Starting phenix.real_space_refine
on Fri Feb 14 15:53:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sea_40408/02_2025/8sea_40408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sea_40408/02_2025/8sea_40408.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sea_40408/02_2025/8sea_40408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sea_40408/02_2025/8sea_40408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sea_40408/02_2025/8sea_40408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sea_40408/02_2025/8sea_40408.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      37      5.16       5
     C    6490      2.51       5
     N    1792      2.21       5
     O    1888      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10208
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7712
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 992, 7712
          Classifications: {'peptide': 992}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 65, 'TRANS': 926}
    Chain: "B"
      Number of atoms: 627
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 627
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 4, 'TRANS': 74}
    Chain: "C"
      Number of atoms: 1243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1243
          Classifications: {'peptide': 152}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133}
    Chain: "D"
      Number of atoms: 603
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 603
          Classifications: {'peptide': 76}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 72}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'GLY%COO:oxt': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 23
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 23
          Classifications: {'RNA': 1}
          Modifications used: {'rna2p': 1}
  Time building chain proxies: 6.63, per 1000 atoms: 0.65
  Number of scatterers: 10208
  At special positions: 0
  Unit cell: (91.652, 104.983, 117.481, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      37     16.00
     P       1     15.00
     O    1888      8.00
     N    1792      7.00
     C    6490      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.29
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 13 sheets defined
      44.9% alpha, 13.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.54
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 32
      removed outlier: 4.059A  pdb=" N   ARG A  29 " --> pdb=" O   PRO A  25 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLN A  31 " --> pdb=" O   MET A  27 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLY A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 55
    Processing helix  chain 'A' and resid 69 through 74
      removed outlier: 3.527A  pdb=" N   ALA A  74 " --> pdb=" O   ASP A  71 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 99
      removed outlier: 4.077A  pdb=" N   GLU A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   LEU A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN A  99 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 119
    Processing helix  chain 'A' and resid 128 through 142
    Processing helix  chain 'A' and resid 197 through 203
      removed outlier: 4.031A  pdb=" N   HIS A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 221
      removed outlier: 3.517A  pdb=" N   ASN A 221 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 218 through 221'
    Processing helix  chain 'A' and resid 266 through 273
      removed outlier: 4.330A  pdb=" N   LEU A 272 " --> pdb=" O   ASP A 268 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLN A 273 " --> pdb=" O   THR A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 280 through 305
    Processing helix  chain 'A' and resid 312 through 326
    Processing helix  chain 'A' and resid 327 through 331
    Processing helix  chain 'A' and resid 342 through 352
    Processing helix  chain 'A' and resid 357 through 378
    Processing helix  chain 'A' and resid 392 through 395
    Processing helix  chain 'A' and resid 404 through 409
    Processing helix  chain 'A' and resid 415 through 423
      removed outlier: 4.640A  pdb=" N   VAL A 421 " --> pdb=" O   GLY A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 433
    Processing helix  chain 'A' and resid 442 through 455
    Processing helix  chain 'A' and resid 473 through 478
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 4.128A  pdb=" N   VAL A 488 " --> pdb=" O   SER A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 504
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.951A  pdb=" N   GLU A 521 " --> pdb=" O   PRO A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 532
      removed outlier: 3.522A  pdb=" N   VAL A 532 " --> pdb=" O   PHE A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 556
      removed outlier: 3.554A  pdb=" N   ARG A 545 " --> pdb=" O   SER A 541 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 593
      removed outlier: 4.306A  pdb=" N   ASP A 593 " --> pdb=" O   ALA A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 607 through 631
      removed outlier: 3.870A  pdb=" N   LEU A 625 " --> pdb=" O   GLU A 621 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ALA A 627 " --> pdb=" O   PHE A 623 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLU A 628 " --> pdb=" O   ARG A 624 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   ASN A 631 " --> pdb=" O   ALA A 627 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 631 through 637
      removed outlier: 3.554A  pdb=" N   HIS A 637 " --> pdb=" O   HIS A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 651
      removed outlier: 4.000A  pdb=" N   THR A 648 " --> pdb=" O   ASP A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 653 through 657
    Processing helix  chain 'A' and resid 672 through 681
    Processing helix  chain 'A' and resid 681 through 692
    Processing helix  chain 'A' and resid 721 through 740
      removed outlier: 3.518A  pdb=" N   LEU A 725 " --> pdb=" O   GLN A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 749 through 757
    Processing helix  chain 'A' and resid 761 through 765
      removed outlier: 4.070A  pdb=" N   MET A 765 " --> pdb=" O   PRO A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 782 through 800
      removed outlier: 3.914A  pdb=" N   GLN A 786 " --> pdb=" O   PHE A 782 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 832
    Processing helix  chain 'A' and resid 838 through 845
      removed outlier: 3.557A  pdb=" N   SER A 842 " --> pdb=" O   ASN A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 853 through 873
    Processing helix  chain 'A' and resid 877 through 881
    Processing helix  chain 'A' and resid 927 through 940
    Processing helix  chain 'A' and resid 959 through 967
    Processing helix  chain 'A' and resid 970 through 980
    Processing helix  chain 'B' and resid 103 through 116
      removed outlier: 3.511A  pdb=" N   LEU B 107 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3 through 17
      removed outlier: 3.701A  pdb=" N   LYS C  16 " --> pdb=" O   GLU C  12 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   LYS C  17 " --> pdb=" O   ASP C  13 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 47
      No H-bonds generated for 'chain 'C' and resid 45 through 47'
    Processing helix  chain 'C' and resid 100 through 114
      removed outlier: 3.873A  pdb=" N   VAL C 104 " --> pdb=" O   LYS C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 122 through 132
    Processing helix  chain 'C' and resid 132 through 148
    Processing helix  chain 'D' and resid 103 through 116
      removed outlier: 3.726A  pdb=" N   LEU D 107 " --> pdb=" O   THR D 103 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLN D 110 " --> pdb=" O   HIS D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 118 through 122
    Processing helix  chain 'D' and resid 136 through 141
      removed outlier: 4.430A  pdb=" N   TYR D 140 " --> pdb=" O   PRO D 136 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106
      removed outlier: 6.301A  pdb=" N   VAL A  35 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   HIS A  62 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   VAL A  37 " --> pdb=" O   HIS A  62 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 121 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   VAL A 155 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106
      removed outlier: 6.301A  pdb=" N   VAL A  35 " --> pdb=" O   THR A  60 " (cutoff:3.500A)
      removed outlier: 7.669A  pdb=" N   HIS A  62 " --> pdb=" O   VAL A  35 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   VAL A  37 " --> pdb=" O   HIS A  62 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   VAL A 121 " --> pdb=" O   ARG A  34 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168
    Processing sheet with id=AA4, first strand: chain 'A' and resid 178 through 179
      removed outlier: 4.492A  pdb=" N   LEU A 208 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 181 through 184
      removed outlier: 3.739A  pdb=" N   LEU A 236 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 214 through 216
    Processing sheet with id=AA7, first strand: chain 'A' and resid 511 through 512
      removed outlier: 6.083A  pdb=" N   VAL A 466 " --> pdb=" O   LEU A 512 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   LEU A 437 " --> pdb=" O   VAL A 467 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   VAL A 535 " --> pdb=" O   LEU A 560 " (cutoff:3.500A)
      removed outlier: 8.528A  pdb=" N   ALA A 562 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 7.163A  pdb=" N   ALA A 537 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   LEU A 559 " --> pdb=" O   PHE A 574 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 904 through 906
    Processing sheet with id=AA9, first strand: chain 'A' and resid 917 through 919
      removed outlier: 6.502A  pdb=" N   LEU A 917 " --> pdb=" O   HIS A1009 " (cutoff:3.500A)
      removed outlier: 7.518A  pdb=" N   GLU A1011 " --> pdb=" O   LEU A 917 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   VAL A 919 " --> pdb=" O   GLU A1011 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   LEU A 946 " --> pdb=" O   LEU A 953 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 93 through 98
      removed outlier: 9.051A  pdb=" N   VAL B 148 " --> pdb=" O   SER B  83 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   LEU B  85 " --> pdb=" O   VAL B 148 " (cutoff:3.500A)
      removed outlier: 7.691A  pdb=" N   MET B 150 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ARG B  87 " --> pdb=" O   MET B 150 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   LEU B 152 " --> pdb=" O   ARG B  87 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 22 through 26
      removed outlier: 6.029A  pdb=" N   ASN C  24 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU C  38 " --> pdb=" O   ASN C  24 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 22 through 26
      removed outlier: 6.029A  pdb=" N   ASN C  24 " --> pdb=" O   LEU C  38 " (cutoff:3.500A)
      removed outlier: 5.189A  pdb=" N   LEU C  38 " --> pdb=" O   ASN C  24 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL C 149 " --> pdb=" O   ALA C  50 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'D' and resid 124 through 126
      removed outlier: 3.508A  pdb=" N   THR D 125 " --> pdb=" O   PHE D 149 " (cutoff:3.500A)

    455 hydrogen bonds defined for protein.
    1281 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.76

  Time building geometry restraints manager: 2.70 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
    1.415  1.624 -0.209 1.50e-02 4.44e+03 1.94e+02
  bond pdb=" C1' AMP B1101 "
       pdb=" C2' AMP B1101 "
    ideal  model  delta    sigma   weight residual
    1.526  1.366  0.160 1.50e-02 4.44e+03 1.13e+02
  bond pdb=" C4' AMP B1101 "
       pdb=" O4' AMP B1101 "
    ideal  model  delta    sigma   weight residual
    1.454  1.295  0.159 1.50e-02 4.44e+03 1.13e+02
  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=" 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 -     2.71: 14137
        2.71 -     5.41: 94
        5.41 -     8.12: 6
        8.12 -    10.82: 1
       10.82 -    13.53: 4
  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
     114.00  127.43  -13.43 1.50e+00 4.44e-01 8.02e+01
  angle pdb=" N9  AMP B1101 "
        pdb=" C1' AMP B1101 "
        pdb=" O4' AMP B1101 "
      ideal   model   delta    sigma   weight residual
     108.20   95.38   12.82 1.50e+00 4.44e-01 7.30e+01
  angle pdb=" C1' AMP B1101 "
        pdb=" O4' AMP B1101 "
        pdb=" C4' AMP B1101 "
      ideal   model   delta    sigma   weight residual
     109.70  104.33    5.37 1.00e+00 1.00e+00 2.88e+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=" C1' AMP B1101 "
        pdb=" C2' AMP B1101 "
        pdb=" C3' AMP B1101 "
      ideal   model   delta    sigma   weight residual
     101.50  105.75   -4.25 1.00e+00 1.00e+00 1.81e+01
  ... (remaining 14237 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    13.84: 5680
       13.84 -    27.68: 436
       27.68 -    41.52: 142
       41.52 -    55.36: 27
       55.36 -    69.21: 14
  Dihedral angle restraints: 6299
    sinusoidal: 2548
      harmonic: 3751
  Sorted by residual:
  dihedral pdb=" C1' AMP B1101 "
           pdb=" C4' AMP B1101 "
           pdb=" O4' AMP B1101 "
           pdb=" C5' AMP B1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -123.00 -152.80   29.80     1      8.00e+00 1.56e-02 1.98e+01
  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
  ... (remaining 6296 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 979
       0.028 -    0.057: 427
       0.057 -    0.085: 98
       0.085 -    0.114: 75
       0.114 -    0.142: 12
  Chirality restraints: 1591
  Sorted by residual:
  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
  chirality pdb=" CA  ILE A 214 "
            pdb=" N   ILE A 214 "
            pdb=" C   ILE A 214 "
            pdb=" CB  ILE A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.19e-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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     26.240
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.500
-------------------------------------------------------------------------------
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   0.209  10460  Z= 0.343
  Angle     :  0.565  13.528  14242  Z= 0.280
  Chirality :  0.038   0.142   1591
  Planarity :  0.004   0.034   1867
  Dihedral  : 11.768  69.205   3873
  Min Nonbonded Distance : 1.270

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  :  7.08 %
    Favored  : 89.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.24), residues: 1291
  helix:  1.74 (0.24), residues: 476
  sheet: -1.21 (0.38), residues: 185
  loop : -0.12 (0.26), residues: 630

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

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

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 144
  time to evaluate  : 1.199 
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: 0.2351
  time to fit residues: 56.8865
Evaluate side-chains
  132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  710 GLN
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue  101 THR
Chi-restraints excluded: chain C residue  117 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.1980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9980
   chunk 74 optimal weight:   30.0000
   chunk 116 optimal weight:    2.9990
   overall best weight:    0.8382

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

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

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.181293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.120342 restraints weight = 13790.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 3.44
r_work: 0.3274 rms_B_bonded: 3.51 restraints_weight: 0.5000
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10460  Z= 0.215
  Angle     :  0.578   6.957  14242  Z= 0.282
  Chirality :  0.040   0.150   1591
  Planarity :  0.004   0.039   1867
  Dihedral  :  6.518  56.106   1441
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  :  9.99 %
    Favored  : 86.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.24), residues: 1291
  helix:  1.64 (0.23), residues: 498
  sheet: -0.99 (0.39), residues: 185
  loop : -0.20 (0.26), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 614 
 HIS   0.003   0.001   HIS A 264 
 PHE   0.009   0.001   PHE A 146 
 TYR   0.016   0.002   TYR D  96 
 ARG   0.006   0.000   ARG C  23 

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

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

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

  2582 Ramachandran restraints generated.
    1291 Oldfield, 0 Emsley, 1291 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 123
  time to evaluate  : 1.098 
Fit side-chains
REVERT: A  170 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.8023 (p0)
REVERT: A  244 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.4515 (m-80)
REVERT: A  282 GLN cc_start: 0.8570 (tt0) cc_final: 0.8307 (tp40)
REVERT: A  540 ASP cc_start: 0.8624 (p0) cc_final: 0.8391 (p0)
REVERT: A  715 LEU cc_start: 0.7041 (tt) cc_final: 0.6746 (tt)
REVERT: A  791 ASN cc_start: 0.7844 (m-40) cc_final: 0.7495 (m-40)
REVERT: B  114 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7904 (mp)
REVERT: B  143 LYS cc_start: 0.8913 (tppp) cc_final: 0.8710 (tppt)
REVERT: B  151 ASN cc_start: 0.9347 (m110) cc_final: 0.9065 (m110)
REVERT: C    5 MET cc_start: 0.8601 (tpp) cc_final: 0.8154 (mmm)
REVERT: C   21 TYR cc_start: 0.8133 (p90) cc_final: 0.7488 (p90)
REVERT: C   47 HIS cc_start: 0.7101 (OUTLIER) cc_final: 0.6430 (p90)
REVERT: C   80 ASP cc_start: 0.8122 (m-30) cc_final: 0.7904 (m-30)
REVERT: C  114 ARG cc_start: 0.7411 (tmm160) cc_final: 0.6162 (tmm160)
  outliers start: 36
  outliers final: 17
  residues processed: 150
  average time/residue: 0.2261
  time to fit residues: 48.6393
Evaluate side-chains
  133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 99 optimal weight:    6.9990
   chunk 71 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 56 optimal weight:    0.0670
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 100 optimal weight:    0.9990
   overall best weight:    0.6920

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.181515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.120772 restraints weight = 13976.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 3.53
r_work: 0.3289 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3289
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10460  Z= 0.188
  Angle     :  0.566   7.365  14242  Z= 0.272
  Chirality :  0.039   0.147   1591
  Planarity :  0.004   0.043   1867
  Dihedral  :  6.379  56.797   1435
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 11.53 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.24), residues: 1291
  helix:  1.74 (0.23), residues: 494
  sheet: -0.96 (0.38), residues: 185
  loop : -0.23 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 966 
 PHE   0.009   0.001   PHE A 146 
 TYR   0.014   0.001   TYR D  96 
 ARG   0.007   0.000   ARG C  23 

*********************** 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
  157 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 122
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6028 (OUTLIER) cc_final: 0.5486 (t80)
REVERT: A  282 GLN cc_start: 0.8542 (tt0) cc_final: 0.8280 (tp40)
REVERT: A  540 ASP cc_start: 0.8641 (p0) cc_final: 0.8352 (p0)
REVERT: A  715 LEU cc_start: 0.7010 (tt) cc_final: 0.6694 (tt)
REVERT: A  765 MET cc_start: 0.0258 (tpt) cc_final: -0.0002 (tpt)
REVERT: A  791 ASN cc_start: 0.7900 (m-40) cc_final: 0.7542 (m-40)
REVERT: B  114 LEU cc_start: 0.8141 (OUTLIER) cc_final: 0.7878 (mp)
REVERT: B  139 GLU cc_start: 0.7789 (tp30) cc_final: 0.7549 (tp30)
REVERT: B  151 ASN cc_start: 0.9351 (m110) cc_final: 0.9074 (m110)
REVERT: C   21 TYR cc_start: 0.8140 (p90) cc_final: 0.7462 (p90)
REVERT: C   47 HIS cc_start: 0.7048 (OUTLIER) cc_final: 0.6424 (p90)
REVERT: C   75 TYR cc_start: 0.7446 (t80) cc_final: 0.7057 (t80)
REVERT: C   80 ASP cc_start: 0.8093 (m-30) cc_final: 0.7823 (m-30)
REVERT: C  114 ARG cc_start: 0.7452 (tmm160) cc_final: 0.7123 (tmm160)
  outliers start: 35
  outliers final: 19
  residues processed: 148
  average time/residue: 0.2242
  time to fit residues: 47.8467
Evaluate side-chains
  132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 110
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  619 PHE
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  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 74 optimal weight:    0.0270
   chunk 67 optimal weight:    0.0170
   chunk 3 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9990
   chunk 10 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 87 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   overall best weight:    0.5676

-------------------------------------------------------------------------------
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 = 0.4246 r_free = 0.4246 target = 0.181994 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.120061 restraints weight = 13784.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3509 rms_B_bonded: 3.42
r_work: 0.3291 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10460  Z= 0.173
  Angle     :  0.561   7.956  14242  Z= 0.267
  Chirality :  0.040   0.280   1591
  Planarity :  0.004   0.038   1867
  Dihedral  :  6.357  58.848   1435
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.99 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.24), residues: 1291
  helix:  1.75 (0.23), residues: 493
  sheet: -0.95 (0.37), residues: 185
  loop : -0.22 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 614 
 HIS   0.002   0.000   HIS A 682 
 PHE   0.011   0.001   PHE A 808 
 TYR   0.019   0.001   TYR A 735 
 ARG   0.008   0.000   ARG C  23 

*********************** 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
  145 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 1.151 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6043 (OUTLIER) cc_final: 0.5499 (t80)
REVERT: A  282 GLN cc_start: 0.8548 (tt0) cc_final: 0.8286 (tp40)
REVERT: A  540 ASP cc_start: 0.8582 (p0) cc_final: 0.8259 (p0)
REVERT: A  715 LEU cc_start: 0.6999 (tt) cc_final: 0.6614 (tt)
REVERT: A  791 ASN cc_start: 0.7903 (m-40) cc_final: 0.7562 (m-40)
REVERT: B  114 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7915 (mp)
REVERT: B  151 ASN cc_start: 0.9339 (m110) cc_final: 0.9070 (m110)
REVERT: C   47 HIS cc_start: 0.7070 (OUTLIER) cc_final: 0.6329 (p-80)
REVERT: C   75 TYR cc_start: 0.7456 (t80) cc_final: 0.7085 (t80)
REVERT: C   80 ASP cc_start: 0.8081 (m-30) cc_final: 0.7838 (m-30)
REVERT: C  114 ARG cc_start: 0.7492 (tmm160) cc_final: 0.7042 (tmt170)
REVERT: C  118 ARG cc_start: 0.9087 (mmp80) cc_final: 0.8876 (mmp80)
REVERT: D  125 THR cc_start: 0.1519 (m) cc_final: 0.1073 (p)
  outliers start: 29
  outliers final: 22
  residues processed: 136
  average time/residue: 0.2250
  time to fit residues: 44.1887
Evaluate side-chains
  136 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 1.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  211 PHE
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  619 PHE
Chi-restraints excluded: chain A residue  827 LEU
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 62 optimal weight:    5.9990
   chunk 117 optimal weight:    0.7980
   chunk 118 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    4.9990
   chunk 101 optimal weight:    0.3980
   chunk 46 optimal weight:    0.3980
   chunk 47 optimal weight:    0.0070
   chunk 11 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.4998

-------------------------------------------------------------------------------
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 = 0.4248 r_free = 0.4248 target = 0.182211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.117942 restraints weight = 13860.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3487 rms_B_bonded: 2.99
r_work: 0.3319 rms_B_bonded: 3.25 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10460  Z= 0.159
  Angle     :  0.541   6.325  14242  Z= 0.258
  Chirality :  0.039   0.182   1591
  Planarity :  0.004   0.063   1867
  Dihedral  :  6.222  57.076   1434
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 13.08 %
    Favored  : 83.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.24), residues: 1291
  helix:  1.83 (0.23), residues: 494
  sheet: -0.91 (0.37), residues: 185
  loop : -0.20 (0.26), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 682 
 PHE   0.009   0.001   PHE A 146 
 TYR   0.018   0.001   TYR C  21 
 ARG   0.010   0.000   ARG C  23 

*********************** 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: 37
    poor density    : 120
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6063 (OUTLIER) cc_final: 0.5538 (t80)
REVERT: A  282 GLN cc_start: 0.8504 (tt0) cc_final: 0.8244 (tp40)
REVERT: A  381 MET cc_start: 0.8163 (tpt) cc_final: 0.7838 (tpt)
REVERT: A  715 LEU cc_start: 0.6889 (tt) cc_final: 0.6551 (tt)
REVERT: A  765 MET cc_start: 0.0507 (tpt) cc_final: 0.0196 (tpt)
REVERT: A  791 ASN cc_start: 0.7893 (m-40) cc_final: 0.7545 (m-40)
REVERT: B  114 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7934 (mp)
REVERT: C    5 MET cc_start: 0.8480 (tpp) cc_final: 0.8146 (mmm)
REVERT: C   21 TYR cc_start: 0.8006 (p90) cc_final: 0.7790 (p90)
REVERT: C   47 HIS cc_start: 0.7045 (OUTLIER) cc_final: 0.6285 (p-80)
REVERT: C   75 TYR cc_start: 0.7443 (t80) cc_final: 0.7018 (t80)
REVERT: C   80 ASP cc_start: 0.8017 (m-30) cc_final: 0.7771 (m-30)
REVERT: C   81 GLU cc_start: 0.8283 (tt0) cc_final: 0.7527 (pt0)
REVERT: C  114 ARG cc_start: 0.7491 (tmm160) cc_final: 0.7044 (tmt170)
REVERT: D  125 THR cc_start: 0.1383 (m) cc_final: 0.0995 (p)
  outliers start: 37
  outliers final: 23
  residues processed: 147
  average time/residue: 0.2221
  time to fit residues: 47.7212
Evaluate side-chains
  134 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  214 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  729 LEU
Chi-restraints excluded: chain A residue  827 LEU
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  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 110 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 16 optimal weight:    7.9990
   chunk 127 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 95 optimal weight:    3.9990
   chunk 39 optimal weight:    0.6980
   chunk 91 optimal weight:    2.9990
   chunk 118 optimal weight:   10.0000
   chunk 74 optimal weight:    0.0670
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.5524

-------------------------------------------------------------------------------
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
D 151 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.178409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.112899 restraints weight = 13865.144|
|-----------------------------------------------------------------------------|
r_work (start): 0.3416 rms_B_bonded: 3.01
r_work: 0.3242 rms_B_bonded: 3.32 restraints_weight: 0.5000
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8200
moved from start:          0.1719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  10460  Z= 0.333
  Angle     :  0.609   8.236  14242  Z= 0.294
  Chirality :  0.041   0.167   1591
  Planarity :  0.004   0.040   1867
  Dihedral  :  6.234  59.385   1430
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  3.81 %
    Allowed  : 13.62 %
    Favored  : 82.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.45 (0.24), residues: 1291
  helix:  1.60 (0.23), residues: 493
  sheet: -1.09 (0.37), residues: 185
  loop : -0.24 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 614 
 HIS   0.005   0.001   HIS A 264 
 PHE   0.014   0.002   PHE A 146 
 TYR   0.013   0.002   TYR C  21 
 ARG   0.009   0.000   ARG C  23 

*********************** 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
  156 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 114
  time to evaluate  : 1.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6084 (OUTLIER) cc_final: 0.5628 (t80)
REVERT: A  282 GLN cc_start: 0.8647 (tt0) cc_final: 0.8342 (tp40)
REVERT: A  715 LEU cc_start: 0.6989 (tt) cc_final: 0.6577 (tt)
REVERT: A  765 MET cc_start: 0.0230 (tpt) cc_final: -0.0077 (tpt)
REVERT: A  791 ASN cc_start: 0.7913 (m-40) cc_final: 0.7571 (m-40)
REVERT: B  114 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7981 (mp)
REVERT: C   21 TYR cc_start: 0.8115 (p90) cc_final: 0.7694 (p90)
REVERT: C   75 TYR cc_start: 0.7552 (t80) cc_final: 0.7135 (t80)
REVERT: C   80 ASP cc_start: 0.8085 (m-30) cc_final: 0.7814 (m-30)
REVERT: C   81 GLU cc_start: 0.8350 (tt0) cc_final: 0.7610 (pt0)
REVERT: C  114 ARG cc_start: 0.7620 (tmm160) cc_final: 0.7173 (tmt170)
REVERT: D  125 THR cc_start: 0.1535 (m) cc_final: 0.1159 (p)
  outliers start: 42
  outliers final: 26
  residues processed: 144
  average time/residue: 0.2553
  time to fit residues: 53.2175
Evaluate side-chains
  135 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 107
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  122 VAL
Chi-restraints excluded: chain A residue  181 ILE
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  591 SER
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  632 HIS
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 63 optimal weight:    8.9990
   chunk 123 optimal weight:    0.9990
   chunk 78 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 87 optimal weight:    0.7980
   chunk 27 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 31 optimal weight:    5.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    0.9384

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.179759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.119293 restraints weight = 13962.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 3.65
r_work: 0.3250 rms_B_bonded: 3.52 restraints_weight: 0.5000
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.1822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10460  Z= 0.222
  Angle     :  0.576   8.860  14242  Z= 0.275
  Chirality :  0.040   0.171   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  5.925  59.370   1426
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 14.62 %
    Favored  : 82.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1291
  helix:  1.69 (0.23), residues: 493
  sheet: -1.12 (0.37), residues: 185
  loop : -0.25 (0.26), residues: 613

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 614 
 HIS   0.003   0.001   HIS A 817 
 PHE   0.018   0.001   PHE D 126 
 TYR   0.011   0.001   TYR A1010 
 ARG   0.009   0.000   ARG C  23 

*********************** 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
  145 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 111
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6132 (OUTLIER) cc_final: 0.5720 (t80)
REVERT: A  282 GLN cc_start: 0.8605 (tt0) cc_final: 0.8340 (tp40)
REVERT: A  381 MET cc_start: 0.8268 (tpt) cc_final: 0.7999 (tpt)
REVERT: A  715 LEU cc_start: 0.7011 (tt) cc_final: 0.6562 (tt)
REVERT: A  738 MET cc_start: 0.6428 (mtp) cc_final: 0.6028 (mtm)
REVERT: A  765 MET cc_start: 0.0376 (tpt) cc_final: 0.0115 (tpt)
REVERT: A  791 ASN cc_start: 0.7898 (m-40) cc_final: 0.7572 (m-40)
REVERT: B  114 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7956 (mp)
REVERT: C    5 MET cc_start: 0.8566 (tpp) cc_final: 0.8133 (mmm)
REVERT: C   21 TYR cc_start: 0.8126 (p90) cc_final: 0.7702 (p90)
REVERT: C   75 TYR cc_start: 0.7516 (t80) cc_final: 0.7082 (t80)
REVERT: C   80 ASP cc_start: 0.8075 (m-30) cc_final: 0.7792 (m-30)
REVERT: C   81 GLU cc_start: 0.8362 (tt0) cc_final: 0.7616 (pt0)
REVERT: C  114 ARG cc_start: 0.7636 (tmm160) cc_final: 0.7170 (tmt170)
REVERT: C  118 ARG cc_start: 0.8968 (mmp80) cc_final: 0.8441 (mmp80)
REVERT: D  125 THR cc_start: 0.1508 (m) cc_final: 0.1140 (p)
  outliers start: 34
  outliers final: 25
  residues processed: 136
  average time/residue: 0.2400
  time to fit residues: 47.3217
Evaluate side-chains
  132 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 105
  time to evaluate  : 1.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   40 LEU
Chi-restraints excluded: chain A residue  105 VAL
Chi-restraints excluded: chain A residue  170 ASP
Chi-restraints excluded: chain A residue  191 ILE
Chi-restraints excluded: chain A residue  229 HIS
Chi-restraints excluded: chain A residue  244 PHE
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  364 LEU
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  977 GLN
Chi-restraints excluded: chain B residue   85 LEU
Chi-restraints excluded: chain B residue  100 LEU
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  117 VAL
Chi-restraints excluded: chain B residue  145 LEU
Chi-restraints excluded: chain C residue   47 HIS
Chi-restraints excluded: chain C residue   87 LEU
Chi-restraints excluded: chain C residue  117 ILE
Chi-restraints excluded: chain C residue  141 GLU
Chi-restraints excluded: chain C residue  143 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 95 optimal weight:    0.5980
   chunk 89 optimal weight:    0.0470
   chunk 98 optimal weight:    0.7980
   chunk 79 optimal weight:    5.9990
   chunk 119 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 8 optimal weight:    0.8980
   chunk 126 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   overall best weight:    0.5678

-------------------------------------------------------------------------------
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 = 0.4235 r_free = 0.4235 target = 0.180766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.120185 restraints weight = 13814.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3515 rms_B_bonded: 3.54
r_work: 0.3277 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.3277
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8147
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10460  Z= 0.173
  Angle     :  0.564   7.212  14242  Z= 0.268
  Chirality :  0.039   0.217   1591
  Planarity :  0.004   0.041   1867
  Dihedral  :  5.799  58.714   1426
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 14.90 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.65 (0.24), residues: 1291
  helix:  1.83 (0.23), residues: 487
  sheet: -1.05 (0.37), residues: 185
  loop : -0.15 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 614 
 HIS   0.003   0.000   HIS A 817 
 PHE   0.016   0.001   PHE D 126 
 TYR   0.012   0.001   TYR A 735 
 ARG   0.008   0.000   ARG C  23 

*********************** 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
  146 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6080 (OUTLIER) cc_final: 0.5667 (t80)
REVERT: A  282 GLN cc_start: 0.8550 (tt0) cc_final: 0.8288 (tp40)
REVERT: A  381 MET cc_start: 0.8223 (tpt) cc_final: 0.7969 (tpt)
REVERT: A  715 LEU cc_start: 0.6935 (tt) cc_final: 0.6544 (tt)
REVERT: A  738 MET cc_start: 0.6533 (mtp) cc_final: 0.6130 (mtm)
REVERT: A  765 MET cc_start: 0.0281 (tpt) cc_final: 0.0065 (tpt)
REVERT: A  791 ASN cc_start: 0.7872 (m-40) cc_final: 0.7226 (t0)
REVERT: B  114 LEU cc_start: 0.8279 (OUTLIER) cc_final: 0.7919 (mp)
REVERT: C    5 MET cc_start: 0.8564 (tpp) cc_final: 0.8124 (mmm)
REVERT: C   21 TYR cc_start: 0.8083 (p90) cc_final: 0.7643 (p90)
REVERT: C   75 TYR cc_start: 0.7445 (t80) cc_final: 0.6985 (t80)
REVERT: C   80 ASP cc_start: 0.8047 (m-30) cc_final: 0.7720 (m-30)
REVERT: C   81 GLU cc_start: 0.8351 (tt0) cc_final: 0.7600 (pt0)
REVERT: C  114 ARG cc_start: 0.7638 (tmm160) cc_final: 0.7196 (tmt170)
  outliers start: 34
  outliers final: 26
  residues processed: 138
  average time/residue: 0.2222
  time to fit residues: 44.0305
Evaluate side-chains
  133 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 105
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
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  468 ASP
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  941 LEU
Chi-restraints excluded: chain A residue  943 VAL
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue  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   56 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 41 optimal weight:    0.9980
   chunk 26 optimal weight:    0.7980
   chunk 73 optimal weight:    2.9990
   chunk 77 optimal weight:   10.0000
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 89 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 95 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.1584

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.179322 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.113808 restraints weight = 13908.362|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 3.05
r_work: 0.3253 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10460  Z= 0.260
  Angle     :  0.604   9.416  14242  Z= 0.288
  Chirality :  0.041   0.363   1591
  Planarity :  0.004   0.043   1867
  Dihedral  :  5.906  59.640   1426
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.17 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.24), residues: 1291
  helix:  1.66 (0.23), residues: 492
  sheet: -1.09 (0.37), residues: 185
  loop : -0.22 (0.26), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 264 
 PHE   0.014   0.001   PHE D 126 
 TYR   0.011   0.001   TYR A 735 
 ARG   0.009   0.000   ARG C  23 

*********************** 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
  141 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 108
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
REVERT: A  244 PHE cc_start: 0.6105 (OUTLIER) cc_final: 0.5752 (t80)
REVERT: A  282 GLN cc_start: 0.8606 (tt0) cc_final: 0.8365 (tp40)
REVERT: A  381 MET cc_start: 0.8264 (tpt) cc_final: 0.7956 (tpt)
REVERT: A  580 GLU cc_start: 0.8515 (OUTLIER) cc_final: 0.8182 (pm20)
REVERT: A  715 LEU cc_start: 0.6936 (tt) cc_final: 0.6544 (tt)
REVERT: A  791 ASN cc_start: 0.7909 (m-40) cc_final: 0.7414 (t0)
REVERT: B  114 LEU cc_start: 0.8218 (OUTLIER) cc_final: 0.7888 (mp)
REVERT: C   21 TYR cc_start: 0.8144 (p90) cc_final: 0.7589 (p90)
REVERT: C   75 TYR cc_start: 0.7490 (t80) cc_final: 0.7034 (t80)
REVERT: C   80 ASP cc_start: 0.8070 (m-30) cc_final: 0.7752 (m-30)
REVERT: C   81 GLU cc_start: 0.8371 (tt0) cc_final: 0.7620 (pt0)
REVERT: C  114 ARG cc_start: 0.7649 (tmm160) cc_final: 0.6756 (tmt170)
REVERT: C  118 ARG cc_start: 0.9034 (mmp80) cc_final: 0.8454 (mmp80)
  outliers start: 33
  outliers final: 26
  residues processed: 134
  average time/residue: 0.2318
  time to fit residues: 44.2172
Evaluate side-chains
  137 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 108
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
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  407 ASP
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  580 GLU
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  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  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  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 111 optimal weight:    0.6980
   chunk 79 optimal weight:    5.9990
   chunk 95 optimal weight:    0.0670
   chunk 119 optimal weight:    0.9990
   chunk 100 optimal weight:    7.9990
   chunk 38 optimal weight:    0.0670
   chunk 61 optimal weight:    8.9990
   chunk 87 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 40 optimal weight:    0.3980
   overall best weight:    0.3856

-------------------------------------------------------------------------------
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 = 0.181860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.121876 restraints weight = 13799.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3541 rms_B_bonded: 3.42
r_work: 0.3294 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2024

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10460  Z= 0.156
  Angle     :  0.571  10.261  14242  Z= 0.270
  Chirality :  0.040   0.392   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  5.736  57.734   1426
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 16.17 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.67 (0.24), residues: 1291
  helix:  1.84 (0.23), residues: 488
  sheet: -1.01 (0.37), residues: 185
  loop : -0.13 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 614 
 HIS   0.005   0.000   HIS A 817 
 PHE   0.015   0.001   PHE D 126 
 TYR   0.012   0.001   TYR A1010 
 ARG   0.010   0.000   ARG C  23 

********************** 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
  138 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
REVERT: A  282 GLN cc_start: 0.8507 (tt0) cc_final: 0.8260 (tp40)
REVERT: A  381 MET cc_start: 0.8207 (tpt) cc_final: 0.7962 (tpt)
REVERT: A  715 LEU cc_start: 0.6914 (tt) cc_final: 0.6534 (tt)
REVERT: A  791 ASN cc_start: 0.7759 (m-40) cc_final: 0.7301 (t0)
REVERT: B   88 ASN cc_start: 0.8357 (t0) cc_final: 0.7829 (t0)
REVERT: C   21 TYR cc_start: 0.8088 (p90) cc_final: 0.7661 (p90)
REVERT: C   75 TYR cc_start: 0.7394 (t80) cc_final: 0.6899 (t80)
REVERT: C   80 ASP cc_start: 0.8071 (m-30) cc_final: 0.7731 (m-30)
REVERT: C   81 GLU cc_start: 0.8352 (tt0) cc_final: 0.7602 (pt0)
REVERT: C  114 ARG cc_start: 0.7665 (tmm160) cc_final: 0.6718 (tmt170)
REVERT: C  118 ARG cc_start: 0.9002 (mmp80) cc_final: 0.8424 (mmp80)
  outliers start: 23
  outliers final: 23
  residues processed: 131
  average time/residue: 0.2333
  time to fit residues: 43.7807
Evaluate side-chains
  136 residues out of total 1101 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 113
  time to evaluate  : 1.140 
-------------------------------------------------------------------------------
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  407 ASP
Chi-restraints excluded: chain A residue  468 ASP
Chi-restraints excluded: chain A residue  630 ILE
Chi-restraints excluded: chain A residue  905 THR
Chi-restraints excluded: chain A residue  912 THR
Chi-restraints excluded: chain A residue  919 VAL
Chi-restraints excluded: chain A residue  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  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 6 optimal weight:    1.9990
   chunk 59 optimal weight:    6.9990
   chunk 118 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 119 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   overall best weight:    1.1384

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.179456 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.118764 restraints weight = 13819.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 3.28
r_work: 0.3253 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3253
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.2044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10460  Z= 0.257
  Angle     :  0.602   9.636  14242  Z= 0.285
  Chirality :  0.041   0.406   1591
  Planarity :  0.004   0.042   1867
  Dihedral  :  5.582  59.799   1422
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.80 %
    Favored  : 95.20 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 15.26 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.22 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.24), residues: 1291
  helix:  1.75 (0.23), residues: 486
  sheet: -1.10 (0.37), residues: 185
  loop : -0.17 (0.26), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 614 
 HIS   0.004   0.001   HIS A 817 
 PHE   0.013   0.001   PHE D 126 
 TYR   0.011   0.001   TYR A 735 
 ARG   0.010   0.000   ARG C  23 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5035.20 seconds
wall clock time: 90 minutes 10.19 seconds (5410.19 seconds total)