Starting phenix.real_space_refine
on Mon Jun  9 17:31:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h1z_51786/06_2025/9h1z_51786_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h1z_51786/06_2025/9h1z_51786.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h1z_51786/06_2025/9h1z_51786.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h1z_51786/06_2025/9h1z_51786.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h1z_51786/06_2025/9h1z_51786_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h1z_51786/06_2025/9h1z_51786_neut.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 sd=   0.165
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      38      5.16       5
     C    7037      2.51       5
     N    1833      2.21       5
     O    1983      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 44 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10892
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 671, 5454
          Classifications: {'peptide': 671}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 630}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 669, 5437
          Classifications: {'peptide': 669}
          Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 39, 'TRANS': 627}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  10617  SG  CYS B 652      54.847  58.539  56.662  1.00139.49           S

  Time building chain proxies: 7.81, per 1000 atoms: 0.72
  Number of scatterers: 10892
  At special positions: 0
  Unit cell: (115.431, 115.431, 91.074, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      38     16.00
     O    1983      8.00
     N    1833      7.00
     C    7037      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: 3.19
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS B 652 "
        pdb="ZN    ZN A 801 " - pdb=" NE2 HIS A 654 "


  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2548

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 7 sheets defined
      55.0% alpha, 8.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 11
    Processing helix  chain 'A' and resid 15 through 24
    Processing helix  chain 'A' and resid 27 through 45
      removed outlier: 4.313A  pdb=" N   GLU A  36 " --> pdb=" O   THR A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 61 through 65
    Processing helix  chain 'A' and resid 86 through 93
      removed outlier: 4.648A  pdb=" N   SER A  93 " --> pdb=" O   GLN A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 108
      removed outlier: 4.134A  pdb=" N   LEU A  98 " --> pdb=" O   GLN A  94 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   CYS A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 3.671A  pdb=" N   LYS A 115 " --> pdb=" O   LYS A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 152
    Processing helix  chain 'A' and resid 156 through 170
      removed outlier: 4.033A  pdb=" N   TYR A 160 " --> pdb=" O   SER A 156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 180
      removed outlier: 4.301A  pdb=" N   VAL A 179 " --> pdb=" O   GLU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 190
      removed outlier: 3.616A  pdb=" N   PHE A 189 " --> pdb=" O   GLN A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 214
    Processing helix  chain 'A' and resid 221 through 237
      removed outlier: 4.313A  pdb=" N   LEU A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 257
      removed outlier: 3.637A  pdb=" N   ARG A 249 " --> pdb=" O   ALA A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 285
      removed outlier: 3.715A  pdb=" N   ILE A 279 " --> pdb=" O   THR A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 320
      removed outlier: 3.876A  pdb=" N   TRP A 308 " --> pdb=" O   ASP A 304 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   GLN A 309 " --> pdb=" O   LYS A 305 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TRP A 310 " --> pdb=" O   ILE A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 343
    Processing helix  chain 'A' and resid 344 through 346
      No H-bonds generated for 'chain 'A' and resid 344 through 346'
    Processing helix  chain 'A' and resid 347 through 356
    Processing helix  chain 'A' and resid 359 through 381
    Processing helix  chain 'A' and resid 424 through 447
      removed outlier: 3.806A  pdb=" N   GLU A 447 " --> pdb=" O   TRP A 443 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 511
      removed outlier: 4.192A  pdb=" N   TYR A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   GLY A 505 " --> pdb=" O   GLU A 501 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LEU A 506 " --> pdb=" O   VAL A 502 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   LEU A 509 " --> pdb=" O   GLY A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 520 through 523
    Processing helix  chain 'A' and resid 524 through 533
    Processing helix  chain 'A' and resid 536 through 558
      removed outlier: 4.027A  pdb=" N   LYS A 556 " --> pdb=" O   GLU A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 561
      No H-bonds generated for 'chain 'A' and resid 559 through 561'
    Processing helix  chain 'A' and resid 565 through 581
      removed outlier: 3.995A  pdb=" N   LEU A 569 " --> pdb=" O   PRO A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 601
    Processing helix  chain 'A' and resid 617 through 628
      removed outlier: 3.685A  pdb=" N   LYS A 622 " --> pdb=" O   GLU A 618 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   SER A 626 " --> pdb=" O   LYS A 622 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 664
      removed outlier: 3.833A  pdb=" N   LEU A 656 " --> pdb=" O   CYS A 652 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 665 through 670
      removed outlier: 5.978A  pdb=" N   CYS A 668 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 7 through 11
    Processing helix  chain 'B' and resid 15 through 24
    Processing helix  chain 'B' and resid 27 through 46
      removed outlier: 4.187A  pdb=" N   LEU B  33 " --> pdb=" O   GLU B  29 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLU B  36 " --> pdb=" O   THR B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 65
    Processing helix  chain 'B' and resid 86 through 91
    Processing helix  chain 'B' and resid 92 through 93
      No H-bonds generated for 'chain 'B' and resid 92 through 93'
    Processing helix  chain 'B' and resid 94 through 109
      removed outlier: 3.801A  pdb=" N   CYS B 108 " --> pdb=" O   LYS B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 116
      removed outlier: 4.487A  pdb=" N   LYS B 115 " --> pdb=" O   LYS B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 152
    Processing helix  chain 'B' and resid 156 through 170
      removed outlier: 3.713A  pdb=" N   TYR B 160 " --> pdb=" O   SER B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 175 through 180
      removed outlier: 4.350A  pdb=" N   VAL B 179 " --> pdb=" O   GLU B 176 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 181 through 190
      removed outlier: 3.666A  pdb=" N   PHE B 189 " --> pdb=" O   GLN B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 214
    Processing helix  chain 'B' and resid 221 through 236
      removed outlier: 4.333A  pdb=" N   LEU B 225 " --> pdb=" O   SER B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 257
    Processing helix  chain 'B' and resid 273 through 285
      removed outlier: 3.779A  pdb=" N   ILE B 279 " --> pdb=" O   THR B 275 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLN B 285 " --> pdb=" O   LEU B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 320
      removed outlier: 3.901A  pdb=" N   TRP B 308 " --> pdb=" O   ASP B 304 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   GLN B 309 " --> pdb=" O   LYS B 305 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   TRP B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 343
    Processing helix  chain 'B' and resid 344 through 346
      No H-bonds generated for 'chain 'B' and resid 344 through 346'
    Processing helix  chain 'B' and resid 347 through 356
      removed outlier: 3.507A  pdb=" N   LYS B 353 " --> pdb=" O   ASP B 349 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 381
    Processing helix  chain 'B' and resid 424 through 447
      removed outlier: 3.847A  pdb=" N   GLU B 447 " --> pdb=" O   TRP B 443 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 511
      removed outlier: 4.211A  pdb=" N   TYR B 503 " --> pdb=" O   SER B 499 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLY B 505 " --> pdb=" O   GLU B 501 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU B 506 " --> pdb=" O   VAL B 502 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LEU B 509 " --> pdb=" O   GLY B 505 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 520 through 523
    Processing helix  chain 'B' and resid 524 through 533
    Processing helix  chain 'B' and resid 536 through 558
      removed outlier: 3.961A  pdb=" N   LYS B 556 " --> pdb=" O   GLU B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 581
      removed outlier: 4.200A  pdb=" N   LEU B 569 " --> pdb=" O   PRO B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 601
    Processing helix  chain 'B' and resid 619 through 629
      removed outlier: 3.668A  pdb=" N   SER B 626 " --> pdb=" O   LYS B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 652 through 664
      removed outlier: 3.908A  pdb=" N   LEU B 656 " --> pdb=" O   CYS B 652 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 665 through 670
      removed outlier: 5.999A  pdb=" N   CYS B 668 " --> pdb=" O   SER B 665 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 60
      removed outlier: 4.064A  pdb=" N   GLY A  56 " --> pdb=" O   PHE A  80 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   GLY A  75 " --> pdb=" O   SER A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 263
    Processing sheet with id=AA3, first strand: chain 'A' and resid 390 through 394
      removed outlier: 4.529A  pdb=" N   SER A 407 " --> pdb=" O   SER A 477 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   SER A 479 " --> pdb=" O   SER A 407 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   LEU A 465 " --> pdb=" O   VAL A 482 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 606 through 607
    Processing sheet with id=AA5, first strand: chain 'B' and resid 54 through 60
      removed outlier: 3.975A  pdb=" N   GLY B  56 " --> pdb=" O   PHE B  80 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 262 through 263
    Processing sheet with id=AA7, first strand: chain 'B' and resid 390 through 394
      removed outlier: 4.500A  pdb=" N   SER B 407 " --> pdb=" O   SER B 477 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   SER B 479 " --> pdb=" O   SER B 407 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   LEU B 465 " --> pdb=" O   VAL B 482 " (cutoff:3.500A)

    543 hydrogen bonds defined for protein.
    1503 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 5.02

  Time building geometry restraints manager: 3.19 seconds

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

  Histogram of bond lengths:
        1.22 -     1.55: 11108
        1.55 -     1.88: 58
        1.88 -     2.21: 0
        2.21 -     2.53: 0
        2.53 -     2.86: 1
  Bond restraints: 11167
  Sorted by residual:
  bond pdb=" C   ASN B 152 "
       pdb=" N   ASN B 154 "
    ideal  model  delta    sigma   weight residual
    1.329  2.864 -1.535 1.40e-02 5.10e+03 1.20e+04
  bond pdb=" C   THR B 631 "
       pdb=" N   ARG B 632 "
    ideal  model  delta    sigma   weight residual
    1.332  1.382 -0.050 1.38e-02 5.25e+03 1.30e+01
  bond pdb=" N   GLU A  47 "
       pdb=" CA  GLU A  47 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.04e-02 9.25e+03 1.10e+01
  bond pdb=" N   VAL B 634 "
       pdb=" CA  VAL B 634 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.19e-02 7.06e+03 9.18e+00
  bond pdb=" N   ASP A 617 "
       pdb=" CA  ASP A 617 "
    ideal  model  delta    sigma   weight residual
    1.453  1.492 -0.039 1.31e-02 5.83e+03 9.05e+00
  ... (remaining 11162 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     8.09: 15121
        8.09 -    16.18: 3
       16.18 -    24.26: 3
       24.26 -    32.35: 0
       32.35 -    40.44: 2
  Bond angle restraints: 15129
  Sorted by residual:
  angle pdb=" O   ASN B 152 "
        pdb=" C   ASN B 152 "
        pdb=" N   ASN B 154 "
      ideal   model   delta    sigma   weight residual
     122.59   85.64   36.95 1.33e+00 5.65e-01 7.72e+02
  angle pdb=" CA  ASN B 152 "
        pdb=" C   ASN B 152 "
        pdb=" N   ASN B 154 "
      ideal   model   delta    sigma   weight residual
     116.84  157.28  -40.44 1.71e+00 3.42e-01 5.59e+02
  angle pdb=" N   PHE B  51 "
        pdb=" CA  PHE B  51 "
        pdb=" CB  PHE B  51 "
      ideal   model   delta    sigma   weight residual
     110.50  131.71  -21.21 1.70e+00 3.46e-01 1.56e+02
  angle pdb=" N   GLN A  50 "
        pdb=" CA  GLN A  50 "
        pdb=" CB  GLN A  50 "
      ideal   model   delta    sigma   weight residual
     110.50  129.01  -18.51 1.70e+00 3.46e-01 1.19e+02
  angle pdb=" N   PHE B  51 "
        pdb=" CA  PHE B  51 "
        pdb=" C   PHE B  51 "
      ideal   model   delta    sigma   weight residual
     111.00   93.54   17.46 2.80e+00 1.28e-01 3.89e+01
  ... (remaining 15124 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 6161
       17.08 -    34.15: 410
       34.15 -    51.23: 99
       51.23 -    68.30: 47
       68.30 -    85.38: 12
  Dihedral angle restraints: 6729
    sinusoidal: 2817
      harmonic: 3912
  Sorted by residual:
  dihedral pdb=" CA  ARG A 288 "
           pdb=" C   ARG A 288 "
           pdb=" N   PRO A 289 "
           pdb=" CA  PRO A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   43.96  -43.96     0      5.00e+00 4.00e-02 7.73e+01
  dihedral pdb=" N   GLN A  50 "
           pdb=" C   GLN A  50 "
           pdb=" CA  GLN A  50 "
           pdb=" CB  GLN A  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  143.71  -20.91     0      2.50e+00 1.60e-01 7.00e+01
  dihedral pdb=" CA  ARG B 288 "
           pdb=" C   ARG B 288 "
           pdb=" N   PRO B 289 "
           pdb=" CA  PRO B 289 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   36.55  -36.55     0      5.00e+00 4.00e-02 5.34e+01
  ... (remaining 6726 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 1635
       0.139 -    0.278: 15
       0.278 -    0.417: 1
       0.417 -    0.556: 0
       0.556 -    0.695: 1
  Chirality restraints: 1652
  Sorted by residual:
  chirality pdb=" CA  GLN A  50 "
            pdb=" N   GLN A  50 "
            pdb=" C   GLN A  50 "
            pdb=" CB  GLN A  50 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.82    0.69 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" CA  PHE B  51 "
            pdb=" N   PHE B  51 "
            pdb=" C   PHE B  51 "
            pdb=" CB  PHE B  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.80e+00
  chirality pdb=" CA  ILE B 635 "
            pdb=" N   ILE B 635 "
            pdb=" C   ILE B 635 "
            pdb=" CB  ILE B 635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1649 not shown)

  Planarity restraints: 1926
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 288 "   -0.385 9.50e-02 1.11e+02   1.73e-01 1.83e+01
        pdb=" NE  ARG A 288 "    0.023 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 288 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 288 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 288 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 245 "    0.016 2.00e-02 2.50e+03   3.28e-02 1.07e+01
        pdb=" C   ALA B 245 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   ALA B 245 "    0.021 2.00e-02 2.50e+03
        pdb=" N   GLU B 246 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 443 "    0.020 2.00e-02 2.50e+03   1.97e-02 9.67e+00
        pdb=" CG  TRP B 443 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 443 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 443 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 443 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 443 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 443 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 443 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 443 "    0.012 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 443 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1923 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.26: 5
        2.26 -     2.92: 4364
        2.92 -     3.58: 15210
        3.58 -     4.24: 23966
        4.24 -     4.90: 41958
  Nonbonded interactions: 85503
  Sorted by model distance:
  nonbonded pdb=" SG  CYS A 262 "
            pdb=" NH2 ARG A 288 "
     model   vdw
     1.599 3.480
  nonbonded pdb=" SG  CYS A 262 "
            pdb=" CZ  ARG A 288 "
     model   vdw
     1.637 3.630
  nonbonded pdb=" NH2 ARG B 238 "
            pdb=" NH1 ARG B 555 "
     model   vdw
     2.044 3.200
  nonbonded pdb=" SG  CYS A 262 "
            pdb=" NH1 ARG A 288 "
     model   vdw
     2.064 3.480
  nonbonded pdb=" NH1 ARG A 288 "
            pdb=" CB  VAL A 290 "
     model   vdw
     2.187 3.550
  ... (remaining 85498 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 7 through 48 or resid 51 through 152 or resid 154 through  \ 
686))
  selection = chain 'B'
}

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:             25.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     31.000
  Find NCS groups from input model:        0.430
  Set up NCS constraints:                  0.050
  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:3.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6365
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      :  0.015   1.535  11169  Z= 1.084
  Angle     :  0.995  40.439  15129  Z= 0.622
  Chirality :  0.054   0.695   1652
  Planarity :  0.010   0.173   1926
  Dihedral  : 13.834  85.381   4181
  Min Nonbonded Distance : 1.599

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.59 %
    Favored  : 92.50 %
  Cbeta Deviations :  0.16 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.56 %
    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: -1.10 (0.21), residues: 1322
  helix: -1.07 (0.18), residues: 606
  sheet: -0.23 (0.46), residues: 134
  loop : -0.22 (0.26), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP B 443 
 HIS   0.007   0.001   HIS A 346 
 PHE   0.018   0.002   PHE A 271 
 TYR   0.019   0.004   TYR B  27 
 ARG   0.019   0.003   ARG B 535 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15847 (  543)
  hydrogen bonds       : angle       7.10535 ( 1503)
  metal coordination   : bond        0.13144 (    2)
  covalent geometry    : bond        0.01536 (11167)
  covalent geometry    : angle       0.99491 (15129)

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

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

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2644 Ramachandran restraints generated.
    1322 Oldfield, 0 Emsley, 1322 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 139
  time to evaluate  : 1.322 
Fit side-chains
REVERT: A  325 ASP cc_start: 0.7842 (t0) cc_final: 0.7585 (t0)
REVERT: A  455 GLU cc_start: 0.7427 (mt-10) cc_final: 0.7193 (tt0)
REVERT: A  470 LYS cc_start: 0.6551 (mtmm) cc_final: 0.6188 (mtpp)
REVERT: A  681 LYS cc_start: 0.8436 (ttpp) cc_final: 0.8031 (pptt)
REVERT: B   86 GLN cc_start: 0.6467 (mp10) cc_final: 0.5997 (mp10)
REVERT: B  109 LEU cc_start: 0.8537 (mm) cc_final: 0.8313 (mm)
REVERT: B  176 GLU cc_start: 0.8602 (tp30) cc_final: 0.8284 (tp30)
REVERT: B  273 ASP cc_start: 0.6036 (t70) cc_final: 0.5743 (t0)
REVERT: B  325 ASP cc_start: 0.7770 (t0) cc_final: 0.7567 (t0)
REVERT: B  601 GLN cc_start: 0.6304 (mm-40) cc_final: 0.6040 (mt0)
REVERT: B  681 LYS cc_start: 0.8544 (ttpp) cc_final: 0.7846 (pptt)
  outliers start: 11
  outliers final: 4
  residues processed: 146
  average time/residue: 0.2345
  time to fit residues: 48.7746
Evaluate side-chains
  114 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ASN
Chi-restraints excluded: chain A residue  143 LEU
Chi-restraints excluded: chain B residue   72 ASN
Chi-restraints excluded: chain B residue  466 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 100 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9980
   chunk 104 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 63 optimal weight:    5.9990
   chunk 77 optimal weight:    6.9990
   chunk 120 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
A 135 ASN
A 136 GLN
A 191 ASN
B 604 GLN
B 629 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151818 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.107687 restraints weight = 12994.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3216 rms_B_bonded: 2.81
r_work: 0.3054 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.1368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  11169  Z= 0.151
  Angle     :  0.632  17.202  15129  Z= 0.337
  Chirality :  0.043   0.265   1652
  Planarity :  0.005   0.043   1926
  Dihedral  :  5.246  46.839   1425
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.91 %
    Favored  : 91.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.08 %
    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:  0.64 (0.23), residues: 1324
  helix:  1.04 (0.21), residues: 620
  sheet:  0.09 (0.42), residues: 146
  loop : -0.05 (0.27), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 651 
 HIS   0.011   0.001   HIS A 654 
 PHE   0.015   0.001   PHE A 382 
 TYR   0.015   0.001   TYR B  27 
 ARG   0.005   0.000   ARG B 632 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04763 (  543)
  hydrogen bonds       : angle       4.66682 ( 1503)
  metal coordination   : bond        0.00536 (    2)
  covalent geometry    : bond        0.00346 (11167)
  covalent geometry    : angle       0.63193 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 1.726 
Fit side-chains
REVERT: A  162 GLU cc_start: 0.8062 (tp30) cc_final: 0.7720 (tp30)
REVERT: A  176 GLU cc_start: 0.8603 (tp30) cc_final: 0.8365 (tt0)
REVERT: A  241 ASN cc_start: 0.9089 (t0) cc_final: 0.8846 (t0)
REVERT: A  272 GLU cc_start: 0.8053 (tp30) cc_final: 0.7550 (mt-10)
REVERT: A  325 ASP cc_start: 0.8157 (t0) cc_final: 0.7865 (t0)
REVERT: A  455 GLU cc_start: 0.7945 (mt-10) cc_final: 0.7063 (tm-30)
REVERT: A  470 LYS cc_start: 0.7568 (mtmm) cc_final: 0.7169 (mtpp)
REVERT: A  681 LYS cc_start: 0.8642 (ttpp) cc_final: 0.8138 (pptt)
REVERT: B   86 GLN cc_start: 0.7249 (mp10) cc_final: 0.6561 (mp10)
REVERT: B  109 LEU cc_start: 0.8703 (mm) cc_final: 0.8458 (mm)
REVERT: B  176 GLU cc_start: 0.8735 (tp30) cc_final: 0.8435 (tp30)
REVERT: B  325 ASP cc_start: 0.8114 (t0) cc_final: 0.7908 (t0)
REVERT: B  455 GLU cc_start: 0.7872 (tt0) cc_final: 0.6683 (tm-30)
REVERT: B  470 LYS cc_start: 0.7461 (mtmm) cc_final: 0.7061 (mtpp)
REVERT: B  681 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8179 (pptt)
  outliers start: 12
  outliers final: 5
  residues processed: 134
  average time/residue: 0.2421
  time to fit residues: 45.9045
Evaluate side-chains
  110 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 105
  time to evaluate  : 1.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  191 ASN
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain B residue  275 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 54 optimal weight:    0.3980
   chunk 22 optimal weight:    0.8980
   chunk 52 optimal weight:    0.7980
   chunk 122 optimal weight:    1.9990
   chunk 15 optimal weight:    6.9990
   chunk 128 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   chunk 90 optimal weight:    3.9990
   chunk 127 optimal weight:    0.7980
   chunk 120 optimal weight:    2.9990
   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 136 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.152386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.108654 restraints weight = 13122.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.84
r_work: 0.3078 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.091  11169  Z= 0.116
  Angle     :  0.551   8.717  15129  Z= 0.291
  Chirality :  0.040   0.232   1652
  Planarity :  0.004   0.043   1926
  Dihedral  :  4.694  52.476   1418
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 2.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.99 %
    Favored  : 90.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  1.08 (0.24), residues: 1324
  helix:  1.53 (0.21), residues: 621
  sheet:  0.17 (0.43), residues: 150
  loop :  0.05 (0.28), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 443 
 HIS   0.004   0.001   HIS A 654 
 PHE   0.021   0.001   PHE B 118 
 TYR   0.009   0.001   TYR B  27 
 ARG   0.002   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04075 (  543)
  hydrogen bonds       : angle       4.33948 ( 1503)
  metal coordination   : bond        0.00070 (    2)
  covalent geometry    : bond        0.00253 (11167)
  covalent geometry    : angle       0.55128 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 121
  time to evaluate  : 1.525 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8638 (mm-40) cc_final: 0.8119 (mp10)
REVERT: A   59 ILE cc_start: 0.8167 (mt) cc_final: 0.7919 (mt)
REVERT: A  162 GLU cc_start: 0.8006 (tp30) cc_final: 0.7679 (tp30)
REVERT: A  241 ASN cc_start: 0.9104 (t0) cc_final: 0.8760 (t0)
REVERT: A  272 GLU cc_start: 0.8012 (tp30) cc_final: 0.7547 (mt-10)
REVERT: A  325 ASP cc_start: 0.8064 (t0) cc_final: 0.7815 (t0)
REVERT: A  455 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7109 (tm-30)
REVERT: A  470 LYS cc_start: 0.7581 (mtmm) cc_final: 0.7175 (mtpp)
REVERT: A  681 LYS cc_start: 0.8628 (ttpp) cc_final: 0.8130 (pptt)
REVERT: B   59 ILE cc_start: 0.8116 (mt) cc_final: 0.7831 (mt)
REVERT: B   86 GLN cc_start: 0.7207 (mp10) cc_final: 0.6481 (mp10)
REVERT: B  109 LEU cc_start: 0.8727 (mm) cc_final: 0.8461 (mm)
REVERT: B  138 ILE cc_start: 0.7869 (OUTLIER) cc_final: 0.7591 (mm)
REVERT: B  176 GLU cc_start: 0.8688 (tp30) cc_final: 0.8295 (tp30)
REVERT: B  238 ARG cc_start: 0.8341 (mpp80) cc_final: 0.8041 (mpt180)
REVERT: B  272 GLU cc_start: 0.7985 (tp30) cc_final: 0.7540 (mt-10)
REVERT: B  455 GLU cc_start: 0.7925 (tt0) cc_final: 0.6729 (tm-30)
REVERT: B  470 LYS cc_start: 0.7524 (mtmm) cc_final: 0.7154 (mtpp)
REVERT: B  681 LYS cc_start: 0.8704 (ttpp) cc_final: 0.8153 (pptt)
  outliers start: 14
  outliers final: 7
  residues processed: 128
  average time/residue: 0.2749
  time to fit residues: 52.7584
Evaluate side-chains
  121 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.761 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 LEU
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  631 THR
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  138 ILE
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  532 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 8 optimal weight:    0.6980
   chunk 104 optimal weight:   10.0000
   chunk 114 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 97 optimal weight:   10.0000
   chunk 56 optimal weight:    2.9990
   chunk 59 optimal weight:    5.9990
   chunk 83 optimal weight:    6.9990
   chunk 2 optimal weight:    9.9990
   chunk 98 optimal weight:    5.9990
   chunk 54 optimal weight:    0.7980
   overall best weight:    2.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
B 384 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.147986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.104163 restraints weight = 13153.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.83
r_work: 0.2997 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.2997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088  11169  Z= 0.201
  Angle     :  0.603   8.302  15129  Z= 0.314
  Chirality :  0.043   0.208   1652
  Planarity :  0.004   0.051   1926
  Dihedral  :  4.798  54.993   1418
  Min Nonbonded Distance : 2.286

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  9.39 %
    Favored  : 89.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.88 (0.24), residues: 1324
  helix:  1.49 (0.21), residues: 619
  sheet:  0.04 (0.45), residues: 148
  loop : -0.21 (0.27), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 651 
 HIS   0.007   0.001   HIS A 654 
 PHE   0.013   0.002   PHE B 118 
 TYR   0.012   0.002   TYR B 160 
 ARG   0.002   0.000   ARG B 428 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04846 (  543)
  hydrogen bonds       : angle       4.35575 ( 1503)
  metal coordination   : bond        0.00253 (    2)
  covalent geometry    : bond        0.00503 (11167)
  covalent geometry    : angle       0.60255 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 109
  time to evaluate  : 1.287 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8679 (mm-40) cc_final: 0.8193 (mp10)
REVERT: A  162 GLU cc_start: 0.8082 (tp30) cc_final: 0.7737 (tp30)
REVERT: A  176 GLU cc_start: 0.8579 (tp30) cc_final: 0.8209 (tt0)
REVERT: A  239 LYS cc_start: 0.7839 (mtpt) cc_final: 0.7604 (mtmm)
REVERT: A  241 ASN cc_start: 0.9126 (t0) cc_final: 0.8757 (t0)
REVERT: A  272 GLU cc_start: 0.8101 (tp30) cc_final: 0.7800 (mt-10)
REVERT: A  455 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7053 (tm-30)
REVERT: A  470 LYS cc_start: 0.7641 (mtmm) cc_final: 0.7239 (mtpp)
REVERT: A  681 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8111 (pptt)
REVERT: B   86 GLN cc_start: 0.7229 (mp10) cc_final: 0.6482 (mp10)
REVERT: B  109 LEU cc_start: 0.8757 (mm) cc_final: 0.8465 (mm)
REVERT: B  176 GLU cc_start: 0.8716 (tp30) cc_final: 0.8402 (tp30)
REVERT: B  272 GLU cc_start: 0.8119 (tp30) cc_final: 0.7639 (mt-10)
REVERT: B  470 LYS cc_start: 0.7554 (mtmm) cc_final: 0.7172 (mtpp)
REVERT: B  681 LYS cc_start: 0.8730 (ttpp) cc_final: 0.8117 (pptt)
  outliers start: 17
  outliers final: 10
  residues processed: 120
  average time/residue: 0.2173
  time to fit residues: 38.6690
Evaluate side-chains
  114 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  407 SER
Chi-restraints excluded: chain B residue  532 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 96 optimal weight:    0.2980
   chunk 10 optimal weight:   10.0000
   chunk 119 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 129 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 185 GLN
B 152 ASN
B 185 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.149402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.106045 restraints weight = 12967.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.77
r_work: 0.3040 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7546
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.066  11169  Z= 0.120
  Angle     :  0.532   8.321  15129  Z= 0.281
  Chirality :  0.040   0.197   1652
  Planarity :  0.004   0.046   1926
  Dihedral  :  4.564  55.708   1418
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 10.71 %
    Favored  : 87.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  1.13 (0.24), residues: 1324
  helix:  1.74 (0.22), residues: 620
  sheet:  0.19 (0.45), residues: 150
  loop : -0.15 (0.28), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 443 
 HIS   0.004   0.001   HIS A 654 
 PHE   0.021   0.001   PHE B 118 
 TYR   0.007   0.001   TYR B 160 
 ARG   0.002   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03971 (  543)
  hydrogen bonds       : angle       4.12523 ( 1503)
  metal coordination   : bond        0.00149 (    2)
  covalent geometry    : bond        0.00271 (11167)
  covalent geometry    : angle       0.53215 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 116
  time to evaluate  : 1.825 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8163 (mp10)
REVERT: A   59 ILE cc_start: 0.8070 (mt) cc_final: 0.7829 (mt)
REVERT: A  162 GLU cc_start: 0.8026 (tp30) cc_final: 0.7711 (tp30)
REVERT: A  176 GLU cc_start: 0.8570 (tp30) cc_final: 0.8176 (tt0)
REVERT: A  239 LYS cc_start: 0.7811 (mtpt) cc_final: 0.7480 (mtmm)
REVERT: A  241 ASN cc_start: 0.9122 (t0) cc_final: 0.8728 (t0)
REVERT: A  272 GLU cc_start: 0.8110 (tp30) cc_final: 0.7843 (mt-10)
REVERT: A  455 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7041 (tm-30)
REVERT: A  470 LYS cc_start: 0.7625 (mtmm) cc_final: 0.7230 (mtpp)
REVERT: B   59 ILE cc_start: 0.8065 (mt) cc_final: 0.7781 (mt)
REVERT: B   86 GLN cc_start: 0.7167 (mp10) cc_final: 0.6617 (mp-120)
REVERT: B  109 LEU cc_start: 0.8769 (mm) cc_final: 0.8465 (mm)
REVERT: B  176 GLU cc_start: 0.8704 (tp30) cc_final: 0.8369 (tp30)
REVERT: B  272 GLU cc_start: 0.8085 (tp30) cc_final: 0.7797 (mt-10)
REVERT: B  455 GLU cc_start: 0.8073 (tt0) cc_final: 0.6891 (tm-30)
REVERT: B  470 LYS cc_start: 0.7529 (mtmm) cc_final: 0.7162 (mtpp)
REVERT: B  681 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8157 (pptt)
  outliers start: 18
  outliers final: 13
  residues processed: 127
  average time/residue: 0.2706
  time to fit residues: 50.6393
Evaluate side-chains
  120 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 ASN
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  532 ILE
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  141 GLU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  532 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 14 optimal weight:    0.0980
   chunk 117 optimal weight:    0.1980
   chunk 97 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 120 optimal weight:    2.9990
   chunk 76 optimal weight:    5.9990
   chunk 21 optimal weight:    0.6980
   chunk 87 optimal weight:    2.9990
   chunk 131 optimal weight:    4.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.108182 restraints weight = 13075.347|
|-----------------------------------------------------------------------------|
r_work (start): 0.3230 rms_B_bonded: 2.83
r_work: 0.3066 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.2402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.061  11169  Z= 0.104
  Angle     :  0.506   9.289  15129  Z= 0.267
  Chirality :  0.039   0.209   1652
  Planarity :  0.004   0.053   1926
  Dihedral  :  4.328  53.353   1418
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 11.37 %
    Favored  : 87.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  1.26 (0.24), residues: 1324
  helix:  1.86 (0.22), residues: 626
  sheet:  0.48 (0.46), residues: 147
  loop : -0.21 (0.28), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 443 
 HIS   0.002   0.001   HIS A 654 
 PHE   0.011   0.001   PHE B 118 
 TYR   0.006   0.001   TYR B 160 
 ARG   0.005   0.000   ARG A 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03497 (  543)
  hydrogen bonds       : angle       3.98952 ( 1503)
  metal coordination   : bond        0.00063 (    2)
  covalent geometry    : bond        0.00223 (11167)
  covalent geometry    : angle       0.50578 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 1.724 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8585 (mm-40) cc_final: 0.8109 (mp10)
REVERT: A   59 ILE cc_start: 0.8072 (mt) cc_final: 0.7820 (mt)
REVERT: A  162 GLU cc_start: 0.8020 (tp30) cc_final: 0.7688 (tp30)
REVERT: A  241 ASN cc_start: 0.9111 (t0) cc_final: 0.8703 (t0)
REVERT: A  272 GLU cc_start: 0.8057 (tp30) cc_final: 0.7820 (mt-10)
REVERT: A  455 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7077 (tm-30)
REVERT: A  470 LYS cc_start: 0.7656 (mtmm) cc_final: 0.7254 (mtpp)
REVERT: A  510 TYR cc_start: 0.7911 (m-80) cc_final: 0.7397 (m-80)
REVERT: A  681 LYS cc_start: 0.8768 (mtmm) cc_final: 0.8159 (pptt)
REVERT: B   59 ILE cc_start: 0.8035 (mt) cc_final: 0.7754 (mt)
REVERT: B   86 GLN cc_start: 0.7171 (mp10) cc_final: 0.6614 (mp-120)
REVERT: B  109 LEU cc_start: 0.8729 (mm) cc_final: 0.8402 (mm)
REVERT: B  176 GLU cc_start: 0.8657 (tp30) cc_final: 0.8335 (tp30)
REVERT: B  272 GLU cc_start: 0.8047 (tp30) cc_final: 0.7775 (mt-10)
REVERT: B  455 GLU cc_start: 0.8116 (tt0) cc_final: 0.6948 (tm-30)
REVERT: B  470 LYS cc_start: 0.7544 (mtmm) cc_final: 0.6963 (mtpp)
REVERT: B  681 LYS cc_start: 0.8723 (ttpp) cc_final: 0.8166 (pptt)
  outliers start: 15
  outliers final: 9
  residues processed: 131
  average time/residue: 0.2794
  time to fit residues: 54.8551
Evaluate side-chains
  116 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   72 ASN
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  259 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 127 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   chunk 46 optimal weight:    7.9990
   chunk 92 optimal weight:    0.9980
   chunk 2 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 87 optimal weight:    8.9990
   chunk 34 optimal weight:    3.9990
   chunk 67 optimal weight:   10.0000
   chunk 50 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0070
   overall best weight:    2.4004

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.146867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.103376 restraints weight = 13286.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.79
r_work: 0.3011 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  11169  Z= 0.181
  Angle     :  0.569   9.138  15129  Z= 0.295
  Chirality :  0.042   0.214   1652
  Planarity :  0.004   0.045   1926
  Dihedral  :  4.528  53.662   1418
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 12.44 %
    Favored  : 86.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  1.03 (0.24), residues: 1324
  helix:  1.68 (0.22), residues: 631
  sheet:  0.36 (0.46), residues: 146
  loop : -0.35 (0.28), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 443 
 HIS   0.006   0.001   HIS A 654 
 PHE   0.012   0.002   PHE B 118 
 TYR   0.012   0.001   TYR A 231 
 ARG   0.003   0.000   ARG A 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04362 (  543)
  hydrogen bonds       : angle       4.09879 ( 1503)
  metal coordination   : bond        0.00192 (    2)
  covalent geometry    : bond        0.00451 (11167)
  covalent geometry    : angle       0.56870 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 2.086 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8576 (mm-40) cc_final: 0.8111 (mp10)
REVERT: A  162 GLU cc_start: 0.8052 (tp30) cc_final: 0.7725 (tp30)
REVERT: A  241 ASN cc_start: 0.9125 (t0) cc_final: 0.8715 (t0)
REVERT: A  272 GLU cc_start: 0.8059 (tp30) cc_final: 0.7838 (mt-10)
REVERT: A  455 GLU cc_start: 0.7956 (mt-10) cc_final: 0.7101 (tm-30)
REVERT: A  470 LYS cc_start: 0.7677 (mtmm) cc_final: 0.7255 (mtpp)
REVERT: A  510 TYR cc_start: 0.8038 (m-80) cc_final: 0.7541 (m-80)
REVERT: A  681 LYS cc_start: 0.8812 (mtmm) cc_final: 0.8177 (pptt)
REVERT: B   86 GLN cc_start: 0.7301 (mp10) cc_final: 0.6740 (mp-120)
REVERT: B  109 LEU cc_start: 0.8728 (mm) cc_final: 0.8405 (mm)
REVERT: B  176 GLU cc_start: 0.8671 (tp30) cc_final: 0.8359 (tp30)
REVERT: B  272 GLU cc_start: 0.8110 (tp30) cc_final: 0.7678 (mt-10)
REVERT: B  470 LYS cc_start: 0.7579 (mtmm) cc_final: 0.7012 (mtpp)
REVERT: B  681 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8209 (pptt)
  outliers start: 15
  outliers final: 14
  residues processed: 116
  average time/residue: 0.2946
  time to fit residues: 50.5103
Evaluate side-chains
  117 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 1.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue   72 ASN
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue   34 ILE
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  407 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 77 optimal weight:    8.9990
   chunk 104 optimal weight:    9.9990
   chunk 72 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   chunk 115 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   chunk 32 optimal weight:    6.9990
   chunk 41 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   overall best weight:    2.1586

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.146704 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.103255 restraints weight = 13055.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3168 rms_B_bonded: 2.77
r_work: 0.3004 rms_B_bonded: 3.36 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2581

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  11169  Z= 0.168
  Angle     :  0.566   9.085  15129  Z= 0.294
  Chirality :  0.042   0.211   1652
  Planarity :  0.004   0.045   1926
  Dihedral  :  4.547  53.380   1418
  Min Nonbonded Distance : 2.201

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 12.36 %
    Favored  : 86.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.96 (0.24), residues: 1324
  helix:  1.69 (0.22), residues: 631
  sheet:  0.27 (0.46), residues: 146
  loop : -0.47 (0.27), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 443 
 HIS   0.006   0.001   HIS A 654 
 PHE   0.025   0.002   PHE A 118 
 TYR   0.011   0.001   TYR A 231 
 ARG   0.003   0.000   ARG A 137 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04361 (  543)
  hydrogen bonds       : angle       4.10599 ( 1503)
  metal coordination   : bond        0.00255 (    2)
  covalent geometry    : bond        0.00415 (11167)
  covalent geometry    : angle       0.56637 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 1.246 
Fit side-chains
REVERT: A   55 GLN cc_start: 0.8621 (mm-40) cc_final: 0.8190 (mp10)
REVERT: A   59 ILE cc_start: 0.8117 (mt) cc_final: 0.7875 (mt)
REVERT: A  162 GLU cc_start: 0.8054 (tp30) cc_final: 0.7724 (tp30)
REVERT: A  220 LEU cc_start: 0.8477 (OUTLIER) cc_final: 0.8277 (tt)
REVERT: A  241 ASN cc_start: 0.9127 (t0) cc_final: 0.8716 (t0)
REVERT: A  272 GLU cc_start: 0.8053 (tp30) cc_final: 0.7843 (mt-10)
REVERT: A  455 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7059 (tm-30)
REVERT: A  470 LYS cc_start: 0.7685 (mtmm) cc_final: 0.7251 (mtpp)
REVERT: A  510 TYR cc_start: 0.8016 (m-80) cc_final: 0.7519 (m-80)
REVERT: A  681 LYS cc_start: 0.8795 (mtmm) cc_final: 0.8168 (pptt)
REVERT: B   21 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8177 (tm-30)
REVERT: B   86 GLN cc_start: 0.7296 (mp10) cc_final: 0.6727 (mp-120)
REVERT: B  109 LEU cc_start: 0.8735 (mm) cc_final: 0.8413 (mm)
REVERT: B  176 GLU cc_start: 0.8671 (tp30) cc_final: 0.8222 (tp30)
REVERT: B  272 GLU cc_start: 0.8095 (tp30) cc_final: 0.7673 (mt-10)
REVERT: B  281 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7346 (mp)
REVERT: B  470 LYS cc_start: 0.7583 (mtmm) cc_final: 0.7003 (mtpp)
  outliers start: 17
  outliers final: 12
  residues processed: 116
  average time/residue: 0.2290
  time to fit residues: 39.2353
Evaluate side-chains
  117 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  259 GLU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  407 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 74 optimal weight:    8.9990
   chunk 3 optimal weight:    9.9990
   chunk 72 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 94 optimal weight:    3.9990
   overall best weight:    0.9788

-------------------------------------------------------------------------------
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 = 0.3788 r_free = 0.3788 target = 0.150657 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.106018 restraints weight = 13388.827|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 2.91
r_work: 0.3073 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7654
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11169  Z= 0.112
  Angle     :  0.525   8.997  15129  Z= 0.276
  Chirality :  0.040   0.203   1652
  Planarity :  0.004   0.043   1926
  Dihedral  :  4.304  52.707   1418
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.69 %
    Favored  : 86.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  1.17 (0.24), residues: 1324
  helix:  1.87 (0.22), residues: 632
  sheet:  0.47 (0.47), residues: 146
  loop : -0.40 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 443 
 HIS   0.004   0.001   HIS A 654 
 PHE   0.027   0.001   PHE A 118 
 TYR   0.006   0.001   TYR B 160 
 ARG   0.002   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03654 (  543)
  hydrogen bonds       : angle       3.94599 ( 1503)
  metal coordination   : bond        0.00187 (    2)
  covalent geometry    : bond        0.00253 (11167)
  covalent geometry    : angle       0.52542 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 112
  time to evaluate  : 1.451 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8570 (mm-40) cc_final: 0.8215 (mp10)
REVERT: A   59 ILE cc_start: 0.8090 (mt) cc_final: 0.7842 (mt)
REVERT: A   74 ASP cc_start: 0.7374 (t0) cc_final: 0.7006 (p0)
REVERT: A  162 GLU cc_start: 0.8061 (tp30) cc_final: 0.7717 (tp30)
REVERT: A  220 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8221 (tt)
REVERT: A  241 ASN cc_start: 0.9090 (t0) cc_final: 0.8666 (t0)
REVERT: A  455 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7159 (tm-30)
REVERT: A  470 LYS cc_start: 0.7792 (mtmm) cc_final: 0.7184 (mtpp)
REVERT: A  510 TYR cc_start: 0.7977 (m-80) cc_final: 0.7562 (m-80)
REVERT: A  681 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8210 (pptt)
REVERT: B   59 ILE cc_start: 0.8095 (mt) cc_final: 0.7840 (mt)
REVERT: B   74 ASP cc_start: 0.7415 (t0) cc_final: 0.7125 (p0)
REVERT: B   86 GLN cc_start: 0.7338 (mp10) cc_final: 0.6749 (mp-120)
REVERT: B  109 LEU cc_start: 0.8773 (mm) cc_final: 0.8463 (mm)
REVERT: B  176 GLU cc_start: 0.8679 (tp30) cc_final: 0.8148 (tt0)
REVERT: B  272 GLU cc_start: 0.8013 (tp30) cc_final: 0.7790 (mt-10)
REVERT: B  281 LEU cc_start: 0.7817 (OUTLIER) cc_final: 0.7445 (mp)
REVERT: B  455 GLU cc_start: 0.8251 (tt0) cc_final: 0.7034 (tm-30)
REVERT: B  470 LYS cc_start: 0.7721 (mtmm) cc_final: 0.7146 (mtpp)
  outliers start: 14
  outliers final: 10
  residues processed: 126
  average time/residue: 0.2258
  time to fit residues: 41.8455
Evaluate side-chains
  119 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  259 GLU
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  407 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 54 optimal weight:    0.1980
   chunk 116 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 91 optimal weight:    5.9990
   chunk 105 optimal weight:    0.0870
   chunk 76 optimal weight:    1.9990
   chunk 86 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 15 optimal weight:    3.9990
   chunk 93 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 475 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.155739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.110813 restraints weight = 13283.082|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 2.95
r_work: 0.3112 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  11169  Z= 0.099
  Angle     :  0.503   8.998  15129  Z= 0.264
  Chirality :  0.039   0.198   1652
  Planarity :  0.004   0.041   1926
  Dihedral  :  4.018  52.074   1418
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 3.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 12.93 %
    Favored  : 86.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  1.25 (0.25), residues: 1324
  helix:  1.90 (0.22), residues: 639
  sheet:  0.66 (0.47), residues: 146
  loop : -0.39 (0.28), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 443 
 HIS   0.002   0.001   HIS B 654 
 PHE   0.026   0.001   PHE A 118 
 TYR   0.005   0.001   TYR B 160 
 ARG   0.002   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03127 (  543)
  hydrogen bonds       : angle       3.82731 ( 1503)
  metal coordination   : bond        0.00165 (    2)
  covalent geometry    : bond        0.00213 (11167)
  covalent geometry    : angle       0.50301 (15129)

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

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

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2648 Ramachandran restraints generated.
    1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 116
  time to evaluate  : 1.994 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 GLN cc_start: 0.8476 (mm-40) cc_final: 0.8177 (mp10)
REVERT: A   59 ILE cc_start: 0.8073 (mt) cc_final: 0.7820 (mt)
REVERT: A   74 ASP cc_start: 0.7343 (t0) cc_final: 0.7094 (p0)
REVERT: A  162 GLU cc_start: 0.8093 (tp30) cc_final: 0.7726 (tp30)
REVERT: A  220 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8176 (tt)
REVERT: A  241 ASN cc_start: 0.9067 (t0) cc_final: 0.8629 (t0)
REVERT: A  455 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7236 (tm-30)
REVERT: A  470 LYS cc_start: 0.7796 (mtmm) cc_final: 0.7195 (mtpp)
REVERT: A  510 TYR cc_start: 0.7854 (m-80) cc_final: 0.7411 (m-80)
REVERT: A  681 LYS cc_start: 0.8830 (mtmm) cc_final: 0.8235 (pptt)
REVERT: B   59 ILE cc_start: 0.8038 (mt) cc_final: 0.7780 (mt)
REVERT: B   86 GLN cc_start: 0.7239 (mp10) cc_final: 0.6891 (mm110)
REVERT: B  109 LEU cc_start: 0.8759 (mm) cc_final: 0.8409 (mm)
REVERT: B  176 GLU cc_start: 0.8640 (tp30) cc_final: 0.8073 (tt0)
REVERT: B  240 ASP cc_start: 0.8601 (p0) cc_final: 0.8054 (m-30)
REVERT: B  281 LEU cc_start: 0.7698 (OUTLIER) cc_final: 0.7289 (mp)
REVERT: B  455 GLU cc_start: 0.8264 (tt0) cc_final: 0.7095 (tm-30)
REVERT: B  470 LYS cc_start: 0.7689 (mtmm) cc_final: 0.7136 (mtpp)
REVERT: B  519 GLU cc_start: 0.7360 (pm20) cc_final: 0.7117 (pm20)
  outliers start: 13
  outliers final: 10
  residues processed: 129
  average time/residue: 0.2276
  time to fit residues: 43.4303
Evaluate side-chains
  115 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 1.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   45 LEU
Chi-restraints excluded: chain A residue   53 LEU
Chi-restraints excluded: chain A residue  129 ILE
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  220 LEU
Chi-restraints excluded: chain A residue  275 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain B residue  129 ILE
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain B residue  275 THR
Chi-restraints excluded: chain B residue  281 LEU
Chi-restraints excluded: chain B residue  407 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 106 optimal weight:    7.9990
   chunk 68 optimal weight:    7.9990
   chunk 6 optimal weight:   10.0000
   chunk 129 optimal weight:    0.7980
   chunk 74 optimal weight:    7.9990
   chunk 93 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 91 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 = 0.3767 r_free = 0.3767 target = 0.149018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.103397 restraints weight = 13406.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 2.95
r_work: 0.3024 rms_B_bonded: 3.53 restraints_weight: 0.5000
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7707
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  11169  Z= 0.195
  Angle     :  0.588   9.167  15129  Z= 0.303
  Chirality :  0.042   0.214   1652
  Planarity :  0.004   0.040   1926
  Dihedral  :  4.356  52.849   1418
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 3.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.55 %
    Favored  : 96.45 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 13.76 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.56 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.97 (0.24), residues: 1324
  helix:  1.69 (0.22), residues: 638
  sheet:  0.39 (0.47), residues: 146
  loop : -0.51 (0.28), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 443 
 HIS   0.005   0.001   HIS A 654 
 PHE   0.026   0.002   PHE A 118 
 TYR   0.012   0.001   TYR A 231 
 ARG   0.003   0.000   ARG A 428 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04397 (  543)
  hydrogen bonds       : angle       4.03514 ( 1503)
  metal coordination   : bond        0.00287 (    2)
  covalent geometry    : bond        0.00481 (11167)
  covalent geometry    : angle       0.58828 (15129)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5591.50 seconds
wall clock time: 101 minutes 59.81 seconds (6119.81 seconds total)