 : 8.70
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.002   0.000   ARG A  87 
 TYR   0.011   0.001   TYR A 603 
 PHE   0.007   0.001   PHE A 146 
 TRP   0.006   0.001   TRP C  95 
 HIS   0.003   0.001   HIS A 948 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 (10460)
  covalent geometry    : angle       0.57751 (14242)
  hydrogen bonds       : bond        0.17714 (  436)
  hydrogen bonds       : angle       6.52220 ( 1281)
  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  : 0.317 
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: 0.0947
  time to fit residues: 23.0713
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  : 0.372 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    8.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    4.9990
   chunk 55 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 522 HIS
A 631 ASN
A 981 GLN
B 102 GLN
B 110 GLN
C  43 GLN
C 103 GLN
D 151 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.179027 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.116634 restraints weight = 13782.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 3.38
r_work: 0.3258 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.1066

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= 0.186
  Angle     :  0.608   6.839  14242  Z= 0.295
  Chirality :  0.041   0.150   1591
  Planarity :  0.004   0.037   1867
  Dihedral  :  6.486  56.231   1441
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 10.35 %
    Favored  : 86.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.24), residues: 1291
  helix:  1.53 (0.23), residues: 497
  sheet: -1.09 (0.38), residues: 185
  loop : -0.25 (0.26), residues: 609

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  23 
 TYR   0.012   0.002   TYR D  96 
 PHE   0.012   0.001   PHE A 146 
 TRP   0.018   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (10460)
  covalent geometry    : angle       0.60813 (14242)
  hydrogen bonds       : bond        0.04575 (  436)
  hydrogen bonds       : angle       5.15737 ( 1281)
  Misc. bond           : bond        0.00324 (    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
  156 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 120
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.5823 (OUTLIER) cc_final: 0.5563 (t80)
REVERT: A  282 GLN cc_start: 0.8623 (tt0) cc_final: 0.8359 (tp40)
REVERT: A  540 ASP cc_start: 0.8645 (p0) cc_final: 0.8419 (p0)
REVERT: A  710 GLN cc_start: 0.2322 (OUTLIER) cc_final: 0.1246 (pp30)
REVERT: A  715 LEU cc_start: 0.7069 (tt) cc_final: 0.6776 (tt)
REVERT: A  738 MET cc_start: 0.6719 (mtp) cc_final: 0.6394 (mtp)
REVERT: A  791 ASN cc_start: 0.7812 (m-40) cc_final: 0.7461 (m-40)
REVERT: B  114 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7860 (mp)
REVERT: C   47 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6502 (p90)
REVERT: C  114 ARG cc_start: 0.7430 (tmm160) cc_final: 0.6178 (tmm160)
  outliers start: 36
  outliers final: 20
  residues processed: 147
  average time/residue: 0.0881
  time to fit residues: 18.6682
Evaluate side-chains
  133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 109
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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  619 PHE
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  710 GLN
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  958 TRP
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 118 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 65 optimal weight:    7.9990
   chunk 119 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 78 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 110 optimal weight:    0.8980
   chunk 16 optimal weight:    9.9990
   chunk 107 optimal weight:    3.9990
   chunk 120 optimal weight:    1.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A 279 GLN
** A 613 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 981 GLN
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  43 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.176730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.116668 restraints weight = 14042.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 3.34
r_work: 0.3194 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.1470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043  10461  Z= 0.249
  Angle     :  0.658   8.015  14242  Z= 0.318
  Chirality :  0.043   0.170   1591
  Planarity :  0.004   0.044   1867
  Dihedral  :  6.691  58.409   1436
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 11.99 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.23), residues: 1291
  helix:  1.31 (0.23), residues: 493
  sheet: -1.26 (0.37), residues: 185
  loop : -0.41 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  23 
 TYR   0.019   0.002   TYR C  21 
 PHE   0.015   0.002   PHE A 146 
 TRP   0.017   0.001   TRP A 614 
 HIS   0.006   0.001   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00605 (10460)
  covalent geometry    : angle       0.65816 (14242)
  hydrogen bonds       : bond        0.04658 (  436)
  hydrogen bonds       : angle       5.05299 ( 1281)
  Misc. bond           : bond        0.00360 (    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
  156 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 114
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6153 (OUTLIER) cc_final: 0.5717 (t80)
REVERT: A  282 GLN cc_start: 0.8693 (tt0) cc_final: 0.8397 (tp40)
REVERT: A  540 ASP cc_start: 0.8804 (p0) cc_final: 0.8501 (p0)
REVERT: A  710 GLN cc_start: 0.2449 (OUTLIER) cc_final: 0.1068 (pp30)
REVERT: A  715 LEU cc_start: 0.7187 (tt) cc_final: 0.6818 (tt)
REVERT: A  791 ASN cc_start: 0.7838 (m-40) cc_final: 0.7535 (m-40)
REVERT: B  114 LEU cc_start: 0.8232 (OUTLIER) cc_final: 0.7892 (mp)
REVERT: C   21 TYR cc_start: 0.8137 (p90) cc_final: 0.7884 (p90)
REVERT: C   47 HIS cc_start: 0.7275 (OUTLIER) cc_final: 0.6663 (p90)
REVERT: C  114 ARG cc_start: 0.7597 (tmm160) cc_final: 0.6226 (tmm160)
  outliers start: 42
  outliers final: 25
  residues processed: 143
  average time/residue: 0.0954
  time to fit residues: 19.8619
Evaluate side-chains
  133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 104
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
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  256 VAL
Chi-restraints excluded: chain A residue  277 VAL
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  573 VAL
Chi-restraints excluded: chain A residue  591 SER
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  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
Chi-restraints excluded: chain C residue  150 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 33 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 45 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 106 optimal weight:    0.9990
   chunk 115 optimal weight:    0.2980
   chunk 111 optimal weight:    0.8980
   chunk 17 optimal weight:    5.9990
   chunk 31 optimal weight:   10.0000
   chunk 34 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.180037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.119094 restraints weight = 13940.432|
|-----------------------------------------------------------------------------|
r_work (start): 0.3490 rms_B_bonded: 3.36
r_work: 0.3257 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.1524

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= 0.119
  Angle     :  0.578   6.487  14242  Z= 0.275
  Chirality :  0.040   0.267   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  6.298  58.923   1434
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 12.44 %
    Favored  : 84.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.24), residues: 1291
  helix:  1.59 (0.23), residues: 494
  sheet: -1.17 (0.37), residues: 184
  loop : -0.36 (0.25), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  23 
 TYR   0.018   0.002   TYR A 735 
 PHE   0.014   0.001   PHE D 126 
 TRP   0.019   0.001   TRP A 614 
 HIS   0.002   0.001   HIS A 966 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (10460)
  covalent geometry    : angle       0.57762 (14242)
  hydrogen bonds       : bond        0.03623 (  436)
  hydrogen bonds       : angle       4.65625 ( 1281)
  Misc. bond           : bond        0.00031 (    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
  155 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 116
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.5754 (t80)
REVERT: A  282 GLN cc_start: 0.8558 (tt0) cc_final: 0.8300 (tp40)
REVERT: A  540 ASP cc_start: 0.8649 (p0) cc_final: 0.8333 (p0)
REVERT: A  710 GLN cc_start: 0.2232 (OUTLIER) cc_final: 0.0908 (pp30)
REVERT: A  715 LEU cc_start: 0.7112 (tt) cc_final: 0.6697 (tt)
REVERT: A  765 MET cc_start: 0.0024 (tpt) cc_final: -0.0403 (tpt)
REVERT: A  791 ASN cc_start: 0.7890 (m-40) cc_final: 0.7544 (m-40)
REVERT: A  973 GLU cc_start: 0.8523 (OUTLIER) cc_final: 0.8266 (pp20)
REVERT: B  114 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7973 (mp)
REVERT: B  139 GLU cc_start: 0.7751 (tp30) cc_final: 0.7532 (tp30)
REVERT: B  151 ASN cc_start: 0.9328 (m110) cc_final: 0.9048 (m110)
REVERT: C    5 MET cc_start: 0.8625 (tpp) cc_final: 0.8207 (mmm)
REVERT: C   21 TYR cc_start: 0.8105 (p90) cc_final: 0.7747 (p90)
REVERT: C   47 HIS cc_start: 0.7142 (OUTLIER) cc_final: 0.6499 (p90)
REVERT: C  114 ARG cc_start: 0.7565 (tmm160) cc_final: 0.7137 (tmt170)
REVERT: C  118 ARG cc_start: 0.9065 (mmp80) cc_final: 0.8570 (mmp80)
  outliers start: 39
  outliers final: 24
  residues processed: 147
  average time/residue: 0.0886
  time to fit residues: 18.8792
Evaluate side-chains
  136 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 107
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
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  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  468 ASP
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  710 GLN
Chi-restraints excluded: chain A residue  729 LEU
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  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 47 optimal weight:    0.1980
   chunk 53 optimal weight:    0.8980
   chunk 104 optimal weight:    0.6980
   chunk 122 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   chunk 8 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.180592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.120907 restraints weight = 13814.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 3.47
r_work: 0.3278 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
moved from start:          0.1657

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= 0.114
  Angle     :  0.562   6.888  14242  Z= 0.266
  Chirality :  0.039   0.188   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  6.043  55.973   1432
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 13.26 %
    Favored  : 83.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.24), residues: 1291
  helix:  1.68 (0.23), residues: 494
  sheet: -1.15 (0.36), residues: 185
  loop : -0.32 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  23 
 TYR   0.013   0.001   TYR A 735 
 PHE   0.013   0.001   PHE A 119 
 TRP   0.021   0.001   TRP A 614 
 HIS   0.002   0.000   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10460)
  covalent geometry    : angle       0.56196 (14242)
  hydrogen bonds       : bond        0.03413 (  436)
  hydrogen bonds       : angle       4.54150 ( 1281)
  Misc. bond           : bond        0.00072 (    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
  157 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 116
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6122 (OUTLIER) cc_final: 0.5641 (t80)
REVERT: A  282 GLN cc_start: 0.8562 (tt0) cc_final: 0.8297 (tp40)
REVERT: A  540 ASP cc_start: 0.8649 (p0) cc_final: 0.8440 (p0)
REVERT: A  580 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8160 (pm20)
REVERT: A  710 GLN cc_start: 0.2348 (OUTLIER) cc_final: 0.0970 (pp30)
REVERT: A  715 LEU cc_start: 0.7051 (tt) cc_final: 0.6627 (tt)
REVERT: A  765 MET cc_start: -0.0141 (tpt) cc_final: -0.0565 (tpt)
REVERT: A  791 ASN cc_start: 0.7921 (m-40) cc_final: 0.7533 (m-40)
REVERT: A  973 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8285 (pp20)
REVERT: B  114 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7963 (mp)
REVERT: B  151 ASN cc_start: 0.9323 (m110) cc_final: 0.9050 (m110)
REVERT: C    5 MET cc_start: 0.8582 (tpp) cc_final: 0.8167 (mmm)
REVERT: C   21 TYR cc_start: 0.8099 (p90) cc_final: 0.7755 (p90)
REVERT: C   47 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6315 (p-80)
REVERT: C  114 ARG cc_start: 0.7583 (tmm160) cc_final: 0.7160 (tmt170)
  outliers start: 41
  outliers final: 27
  residues processed: 148
  average time/residue: 0.0946
  time to fit residues: 20.1778
Evaluate side-chains
  141 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 108
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
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  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  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  710 GLN
Chi-restraints excluded: chain A residue  729 LEU
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 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    0.5980
   chunk 85 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0270
   chunk 96 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9990
   chunk 88 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 8 optimal weight:    4.9990
   chunk 116 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 = 0.4241 r_free = 0.4241 target = 0.181073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.115401 restraints weight = 13911.164|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.63
r_work: 0.3312 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 4.81 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.1754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10461  Z= 0.112
  Angle     :  0.558   6.138  14242  Z= 0.266
  Chirality :  0.039   0.178   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  5.864  56.341   1430
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  4.00 %
    Allowed  : 14.26 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.24), residues: 1291
  helix:  1.72 (0.23), residues: 494
  sheet: -1.07 (0.37), residues: 185
  loop : -0.29 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  23 
 TYR   0.013   0.001   TYR A 735 
 PHE   0.009   0.001   PHE A 146 
 TRP   0.022   0.001   TRP A 614 
 HIS   0.002   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10460)
  covalent geometry    : angle       0.55846 (14242)
  hydrogen bonds       : bond        0.03288 (  436)
  hydrogen bonds       : angle       4.42479 ( 1281)
  Misc. bond           : bond        0.00058 (    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
  160 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 116
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6152 (OUTLIER) cc_final: 0.5664 (t80)
REVERT: A  282 GLN cc_start: 0.8653 (tt0) cc_final: 0.8351 (tp40)
REVERT: A  540 ASP cc_start: 0.8723 (p0) cc_final: 0.8508 (p0)
REVERT: A  580 GLU cc_start: 0.8722 (OUTLIER) cc_final: 0.8399 (pm20)
REVERT: A  710 GLN cc_start: 0.2459 (OUTLIER) cc_final: 0.1041 (pp30)
REVERT: A  715 LEU cc_start: 0.7148 (tt) cc_final: 0.6703 (tt)
REVERT: A  765 MET cc_start: 0.0260 (tpt) cc_final: -0.0104 (tpt)
REVERT: A  791 ASN cc_start: 0.7803 (m-40) cc_final: 0.7457 (m-40)
REVERT: A  973 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8351 (pp20)
REVERT: B   88 ASN cc_start: 0.8303 (t0) cc_final: 0.7903 (t0)
REVERT: B  114 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7931 (mp)
REVERT: B  140 TYR cc_start: 0.8483 (m-10) cc_final: 0.8250 (m-10)
REVERT: B  151 ASN cc_start: 0.9376 (m110) cc_final: 0.9051 (m-40)
REVERT: C    5 MET cc_start: 0.8585 (tpp) cc_final: 0.8181 (mmm)
REVERT: C   21 TYR cc_start: 0.8215 (p90) cc_final: 0.7751 (p90)
REVERT: C   47 HIS cc_start: 0.7064 (OUTLIER) cc_final: 0.6296 (p-80)
REVERT: C  114 ARG cc_start: 0.7701 (tmm160) cc_final: 0.7251 (tmt170)
REVERT: D  125 THR cc_start: 0.1490 (OUTLIER) cc_final: 0.1101 (p)
  outliers start: 44
  outliers final: 28
  residues processed: 151
  average time/residue: 0.0915
  time to fit residues: 20.0628
Evaluate side-chains
  144 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
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  191 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  253 ILE
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  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  710 GLN
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    3.9990
   chunk 105 optimal weight:    0.3980
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.179611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.119246 restraints weight = 13749.897|
|-----------------------------------------------------------------------------|
r_work (start): 0.3519 rms_B_bonded: 3.40
r_work: 0.3276 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10461  Z= 0.130
  Angle     :  0.579   9.023  14242  Z= 0.272
  Chirality :  0.040   0.298   1591
  Planarity :  0.004   0.043   1867
  Dihedral  :  5.865  56.992   1430
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 14.99 %
    Favored  : 81.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.24), residues: 1291
  helix:  1.72 (0.23), residues: 493
  sheet: -1.08 (0.37), residues: 185
  loop : -0.31 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  23 
 TYR   0.011   0.001   TYR A 735 
 PHE   0.011   0.001   PHE A 146 
 TRP   0.024   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 264 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10460)
  covalent geometry    : angle       0.57880 (14242)
  hydrogen bonds       : bond        0.03347 (  436)
  hydrogen bonds       : angle       4.42187 ( 1281)
  Misc. bond           : bond        0.00063 (    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
  154 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 113
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6181 (OUTLIER) cc_final: 0.5760 (t80)
REVERT: A  282 GLN cc_start: 0.8553 (tt0) cc_final: 0.8302 (tp40)
REVERT: A  436 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8806 (tp)
REVERT: A  580 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8173 (pm20)
REVERT: A  710 GLN cc_start: 0.2235 (OUTLIER) cc_final: 0.0818 (pp30)
REVERT: A  715 LEU cc_start: 0.7003 (tt) cc_final: 0.6582 (tt)
REVERT: A  738 MET cc_start: 0.6398 (mtp) cc_final: 0.6118 (mtp)
REVERT: A  765 MET cc_start: 0.0495 (tpt) cc_final: 0.0202 (tpt)
REVERT: A  791 ASN cc_start: 0.7803 (m-40) cc_final: 0.7447 (m-40)
REVERT: A  973 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8277 (pp20)
REVERT: B  114 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7881 (mp)
REVERT: B  151 ASN cc_start: 0.9328 (m110) cc_final: 0.9049 (m110)
REVERT: C   21 TYR cc_start: 0.8159 (p90) cc_final: 0.7741 (p90)
REVERT: C   47 HIS cc_start: 0.7081 (OUTLIER) cc_final: 0.6323 (p-80)
REVERT: C  114 ARG cc_start: 0.7653 (tmm160) cc_final: 0.7213 (tmt170)
REVERT: C  118 ARG cc_start: 0.9052 (mmp80) cc_final: 0.8485 (mmp80)
REVERT: D  125 THR cc_start: 0.1374 (OUTLIER) cc_final: 0.1010 (p)
  outliers start: 41
  outliers final: 28
  residues processed: 147
  average time/residue: 0.0841
  time to fit residues: 18.2848
Evaluate side-chains
  144 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
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  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  710 GLN
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 127 optimal weight:    3.9990
   chunk 117 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0370
   chunk 87 optimal weight:    0.5980
   chunk 95 optimal weight:    2.9990
   chunk 29 optimal weight:    0.5980
   chunk 88 optimal weight:    0.0970
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.4456

-------------------------------------------------------------------------------
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**
C  43 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.182127 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122794 restraints weight = 13852.217|
|-----------------------------------------------------------------------------|
r_work (start): 0.3549 rms_B_bonded: 3.24
r_work: 0.3311 rms_B_bonded: 3.29 restraints_weight: 0.5000
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10461  Z= 0.102
  Angle     :  0.571  10.166  14242  Z= 0.267
  Chirality :  0.040   0.340   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  5.720  57.709   1429
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 15.71 %
    Favored  : 80.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.24), residues: 1291
  helix:  1.83 (0.23), residues: 488
  sheet: -1.03 (0.37), residues: 185
  loop : -0.22 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  23 
 TYR   0.012   0.001   TYR A 735 
 PHE   0.008   0.001   PHE C  63 
 TRP   0.026   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 (10460)
  covalent geometry    : angle       0.57062 (14242)
  hydrogen bonds       : bond        0.03081 (  436)
  hydrogen bonds       : angle       4.28583 ( 1281)
  Misc. bond           : bond        0.00050 (    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
  155 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 117
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6159 (OUTLIER) cc_final: 0.5765 (t80)
REVERT: A  282 GLN cc_start: 0.8472 (tt0) cc_final: 0.8226 (tp40)
REVERT: A  436 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8800 (tp)
REVERT: A  580 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8191 (pm20)
REVERT: A  710 GLN cc_start: 0.2233 (OUTLIER) cc_final: 0.0845 (pp30)
REVERT: A  715 LEU cc_start: 0.6881 (tt) cc_final: 0.6497 (tt)
REVERT: A  738 MET cc_start: 0.6358 (mtp) cc_final: 0.5984 (mtm)
REVERT: A  765 MET cc_start: 0.0563 (tpt) cc_final: 0.0295 (tpt)
REVERT: A  791 ASN cc_start: 0.7761 (m-40) cc_final: 0.7413 (m-40)
REVERT: B  114 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7803 (mp)
REVERT: C    5 MET cc_start: 0.8459 (tpp) cc_final: 0.8096 (mmm)
REVERT: C   21 TYR cc_start: 0.8116 (p90) cc_final: 0.7701 (p90)
REVERT: C   47 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6293 (p-80)
REVERT: C  114 ARG cc_start: 0.7629 (tmm160) cc_final: 0.6701 (tmt170)
REVERT: D  125 THR cc_start: 0.1225 (OUTLIER) cc_final: 0.0896 (p)
  outliers start: 38
  outliers final: 26
  residues processed: 150
  average time/residue: 0.0906
  time to fit residues: 19.7314
Evaluate side-chains
  144 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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  253 ILE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
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  710 GLN
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  943 VAL
Chi-restraints excluded: chain A residue  972 THR
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 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 20 optimal weight:    6.9990
   chunk 3 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 107 optimal weight:    0.0000
   chunk 99 optimal weight:    6.9990
   chunk 16 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9990
   chunk 95 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.6586

-------------------------------------------------------------------------------
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 = 0.4239 r_free = 0.4239 target = 0.181120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.121420 restraints weight = 13889.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 3.23
r_work: 0.3290 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1982

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= 0.118
  Angle     :  0.584   8.577  14242  Z= 0.274
  Chirality :  0.040   0.371   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  5.649  58.223   1429
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 15.99 %
    Favored  : 80.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1291
  helix:  1.84 (0.23), residues: 488
  sheet: -1.07 (0.37), residues: 185
  loop : -0.20 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG C  23 
 TYR   0.013   0.001   TYR A 735 
 PHE   0.010   0.001   PHE A 146 
 TRP   0.021   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10460)
  covalent geometry    : angle       0.58356 (14242)
  hydrogen bonds       : bond        0.03187 (  436)
  hydrogen bonds       : angle       4.31298 ( 1281)
  Misc. bond           : bond        0.00052 (    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
  147 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 113
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 GLN cc_start: 0.8510 (tt0) cc_final: 0.8263 (tp40)
REVERT: A  436 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8794 (tp)
REVERT: A  580 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8187 (pm20)
REVERT: A  623 PHE cc_start: 0.6982 (m-10) cc_final: 0.6779 (m-10)
REVERT: A  710 GLN cc_start: 0.2254 (OUTLIER) cc_final: 0.0868 (pp30)
REVERT: A  715 LEU cc_start: 0.6906 (tt) cc_final: 0.6573 (tt)
REVERT: A  738 MET cc_start: 0.6497 (mtp) cc_final: 0.6116 (mtm)
REVERT: A  765 MET cc_start: 0.0553 (tpt) cc_final: 0.0329 (tpt)
REVERT: A  791 ASN cc_start: 0.7768 (m-40) cc_final: 0.7404 (m-40)
REVERT: B   88 ASN cc_start: 0.8156 (t0) cc_final: 0.6991 (t0)
REVERT: C   21 TYR cc_start: 0.8106 (p90) cc_final: 0.7686 (p90)
REVERT: C  114 ARG cc_start: 0.7653 (tmm160) cc_final: 0.7338 (tmm160)
REVERT: C  118 ARG cc_start: 0.9016 (mmp80) cc_final: 0.8452 (mmp80)
REVERT: D  125 THR cc_start: 0.1209 (OUTLIER) cc_final: 0.0874 (p)
  outliers start: 34
  outliers final: 29
  residues processed: 140
  average time/residue: 0.0926
  time to fit residues: 18.7048
Evaluate side-chains
  144 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 111
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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  253 ILE
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  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  710 GLN
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  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  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 20 optimal weight:    0.6980
   chunk 2 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 119 optimal weight:    9.9990
   chunk 34 optimal weight:    0.5980
   chunk 16 optimal weight:    0.2980
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 62 optimal weight:    0.8980
   chunk 83 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4243 r_free = 0.4243 target = 0.181439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.121572 restraints weight = 13776.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3533 rms_B_bonded: 3.32
r_work: 0.3290 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.3290
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.2032

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= 0.114
  Angle     :  0.583   8.652  14242  Z= 0.274
  Chirality :  0.040   0.369   1591
  Planarity :  0.004   0.041   1867
  Dihedral  :  5.337  58.879   1425
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.62 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1291
  helix:  1.84 (0.23), residues: 488
  sheet: -1.09 (0.37), residues: 185
  loop : -0.19 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  23 
 TYR   0.012   0.001   TYR A 735 
 PHE   0.009   0.001   PHE A 146 
 TRP   0.026   0.001   TRP A 614 
 HIS   0.004   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10460)
  covalent geometry    : angle       0.58317 (14242)
  hydrogen bonds       : bond        0.03127 (  436)
  hydrogen bonds       : angle       4.28462 ( 1281)
  Misc. bond           : bond        0.00048 (    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
  141 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 112
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 GLN cc_start: 0.8519 (tt0) cc_final: 0.8260 (tp40)
REVERT: A  436 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8797 (tp)
REVERT: A  580 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8224 (pm20)
REVERT: A  710 GLN cc_start: 0.2271 (OUTLIER) cc_final: 0.0915 (pp30)
REVERT: A  715 LEU cc_start: 0.6903 (tt) cc_final: 0.6572 (tt)
REVERT: A  765 MET cc_start: 0.0590 (tpt) cc_final: -0.0090 (tpt)
REVERT: A  791 ASN cc_start: 0.7766 (m-40) cc_final: 0.7414 (m-40)
REVERT: A  834 ILE cc_start: 0.7185 (mm) cc_final: 0.6981 (mm)
REVERT: C   21 TYR cc_start: 0.8098 (p90) cc_final: 0.7679 (p90)
REVERT: C   80 ASP cc_start: 0.7585 (m-30) cc_final: 0.7346 (m-30)
REVERT: C  114 ARG cc_start: 0.7636 (tmm160) cc_final: 0.6700 (tmt170)
REVERT: C  118 ARG cc_start: 0.8992 (mmp80) cc_final: 0.8371 (mmp80)
  outliers start: 29
  outliers final: 24
  residues processed: 135
  average time/residue: 0.0974
  time to fit residues: 18.8895
Evaluate side-chains
  139 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
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  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  436 LEU
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  710 GLN
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  943 VAL
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  145 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
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 82 optimal weight:    9.9990
   chunk 44 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 108 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9980
   chunk 98 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0970
   chunk 94 optimal weight:    0.6980
   overall best weight:    0.6978

-------------------------------------------------------------------------------
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**
A 710 GLN
B  88 ASN
** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.181231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.116405 restraints weight = 13864.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 2.95
r_work: 0.3299 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work: 0.3160 rms_B_bonded: 4.92 restraints_weight: 0.2500
r_work (final): 0.3160
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.2088

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= 0.121
  Angle     :  0.582   7.984  14242  Z= 0.273
  Chirality :  0.040   0.361   1591
  Planarity :  0.004   0.040   1867
  Dihedral  :  5.317  59.760   1425
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 16.53 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.24), residues: 1291
  helix:  1.87 (0.23), residues: 487
  sheet: -1.11 (0.37), residues: 185
  loop : -0.21 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C  23 
 TYR   0.012   0.001   TYR A 735 
 PHE   0.010   0.001   PHE A 146 
 TRP   0.025   0.001   TRP A 614 
 HIS   0.004   0.000   HIS A 817 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10460)
  covalent geometry    : angle       0.58241 (14242)
  hydrogen bonds       : bond        0.03197 (  436)
  hydrogen bonds       : angle       4.28686 ( 1281)
  Misc. bond           : bond        0.00053 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2617.74 seconds
wall clock time: 45 minutes 39.18 seconds (2739.18 seconds total)