Starting phenix.real_space_refine
on Sun Jan 19 07:25:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rkt_19282/01_2025/8rkt_19282.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rkt_19282/01_2025/8rkt_19282.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rkt_19282/01_2025/8rkt_19282.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rkt_19282/01_2025/8rkt_19282.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rkt_19282/01_2025/8rkt_19282.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rkt_19282/01_2025/8rkt_19282.cif"
  }
  resolution = 2.35
  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
-------------------------------------------------------------------------------
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=   0.002 sd=   0.075
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     310      5.49       5
     Mg      1      5.21       5
     S      30      5.16       5
     C    7329      2.51       5
     N    2427      2.21       5
     O    3695      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 13794
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "1"
      Number of atoms: 5239
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 246, 5239
          Classifications: {'RNA': 246}
          Modifications used: {'5*END': 1, 'rna2p_pur': 21, 'rna2p_pyr': 17, 'rna3p_pur': 107, 'rna3p_pyr': 101}
          Link IDs: {'rna2p': 38, 'rna3p': 207}
    Chain: "2"
      Number of atoms: 696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 696
          Classifications: {'DNA': 34}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 33}
    Chain: "3"
      Number of atoms: 647
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 647
          Classifications: {'DNA': 32}
          Link IDs: {'rna3p': 31}
    Chain: "A"
      Number of atoms: 4872
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 602, 4872
          Classifications: {'peptide': 602}
          Link IDs: {'PTRANS': 18, 'TRANS': 583}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 708
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 87, 708
          Classifications: {'peptide': 87}
          Link IDs: {'TRANS': 86}
    Chain: "C"
      Number of atoms: 1306
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 164, 1306
          Classifications: {'peptide': 164}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 150}
    Chain: "1"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "1"
      Number of atoms: 160
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 160, 160
          Classifications: {'water': 160}
          Link IDs: {None: 159}
    Chain: "2"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 7
          Classifications: {'water': 7}
          Link IDs: {None: 6}
    Chain: "3"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 33
          Classifications: {'water': 33}
          Link IDs: {None: 32}
    Chain: "A"
      Number of atoms: 93
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 93
          Classifications: {'water': 93}
          Link IDs: {None: 92}
    Chain: "B"
      Number of atoms: 13
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 13, 13
          Classifications: {'water': 13}
          Link IDs: {None: 12}
    Chain: "C"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 17, 17
          Classifications: {'water': 17}
          Link IDs: {None: 16}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  13205  SG  CYS C 133      40.436 123.263  33.806  1.00 30.64           S
  ATOM  13226  SG  CYS C 136      38.341 120.320  32.674  1.00 34.07           S
  ATOM  13342  SG  CYS C 151      41.754 120.712  31.254  1.00 40.26           S
  ATOM  13369  SG  CYS C 154      39.055 123.236  30.327  1.00 46.87           S
  ATOM  12930  SG  CYS C 100      51.117 131.217  40.191  1.00 34.05           S
  ATOM  12945  SG  CYS C 103      54.710 131.386  39.195  1.00 29.68           S
  ATOM  13114  SG  CYS C 122      53.673 132.699  42.623  1.00 35.65           S

  Time building chain proxies: 9.09, per 1000 atoms: 0.66
  Number of scatterers: 13794
  At special positions: 0
  Unit cell: (116.48, 144.144, 117.936, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S      30     16.00
     P     310     15.00
     Mg      1     11.99
     O    3695      8.00
     N    2427      7.00
     C    7329      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.46
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 200 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 136 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 133 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 151 "
        pdb="ZN    ZN C 200 " - pdb=" SG  CYS C 154 "
      pdb="  ZN C 201 "
        pdb="ZN    ZN C 201 " - pdb=" ND1 HIS C 125 "
        pdb="ZN    ZN C 201 " - pdb=" SG  CYS C 100 "
        pdb="ZN    ZN C 201 " - pdb=" SG  CYS C 103 "
        pdb="ZN    ZN C 201 " - pdb=" SG  CYS C 122 "
      Number of angles added : 9


  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1616

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 3 sheets defined
      62.8% alpha, 7.9% beta
      109 base pairs and 188 stacking pairs defined.
    Time for finding SS restraints: 6.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 27
    Processing helix  chain 'A' and resid 27 through 40
    Processing helix  chain 'A' and resid 44 through 52
      removed outlier: 3.532A  pdb=" N   GLN A  50 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 67
      Proline residue:  A  65  - end of helix
    Processing helix  chain 'A' and resid 76 through 115
    Processing helix  chain 'A' and resid 117 through 126
      removed outlier: 3.730A  pdb=" N   GLU A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 128 through 144
    Processing helix  chain 'A' and resid 174 through 185
      removed outlier: 3.641A  pdb=" N   GLN A 183 " --> pdb=" O   PHE A 179 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   GLU A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   THR A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 200
      removed outlier: 3.531A  pdb=" N   ASN A 200 " --> pdb=" O   TYR A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 232
    Processing helix  chain 'A' and resid 244 through 257
      removed outlier: 3.500A  pdb=" N   LEU A 248 " --> pdb=" O   ASN A 244 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 274
    Processing helix  chain 'A' and resid 287 through 289
      No H-bonds generated for 'chain 'A' and resid 287 through 289'
    Processing helix  chain 'A' and resid 318 through 338
      removed outlier: 4.167A  pdb=" N   HIS A 323 " --> pdb=" O   ASN A 319 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   TRP A 324 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   PHE A 325 " --> pdb=" O   GLN A 321 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 347
    Processing helix  chain 'A' and resid 364 through 369
    Processing helix  chain 'A' and resid 380 through 382
      No H-bonds generated for 'chain 'A' and resid 380 through 382'
    Processing helix  chain 'A' and resid 383 through 406
      removed outlier: 3.583A  pdb=" N   LYS A 406 " --> pdb=" O   ILE A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 413 through 429
    Processing helix  chain 'A' and resid 476 through 482
    Processing helix  chain 'A' and resid 485 through 508
      removed outlier: 4.086A  pdb=" N   ASN A 489 " --> pdb=" O   TYR A 485 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A 507 " --> pdb=" O   HIS A 503 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASN A 508 " --> pdb=" O   LYS A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 516 through 538
    Processing helix  chain 'A' and resid 550 through 567
      removed outlier: 3.600A  pdb=" N   GLN A 565 " --> pdb=" O   ALA A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 577
    Processing helix  chain 'A' and resid 578 through 588
    Processing helix  chain 'A' and resid 589 through 604
    Processing helix  chain 'A' and resid 618 through 633
    Processing helix  chain 'B' and resid 5 through 17
    Processing helix  chain 'B' and resid 25 through 47
      removed outlier: 3.566A  pdb=" N   ALA B  46 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 73
      removed outlier: 3.641A  pdb=" N   GLY B  56 " --> pdb=" O   SER B  52 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   LYS B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 87
    Processing helix  chain 'C' and resid 21 through 33
    Processing helix  chain 'C' and resid 36 through 45
    Processing helix  chain 'C' and resid 48 through 55
      removed outlier: 3.568A  pdb=" N   ARG C  52 " --> pdb=" O   ALA C  48 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ARG C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 63 through 74
      removed outlier: 3.841A  pdb=" N   VAL C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 77 through 83
    Processing helix  chain 'C' and resid 111 through 116
    Processing helix  chain 'C' and resid 142 through 146
    Processing helix  chain 'C' and resid 159 through 165
      removed outlier: 3.544A  pdb=" N   ALA C 162 " --> pdb=" O   ALA C 159 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN C 165 " --> pdb=" O   ALA C 162 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 283 through 285
      removed outlier: 6.562A  pdb=" N   LEU A 349 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   ASP A 378 " --> pdb=" O   LEU A 349 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN A 351 " --> pdb=" O   CYS A 376 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU A 371 " --> pdb=" O   LEU A  10 " (cutoff:3.500A)
      removed outlier: 5.169A  pdb=" N   LEU A 301 " --> pdb=" O   VAL A 315 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 470 through 475
      removed outlier: 6.558A  pdb=" N   VAL A 463 " --> pdb=" O   LEU A 472 " (cutoff:3.500A)
      removed outlier: 4.535A  pdb=" N   TYR A 474 " --> pdb=" O   VAL A 461 " (cutoff:3.500A)
      removed outlier: 6.887A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 474 " (cutoff:3.500A)
      removed outlier: 6.541A  pdb=" N   SER A 445 " --> pdb=" O   ALA A 540 " (cutoff:3.500A)
      removed outlier: 6.011A  pdb=" N   SER A 542 " --> pdb=" O   SER A 445 " (cutoff:3.500A)
      removed outlier: 7.118A  pdb=" N   ILE A 447 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
      removed outlier: 8.026A  pdb=" N   VAL A 544 " --> pdb=" O   ILE A 447 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   VAL A 449 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 8.939A  pdb=" N   VAL A 451 " --> pdb=" O   PRO A 546 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 121 through 122

    404 hydrogen bonds defined for protein.
    1164 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      277 hydrogen bonds
      522 hydrogen bond angles
      0 basepair planarities
      109 basepair parallelities
      188 stacking parallelities
  Total time for adding SS restraints: 7.26

  Time building geometry restraints manager: 4.02 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1889
        1.32 -     1.45: 5358
        1.45 -     1.57: 6467
        1.57 -     1.69: 619
        1.69 -     1.81: 44
  Bond restraints: 14377
  Sorted by residual:
  bond pdb=" CE1 HIS C  94 "
       pdb=" NE2 HIS C  94 "
    ideal  model  delta    sigma   weight residual
    1.321  1.356 -0.035 1.00e-02 1.00e+04 1.20e+01
  bond pdb=" N   ILE C  97 "
       pdb=" CA  ILE C  97 "
    ideal  model  delta    sigma   weight residual
    1.458  1.500 -0.042 1.20e-02 6.94e+03 1.20e+01
  bond pdb=" N   GLN C  93 "
       pdb=" CA  GLN C  93 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.86e+00
  bond pdb=" N   GLU C  95 "
       pdb=" CA  GLU C  95 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.41e-02 5.03e+03 4.80e+00
  bond pdb=" N   HIS C  94 "
       pdb=" CA  HIS C  94 "
    ideal  model  delta    sigma   weight residual
    1.458  1.484 -0.026 1.28e-02 6.10e+03 4.28e+00
  ... (remaining 14372 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.29: 20126
        2.29 -     4.58: 716
        4.58 -     6.86: 53
        6.86 -     9.15: 2
        9.15 -    11.44: 1
  Bond angle restraints: 20898
  Sorted by residual:
  angle pdb=" C3'  DT 3 130 "
        pdb=" O3'  DT 3 130 "
        pdb=" P    DC 3 131 "
      ideal   model   delta    sigma   weight residual
     120.20  108.76   11.44 1.50e+00 4.44e-01 5.82e+01
  angle pdb=" O3'   A 1 196 "
        pdb=" C3'   A 1 196 "
        pdb=" C2'   A 1 196 "
      ideal   model   delta    sigma   weight residual
     109.50  118.10   -8.60 1.50e+00 4.44e-01 3.29e+01
  angle pdb=" C3'  DT 3 129 "
        pdb=" O3'  DT 3 129 "
        pdb=" P    DT 3 130 "
      ideal   model   delta    sigma   weight residual
     120.20  113.20    7.00 1.50e+00 4.44e-01 2.18e+01
  angle pdb=" C4'  DA 2   5 "
        pdb=" C3'  DA 2   5 "
        pdb=" O3'  DA 2   5 "
      ideal   model   delta    sigma   weight residual
     110.00  116.80   -6.80 1.50e+00 4.44e-01 2.06e+01
  angle pdb=" C4'   A 1 196 "
        pdb=" C3'   A 1 196 "
        pdb=" O3'   A 1 196 "
      ideal   model   delta    sigma   weight residual
     109.40  116.05   -6.65 1.50e+00 4.44e-01 1.96e+01
  ... (remaining 20893 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.96: 8063
       35.96 -    71.91: 729
       71.91 -   107.87: 37
      107.87 -   143.82: 6
      143.82 -   179.78: 7
  Dihedral angle restraints: 8842
    sinusoidal: 6355
      harmonic: 2487
  Sorted by residual:
  dihedral pdb=" O4'   U 1 170 "
           pdb=" C1'   U 1 170 "
           pdb=" N1    U 1 170 "
           pdb=" C2    U 1 170 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   33.10  166.90     1      1.50e+01 4.44e-03 8.42e+01
  dihedral pdb=" O4'   U 1  41 "
           pdb=" C1'   U 1  41 "
           pdb=" N1    U 1  41 "
           pdb=" C2    U 1  41 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   36.46  163.54     1      1.50e+01 4.44e-03 8.36e+01
  dihedral pdb=" O4'   U 1  39 "
           pdb=" C1'   U 1  39 "
           pdb=" N1    U 1  39 "
           pdb=" C2    U 1  39 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   38.24  161.76     1      1.50e+01 4.44e-03 8.32e+01
  ... (remaining 8839 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.124: 2348
       0.124 -    0.249: 155
       0.249 -    0.373: 15
       0.373 -    0.498: 5
       0.498 -    0.622: 1
  Chirality restraints: 2524
  Sorted by residual:
  chirality pdb=" C3'   A 1 196 "
            pdb=" C4'   A 1 196 "
            pdb=" O3'   A 1 196 "
            pdb=" C2'   A 1 196 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.12   -0.62 2.00e-01 2.50e+01 9.67e+00
  chirality pdb=" C3'  DA 2   5 "
            pdb=" C4'  DA 2   5 "
            pdb=" O3'  DA 2   5 "
            pdb=" C2'  DA 2   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.17   -0.49 2.00e-01 2.50e+01 6.03e+00
  chirality pdb=" P    DT 3 129 "
            pdb=" OP1  DT 3 129 "
            pdb=" OP2  DT 3 129 "
            pdb=" O5'  DT 3 129 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.80   -0.45 2.00e-01 2.50e+01 5.10e+00
  ... (remaining 2521 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 1  99 "    0.084 2.00e-02 2.50e+03   4.90e-02 5.41e+01
        pdb=" N1    C 1  99 "   -0.074 2.00e-02 2.50e+03
        pdb=" C2    C 1  99 "   -0.024 2.00e-02 2.50e+03
        pdb=" O2    C 1  99 "    0.004 2.00e-02 2.50e+03
        pdb=" N3    C 1  99 "    0.002 2.00e-02 2.50e+03
        pdb=" C4    C 1  99 "    0.004 2.00e-02 2.50e+03
        pdb=" N4    C 1  99 "    0.013 2.00e-02 2.50e+03
        pdb=" C5    C 1  99 "    0.059 2.00e-02 2.50e+03
        pdb=" C6    C 1  99 "   -0.068 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U 1 127 "   -0.079 2.00e-02 2.50e+03   4.75e-02 5.08e+01
        pdb=" N1    U 1 127 "    0.074 2.00e-02 2.50e+03
        pdb=" C2    U 1 127 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    U 1 127 "    0.005 2.00e-02 2.50e+03
        pdb=" N3    U 1 127 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    U 1 127 "   -0.007 2.00e-02 2.50e+03
        pdb=" O4    U 1 127 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    U 1 127 "   -0.057 2.00e-02 2.50e+03
        pdb=" C6    U 1 127 "    0.072 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C 1 245 "    0.063 2.00e-02 2.50e+03   3.96e-02 3.52e+01
        pdb=" N1    C 1 245 "   -0.051 2.00e-02 2.50e+03
        pdb=" C2    C 1 245 "    0.006 2.00e-02 2.50e+03
        pdb=" O2    C 1 245 "   -0.011 2.00e-02 2.50e+03
        pdb=" N3    C 1 245 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    C 1 245 "    0.003 2.00e-02 2.50e+03
        pdb=" N4    C 1 245 "    0.006 2.00e-02 2.50e+03
        pdb=" C5    C 1 245 "    0.053 2.00e-02 2.50e+03
        pdb=" C6    C 1 245 "   -0.068 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 240
        2.62 -     3.19: 11521
        3.19 -     3.76: 26435
        3.76 -     4.33: 36697
        4.33 -     4.90: 50343
  Nonbonded interactions: 125236
  Sorted by model distance:
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH 1 447 "
     model   vdw
     2.046 2.170
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH C 317 "
     model   vdw
     2.056 2.170
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH 1 492 "
     model   vdw
     2.058 2.170
  nonbonded pdb="MG    MG 1 300 "
            pdb=" O   HOH 1 527 "
     model   vdw
     2.071 2.170
  nonbonded pdb=" OP1   A 1 173 "
            pdb="MG    MG 1 300 "
     model   vdw
     2.185 2.170
  ... (remaining 125231 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.650
  Check model and map are aligned:         0.110
  Set scattering table:                    0.150
  Process input model:                     42.620
  Find NCS groups from input model:        0.110
  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:12.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   57.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  14377  Z= 0.332
  Angle     :  0.955  11.440  20898  Z= 0.597
  Chirality :  0.071   0.622   2524
  Planarity :  0.012   0.118   1532
  Dihedral  : 22.001 179.780   7226
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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: -0.24 (0.26), residues: 843
  helix: -0.20 (0.20), residues: 493
  sheet:  0.11 (0.63), residues: 62
  loop :  0.22 (0.37), residues: 288

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A  94 
 HIS   0.015   0.002   HIS A 353 
 PHE   0.027   0.003   PHE A  13 
 TYR   0.022   0.005   TYR A  91 
 ARG   0.021   0.004   ARG A 490 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.999 
Fit side-chains
REVERT: A   24 MET cc_start: 0.9093 (mtp) cc_final: 0.8777 (mtp)
REVERT: A  226 GLN cc_start: 0.8022 (tt0) cc_final: 0.7812 (tm-30)
REVERT: A  252 LEU cc_start: 0.8776 (mt) cc_final: 0.8568 (mp)
REVERT: A  260 GLU cc_start: 0.7600 (pt0) cc_final: 0.7381 (pt0)
REVERT: A  267 ARG cc_start: 0.8076 (mtm110) cc_final: 0.7866 (mtp180)
REVERT: A  397 GLU cc_start: 0.8185 (tt0) cc_final: 0.7877 (tt0)
REVERT: A  416 GLN cc_start: 0.7708 (tp40) cc_final: 0.7398 (tp-100)
REVERT: A  496 GLN cc_start: 0.8474 (mt0) cc_final: 0.8251 (mt0)
REVERT: A  612 LYS cc_start: 0.7488 (tppt) cc_final: 0.7067 (ttpt)
REVERT: A  621 ASP cc_start: 0.7717 (t0) cc_final: 0.7500 (t70)
REVERT: B    9 LYS cc_start: 0.6910 (ttpt) cc_final: 0.6095 (ttpt)
REVERT: C   93 GLN cc_start: 0.8254 (mt0) cc_final: 0.7264 (pm20)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 2.1702
  time to fit residues: 289.3204
Evaluate side-chains
  101 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 86 optimal weight:   10.0000
   chunk 47 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 58 optimal weight:   10.0000
   chunk 46 optimal weight:    6.9990
   chunk 89 optimal weight:   10.0000
   chunk 34 optimal weight:    4.9990
   chunk 54 optimal weight:    7.9990
   chunk 66 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 423 GLN
A 431 ASN
B  10 GLN
B  80 GLN
C 135 ASN
C 137 GLN
C 165 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.175864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.133500 restraints weight = 12078.588|
|-----------------------------------------------------------------------------|
r_work (start): 0.3497 rms_B_bonded: 0.84
r_work: 0.3275 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.3173 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8534
moved from start:          0.1422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  14377  Z= 0.308
  Angle     :  0.689   6.825  20898  Z= 0.377
  Chirality :  0.044   0.346   2524
  Planarity :  0.005   0.045   1532
  Dihedral  : 23.946 178.743   5469
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  :  7.40 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.29), residues: 843
  helix:  1.29 (0.22), residues: 504
  sheet:  0.80 (0.66), residues: 65
  loop :  0.63 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 382 
 HIS   0.010   0.002   HIS A 353 
 PHE   0.023   0.003   PHE A 214 
 TYR   0.022   0.002   TYR A  91 
 ARG   0.004   0.001   ARG A 218 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 1.034 
Fit side-chains
REVERT: A  252 LEU cc_start: 0.8730 (mt) cc_final: 0.8486 (mp)
REVERT: A  341 GLN cc_start: 0.8004 (OUTLIER) cc_final: 0.7621 (mp-120)
REVERT: A  397 GLU cc_start: 0.8064 (tt0) cc_final: 0.7858 (tt0)
REVERT: A  416 GLN cc_start: 0.7703 (tp40) cc_final: 0.7465 (tp-100)
REVERT: A  566 LYS cc_start: 0.8256 (tttp) cc_final: 0.7968 (ttmp)
REVERT: B    9 LYS cc_start: 0.7125 (ttpt) cc_final: 0.6589 (ttpt)
REVERT: C   93 GLN cc_start: 0.8612 (mt0) cc_final: 0.7198 (pm20)
  outliers start: 8
  outliers final: 4
  residues processed: 95
  average time/residue: 2.1943
  time to fit residues: 221.5982
Evaluate side-chains
  93 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 88
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain B residue   76 ARG
Chi-restraints excluded: chain C residue   73 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 44 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 109 optimal weight:    5.9990
   chunk 87 optimal weight:    9.9990
   chunk 93 optimal weight:    6.9990
   chunk 89 optimal weight:    0.6980
   chunk 111 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 ASN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.176818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.134619 restraints weight = 12127.040|
|-----------------------------------------------------------------------------|
r_work (start): 0.3514 rms_B_bonded: 0.79
r_work: 0.3293 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3191 rms_B_bonded: 3.61 restraints_weight: 0.2500
r_work (final): 0.3191
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.1787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14377  Z= 0.243
  Angle     :  0.617   7.226  20898  Z= 0.339
  Chirality :  0.040   0.329   2524
  Planarity :  0.004   0.034   1532
  Dihedral  : 23.881 179.991   5469
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  :  9.15 %
    Favored  : 89.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.81 (0.29), residues: 843
  helix:  1.66 (0.22), residues: 503
  sheet:  0.74 (0.65), residues: 65
  loop :  0.65 (0.41), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 382 
 HIS   0.007   0.001   HIS A 353 
 PHE   0.019   0.002   PHE A 214 
 TYR   0.019   0.002   TYR A  91 
 ARG   0.003   0.001   ARG A 492 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 94
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8299 (mt-10) cc_final: 0.8077 (mt-10)
REVERT: A  252 LEU cc_start: 0.8718 (mt) cc_final: 0.8487 (mp)
REVERT: A  336 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7689 (mtt180)
REVERT: A  341 GLN cc_start: 0.8043 (OUTLIER) cc_final: 0.7661 (mp-120)
REVERT: A  397 GLU cc_start: 0.8102 (tt0) cc_final: 0.7892 (tt0)
REVERT: A  566 LYS cc_start: 0.8289 (tttp) cc_final: 0.8005 (ttmp)
REVERT: A  612 LYS cc_start: 0.7700 (tptt) cc_final: 0.7339 (ttpt)
REVERT: B    9 LYS cc_start: 0.7073 (ttpt) cc_final: 0.6536 (ttpt)
REVERT: B   76 ARG cc_start: 0.7790 (OUTLIER) cc_final: 0.7324 (mtt90)
REVERT: C   93 GLN cc_start: 0.8605 (mt0) cc_final: 0.7276 (pm20)
  outliers start: 13
  outliers final: 4
  residues processed: 98
  average time/residue: 2.3214
  time to fit residues: 240.9892
Evaluate side-chains
  100 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain B residue   76 ARG
Chi-restraints excluded: chain C residue   73 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 7 optimal weight:   10.0000
   chunk 98 optimal weight:   20.0000
   chunk 50 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 14 optimal weight:   10.0000
   chunk 103 optimal weight:    6.9990
   chunk 35 optimal weight:    9.9990
   chunk 21 optimal weight:   40.0000
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 ASN
A 620 HIS
B  80 GLN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.174730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.132385 restraints weight = 12081.101|
|-----------------------------------------------------------------------------|
r_work (start): 0.3485 rms_B_bonded: 0.85
r_work: 0.3265 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.3161 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8562
moved from start:          0.1895

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  14377  Z= 0.325
  Angle     :  0.683   8.402  20898  Z= 0.369
  Chirality :  0.043   0.362   2524
  Planarity :  0.005   0.038   1532
  Dihedral  : 23.966 179.751   5469
  Min Nonbonded Distance : 1.876

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.95 %
    Favored  : 99.05 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.23 %
    Favored  : 88.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.29), residues: 843
  helix:  1.51 (0.22), residues: 504
  sheet:  0.71 (0.65), residues: 65
  loop :  0.55 (0.40), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 382 
 HIS   0.005   0.001   HIS C  24 
 PHE   0.022   0.002   PHE A 214 
 TYR   0.021   0.002   TYR A  91 
 ARG   0.004   0.001   ARG B  54 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.466 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8064 (mt-10)
REVERT: A  252 LEU cc_start: 0.8762 (mt) cc_final: 0.8522 (mp)
REVERT: A  336 ARG cc_start: 0.8017 (OUTLIER) cc_final: 0.7709 (mtt180)
REVERT: A  341 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7702 (mp-120)
REVERT: A  397 GLU cc_start: 0.8123 (tt0) cc_final: 0.7899 (tt0)
REVERT: A  477 ILE cc_start: 0.9032 (OUTLIER) cc_final: 0.8779 (tp)
REVERT: B    9 LYS cc_start: 0.7267 (ttpt) cc_final: 0.6480 (ttpt)
REVERT: B   76 ARG cc_start: 0.7765 (OUTLIER) cc_final: 0.7368 (mtt90)
REVERT: C   93 GLN cc_start: 0.8627 (mt0) cc_final: 0.7278 (pm20)
  outliers start: 13
  outliers final: 4
  residues processed: 96
  average time/residue: 2.2183
  time to fit residues: 226.2753
Evaluate side-chains
  95 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 87
  time to evaluate  : 1.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   76 ARG
Chi-restraints excluded: chain C residue   73 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 41 optimal weight:    5.9990
   chunk 93 optimal weight:    2.9990
   chunk 36 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 15 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 64 optimal weight:   10.0000
   chunk 3 optimal weight:   20.0000
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 431 ASN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.176014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.133563 restraints weight = 12121.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 0.81
r_work: 0.3285 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1971

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  14377  Z= 0.259
  Angle     :  0.627   8.310  20898  Z= 0.342
  Chirality :  0.040   0.332   2524
  Planarity :  0.004   0.035   1532
  Dihedral  : 23.932 179.574   5469
  Min Nonbonded Distance : 1.905

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 10.77 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.75 (0.29), residues: 843
  helix:  1.64 (0.22), residues: 505
  sheet:  0.75 (0.66), residues: 65
  loop :  0.52 (0.39), residues: 273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 382 
 HIS   0.004   0.001   HIS A 620 
 PHE   0.019   0.002   PHE A 214 
 TYR   0.019   0.002   TYR A  91 
 ARG   0.003   0.000   ARG A 275 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 1.072 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8266 (mt-10) cc_final: 0.8052 (mt-10)
REVERT: A  252 LEU cc_start: 0.8726 (mt) cc_final: 0.8481 (mp)
REVERT: A  336 ARG cc_start: 0.7964 (OUTLIER) cc_final: 0.7682 (mtt180)
REVERT: A  341 GLN cc_start: 0.8045 (OUTLIER) cc_final: 0.7686 (mp-120)
REVERT: A  477 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8744 (tp)
REVERT: A  566 LYS cc_start: 0.8301 (tttp) cc_final: 0.7992 (ttmp)
REVERT: B    9 LYS cc_start: 0.7280 (ttpt) cc_final: 0.6482 (ttpt)
REVERT: B   15 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7537 (t0)
REVERT: B   76 ARG cc_start: 0.7771 (OUTLIER) cc_final: 0.7365 (mtt90)
REVERT: C   93 GLN cc_start: 0.8634 (mt0) cc_final: 0.7281 (pm20)
  outliers start: 16
  outliers final: 4
  residues processed: 97
  average time/residue: 2.1790
  time to fit residues: 223.9207
Evaluate side-chains
  99 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  216 LYS
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain B residue   76 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 94 optimal weight:    9.9990
   chunk 110 optimal weight:   10.0000
   chunk 49 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   chunk 6 optimal weight:   20.0000
   chunk 97 optimal weight:    8.9990
   chunk 79 optimal weight:    2.9990
   overall best weight:    3.5188

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

Flipped N/Q/H residues before XYZ refinement:
A 431 ASN
A 500 HIS
A 620 HIS
B  80 GLN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.175925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.133505 restraints weight = 12163.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3489 rms_B_bonded: 0.81
r_work: 0.3258 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3155 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8538
moved from start:          0.2073

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  14377  Z= 0.235
  Angle     :  0.603   7.736  20898  Z= 0.329
  Chirality :  0.039   0.324   2524
  Planarity :  0.004   0.036   1532
  Dihedral  : 23.902 179.324   5469
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 5.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 12.25 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.29), residues: 843
  helix:  1.76 (0.22), residues: 505
  sheet:  0.80 (0.67), residues: 63
  loop :  0.49 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A  21 
 HIS   0.004   0.001   HIS A 620 
 PHE   0.017   0.002   PHE A  13 
 TYR   0.019   0.002   TYR A  91 
 ARG   0.003   0.000   ARG B  39 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8047 (mt-10)
REVERT: A  252 LEU cc_start: 0.8711 (mt) cc_final: 0.8482 (mp)
REVERT: A  336 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7680 (mtt180)
REVERT: A  341 GLN cc_start: 0.8054 (OUTLIER) cc_final: 0.7677 (mp-120)
REVERT: A  566 LYS cc_start: 0.8288 (tttp) cc_final: 0.7965 (ttmp)
REVERT: B    9 LYS cc_start: 0.7144 (ttpt) cc_final: 0.6336 (ttpt)
REVERT: C   93 GLN cc_start: 0.8628 (mt0) cc_final: 0.7258 (pm20)
  outliers start: 11
  outliers final: 1
  residues processed: 92
  average time/residue: 2.2635
  time to fit residues: 220.3545
Evaluate side-chains
  92 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 1.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 64 optimal weight:    9.9990
   chunk 37 optimal weight:    0.8980
   chunk 75 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 84 optimal weight:    7.9990
   chunk 60 optimal weight:    0.9980
   chunk 28 optimal weight:    8.9990
   chunk 50 optimal weight:    4.9990
   chunk 21 optimal weight:   40.0000
   overall best weight:    2.7786

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

Flipped N/Q/H residues before XYZ refinement:
A 431 ASN
A 620 HIS
B  47 ASN
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.176922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134677 restraints weight = 12130.695|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 0.81
r_work: 0.3271 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3163 rms_B_bonded: 3.87 restraints_weight: 0.2500
r_work (final): 0.3163
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
moved from start:          0.2147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  14377  Z= 0.203
  Angle     :  0.581   7.303  20898  Z= 0.318
  Chirality :  0.037   0.310   2524
  Planarity :  0.004   0.037   1532
  Dihedral  : 23.893 179.132   5469
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.84 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.29), residues: 843
  helix:  1.89 (0.22), residues: 504
  sheet:  0.81 (0.68), residues: 63
  loop :  0.48 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  21 
 HIS   0.004   0.001   HIS A 620 
 PHE   0.016   0.002   PHE A  13 
 TYR   0.018   0.002   TYR A  91 
 ARG   0.002   0.000   ARG B  39 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 1.151 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8263 (mt-10) cc_final: 0.8057 (mt-10)
REVERT: A  246 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7995 (ttmm)
REVERT: A  252 LEU cc_start: 0.8694 (mt) cc_final: 0.8450 (mp)
REVERT: A  336 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7694 (mtt180)
REVERT: A  341 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7674 (mp-120)
REVERT: A  477 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8715 (tp)
REVERT: A  566 LYS cc_start: 0.8265 (tttp) cc_final: 0.7948 (ttmp)
REVERT: B    9 LYS cc_start: 0.7154 (ttpt) cc_final: 0.6360 (ttpt)
REVERT: C   83 GLN cc_start: 0.8123 (OUTLIER) cc_final: 0.7914 (mt0)
REVERT: C   93 GLN cc_start: 0.8623 (mt0) cc_final: 0.7254 (pm20)
REVERT: C  161 MET cc_start: 0.8563 (mtm) cc_final: 0.8234 (mtt)
  outliers start: 12
  outliers final: 2
  residues processed: 96
  average time/residue: 2.2158
  time to fit residues: 225.4362
Evaluate side-chains
  98 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 91
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain C residue   83 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:   40.0000
   chunk 68 optimal weight:    5.9990
   chunk 101 optimal weight:    6.9990
   chunk 26 optimal weight:   20.0000
   chunk 80 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 64 optimal weight:   20.0000
   chunk 77 optimal weight:    6.9990
   chunk 48 optimal weight:    6.9990
   chunk 16 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 431 ASN
A 620 HIS
B  80 GLN
C 135 ASN
C 137 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.174046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.131841 restraints weight = 12180.693|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 0.93
r_work: 0.3241 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3133 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8576
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044  14377  Z= 0.337
  Angle     :  0.684   7.809  20898  Z= 0.367
  Chirality :  0.043   0.364   2524
  Planarity :  0.005   0.038   1532
  Dihedral  : 23.988 179.469   5469
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 11.98 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.29), residues: 843
  helix:  1.57 (0.22), residues: 508
  sheet:  0.74 (0.67), residues: 63
  loop :  0.45 (0.39), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  21 
 HIS   0.005   0.001   HIS A 620 
 PHE   0.020   0.002   PHE A 214 
 TYR   0.021   0.003   TYR A  91 
 ARG   0.005   0.001   ARG B  39 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 1.160 
Fit side-chains
REVERT: A  230 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8068 (mt-10)
REVERT: A  252 LEU cc_start: 0.8777 (mt) cc_final: 0.8534 (mp)
REVERT: A  275 ARG cc_start: 0.7643 (tmm160) cc_final: 0.6968 (tpp80)
REVERT: A  336 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7675 (mtt180)
REVERT: A  341 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7714 (mp-120)
REVERT: A  420 GLN cc_start: 0.7613 (OUTLIER) cc_final: 0.7364 (tm-30)
REVERT: A  477 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8797 (tp)
REVERT: B    9 LYS cc_start: 0.7257 (ttpt) cc_final: 0.6361 (ttpt)
REVERT: B   15 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7568 (t0)
REVERT: C   93 GLN cc_start: 0.8623 (mt0) cc_final: 0.7262 (pm20)
  outliers start: 12
  outliers final: 4
  residues processed: 93
  average time/residue: 2.2608
  time to fit residues: 222.3269
Evaluate side-chains
  96 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 1.041 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  246 LYS
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  420 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   15 ASN
Chi-restraints excluded: chain C residue  163 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 1 optimal weight:   30.0000
   chunk 33 optimal weight:    1.9990
   chunk 105 optimal weight:    7.9990
   chunk 112 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 48 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    8.9990
   chunk 7 optimal weight:   10.0000
   overall best weight:    1.5786

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

Flipped N/Q/H residues before XYZ refinement:
A 431 ASN
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.179664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.138337 restraints weight = 12195.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 0.79
r_work: 0.3331 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3231 rms_B_bonded: 3.78 restraints_weight: 0.2500
r_work (final): 0.3231
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.2358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14377  Z= 0.158
  Angle     :  0.546   6.232  20898  Z= 0.299
  Chirality :  0.035   0.285   2524
  Planarity :  0.004   0.039   1532
  Dihedral  : 23.864 179.949   5469
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.52 %
    Favored  : 86.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.17 (0.29), residues: 843
  helix:  2.07 (0.22), residues: 504
  sheet:  0.81 (0.68), residues: 63
  loop :  0.54 (0.39), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  21 
 HIS   0.004   0.001   HIS A 620 
 PHE   0.014   0.001   PHE A  13 
 TYR   0.016   0.001   TYR A  91 
 ARG   0.004   0.000   ARG B  39 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 1.118 
Fit side-chains
REVERT: A  144 MET cc_start: 0.4314 (pp-130) cc_final: 0.4060 (mtm)
REVERT: A  252 LEU cc_start: 0.8673 (mt) cc_final: 0.8415 (mp)
REVERT: A  275 ARG cc_start: 0.7576 (tmm160) cc_final: 0.6889 (tpp80)
REVERT: A  336 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7674 (mtt180)
REVERT: A  341 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7713 (mp-120)
REVERT: A  420 GLN cc_start: 0.7515 (OUTLIER) cc_final: 0.7260 (tm-30)
REVERT: A  566 LYS cc_start: 0.8168 (tttp) cc_final: 0.7890 (ttmp)
REVERT: B    9 LYS cc_start: 0.7137 (ttpt) cc_final: 0.6330 (ttpt)
REVERT: B   15 ASN cc_start: 0.8041 (OUTLIER) cc_final: 0.7648 (t0)
REVERT: C   93 GLN cc_start: 0.8557 (mt0) cc_final: 0.7219 (pm20)
  outliers start: 9
  outliers final: 2
  residues processed: 92
  average time/residue: 2.2622
  time to fit residues: 220.5640
Evaluate side-chains
  95 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 89
  time to evaluate  : 1.070 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  420 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain B residue   15 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 79 optimal weight:    7.9990
   chunk 81 optimal weight:    0.6980
   chunk 9 optimal weight:   10.0000
   chunk 94 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 29 optimal weight:    8.9990
   chunk 55 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 109 optimal weight:    0.9980
   overall best weight:    3.7386

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

Flipped N/Q/H residues before XYZ refinement:
A 423 GLN
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.176010 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.134277 restraints weight = 12207.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 0.82
r_work: 0.3273 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3170 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  14377  Z= 0.248
  Angle     :  0.610   6.807  20898  Z= 0.331
  Chirality :  0.039   0.327   2524
  Planarity :  0.004   0.037   1532
  Dihedral  : 23.908 179.078   5469
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.07 %
    Favored  : 98.93 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 12.52 %
    Favored  : 86.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.05 (0.29), residues: 843
  helix:  1.95 (0.22), residues: 505
  sheet:  0.72 (0.67), residues: 63
  loop :  0.54 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A  21 
 HIS   0.003   0.001   HIS C  24 
 PHE   0.017   0.002   PHE A  13 
 TYR   0.019   0.002   TYR A  91 
 ARG   0.006   0.001   ARG A 100 

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

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

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1686 Ramachandran restraints generated.
    843 Oldfield, 0 Emsley, 843 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 96
  time to evaluate  : 1.056 
Fit side-chains
REVERT: A  226 GLN cc_start: 0.8070 (tm-30) cc_final: 0.7774 (tp-100)
REVERT: A  252 LEU cc_start: 0.8718 (mt) cc_final: 0.8474 (mp)
REVERT: A  275 ARG cc_start: 0.7607 (tmm160) cc_final: 0.6918 (tpp80)
REVERT: A  336 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7663 (mtt180)
REVERT: A  341 GLN cc_start: 0.8027 (OUTLIER) cc_final: 0.7677 (mp-120)
REVERT: A  477 ILE cc_start: 0.8996 (OUTLIER) cc_final: 0.8728 (tp)
REVERT: A  566 LYS cc_start: 0.8300 (tttp) cc_final: 0.8011 (ttmp)
REVERT: B    9 LYS cc_start: 0.7196 (ttpt) cc_final: 0.6321 (ttpt)
REVERT: B   15 ASN cc_start: 0.8044 (OUTLIER) cc_final: 0.7551 (t0)
REVERT: C   93 GLN cc_start: 0.8606 (mt0) cc_final: 0.7228 (pm20)
  outliers start: 8
  outliers final: 2
  residues processed: 97
  average time/residue: 2.2058
  time to fit residues: 226.6873
Evaluate side-chains
  97 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 91
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  336 ARG
Chi-restraints excluded: chain A residue  341 GLN
Chi-restraints excluded: chain A residue  438 GLN
Chi-restraints excluded: chain A residue  470 LYS
Chi-restraints excluded: chain A residue  477 ILE
Chi-restraints excluded: chain B residue   15 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 111 optimal weight:    6.9990
   chunk 18 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 72 optimal weight:    0.3980
   chunk 66 optimal weight:    6.9990
   chunk 89 optimal weight:    8.9990
   chunk 113 optimal weight:    0.3980
   chunk 2 optimal weight:   40.0000
   chunk 13 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    2.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 620 HIS
B  80 GLN
C 137 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.177143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.135584 restraints weight = 12303.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3516 rms_B_bonded: 0.81
r_work: 0.3282 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8522
moved from start:          0.2303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14377  Z= 0.206
  Angle     :  0.580   6.526  20898  Z= 0.317
  Chirality :  0.037   0.309   2524
  Planarity :  0.004   0.037   1532
  Dihedral  : 23.892 179.230   5469
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.19 %
    Favored  : 98.81 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.92 %
    Favored  : 85.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    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:  2.12 (0.29), residues: 843
  helix:  2.02 (0.22), residues: 505
  sheet:  0.65 (0.67), residues: 63
  loop :  0.55 (0.39), residues: 275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 111 
 HIS   0.004   0.001   HIS A 620 
 PHE   0.015   0.002   PHE A  13 
 TYR   0.018   0.002   TYR A  91 
 ARG   0.005   0.000   ARG A 100 

===============================================================================
Job complete
usr+sys time: 12122.17 seconds
wall clock time: 214 minutes 51.77 seconds (12891.77 seconds total)