Starting phenix.real_space_refine
on Sun Jun 22 07:58:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tdf_25827/06_2025/7tdf_25827.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tdf_25827/06_2025/7tdf_25827.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tdf_25827/06_2025/7tdf_25827.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tdf_25827/06_2025/7tdf_25827.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tdf_25827/06_2025/7tdf_25827.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tdf_25827/06_2025/7tdf_25827.cif"
  }
  resolution = 2.7
  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=   0.001 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 7502 atoms to isotropic.
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
     S      44      5.16       5
     C    6520      2.51       5
     N    1502      2.21       5
     O    1708      1.98       5
     H    9792      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 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: 19566
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 9783
          Classifications: {'peptide': 594}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 577}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
    Chain: "B"
      Number of atoms: 9783
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 594, 9783
          Classifications: {'peptide': 594}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 577}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 10
          Unresolved non-hydrogen angles: 13
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 9.88, per 1000 atoms: 0.50
  Number of scatterers: 19566
  At special positions: 0
  Unit cell: (111.055, 86.005, 106.045, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     O    1708      8.00
     N    1502      7.00
     C    6520      6.00
     H    9792      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 101 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  93 " - pdb=" SG  CYS B 101 " distance=2.04

  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: 5.02
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 1 sheets defined
      83.8% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 21 through 28
    Processing helix  chain 'A' and resid 29 through 44
    Processing helix  chain 'A' and resid 48 through 53
    Processing helix  chain 'A' and resid 58 through 70
      removed outlier: 3.826A  pdb=" N   LEU A  70 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 84
    Processing helix  chain 'A' and resid 85 through 88
      removed outlier: 3.752A  pdb=" N   GLU A  88 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 85 through 88'
    Processing helix  chain 'A' and resid 90 through 95
      removed outlier: 3.688A  pdb=" N   GLU A  94 " --> pdb=" O   PRO A  90 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   LYS A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 90 through 95'
    Processing helix  chain 'A' and resid 116 through 137
    Processing helix  chain 'A' and resid 138 through 141
    Processing helix  chain 'A' and resid 143 through 148
    Processing helix  chain 'A' and resid 150 through 172
      removed outlier: 3.891A  pdb=" N   ASP A 170 " --> pdb=" O   ASP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 199
      removed outlier: 3.567A  pdb=" N   VAL A 192 " --> pdb=" O   PRO A 188 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ILE A 199 " --> pdb=" O   PHE A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 238
      removed outlier: 3.579A  pdb=" N   GLY A 211 " --> pdb=" O   VAL A 207 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET A 212 " --> pdb=" O   LEU A 208 " (cutoff:3.500A)
      removed outlier: 4.777A  pdb=" N   GLY A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 4.956A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ASN A 218 " --> pdb=" O   GLY A 214 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ILE A 219 " --> pdb=" O   THR A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 250 through 263
      removed outlier: 3.535A  pdb=" N   THR A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 270
      No H-bonds generated for 'chain 'A' and resid 268 through 270'
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 280 through 295
      removed outlier: 4.365A  pdb=" N   PHE A 284 " --> pdb=" O   TRP A 280 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   PHE A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 335
      removed outlier: 3.671A  pdb=" N   ILE A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 356
    Processing helix  chain 'A' and resid 385 through 399
      removed outlier: 4.000A  pdb=" N   LEU A 397 " --> pdb=" O   GLN A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 452
      removed outlier: 4.200A  pdb=" N   TYR A 434 " --> pdb=" O   PRO A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 487
    Processing helix  chain 'A' and resid 487 through 492
    Processing helix  chain 'A' and resid 494 through 510
      removed outlier: 3.795A  pdb=" N   PHE A 499 " --> pdb=" O   GLY A 495 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU A 502 " --> pdb=" O   ARG A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 539
      removed outlier: 3.687A  pdb=" N   LEU A 533 " --> pdb=" O   TRP A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 547
    Processing helix  chain 'A' and resid 548 through 565
      removed outlier: 4.743A  pdb=" N   ALA A 553 " --> pdb=" O   GLN A 549 " (cutoff:3.500A)
      removed outlier: 6.009A  pdb=" N   PHE A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      Proline residue:  A 563  - end of helix
    Processing helix  chain 'A' and resid 565 through 588
    Processing helix  chain 'A' and resid 596 through 601
    Processing helix  chain 'A' and resid 615 through 628
    Processing helix  chain 'A' and resid 632 through 644
      removed outlier: 3.676A  pdb=" N   MET A 636 " --> pdb=" O   TRP A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 647
      No H-bonds generated for 'chain 'A' and resid 645 through 647'
    Processing helix  chain 'A' and resid 648 through 660
      removed outlier: 4.211A  pdb=" N   PHE A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 686
    Processing helix  chain 'B' and resid 21 through 28
    Processing helix  chain 'B' and resid 29 through 43
    Processing helix  chain 'B' and resid 48 through 53
    Processing helix  chain 'B' and resid 57 through 70
      removed outlier: 3.667A  pdb=" N   ARG B  62 " --> pdb=" O   GLY B  58 " (cutoff:3.500A)
      removed outlier: 5.454A  pdb=" N   TYR B  63 " --> pdb=" O   GLU B  59 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU B  70 " --> pdb=" O   ILE B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 70 through 84
    Processing helix  chain 'B' and resid 85 through 88
      removed outlier: 3.798A  pdb=" N   GLU B  88 " --> pdb=" O   ASN B  85 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 85 through 88'
    Processing helix  chain 'B' and resid 90 through 95
      removed outlier: 3.589A  pdb=" N   GLU B  94 " --> pdb=" O   PRO B  90 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   LYS B  95 " --> pdb=" O   LEU B  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 90 through 95'
    Processing helix  chain 'B' and resid 116 through 137
    Processing helix  chain 'B' and resid 138 through 141
    Processing helix  chain 'B' and resid 143 through 148
    Processing helix  chain 'B' and resid 150 through 172
      removed outlier: 3.937A  pdb=" N   ASP B 170 " --> pdb=" O   ASP B 166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 186 through 199
      removed outlier: 3.540A  pdb=" N   VAL B 192 " --> pdb=" O   PRO B 188 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ILE B 199 " --> pdb=" O   PHE B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 238
      removed outlier: 3.532A  pdb=" N   MET B 212 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   GLY B 214 " --> pdb=" O   SER B 210 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   THR B 215 " --> pdb=" O   GLY B 211 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ASN B 218 " --> pdb=" O   GLY B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
    Processing helix  chain 'B' and resid 250 through 263
      removed outlier: 3.540A  pdb=" N   THR B 263 " --> pdb=" O   PHE B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 268 through 270
      No H-bonds generated for 'chain 'B' and resid 268 through 270'
    Processing helix  chain 'B' and resid 271 through 278
    Processing helix  chain 'B' and resid 281 through 295
      removed outlier: 3.721A  pdb=" N   PHE B 285 " --> pdb=" O   SER B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 295 through 335
    Processing helix  chain 'B' and resid 343 through 356
    Processing helix  chain 'B' and resid 384 through 398
      removed outlier: 3.669A  pdb=" N   ILE B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   ALA B 396 " --> pdb=" O   CYS B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 430 through 452
      removed outlier: 4.089A  pdb=" N   TYR B 434 " --> pdb=" O   PRO B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 487
    Processing helix  chain 'B' and resid 487 through 492
    Processing helix  chain 'B' and resid 494 through 510
      removed outlier: 3.697A  pdb=" N   PHE B 499 " --> pdb=" O   GLY B 495 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   LEU B 502 " --> pdb=" O   ARG B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 529 through 539
      removed outlier: 3.503A  pdb=" N   LEU B 533 " --> pdb=" O   TRP B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 547
    Processing helix  chain 'B' and resid 548 through 565
      removed outlier: 4.639A  pdb=" N   ALA B 553 " --> pdb=" O   GLN B 549 " (cutoff:3.500A)
      removed outlier: 5.924A  pdb=" N   PHE B 554 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      Proline residue:  B 563  - end of helix
    Processing helix  chain 'B' and resid 565 through 588
    Processing helix  chain 'B' and resid 597 through 601
    Processing helix  chain 'B' and resid 615 through 628
    Processing helix  chain 'B' and resid 632 through 644
      removed outlier: 3.718A  pdb=" N   MET B 636 " --> pdb=" O   TRP B 632 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 645 through 647
      No H-bonds generated for 'chain 'B' and resid 645 through 647'
    Processing helix  chain 'B' and resid 648 through 660
      removed outlier: 4.187A  pdb=" N   PHE B 652 " --> pdb=" O   SER B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 662 through 686
    Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342

    673 hydrogen bonds defined for protein.
    1965 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: 6.94

  Time building geometry restraints manager: 6.14 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 9780
        1.03 -     1.23: 62
        1.23 -     1.42: 4316
        1.42 -     1.62: 5592
        1.62 -     1.82: 72
  Bond restraints: 19822
  Sorted by residual:
  bond pdb=" N   GLY B 527 "
       pdb=" CA  GLY B 527 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.31e+00
  bond pdb=" N   GLY A 527 "
       pdb=" CA  GLY A 527 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.12e+00
  bond pdb=" CB  PRO A  99 "
       pdb=" CG  PRO A  99 "
    ideal  model  delta    sigma   weight residual
    1.506  1.427  0.079 3.90e-02 6.57e+02 4.15e+00
  bond pdb=" CB  PRO B  99 "
       pdb=" CG  PRO B  99 "
    ideal  model  delta    sigma   weight residual
    1.506  1.434  0.072 3.90e-02 6.57e+02 3.41e+00
  bond pdb=" N   TRP A 464 "
       pdb=" CA  TRP A 464 "
    ideal  model  delta    sigma   weight residual
    1.458  1.492 -0.034 1.90e-02 2.77e+03 3.14e+00
  ... (remaining 19817 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.29: 32948
        1.29 -     2.58: 2621
        2.58 -     3.87: 127
        3.87 -     5.16: 41
        5.16 -     6.44: 7
  Bond angle restraints: 35744
  Sorted by residual:
  angle pdb=" N   ASN B  96 "
        pdb=" CA  ASN B  96 "
        pdb=" C   ASN B  96 "
      ideal   model   delta    sigma   weight residual
     109.81  116.25   -6.44 2.21e+00 2.05e-01 8.50e+00
  angle pdb=" N   VAL B 586 "
        pdb=" CA  VAL B 586 "
        pdb=" C   VAL B 586 "
      ideal   model   delta    sigma   weight residual
     109.34  115.12   -5.78 2.08e+00 2.31e-01 7.71e+00
  angle pdb=" CA  TYR B 123 "
        pdb=" CB  TYR B 123 "
        pdb=" CG  TYR B 123 "
      ideal   model   delta    sigma   weight residual
     113.90  118.80   -4.90 1.80e+00 3.09e-01 7.41e+00
  angle pdb=" N   ASN A  96 "
        pdb=" CA  ASN A  96 "
        pdb=" C   ASN A  96 "
      ideal   model   delta    sigma   weight residual
     109.81  115.57   -5.76 2.21e+00 2.05e-01 6.80e+00
  angle pdb=" CA  TYR A 123 "
        pdb=" CB  TYR A 123 "
        pdb=" CG  TYR A 123 "
      ideal   model   delta    sigma   weight residual
     113.90  118.52   -4.62 1.80e+00 3.09e-01 6.59e+00
  ... (remaining 35739 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 8572
       17.99 -    35.98: 460
       35.98 -    53.98: 144
       53.98 -    71.97: 142
       71.97 -    89.96: 6
  Dihedral angle restraints: 9324
    sinusoidal: 4840
      harmonic: 4484
  Sorted by residual:
  dihedral pdb=" CA  GLU A 600 "
           pdb=" C   GLU A 600 "
           pdb=" N   THR A 601 "
           pdb=" CA  THR A 601 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.72  -29.28     0      5.00e+00 4.00e-02 3.43e+01
  dihedral pdb=" CA  GLN A 400 "
           pdb=" C   GLN A 400 "
           pdb=" N   LYS A 401 "
           pdb=" CA  LYS A 401 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.48   28.52     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  ARG A  20 "
           pdb=" C   ARG A  20 "
           pdb=" N   ARG A  21 "
           pdb=" CA  ARG A  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.60  -27.40     0      5.00e+00 4.00e-02 3.00e+01
  ... (remaining 9321 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 861
       0.035 -    0.069: 524
       0.069 -    0.104: 125
       0.104 -    0.139: 28
       0.139 -    0.173: 14
  Chirality restraints: 1552
  Sorted by residual:
  chirality pdb=" CA  PRO A 563 "
            pdb=" N   PRO A 563 "
            pdb=" C   PRO A 563 "
            pdb=" CB  PRO A 563 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.55    0.17 2.00e-01 2.50e+01 7.51e-01
  chirality pdb=" CA  ARG B 358 "
            pdb=" N   ARG B 358 "
            pdb=" C   ARG B 358 "
            pdb=" CB  ARG B 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.79e-01
  chirality pdb=" CA  PRO A 138 "
            pdb=" N   PRO A 138 "
            pdb=" C   PRO A 138 "
            pdb=" CB  PRO A 138 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.28e-01
  ... (remaining 1549 not shown)

  Planarity restraints: 2812
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 400 "    0.029 2.00e-02 2.50e+03   3.73e-02 2.09e+01
        pdb=" CD  GLN A 400 "   -0.023 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 400 "   -0.002 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 400 "   -0.061 2.00e-02 2.50e+03
        pdb="HE21 GLN A 400 "   -0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN A 400 "    0.057 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLN A 353 "   -0.025 2.00e-02 2.50e+03   3.56e-02 1.90e+01
        pdb=" CD  GLN A 353 "    0.009 2.00e-02 2.50e+03
        pdb=" OE1 GLN A 353 "    0.007 2.00e-02 2.50e+03
        pdb=" NE2 GLN A 353 "    0.062 2.00e-02 2.50e+03
        pdb="HE21 GLN A 353 "    0.001 2.00e-02 2.50e+03
        pdb="HE22 GLN A 353 "   -0.055 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 618 "    0.029 2.00e-02 2.50e+03   3.46e-02 1.79e+01
        pdb=" CG  ASN B 618 "   -0.026 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 618 "   -0.000 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 618 "   -0.054 2.00e-02 2.50e+03
        pdb="HD21 ASN B 618 "   -0.001 2.00e-02 2.50e+03
        pdb="HD22 ASN B 618 "    0.052 2.00e-02 2.50e+03
  ... (remaining 2809 not shown)

  Histogram of nonbonded interaction distances:
        1.56 -     2.17: 757
        2.17 -     2.77: 37991
        2.77 -     3.38: 55461
        3.38 -     3.99: 69546
        3.99 -     4.60: 109924
  Nonbonded interactions: 273679
  Sorted by model distance:
  nonbonded pdb=" HG1 THR B 452 "
            pdb=" OD1 ASN B 454 "
     model   vdw
     1.556 2.450
  nonbonded pdb=" O   GLN B  54 "
            pdb=" HG  SER B  55 "
     model   vdw
     1.568 2.450
  nonbonded pdb=" HG1 THR A 452 "
            pdb=" OD1 ASN A 454 "
     model   vdw
     1.569 2.450
  nonbonded pdb="HH11 ARG B 104 "
            pdb=" O   GLY B 110 "
     model   vdw
     1.574 2.450
  nonbonded pdb="HH11 ARG A 104 "
            pdb=" O   GLY A 110 "
     model   vdw
     1.583 2.450
  ... (remaining 273674 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  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:             3.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.170
  Construct map_model_manager:             0.320
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.120
  Set scattering table:                    0.170
  Process input model:                     42.150
  Find NCS groups from input model:        0.410
  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:13.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   61.630
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7470
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  10032  Z= 0.270
  Angle     :  0.736   6.444  13638  Z= 0.454
  Chirality :  0.046   0.173   1552
  Planarity :  0.008   0.131   1666
  Dihedral  : 12.557  89.961   3514
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 2.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.52 %
    Favored  : 96.48 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  5.29 %
    Favored  : 94.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.24), residues: 1164
  helix: -0.11 (0.16), residues: 864
  sheet:  None (None), residues: 0
  loop :  1.07 (0.43), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.004   TRP A 271 
 HIS   0.003   0.001   HIS B  27 
 PHE   0.016   0.003   PHE B  57 
 TYR   0.025   0.005   TYR A 532 
 ARG   0.016   0.003   ARG B 279 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11770 (  673)
  hydrogen bonds       : angle       5.87021 ( 1965)
  SS BOND              : bond        0.00631 (    2)
  SS BOND              : angle       1.46241 (    4)
  covalent geometry    : bond        0.00623 (10030)
  covalent geometry    : angle       0.73547 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  263 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 261
  time to evaluate  : 1.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.7863 (t0) cc_final: 0.7452 (t0)
REVERT: A  208 LEU cc_start: 0.8415 (tt) cc_final: 0.8192 (tp)
REVERT: A  490 ASN cc_start: 0.8097 (t0) cc_final: 0.7777 (t0)
REVERT: A  538 MET cc_start: 0.6634 (tmt) cc_final: 0.6314 (tmt)
REVERT: B  324 ARG cc_start: 0.7449 (mtp85) cc_final: 0.7224 (mtp85)
REVERT: B  538 MET cc_start: 0.6887 (tmt) cc_final: 0.6379 (tmt)
  outliers start: 2
  outliers final: 1
  residues processed: 262
  average time/residue: 2.7805
  time to fit residues: 778.2512
Evaluate side-chains
  226 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 1.920 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   57 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 92 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 56 optimal weight:    0.1980
   chunk 68 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B 592 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.116916 restraints weight = 35459.151|
|-----------------------------------------------------------------------------|
r_work (start): 0.3456 rms_B_bonded: 1.68
r_work: 0.3339 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3196 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10032  Z= 0.194
  Angle     :  0.600   6.459  13638  Z= 0.326
  Chirality :  0.039   0.135   1552
  Planarity :  0.004   0.044   1666
  Dihedral  :  4.825  28.087   1292
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.81 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.40 (0.25), residues: 1164
  helix:  1.02 (0.17), residues: 882
  sheet:  None (None), residues: 0
  loop :  1.02 (0.43), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 223 
 HIS   0.002   0.001   HIS B  27 
 PHE   0.015   0.002   PHE A 599 
 TYR   0.016   0.002   TYR A 568 
 ARG   0.010   0.001   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05910 (  673)
  hydrogen bonds       : angle       4.78037 ( 1965)
  SS BOND              : bond        0.00260 (    2)
  SS BOND              : angle       0.87913 (    4)
  covalent geometry    : bond        0.00446 (10030)
  covalent geometry    : angle       0.59958 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  238 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 224
  time to evaluate  : 1.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8202 (t0) cc_final: 0.7803 (t0)
REVERT: A  490 ASN cc_start: 0.8077 (t0) cc_final: 0.7723 (t0)
REVERT: A  531 ARG cc_start: 0.6694 (ttm-80) cc_final: 0.6439 (ttm-80)
REVERT: A  538 MET cc_start: 0.6634 (tmt) cc_final: 0.6335 (tmt)
REVERT: A  602 GLU cc_start: 0.7370 (tt0) cc_final: 0.7161 (tt0)
REVERT: A  682 GLU cc_start: 0.7758 (mt-10) cc_final: 0.7532 (mt-10)
REVERT: B   39 ASP cc_start: 0.7748 (t0) cc_final: 0.7496 (t70)
REVERT: B   65 PHE cc_start: 0.7799 (m-80) cc_final: 0.7563 (m-80)
REVERT: B   66 ILE cc_start: 0.8347 (pt) cc_final: 0.7817 (mt)
REVERT: B   69 ARG cc_start: 0.7872 (ttm170) cc_final: 0.7567 (mtm110)
REVERT: B  103 ASP cc_start: 0.8261 (t0) cc_final: 0.7924 (t0)
REVERT: B  151 ARG cc_start: 0.7222 (tmt170) cc_final: 0.6986 (tmt170)
REVERT: B  166 ASP cc_start: 0.7518 (m-30) cc_final: 0.7279 (m-30)
REVERT: B  538 MET cc_start: 0.6936 (tmt) cc_final: 0.6416 (tmt)
REVERT: B  552 ARG cc_start: 0.8111 (ttt180) cc_final: 0.7899 (tmt170)
  outliers start: 14
  outliers final: 6
  residues processed: 230
  average time/residue: 2.9483
  time to fit residues: 722.5608
Evaluate side-chains
  214 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 208
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 SER
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  224 MET
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  605 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 78 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 104 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 116 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
B 339 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.141998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.116188 restraints weight = 35094.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.69
r_work: 0.3319 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3178 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.2576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047  10032  Z= 0.233
  Angle     :  0.572   6.177  13638  Z= 0.312
  Chirality :  0.040   0.141   1552
  Planarity :  0.004   0.046   1666
  Dihedral  :  4.644  27.476   1292
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 3.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.23 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.25), residues: 1164
  helix:  1.32 (0.17), residues: 882
  sheet:  None (None), residues: 0
  loop :  0.76 (0.44), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.003   0.001   HIS B  27 
 PHE   0.022   0.002   PHE B 399 
 TYR   0.018   0.002   TYR A 568 
 ARG   0.003   0.000   ARG A 203 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05977 (  673)
  hydrogen bonds       : angle       4.58647 ( 1965)
  SS BOND              : bond        0.00306 (    2)
  SS BOND              : angle       1.10637 (    4)
  covalent geometry    : bond        0.00553 (10030)
  covalent geometry    : angle       0.57219 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  232 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 215
  time to evaluate  : 1.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8235 (t0) cc_final: 0.7893 (t0)
REVERT: A  323 LYS cc_start: 0.8539 (ttpp) cc_final: 0.8158 (ttpp)
REVERT: A  490 ASN cc_start: 0.8102 (t0) cc_final: 0.7754 (t0)
REVERT: A  531 ARG cc_start: 0.6757 (ttm-80) cc_final: 0.6431 (ttm-80)
REVERT: A  538 MET cc_start: 0.6665 (tmt) cc_final: 0.6294 (tmt)
REVERT: A  585 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.7875 (tm-30)
REVERT: A  602 GLU cc_start: 0.7323 (tt0) cc_final: 0.7111 (tt0)
REVERT: B   39 ASP cc_start: 0.7691 (t0) cc_final: 0.7412 (t70)
REVERT: B   66 ILE cc_start: 0.8337 (pt) cc_final: 0.8079 (mt)
REVERT: B   94 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7085 (mp0)
REVERT: B  151 ARG cc_start: 0.7212 (tmt170) cc_final: 0.6976 (tmt170)
REVERT: B  200 ARG cc_start: 0.7774 (ttm-80) cc_final: 0.7509 (ttt-90)
REVERT: B  538 MET cc_start: 0.6968 (tmt) cc_final: 0.6464 (tmt)
REVERT: B  552 ARG cc_start: 0.8052 (ttt180) cc_final: 0.7851 (tmt170)
REVERT: B  680 ASP cc_start: 0.7770 (m-30) cc_final: 0.7536 (m-30)
  outliers start: 17
  outliers final: 6
  residues processed: 222
  average time/residue: 2.9971
  time to fit residues: 708.1955
Evaluate side-chains
  211 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 203
  time to evaluate  : 1.584 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  306 ASP
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  605 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 96 optimal weight:    1.9990
   chunk 14 optimal weight:    0.7980
   chunk 13 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 80 optimal weight:    0.0870
   chunk 25 optimal weight:    0.0870
   overall best weight:    0.3936

-------------------------------------------------------------------------------
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 = 0.3818 r_free = 0.3818 target = 0.142567 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.117314 restraints weight = 35832.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3460 rms_B_bonded: 1.67
r_work: 0.3349 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3208 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3208
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10032  Z= 0.139
  Angle     :  0.517   6.224  13638  Z= 0.280
  Chirality :  0.035   0.126   1552
  Planarity :  0.004   0.053   1666
  Dihedral  :  4.363  25.387   1292
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.37 %
    Favored  : 84.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.26), residues: 1164
  helix:  1.60 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  0.79 (0.45), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.002   0.001   HIS B  27 
 PHE   0.015   0.001   PHE A 554 
 TYR   0.013   0.001   TYR A 256 
 ARG   0.012   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05138 (  673)
  hydrogen bonds       : angle       4.36523 ( 1965)
  SS BOND              : bond        0.00241 (    2)
  SS BOND              : angle       1.18562 (    4)
  covalent geometry    : bond        0.00311 (10030)
  covalent geometry    : angle       0.51652 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  226 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 211
  time to evaluate  : 1.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8203 (t0) cc_final: 0.7767 (t0)
REVERT: A  127 THR cc_start: 0.8453 (m) cc_final: 0.6947 (t)
REVERT: A  490 ASN cc_start: 0.8046 (t0) cc_final: 0.7685 (t0)
REVERT: A  538 MET cc_start: 0.6636 (tmt) cc_final: 0.6345 (tmt)
REVERT: B   39 ASP cc_start: 0.7663 (t0) cc_final: 0.7372 (t70)
REVERT: B   65 PHE cc_start: 0.7781 (m-80) cc_final: 0.7420 (m-80)
REVERT: B   66 ILE cc_start: 0.8337 (pt) cc_final: 0.8070 (mt)
REVERT: B  151 ARG cc_start: 0.7104 (tmt170) cc_final: 0.6899 (tmt170)
REVERT: B  166 ASP cc_start: 0.7391 (m-30) cc_final: 0.7030 (m-30)
REVERT: B  538 MET cc_start: 0.6955 (tmt) cc_final: 0.6540 (tmt)
REVERT: B  680 ASP cc_start: 0.7688 (m-30) cc_final: 0.7454 (m-30)
  outliers start: 15
  outliers final: 4
  residues processed: 218
  average time/residue: 2.8697
  time to fit residues: 667.2599
Evaluate side-chains
  218 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 214
  time to evaluate  : 1.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  605 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 110 optimal weight:    0.9990
   chunk 66 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:    0.5980
   chunk 82 optimal weight:    0.9980
   chunk 44 optimal weight:    4.9990
   chunk 111 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.140982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.115497 restraints weight = 35692.478|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 1.68
r_work: 0.3326 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  10032  Z= 0.222
  Angle     :  0.557   6.121  13638  Z= 0.302
  Chirality :  0.039   0.141   1552
  Planarity :  0.004   0.048   1666
  Dihedral  :  4.412  25.646   1292
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 3.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 14.46 %
    Favored  : 84.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.95 (0.25), residues: 1164
  helix:  1.57 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  0.63 (0.44), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.003   0.001   HIS B  27 
 PHE   0.018   0.002   PHE A 599 
 TYR   0.017   0.002   TYR A 141 
 ARG   0.005   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05645 (  673)
  hydrogen bonds       : angle       4.41429 ( 1965)
  SS BOND              : bond        0.00490 (    2)
  SS BOND              : angle       2.41725 (    4)
  covalent geometry    : bond        0.00527 (10030)
  covalent geometry    : angle       0.55541 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  231 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 216
  time to evaluate  : 1.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8230 (t0) cc_final: 0.7909 (t0)
REVERT: A  127 THR cc_start: 0.8526 (m) cc_final: 0.7640 (p)
REVERT: A  314 LYS cc_start: 0.8454 (mtpp) cc_final: 0.8247 (mtmt)
REVERT: A  490 ASN cc_start: 0.8066 (t0) cc_final: 0.7715 (t0)
REVERT: B   39 ASP cc_start: 0.7696 (t0) cc_final: 0.7385 (t70)
REVERT: B   65 PHE cc_start: 0.7868 (m-80) cc_final: 0.7509 (m-80)
REVERT: B   66 ILE cc_start: 0.8341 (pt) cc_final: 0.8086 (mt)
REVERT: B  151 ARG cc_start: 0.7140 (tmt170) cc_final: 0.6921 (tmt170)
REVERT: B  538 MET cc_start: 0.7015 (tmt) cc_final: 0.6503 (tmt)
  outliers start: 15
  outliers final: 9
  residues processed: 226
  average time/residue: 2.8247
  time to fit residues: 681.6068
Evaluate side-chains
  213 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 204
  time to evaluate  : 1.510 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  562 ILE
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  605 GLU
Chi-restraints excluded: chain B residue  650 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 50 optimal weight:    0.0030
   chunk 63 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9980
   chunk 31 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0980
   overall best weight:    0.5190

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

Flipped N/Q/H residues before XYZ refinement:
B 315 GLN
B 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.141633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.116351 restraints weight = 35526.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.3457 rms_B_bonded: 1.68
r_work: 0.3339 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.3097

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  10032  Z= 0.153
  Angle     :  0.520   5.874  13638  Z= 0.281
  Chirality :  0.036   0.126   1552
  Planarity :  0.004   0.058   1666
  Dihedral  :  4.265  24.645   1292
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 14.93 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.13 (0.26), residues: 1164
  helix:  1.72 (0.17), residues: 886
  sheet:  None (None), residues: 0
  loop :  0.61 (0.44), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 223 
 HIS   0.002   0.001   HIS B  27 
 PHE   0.014   0.001   PHE B 599 
 TYR   0.014   0.001   TYR A 256 
 ARG   0.011   0.000   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05144 (  673)
  hydrogen bonds       : angle       4.30130 ( 1965)
  SS BOND              : bond        0.00362 (    2)
  SS BOND              : angle       1.83076 (    4)
  covalent geometry    : bond        0.00352 (10030)
  covalent geometry    : angle       0.51941 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  225 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 208
  time to evaluate  : 1.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 THR cc_start: 0.8464 (m) cc_final: 0.6911 (t)
REVERT: A  490 ASN cc_start: 0.8032 (t0) cc_final: 0.7682 (t0)
REVERT: A  538 MET cc_start: 0.6698 (tmt) cc_final: 0.6226 (tmt)
REVERT: B   39 ASP cc_start: 0.7736 (t0) cc_final: 0.7422 (t70)
REVERT: B   65 PHE cc_start: 0.7875 (m-80) cc_final: 0.7490 (m-80)
REVERT: B   66 ILE cc_start: 0.8340 (pt) cc_final: 0.8089 (mt)
REVERT: B   94 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7201 (mp0)
REVERT: B  151 ARG cc_start: 0.7104 (tmt170) cc_final: 0.6903 (tmt170)
REVERT: B  538 MET cc_start: 0.7045 (tmt) cc_final: 0.6571 (tmt)
  outliers start: 17
  outliers final: 7
  residues processed: 218
  average time/residue: 2.8349
  time to fit residues: 660.4267
Evaluate side-chains
  210 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 202
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  208 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   chunk 97 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 106 optimal weight:    0.0980
   chunk 96 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.141901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.116694 restraints weight = 35481.097|
|-----------------------------------------------------------------------------|
r_work (start): 0.3447 rms_B_bonded: 1.67
r_work: 0.3329 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3188 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3188
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.3211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10032  Z= 0.186
  Angle     :  0.536   5.810  13638  Z= 0.291
  Chirality :  0.037   0.134   1552
  Planarity :  0.005   0.058   1666
  Dihedral  :  4.259  24.187   1292
  Min Nonbonded Distance : 2.389

Molprobity Statistics.
  All-atom Clashscore : 3.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 15.50 %
    Favored  : 82.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.26), residues: 1164
  helix:  1.69 (0.17), residues: 890
  sheet:  None (None), residues: 0
  loop :  0.65 (0.45), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 223 
 HIS   0.003   0.001   HIS B  27 
 PHE   0.028   0.002   PHE B 554 
 TYR   0.015   0.002   TYR A 256 
 ARG   0.012   0.001   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05281 (  673)
  hydrogen bonds       : angle       4.32068 ( 1965)
  SS BOND              : bond        0.00416 (    2)
  SS BOND              : angle       1.87313 (    4)
  covalent geometry    : bond        0.00436 (10030)
  covalent geometry    : angle       0.53554 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  220 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 203
  time to evaluate  : 1.452 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  127 THR cc_start: 0.8493 (m) cc_final: 0.6906 (t)
REVERT: A  490 ASN cc_start: 0.8038 (t0) cc_final: 0.7686 (t0)
REVERT: A  538 MET cc_start: 0.6709 (tmt) cc_final: 0.6237 (tmt)
REVERT: A  682 GLU cc_start: 0.7731 (OUTLIER) cc_final: 0.7367 (mt-10)
REVERT: B   39 ASP cc_start: 0.7721 (t0) cc_final: 0.7414 (t70)
REVERT: B   66 ILE cc_start: 0.8345 (pt) cc_final: 0.8094 (mt)
REVERT: B   94 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7220 (mp0)
REVERT: B  166 ASP cc_start: 0.7417 (m-30) cc_final: 0.7080 (m-30)
REVERT: B  538 MET cc_start: 0.7056 (tmt) cc_final: 0.6585 (tmt)
REVERT: B  546 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7892 (mtt)
  outliers start: 17
  outliers final: 10
  residues processed: 216
  average time/residue: 2.8425
  time to fit residues: 655.5102
Evaluate side-chains
  222 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 209
  time to evaluate  : 1.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  546 MET
Chi-restraints excluded: chain B residue  650 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 76 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 393 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 267 ASN
B 315 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.140539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.115870 restraints weight = 35754.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 1.63
r_work: 0.3330 rms_B_bonded: 2.03 restraints_weight: 0.5000
r_work: 0.3192 rms_B_bonded: 3.55 restraints_weight: 0.2500
r_work (final): 0.3192
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7877
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  10032  Z= 0.206
  Angle     :  0.551   5.767  13638  Z= 0.297
  Chirality :  0.038   0.137   1552
  Planarity :  0.005   0.066   1666
  Dihedral  :  4.296  24.301   1292
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 15.88 %
    Favored  : 82.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.26), residues: 1164
  helix:  1.74 (0.17), residues: 884
  sheet:  None (None), residues: 0
  loop :  0.47 (0.44), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 223 
 HIS   0.003   0.001   HIS B  27 
 PHE   0.020   0.002   PHE B  65 
 TYR   0.015   0.002   TYR A 141 
 ARG   0.013   0.001   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05398 (  673)
  hydrogen bonds       : angle       4.34603 ( 1965)
  SS BOND              : bond        0.00457 (    2)
  SS BOND              : angle       1.96531 (    4)
  covalent geometry    : bond        0.00490 (10030)
  covalent geometry    : angle       0.54985 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  223 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 205
  time to evaluate  : 1.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8208 (t0) cc_final: 0.7853 (t0)
REVERT: A  127 THR cc_start: 0.8495 (m) cc_final: 0.6892 (t)
REVERT: A  490 ASN cc_start: 0.8041 (t0) cc_final: 0.7692 (t0)
REVERT: B   39 ASP cc_start: 0.7729 (t0) cc_final: 0.7418 (t70)
REVERT: B   65 PHE cc_start: 0.7856 (m-80) cc_final: 0.7509 (m-80)
REVERT: B   66 ILE cc_start: 0.8346 (pt) cc_final: 0.8109 (mt)
REVERT: B   94 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7209 (mp0)
REVERT: B  538 MET cc_start: 0.7041 (tmt) cc_final: 0.6707 (tmt)
REVERT: B  546 MET cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (mtt)
  outliers start: 18
  outliers final: 12
  residues processed: 216
  average time/residue: 2.7305
  time to fit residues: 630.5273
Evaluate side-chains
  217 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 203
  time to evaluate  : 1.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  339 ASN
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  165 VAL
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  546 MET
Chi-restraints excluded: chain B residue  650 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   chunk 23 optimal weight:    0.6980
   chunk 57 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 24 optimal weight:    0.4980
   chunk 42 optimal weight:    0.8980
   chunk 59 optimal weight:    2.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B 315 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.142023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.116937 restraints weight = 35530.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.3443 rms_B_bonded: 1.67
r_work: 0.3327 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3186 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  10032  Z= 0.181
  Angle     :  0.538   5.708  13638  Z= 0.291
  Chirality :  0.037   0.132   1552
  Planarity :  0.005   0.070   1666
  Dihedral  :  4.241  24.001   1292
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 16.35 %
    Favored  : 82.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.26), residues: 1164
  helix:  1.76 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop :  0.59 (0.45), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.003   0.001   HIS A 134 
 PHE   0.019   0.001   PHE A  67 
 TYR   0.015   0.002   TYR A 256 
 ARG   0.012   0.001   ARG B 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05244 (  673)
  hydrogen bonds       : angle       4.31682 ( 1965)
  SS BOND              : bond        0.00425 (    2)
  SS BOND              : angle       1.79735 (    4)
  covalent geometry    : bond        0.00428 (10030)
  covalent geometry    : angle       0.53722 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  220 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 206
  time to evaluate  : 1.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8206 (t0) cc_final: 0.7849 (t0)
REVERT: A  127 THR cc_start: 0.8495 (m) cc_final: 0.6876 (t)
REVERT: A  490 ASN cc_start: 0.8025 (t0) cc_final: 0.7664 (t0)
REVERT: B   39 ASP cc_start: 0.7739 (t0) cc_final: 0.7419 (t70)
REVERT: B   65 PHE cc_start: 0.7890 (m-80) cc_final: 0.7506 (m-80)
REVERT: B   66 ILE cc_start: 0.8344 (pt) cc_final: 0.8112 (mt)
REVERT: B   94 GLU cc_start: 0.7965 (OUTLIER) cc_final: 0.7253 (mp0)
REVERT: B  538 MET cc_start: 0.7047 (tmt) cc_final: 0.6717 (tmt)
  outliers start: 14
  outliers final: 11
  residues processed: 216
  average time/residue: 3.0291
  time to fit residues: 700.5065
Evaluate side-chains
  215 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 203
  time to evaluate  : 1.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  208 LEU
Chi-restraints excluded: chain B residue  470 VAL
Chi-restraints excluded: chain B residue  650 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 113 optimal weight:    0.9980
   chunk 106 optimal weight:    0.6980
   chunk 75 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 66 optimal weight:    0.0980
   chunk 69 optimal weight:    0.9990
   chunk 85 optimal weight:    0.6980
   chunk 60 optimal weight:    0.4980
   chunk 77 optimal weight:    0.9980
   chunk 26 optimal weight:    0.4980
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
B 315 GLN
B 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.141306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116668 restraints weight = 35579.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.63
r_work: 0.3342 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.53 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10032  Z= 0.154
  Angle     :  0.531   5.738  13638  Z= 0.286
  Chirality :  0.036   0.126   1552
  Planarity :  0.005   0.089   1666
  Dihedral  :  4.185  23.184   1292
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.84 %
    Favored  : 97.16 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.92 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.28 (0.26), residues: 1164
  helix:  1.83 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop :  0.64 (0.45), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 223 
 HIS   0.002   0.001   HIS A 134 
 PHE   0.015   0.001   PHE B  65 
 TYR   0.014   0.001   TYR A 256 
 ARG   0.013   0.001   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05033 (  673)
  hydrogen bonds       : angle       4.26521 ( 1965)
  SS BOND              : bond        0.00331 (    2)
  SS BOND              : angle       1.58549 (    4)
  covalent geometry    : bond        0.00355 (10030)
  covalent geometry    : angle       0.53075 (13634)

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

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

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2328 Ramachandran restraints generated.
    1164 Oldfield, 0 Emsley, 1164 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue ILE  342 is missing expected H atoms. Skipping.
Residue ILE  342 is missing expected H atoms. Skipping.
Evaluate side-chains
  216 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 204
  time to evaluate  : 1.616 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 ASP cc_start: 0.8189 (t0) cc_final: 0.7832 (t0)
REVERT: A  127 THR cc_start: 0.8487 (m) cc_final: 0.6873 (t)
REVERT: A  325 ARG cc_start: 0.8356 (mtp-110) cc_final: 0.8155 (mtp-110)
REVERT: A  490 ASN cc_start: 0.8017 (t0) cc_final: 0.7656 (t0)
REVERT: A  538 MET cc_start: 0.6700 (tmt) cc_final: 0.6367 (tmt)
REVERT: A  682 GLU cc_start: 0.7761 (OUTLIER) cc_final: 0.7401 (mt-10)
REVERT: B   39 ASP cc_start: 0.7711 (t0) cc_final: 0.7393 (t70)
REVERT: B   65 PHE cc_start: 0.7885 (m-80) cc_final: 0.7517 (m-80)
REVERT: B   66 ILE cc_start: 0.8337 (pt) cc_final: 0.8111 (mt)
REVERT: B   94 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7281 (mp0)
REVERT: B  139 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8185 (tt)
REVERT: B  538 MET cc_start: 0.7054 (tmt) cc_final: 0.6730 (tmt)
  outliers start: 12
  outliers final: 8
  residues processed: 211
  average time/residue: 3.0605
  time to fit residues: 692.7389
Evaluate side-chains
  211 residues out of total 1062 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 200
  time to evaluate  : 1.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ARG
Chi-restraints excluded: chain A residue  169 VAL
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  682 GLU
Chi-restraints excluded: chain B residue   57 PHE
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain B residue  169 VAL
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  208 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 47 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 88 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 115 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   chunk 32 optimal weight:    0.8980
   chunk 117 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 315 GLN
B 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.141540 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.116244 restraints weight = 35722.634|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 1.68
r_work: 0.3325 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3185 rms_B_bonded: 3.62 restraints_weight: 0.2500
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.066  10032  Z= 0.204
  Angle     :  0.554   5.636  13638  Z= 0.299
  Chirality :  0.038   0.137   1552
  Planarity :  0.005   0.068   1666
  Dihedral  :  4.226  23.553   1292
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 16.92 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.26), residues: 1164
  helix:  1.77 (0.17), residues: 888
  sheet:  None (None), residues: 0
  loop :  0.56 (0.45), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 223 
 HIS   0.002   0.001   HIS B  27 
 PHE   0.020   0.002   PHE A  67 
 TYR   0.015   0.002   TYR A 568 
 ARG   0.013   0.001   ARG A 325 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05358 (  673)
  hydrogen bonds       : angle       4.32685 ( 1965)
  SS BOND              : bond        0.00485 (    2)
  SS BOND              : angle       1.96775 (    4)
  covalent geometry    : bond        0.00488 (10030)
  covalent geometry    : angle       0.55319 (13634)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 17384.45 seconds
wall clock time: 296 minutes 12.95 seconds (17772.95 seconds total)