Starting phenix.real_space_refine
on Wed Sep 17 06:36:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ca4_45380/09_2025/9ca4_45380_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ca4_45380/09_2025/9ca4_45380.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ca4_45380/09_2025/9ca4_45380.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ca4_45380/09_2025/9ca4_45380.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ca4_45380/09_2025/9ca4_45380_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ca4_45380/09_2025/9ca4_45380_neut.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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: 6
    Type Number    sf(0)   Gaussians
     Mn      2      7.51       5
     P       8      5.49       5
     S      39      5.16       5
     C    3905      2.51       5
     N    1076      2.21       5
     O    1200      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6230
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4843
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 612, 4843
          Classifications: {'peptide': 612}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 581}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'PTR:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1219
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1219
          Classifications: {'peptide': 161}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 153}
    Chain: "E"
      Number of atoms: 128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 128
          Classifications: {'RNA': 6}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 3, 'rna3p_pyr': 2}
          Link IDs: {'rna2p': 1, 'rna3p': 4}
    Chain: "G"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Classifications: {'RNA': 2}
          Modifications used: {'5*END': 1, 'rna2p_pyr': 1}
          Link IDs: {'rna3p': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.48, per 1000 atoms: 0.24
  Number of scatterers: 6230
  At special positions: 0
  Unit cell: (73.87, 87.98, 135.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Mn      2     24.99
     S      39     16.00
     P       8     15.00
     O    1200      8.00
     N    1076      7.00
     C    3905      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: 0.58
  Conformation dependent library (CDL) restraints added in 346.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1442

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 5 sheets defined
      42.6% alpha, 16.7% beta
      0 base pairs and 4 stacking pairs defined.
    Time for finding SS restraints: 0.63
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 20
    Processing helix  chain 'A' and resid 77 through 82
      removed outlier: 3.858A  pdb=" N   PHE A  82 " --> pdb=" O   ALA A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 106
    Processing helix  chain 'A' and resid 119 through 134
    Processing helix  chain 'A' and resid 156 through 166
    Processing helix  chain 'A' and resid 171 through 204
      removed outlier: 4.253A  pdb=" N   ALA A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 4.567A  pdb=" N   GLY A 189 " --> pdb=" O   ASP A 185 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   PHE A 192 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLY A 202 " --> pdb=" O   LYS A 198 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   LYS A 203 " --> pdb=" O   TYR A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 208
    Processing helix  chain 'A' and resid 218 through 234
      removed outlier: 3.620A  pdb=" N   CYS A 225 " --> pdb=" O   THR A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 276
    Processing helix  chain 'A' and resid 302 through 311
    Processing helix  chain 'A' and resid 317 through 332
    Processing helix  chain 'A' and resid 349 through 356
    Processing helix  chain 'A' and resid 357 through 360
      removed outlier: 3.602A  pdb=" N   HIS A 360 " --> pdb=" O   GLN A 357 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 357 through 360'
    Processing helix  chain 'A' and resid 363 through 373
      removed outlier: 3.565A  pdb=" N   ALA A 372 " --> pdb=" O   LYS A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 402
      removed outlier: 3.561A  pdb=" N   LEU A 401 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.746A  pdb=" N   ARG A 407 " --> pdb=" O   GLY A 403 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 408 " --> pdb=" O   ASP A 404 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ILE A 417 " --> pdb=" O   THR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 454
      removed outlier: 3.743A  pdb=" N   GLU A 454 " --> pdb=" O   GLY A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 506
      removed outlier: 3.727A  pdb=" N   THR A 501 " --> pdb=" O   ALA A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 524
      removed outlier: 4.221A  pdb=" N   VAL A 516 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 552
      removed outlier: 3.756A  pdb=" N   VAL A 543 " --> pdb=" O   ASN A 539 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   LEU A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS A 550 " --> pdb=" O   HIS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 553 through 557
      removed outlier: 4.570A  pdb=" N   LEU A 557 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 573
      removed outlier: 4.198A  pdb=" N   SER A 562 " --> pdb=" O   PRO A 558 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   ILE A 571 " --> pdb=" O   GLN A 567 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ALA A 572 " --> pdb=" O   LEU A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 599
      removed outlier: 3.737A  pdb=" N   LYS A 592 " --> pdb=" O   VAL A 588 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER A 599 " --> pdb=" O   TYR A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 600 through 611
      removed outlier: 3.873A  pdb=" N   ASP A 604 " --> pdb=" O   ILE A 600 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU A 605 " --> pdb=" O   ALA A 601 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LEU A 606 " --> pdb=" O   GLY A 602 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   VAL A 609 " --> pdb=" O   GLU A 605 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   SER A 610 " --> pdb=" O   LEU A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 13
    Processing helix  chain 'B' and resid 19 through 25
      removed outlier: 3.577A  pdb=" N   THR B  25 " --> pdb=" O   ILE B  21 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 43
      removed outlier: 4.530A  pdb=" N   LEU B  38 " --> pdb=" O   ASN B  34 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ILE B  39 " --> pdb=" O   ASP B  35 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   ALA B  40 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   ASN B  42 " --> pdb=" O   LEU B  38 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 143 through 147
      removed outlier: 3.553A  pdb=" N   ASN B 146 " --> pdb=" O   ASN B 143 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   THR B 147 " --> pdb=" O   ASP B 144 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 143 through 147'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 29
      removed outlier: 6.627A  pdb=" N   LYS A   2 " --> pdb=" O   ARG A  51 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   LYS A  53 " --> pdb=" O   LYS A   2 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   VAL A   4 " --> pdb=" O   LYS A  53 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   THR A  55 " --> pdb=" O   VAL A   4 " (cutoff:3.500A)
      removed outlier: 6.167A  pdb=" N   MET A   6 " --> pdb=" O   THR A  55 " (cutoff:3.500A)
      removed outlier: 7.145A  pdb=" N   THR A   3 " --> pdb=" O   TYR A 111 " (cutoff:3.500A)
      removed outlier: 8.384A  pdb=" N   VAL A 113 " --> pdb=" O   THR A   3 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LEU A   5 " --> pdb=" O   VAL A 113 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   ILE A 112 " --> pdb=" O   PHE A 148 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 66
    Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 449
      removed outlier: 6.904A  pdb=" N   LYS A 425 " --> pdb=" O   LEU A 448 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   ALA A 245 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   TRP A 259 " --> pdb=" O   LEU A 243 " (cutoff:3.500A)
      removed outlier: 7.584A  pdb=" N   LEU A 243 " --> pdb=" O   TRP A 259 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 480 " --> pdb=" O   LYS A 246 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ASN A 248 " --> pdb=" O   VAL A 478 " (cutoff:3.500A)
      removed outlier: 5.661A  pdb=" N   VAL A 478 " --> pdb=" O   ASN A 248 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   PHE A 476 " --> pdb=" O   ALA A 283 " (cutoff:3.500A)
      removed outlier: 6.065A  pdb=" N   VAL A 285 " --> pdb=" O   ARG A 434 " (cutoff:3.500A)
      removed outlier: 6.699A  pdb=" N   ARG A 434 " --> pdb=" O   VAL A 285 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A 287 " --> pdb=" O   SER A 432 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   THR A 430 " --> pdb=" O   SER A 289 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 527 through 530
    Processing sheet with id=AA5, first strand: chain 'B' and resid 64 through 65
      removed outlier: 4.499A  pdb=" N   ASP B 134 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 9.337A  pdb=" N   LEU B 140 " --> pdb=" O   SER B 105 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   THR B 107 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   LEU B 142 " --> pdb=" O   THR B 107 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   VAL B 109 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 5.980A  pdb=" N   LYS B 126 " --> pdb=" O   LEU B 150 " (cutoff:3.500A)

    250 hydrogen bonds defined for protein.
    705 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      4 stacking parallelities
  Total time for adding SS restraints: 1.01

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1728
        1.33 -     1.45: 1037
        1.45 -     1.57: 3531
        1.57 -     1.69: 13
        1.69 -     1.81: 62
  Bond restraints: 6371
  Sorted by residual:
  bond pdb=" OH  PTR A 336 "
       pdb=" P   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.769  1.608  0.161 2.00e-02 2.50e+03 6.48e+01
  bond pdb=" C   SER A 335 "
       pdb=" N   PTR A 336 "
    ideal  model  delta    sigma   weight residual
    1.329  1.430 -0.101 1.40e-02 5.10e+03 5.23e+01
  bond pdb=" N   GLU A 465 "
       pdb=" CA  GLU A 465 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.035 1.29e-02 6.01e+03 7.57e+00
  bond pdb=" O3'   U E  -1 "
       pdb=" P     A E   0 "
    ideal  model  delta    sigma   weight residual
    1.607  1.567  0.040 1.50e-02 4.44e+03 6.98e+00
  bond pdb=" N   ASN A  71 "
       pdb=" CA  ASN A  71 "
    ideal  model  delta    sigma   weight residual
    1.457  1.485 -0.028 1.29e-02 6.01e+03 4.70e+00
  ... (remaining 6366 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     7.59: 8650
        7.59 -    15.18: 4
       15.18 -    22.77: 1
       22.77 -    30.36: 0
       30.36 -    37.96: 2
  Bond angle restraints: 8657
  Sorted by residual:
  angle pdb=" O   SER A 335 "
        pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
      ideal   model   delta    sigma   weight residual
     123.00   85.04   37.96 1.60e+00 3.91e-01 5.63e+02
  angle pdb=" CA  SER A 335 "
        pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
      ideal   model   delta    sigma   weight residual
     116.20  149.47  -33.27 2.00e+00 2.50e-01 2.77e+02
  angle pdb=" C   SER A 335 "
        pdb=" N   PTR A 336 "
        pdb=" CA  PTR A 336 "
      ideal   model   delta    sigma   weight residual
     121.70  138.72  -17.02 1.80e+00 3.09e-01 8.94e+01
  angle pdb=" C   GLU A 465 "
        pdb=" N   SER A 466 "
        pdb=" CA  SER A 466 "
      ideal   model   delta    sigma   weight residual
     122.95  114.97    7.98 1.44e+00 4.82e-01 3.07e+01
  angle pdb=" C   ASN A  71 "
        pdb=" CA  ASN A  71 "
        pdb=" CB  ASN A  71 "
      ideal   model   delta    sigma   weight residual
     110.42  101.56    8.86 1.99e+00 2.53e-01 1.98e+01
  ... (remaining 8652 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 3423
       17.54 -    35.08: 344
       35.08 -    52.61: 79
       52.61 -    70.15: 15
       70.15 -    87.69: 5
  Dihedral angle restraints: 3866
    sinusoidal: 1632
      harmonic: 2234
  Sorted by residual:
  dihedral pdb=" CA  SER A 335 "
           pdb=" C   SER A 335 "
           pdb=" N   PTR A 336 "
           pdb=" CA  PTR A 336 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.64  -28.36     0      5.00e+00 4.00e-02 3.22e+01
  dihedral pdb=" O4'   A E   0 "
           pdb=" C2'   A E   0 "
           pdb=" C1'   A E   0 "
           pdb=" C3'   A E   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00   -1.81   26.81     1      8.00e+00 1.56e-02 1.61e+01
  dihedral pdb=" C4'   A E   0 "
           pdb=" O4'   A E   0 "
           pdb=" C1'   A E   0 "
           pdb=" C2'   A E   0 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -22.17   25.17     1      8.00e+00 1.56e-02 1.42e+01
  ... (remaining 3863 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 731
       0.044 -    0.088: 179
       0.088 -    0.131: 55
       0.131 -    0.175: 10
       0.175 -    0.219: 2
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" C3'   A E   0 "
            pdb=" C4'   A E   0 "
            pdb=" O3'   A E   0 "
            pdb=" C2'   A E   0 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.70    0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CA  LEU A 134 "
            pdb=" N   LEU A 134 "
            pdb=" C   LEU A 134 "
            pdb=" CB  LEU A 134 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.75e-01
  chirality pdb=" C3'   A E   1 "
            pdb=" C4'   A E   1 "
            pdb=" O3'   A E   1 "
            pdb=" C2'   A E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.65    0.17 2.00e-01 2.50e+01 7.06e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1090
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 335 "    0.048 2.00e-02 2.50e+03   6.95e-02 4.83e+01
        pdb=" C   SER A 335 "   -0.120 2.00e-02 2.50e+03
        pdb=" O   SER A 335 "    0.028 2.00e-02 2.50e+03
        pdb=" N   PTR A 336 "    0.044 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 456 "    0.051 5.00e-02 4.00e+02   7.68e-02 9.43e+00
        pdb=" N   PRO A 457 "   -0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO A 457 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A 457 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 464 "   -0.015 2.00e-02 2.50e+03   2.83e-02 7.99e+00
        pdb=" C   GLU A 464 "    0.049 2.00e-02 2.50e+03
        pdb=" O   GLU A 464 "   -0.018 2.00e-02 2.50e+03
        pdb=" N   GLU A 465 "   -0.016 2.00e-02 2.50e+03
  ... (remaining 1087 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 85
        2.65 -     3.21: 5606
        3.21 -     3.78: 8814
        3.78 -     4.34: 11790
        4.34 -     4.90: 19739
  Nonbonded interactions: 46034
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A   9 "
            pdb="MN    MN A 702 "
     model   vdw
     2.091 2.320
  nonbonded pdb=" OE2 GLU A 340 "
            pdb=" OD2 ASP A 511 "
     model   vdw
     2.114 3.040
  nonbonded pdb=" OD2 ASP A 117 "
            pdb="MN    MN A 702 "
     model   vdw
     2.164 2.320
  nonbonded pdb=" OD2 ASP A 511 "
            pdb="MN    MN A 701 "
     model   vdw
     2.168 2.320
  nonbonded pdb=" O   ASP A 185 "
            pdb=" O2'   U E  -1 "
     model   vdw
     2.199 3.040
  ... (remaining 46029 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:             2.830
  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:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.650
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
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   0.203   6372  Z= 0.346
  Angle     :  0.870  37.956   8657  Z= 0.483
  Chirality :  0.044   0.219    977
  Planarity :  0.006   0.077   1090
  Dihedral  : 14.819  87.692   2424
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.22 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.30), residues: 766
  helix:  0.35 (0.30), residues: 291
  sheet:  0.26 (0.48), residues: 137
  loop : -0.93 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 434 
 TYR   0.016   0.002   TYR A 240 
 PHE   0.018   0.002   PHE A 265 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 ( 6371)
  covalent geometry    : angle       0.86963 ( 8657)
  hydrogen bonds       : bond        0.19650 (  250)
  hydrogen bonds       : angle       5.89950 (  705)
  Misc. bond           : bond        0.20258 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ASN cc_start: 0.7593 (t0) cc_final: 0.7389 (t0)
REVERT: A  185 ASP cc_start: 0.7302 (m-30) cc_final: 0.7096 (m-30)
REVERT: A  285 VAL cc_start: 0.8386 (p) cc_final: 0.8097 (m)
REVERT: A  431 ILE cc_start: 0.8354 (mm) cc_final: 0.8136 (mt)
REVERT: A  505 LYS cc_start: 0.8703 (ttmm) cc_final: 0.8304 (ttpp)
REVERT: A  528 THR cc_start: 0.7886 (p) cc_final: 0.7465 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0665
  time to fit residues: 19.1049
Evaluate side-chains
  204 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0050
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.2980
   chunk 74 optimal weight:    0.0470
   overall best weight:    0.2492

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.125039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.111147 restraints weight = 10233.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3544 rms_B_bonded: 2.59
r_work: 0.3422 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7711
moved from start:          0.1406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6372  Z= 0.121
  Angle     :  0.582  11.038   8657  Z= 0.298
  Chirality :  0.042   0.242    977
  Planarity :  0.005   0.058   1090
  Dihedral  :  8.276  73.434    940
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 13.81 %
    Favored  : 85.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.02 (0.30), residues: 766
  helix:  0.78 (0.30), residues: 292
  sheet:  0.50 (0.49), residues: 128
  loop : -0.86 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 434 
 TYR   0.011   0.001   TYR A 240 
 PHE   0.031   0.002   PHE A 214 
 TRP   0.007   0.001   TRP A 458 
 HIS   0.001   0.000   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 6371)
  covalent geometry    : angle       0.58188 ( 8657)
  hydrogen bonds       : bond        0.04815 (  250)
  hydrogen bonds       : angle       4.56155 (  705)
  Misc. bond           : bond        0.00062 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 191
  time to evaluate  : 0.221 
Fit side-chains
   revert: symmetry clash
REVERT: A   21 LEU cc_start: 0.8239 (tp) cc_final: 0.8006 (tt)
REVERT: A   93 ASN cc_start: 0.8074 (t0) cc_final: 0.7823 (t0)
REVERT: A  124 ASN cc_start: 0.8180 (t0) cc_final: 0.7932 (t0)
REVERT: A  159 ASP cc_start: 0.7792 (m-30) cc_final: 0.7487 (t0)
REVERT: A  185 ASP cc_start: 0.7728 (m-30) cc_final: 0.7491 (m-30)
REVERT: A  234 SER cc_start: 0.8728 (t) cc_final: 0.8483 (p)
REVERT: A  284 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7106 (mm-40)
REVERT: A  306 MET cc_start: 0.8140 (ttp) cc_final: 0.7885 (ttp)
REVERT: A  431 ILE cc_start: 0.8364 (mm) cc_final: 0.8151 (mt)
REVERT: A  465 GLU cc_start: 0.8131 (tp30) cc_final: 0.7398 (tt0)
REVERT: A  526 TYR cc_start: 0.8608 (m-10) cc_final: 0.8203 (m-10)
REVERT: A  530 GLU cc_start: 0.7083 (pm20) cc_final: 0.6742 (pm20)
REVERT: A  569 ASN cc_start: 0.8810 (t0) cc_final: 0.8527 (t0)
REVERT: A  579 ARG cc_start: 0.8047 (mmm-85) cc_final: 0.7639 (mmm-85)
  outliers start: 5
  outliers final: 3
  residues processed: 191
  average time/residue: 0.0724
  time to fit residues: 18.6737
Evaluate side-chains
  188 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 185
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain B residue  119 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 20 optimal weight:    0.0570
   chunk 27 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 55 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9980
   chunk 21 optimal weight:    0.3980
   chunk 16 optimal weight:    0.6980
   chunk 76 optimal weight:    0.0570
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
A  71 ASN
A 347 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.124514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.110631 restraints weight = 10141.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.3532 rms_B_bonded: 2.58
r_work: 0.3409 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6372  Z= 0.131
  Angle     :  0.543   9.864   8657  Z= 0.278
  Chirality :  0.042   0.213    977
  Planarity :  0.005   0.056   1090
  Dihedral  :  7.888  73.230    940
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.96 %
    Favored  : 83.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.15 (0.31), residues: 766
  helix:  0.96 (0.31), residues: 292
  sheet:  0.65 (0.49), residues: 128
  loop : -0.83 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 151 
 TYR   0.015   0.001   TYR A 240 
 PHE   0.024   0.002   PHE A 235 
 TRP   0.016   0.001   TRP A 241 
 HIS   0.002   0.000   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 6371)
  covalent geometry    : angle       0.54297 ( 8657)
  hydrogen bonds       : bond        0.04510 (  250)
  hydrogen bonds       : angle       4.35812 (  705)
  Misc. bond           : bond        0.00002 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A   21 LEU cc_start: 0.8325 (tp) cc_final: 0.8078 (tt)
REVERT: A  159 ASP cc_start: 0.7823 (m-30) cc_final: 0.7508 (t0)
REVERT: A  185 ASP cc_start: 0.7793 (m-30) cc_final: 0.7448 (m-30)
REVERT: A  234 SER cc_start: 0.8703 (t) cc_final: 0.8404 (p)
REVERT: A  284 GLN cc_start: 0.7715 (mm-40) cc_final: 0.7224 (mm-40)
REVERT: A  431 ILE cc_start: 0.8394 (mm) cc_final: 0.8184 (mt)
REVERT: A  465 GLU cc_start: 0.8118 (tp30) cc_final: 0.7456 (tt0)
REVERT: A  503 MET cc_start: 0.8253 (mtp) cc_final: 0.8013 (mtm)
REVERT: A  526 TYR cc_start: 0.8592 (m-10) cc_final: 0.8174 (m-10)
REVERT: A  530 GLU cc_start: 0.7101 (pm20) cc_final: 0.6882 (pm20)
REVERT: A  569 ASN cc_start: 0.8751 (t0) cc_final: 0.8411 (t0)
REVERT: A  579 ARG cc_start: 0.8017 (mmm-85) cc_final: 0.7644 (mmm-85)
  outliers start: 14
  outliers final: 13
  residues processed: 189
  average time/residue: 0.0709
  time to fit residues: 18.0888
Evaluate side-chains
  195 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 182
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   71 ASN
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 48 optimal weight:    0.9980
   chunk 60 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.2980
   chunk 53 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.4138

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.124642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.110686 restraints weight = 10224.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.61
r_work: 0.3409 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6372  Z= 0.127
  Angle     :  0.540  11.021   8657  Z= 0.273
  Chirality :  0.041   0.193    977
  Planarity :  0.004   0.055   1090
  Dihedral  :  7.778  73.185    940
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.22 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.30), residues: 766
  helix:  0.99 (0.31), residues: 292
  sheet:  0.46 (0.47), residues: 134
  loop : -0.82 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 151 
 TYR   0.013   0.001   TYR A 240 
 PHE   0.028   0.002   PHE A 214 
 TRP   0.010   0.001   TRP A 241 
 HIS   0.002   0.000   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6371)
  covalent geometry    : angle       0.53974 ( 8657)
  hydrogen bonds       : bond        0.04307 (  250)
  hydrogen bonds       : angle       4.27277 (  705)
  Misc. bond           : bond        0.00003 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 189
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   21 LEU cc_start: 0.8337 (tp) cc_final: 0.8118 (tt)
REVERT: A  124 ASN cc_start: 0.8235 (t0) cc_final: 0.7841 (t0)
REVERT: A  159 ASP cc_start: 0.7859 (m-30) cc_final: 0.7533 (t0)
REVERT: A  185 ASP cc_start: 0.7779 (m-30) cc_final: 0.7449 (m-30)
REVERT: A  232 ILE cc_start: 0.8627 (mm) cc_final: 0.8302 (tp)
REVERT: A  234 SER cc_start: 0.8724 (t) cc_final: 0.8396 (p)
REVERT: A  250 ASP cc_start: 0.8247 (m-30) cc_final: 0.8012 (m-30)
REVERT: A  284 GLN cc_start: 0.7728 (mm-40) cc_final: 0.7253 (mm-40)
REVERT: A  431 ILE cc_start: 0.8372 (mm) cc_final: 0.8166 (mt)
REVERT: A  526 TYR cc_start: 0.8584 (m-10) cc_final: 0.8168 (m-10)
REVERT: A  530 GLU cc_start: 0.7131 (pm20) cc_final: 0.6901 (pm20)
REVERT: A  579 ARG cc_start: 0.8001 (mmm-85) cc_final: 0.7607 (mmm-85)
  outliers start: 17
  outliers final: 14
  residues processed: 191
  average time/residue: 0.0757
  time to fit residues: 19.4705
Evaluate side-chains
  202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 188
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0030
   overall best weight:    0.6790

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.122533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.108729 restraints weight = 10372.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 2.63
r_work: 0.3374 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7768
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6372  Z= 0.181
  Angle     :  0.562  11.210   8657  Z= 0.288
  Chirality :  0.043   0.163    977
  Planarity :  0.004   0.057   1090
  Dihedral  :  7.790  72.952    940
  Min Nonbonded Distance : 2.140

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 16.97 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.30), residues: 766
  helix:  0.88 (0.31), residues: 294
  sheet:  0.44 (0.47), residues: 134
  loop : -0.74 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 151 
 TYR   0.016   0.002   TYR A 426 
 PHE   0.020   0.002   PHE A 235 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.003   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 6371)
  covalent geometry    : angle       0.56215 ( 8657)
  hydrogen bonds       : bond        0.04897 (  250)
  hydrogen bonds       : angle       4.34579 (  705)
  Misc. bond           : bond        0.00001 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 198
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
REVERT: A  124 ASN cc_start: 0.8286 (t0) cc_final: 0.7984 (t0)
REVERT: A  159 ASP cc_start: 0.7890 (m-30) cc_final: 0.7529 (t0)
REVERT: A  169 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7191 (mm-30)
REVERT: A  185 ASP cc_start: 0.7816 (m-30) cc_final: 0.7493 (m-30)
REVERT: A  234 SER cc_start: 0.8754 (t) cc_final: 0.8420 (p)
REVERT: A  250 ASP cc_start: 0.8338 (m-30) cc_final: 0.8087 (m-30)
REVERT: A  284 GLN cc_start: 0.7773 (mm-40) cc_final: 0.7294 (mm-40)
REVERT: A  285 VAL cc_start: 0.8497 (OUTLIER) cc_final: 0.8135 (m)
REVERT: A  431 ILE cc_start: 0.8381 (mm) cc_final: 0.8173 (mt)
REVERT: A  465 GLU cc_start: 0.8190 (tp30) cc_final: 0.7924 (tp30)
REVERT: A  505 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8519 (ttmm)
REVERT: A  526 TYR cc_start: 0.8598 (m-10) cc_final: 0.8191 (m-10)
REVERT: A  530 GLU cc_start: 0.7107 (pm20) cc_final: 0.6795 (pm20)
REVERT: A  552 ASP cc_start: 0.7763 (t0) cc_final: 0.7444 (t0)
REVERT: A  579 ARG cc_start: 0.8035 (mmm-85) cc_final: 0.7638 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7689 (m90) cc_final: 0.7445 (m90)
  outliers start: 18
  outliers final: 15
  residues processed: 201
  average time/residue: 0.0807
  time to fit residues: 21.3073
Evaluate side-chains
  210 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 194
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0670
   chunk 31 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 59 optimal weight:    0.8980
   chunk 43 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0980
   chunk 24 optimal weight:    0.7980
   overall best weight:    0.4518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.123851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.110066 restraints weight = 10215.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3523 rms_B_bonded: 2.60
r_work: 0.3400 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.2061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6372  Z= 0.136
  Angle     :  0.557  11.843   8657  Z= 0.279
  Chirality :  0.042   0.186    977
  Planarity :  0.005   0.064   1090
  Dihedral  :  7.679  73.112    940
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 19.37 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.30), residues: 766
  helix:  0.89 (0.31), residues: 294
  sheet:  0.45 (0.47), residues: 134
  loop : -0.73 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 369 
 TYR   0.013   0.001   TYR A 240 
 PHE   0.019   0.002   PHE A 152 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6371)
  covalent geometry    : angle       0.55667 ( 8657)
  hydrogen bonds       : bond        0.04393 (  250)
  hydrogen bonds       : angle       4.23914 (  705)
  Misc. bond           : bond        0.00006 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A   54 MET cc_start: 0.8025 (ttt) cc_final: 0.7628 (ttt)
REVERT: A   93 ASN cc_start: 0.8177 (t0) cc_final: 0.7782 (t0)
REVERT: A  124 ASN cc_start: 0.8263 (t0) cc_final: 0.7955 (t0)
REVERT: A  159 ASP cc_start: 0.7918 (m-30) cc_final: 0.7581 (t0)
REVERT: A  169 GLU cc_start: 0.7425 (mm-30) cc_final: 0.7199 (mm-30)
REVERT: A  185 ASP cc_start: 0.7800 (m-30) cc_final: 0.7458 (m-30)
REVERT: A  234 SER cc_start: 0.8738 (t) cc_final: 0.8413 (p)
REVERT: A  284 GLN cc_start: 0.7755 (mm-40) cc_final: 0.7302 (mm-40)
REVERT: A  285 VAL cc_start: 0.8525 (OUTLIER) cc_final: 0.8169 (m)
REVERT: A  431 ILE cc_start: 0.8360 (mm) cc_final: 0.8156 (mt)
REVERT: A  505 LYS cc_start: 0.8863 (ttmm) cc_final: 0.8523 (ttmm)
REVERT: A  526 TYR cc_start: 0.8572 (m-10) cc_final: 0.8175 (m-10)
REVERT: A  530 GLU cc_start: 0.7102 (pm20) cc_final: 0.6792 (pm20)
REVERT: A  579 ARG cc_start: 0.8008 (mmm-85) cc_final: 0.7612 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7655 (m90) cc_final: 0.7408 (m90)
  outliers start: 18
  outliers final: 15
  residues processed: 196
  average time/residue: 0.0810
  time to fit residues: 21.0868
Evaluate side-chains
  208 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 192
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 18 optimal weight:    0.5980
   chunk 3 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 22 optimal weight:    0.7980
   chunk 63 optimal weight:    0.3980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 539 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.121957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.108184 restraints weight = 10237.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3496 rms_B_bonded: 2.63
r_work: 0.3373 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6372  Z= 0.199
  Angle     :  0.590  12.181   8657  Z= 0.300
  Chirality :  0.043   0.171    977
  Planarity :  0.005   0.063   1090
  Dihedral  :  7.791  72.961    940
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 6.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.57 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.06 (0.30), residues: 766
  helix:  0.82 (0.31), residues: 294
  sheet:  0.42 (0.47), residues: 134
  loop : -0.76 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 369 
 TYR   0.019   0.002   TYR A 240 
 PHE   0.033   0.002   PHE A 235 
 TRP   0.009   0.001   TRP A 406 
 HIS   0.004   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 ( 6371)
  covalent geometry    : angle       0.58978 ( 8657)
  hydrogen bonds       : bond        0.05004 (  250)
  hydrogen bonds       : angle       4.39103 (  705)
  Misc. bond           : bond        0.00013 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 192
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A   54 MET cc_start: 0.8018 (ttt) cc_final: 0.7623 (ttt)
REVERT: A   93 ASN cc_start: 0.8204 (t0) cc_final: 0.7806 (t0)
REVERT: A  124 ASN cc_start: 0.8318 (t0) cc_final: 0.7978 (t0)
REVERT: A  134 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8679 (mp)
REVERT: A  159 ASP cc_start: 0.7939 (m-30) cc_final: 0.7597 (t0)
REVERT: A  162 ASN cc_start: 0.7700 (t0) cc_final: 0.7482 (t0)
REVERT: A  185 ASP cc_start: 0.7829 (m-30) cc_final: 0.7503 (m-30)
REVERT: A  234 SER cc_start: 0.8762 (t) cc_final: 0.8417 (p)
REVERT: A  284 GLN cc_start: 0.7793 (mm-40) cc_final: 0.7388 (mm-40)
REVERT: A  285 VAL cc_start: 0.8530 (OUTLIER) cc_final: 0.8174 (m)
REVERT: A  306 MET cc_start: 0.8074 (ttp) cc_final: 0.7848 (ttp)
REVERT: A  431 ILE cc_start: 0.8393 (mm) cc_final: 0.8191 (mt)
REVERT: A  465 GLU cc_start: 0.8167 (tp30) cc_final: 0.7911 (tp30)
REVERT: A  505 LYS cc_start: 0.8859 (ttmm) cc_final: 0.8511 (ttmm)
REVERT: A  526 TYR cc_start: 0.8592 (m-10) cc_final: 0.8204 (m-10)
REVERT: A  530 GLU cc_start: 0.7121 (pm20) cc_final: 0.6804 (pm20)
REVERT: A  579 ARG cc_start: 0.8041 (mmm-85) cc_final: 0.7665 (mmm-85)
REVERT: B  156 HIS cc_start: 0.7684 (m90) cc_final: 0.7437 (m90)
  outliers start: 21
  outliers final: 15
  residues processed: 199
  average time/residue: 0.0799
  time to fit residues: 20.9467
Evaluate side-chains
  207 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 190
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 52 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 22 optimal weight:    0.2980
   chunk 25 optimal weight:    0.3980
   chunk 17 optimal weight:    0.3980
   chunk 15 optimal weight:    0.9980
   chunk 76 optimal weight:    0.0040
   chunk 33 optimal weight:    0.9990
   chunk 60 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.3392

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.124365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.110487 restraints weight = 10263.132|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 2.62
r_work: 0.3412 rms_B_bonded: 3.07 restraints_weight: 0.5000
r_work (final): 0.3412
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   6372  Z= 0.117
  Angle     :  0.544  12.764   8657  Z= 0.273
  Chirality :  0.041   0.201    977
  Planarity :  0.004   0.058   1090
  Dihedral  :  7.585  73.184    940
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.02 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.17 (0.31), residues: 766
  helix:  0.93 (0.31), residues: 300
  sheet:  0.50 (0.47), residues: 134
  loop : -0.75 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 369 
 TYR   0.013   0.001   TYR A 240 
 PHE   0.026   0.002   PHE A 235 
 TRP   0.008   0.001   TRP A 458 
 HIS   0.002   0.000   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 6371)
  covalent geometry    : angle       0.54380 ( 8657)
  hydrogen bonds       : bond        0.04127 (  250)
  hydrogen bonds       : angle       4.11877 (  705)
  Misc. bond           : bond        0.00009 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A   54 MET cc_start: 0.7945 (ttt) cc_final: 0.7565 (ttt)
REVERT: A   93 ASN cc_start: 0.8151 (t0) cc_final: 0.7756 (t0)
REVERT: A  124 ASN cc_start: 0.8267 (t0) cc_final: 0.7992 (t0)
REVERT: A  159 ASP cc_start: 0.7916 (m-30) cc_final: 0.7559 (t0)
REVERT: A  185 ASP cc_start: 0.7779 (m-30) cc_final: 0.7427 (m-30)
REVERT: A  234 SER cc_start: 0.8744 (t) cc_final: 0.8396 (p)
REVERT: A  284 GLN cc_start: 0.7737 (mm-40) cc_final: 0.7384 (mm-40)
REVERT: A  285 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8181 (m)
REVERT: A  431 ILE cc_start: 0.8355 (mm) cc_final: 0.8152 (mt)
REVERT: A  465 GLU cc_start: 0.8225 (tp30) cc_final: 0.7914 (tp30)
REVERT: A  526 TYR cc_start: 0.8586 (m-10) cc_final: 0.8281 (m-10)
REVERT: A  530 GLU cc_start: 0.7184 (pm20) cc_final: 0.6894 (pm20)
REVERT: A  579 ARG cc_start: 0.8005 (mmm-85) cc_final: 0.7638 (mmm-85)
REVERT: B  111 PHE cc_start: 0.7596 (OUTLIER) cc_final: 0.7159 (m-80)
REVERT: B  156 HIS cc_start: 0.7614 (m90) cc_final: 0.7372 (m90)
  outliers start: 20
  outliers final: 14
  residues processed: 188
  average time/residue: 0.0789
  time to fit residues: 19.5030
Evaluate side-chains
  198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 60 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9990
   chunk 64 optimal weight:    0.0970
   chunk 31 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.122377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.108732 restraints weight = 10252.791|
|-----------------------------------------------------------------------------|
r_work (start): 0.3500 rms_B_bonded: 2.62
r_work: 0.3375 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3375
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6372  Z= 0.191
  Angle     :  0.589  12.380   8657  Z= 0.299
  Chirality :  0.043   0.174    977
  Planarity :  0.005   0.059   1090
  Dihedral  :  7.710  72.963    940
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 21.62 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.09 (0.30), residues: 766
  helix:  0.86 (0.30), residues: 298
  sheet:  0.43 (0.47), residues: 134
  loop : -0.77 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 369 
 TYR   0.018   0.002   TYR A 240 
 PHE   0.030   0.002   PHE A 235 
 TRP   0.009   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6371)
  covalent geometry    : angle       0.58874 ( 8657)
  hydrogen bonds       : bond        0.04911 (  250)
  hydrogen bonds       : angle       4.29749 (  705)
  Misc. bond           : bond        0.00017 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 183
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
REVERT: A   54 MET cc_start: 0.7980 (ttt) cc_final: 0.7602 (ttt)
REVERT: A   70 TYR cc_start: 0.8129 (m-80) cc_final: 0.7796 (m-80)
REVERT: A   93 ASN cc_start: 0.8181 (t0) cc_final: 0.7779 (t0)
REVERT: A  124 ASN cc_start: 0.8336 (t0) cc_final: 0.8018 (t0)
REVERT: A  145 LYS cc_start: 0.8185 (ttpp) cc_final: 0.7749 (tttt)
REVERT: A  159 ASP cc_start: 0.7899 (m-30) cc_final: 0.7562 (t0)
REVERT: A  185 ASP cc_start: 0.7809 (m-30) cc_final: 0.7462 (m-30)
REVERT: A  234 SER cc_start: 0.8737 (t) cc_final: 0.8391 (p)
REVERT: A  284 GLN cc_start: 0.7776 (mm-40) cc_final: 0.7405 (mm-40)
REVERT: A  285 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8191 (m)
REVERT: A  306 MET cc_start: 0.8063 (ttp) cc_final: 0.7835 (ttp)
REVERT: A  431 ILE cc_start: 0.8388 (mm) cc_final: 0.8187 (mt)
REVERT: A  526 TYR cc_start: 0.8620 (m-10) cc_final: 0.8238 (m-10)
REVERT: A  530 GLU cc_start: 0.7183 (pm20) cc_final: 0.6881 (pm20)
REVERT: A  579 ARG cc_start: 0.8052 (mmm-85) cc_final: 0.7697 (mmm-85)
REVERT: B  111 PHE cc_start: 0.7711 (OUTLIER) cc_final: 0.7284 (m-80)
REVERT: B  156 HIS cc_start: 0.7610 (m90) cc_final: 0.7400 (m90)
  outliers start: 16
  outliers final: 13
  residues processed: 187
  average time/residue: 0.0817
  time to fit residues: 20.2993
Evaluate side-chains
  199 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 184
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  255 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 66 optimal weight:    0.0470
   chunk 10 optimal weight:    0.0980
   chunk 74 optimal weight:    0.5980
   chunk 76 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 21 optimal weight:    0.5980
   chunk 38 optimal weight:    0.5980
   chunk 3 optimal weight:    0.8980
   chunk 4 optimal weight:    0.7980
   overall best weight:    0.3878

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.123941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.110277 restraints weight = 10159.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 2.60
r_work: 0.3409 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7738
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6372  Z= 0.125
  Angle     :  0.558  12.923   8657  Z= 0.279
  Chirality :  0.041   0.197    977
  Planarity :  0.005   0.069   1090
  Dihedral  :  7.606  73.154    940
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 22.22 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.13 (0.30), residues: 766
  helix:  0.90 (0.30), residues: 298
  sheet:  0.46 (0.47), residues: 134
  loop : -0.76 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 369 
 TYR   0.014   0.001   TYR A 240 
 PHE   0.027   0.002   PHE A 235 
 TRP   0.009   0.001   TRP A 458 
 HIS   0.002   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6371)
  covalent geometry    : angle       0.55763 ( 8657)
  hydrogen bonds       : bond        0.04267 (  250)
  hydrogen bonds       : angle       4.15891 (  705)
  Misc. bond           : bond        0.00018 (    1)

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

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

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1532 Ramachandran restraints generated.
    766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 182
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   54 MET cc_start: 0.7977 (ttt) cc_final: 0.7591 (ttt)
REVERT: A   70 TYR cc_start: 0.8091 (m-80) cc_final: 0.7757 (m-80)
REVERT: A   93 ASN cc_start: 0.8149 (t0) cc_final: 0.7751 (t0)
REVERT: A  105 GLU cc_start: 0.7492 (tp30) cc_final: 0.7225 (tp30)
REVERT: A  124 ASN cc_start: 0.8312 (t0) cc_final: 0.8019 (t0)
REVERT: A  134 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8674 (mp)
REVERT: A  159 ASP cc_start: 0.7867 (m-30) cc_final: 0.7543 (t0)
REVERT: A  164 MET cc_start: 0.8549 (tpp) cc_final: 0.7691 (tpp)
REVERT: A  185 ASP cc_start: 0.7780 (m-30) cc_final: 0.7428 (m-30)
REVERT: A  234 SER cc_start: 0.8724 (t) cc_final: 0.8373 (p)
REVERT: A  284 GLN cc_start: 0.7745 (mm-40) cc_final: 0.7443 (mm-40)
REVERT: A  285 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8218 (m)
REVERT: A  306 MET cc_start: 0.8087 (ttp) cc_final: 0.7850 (ttp)
REVERT: A  404 ASP cc_start: 0.8125 (m-30) cc_final: 0.7856 (t0)
REVERT: A  431 ILE cc_start: 0.8363 (mm) cc_final: 0.8160 (mt)
REVERT: A  465 GLU cc_start: 0.8199 (tp30) cc_final: 0.7696 (tt0)
REVERT: A  526 TYR cc_start: 0.8578 (m-10) cc_final: 0.8234 (m-10)
REVERT: A  530 GLU cc_start: 0.7183 (pm20) cc_final: 0.6877 (pm20)
REVERT: A  579 ARG cc_start: 0.8032 (mmm-85) cc_final: 0.7680 (mmm-85)
REVERT: B  111 PHE cc_start: 0.7633 (OUTLIER) cc_final: 0.7221 (m-80)
REVERT: B  156 HIS cc_start: 0.7599 (m90) cc_final: 0.7387 (m90)
  outliers start: 16
  outliers final: 13
  residues processed: 186
  average time/residue: 0.0783
  time to fit residues: 19.2379
Evaluate side-chains
  197 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 181
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 MET
Chi-restraints excluded: chain A residue   67 LEU
Chi-restraints excluded: chain A residue  134 LEU
Chi-restraints excluded: chain A residue  227 GLU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  603 MET
Chi-restraints excluded: chain B residue   62 VAL
Chi-restraints excluded: chain B residue   70 VAL
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  111 PHE
Chi-restraints excluded: chain B residue  119 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  154 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 77
   random chunks:
   chunk 14 optimal weight:    0.0370
   chunk 30 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 16 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 73 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 49 optimal weight:    0.8980
   chunk 7 optimal weight:    0.6980
   overall best weight:    0.5658

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.123379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.109801 restraints weight = 10226.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3517 rms_B_bonded: 2.61
r_work: 0.3394 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7757
moved from start:          0.2442

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   6372  Z= 0.159
  Angle     :  0.576  12.681   8657  Z= 0.291
  Chirality :  0.042   0.190    977
  Planarity :  0.005   0.070   1090
  Dihedral  :  7.632  73.066    940
  Min Nonbonded Distance : 2.163

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 21.62 %
    Favored  : 75.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.30), residues: 766
  helix:  0.84 (0.30), residues: 300
  sheet:  0.49 (0.47), residues: 134
  loop : -0.76 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 369 
 TYR   0.016   0.001   TYR A 240 
 PHE   0.028   0.002   PHE A 235 
 TRP   0.009   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 6371)
  covalent geometry    : angle       0.57624 ( 8657)
  hydrogen bonds       : bond        0.04560 (  250)
  hydrogen bonds       : angle       4.22219 (  705)
  Misc. bond           : bond        0.00019 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1595.70 seconds
wall clock time: 28 minutes 7.00 seconds (1687.00 seconds total)