Starting phenix.real_space_refine
on Sun May  3 05:02:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xvg_67288/05_2026/9xvg_67288.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xvg_67288/05_2026/9xvg_67288.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.49
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xvg_67288/05_2026/9xvg_67288.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xvg_67288/05_2026/9xvg_67288.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xvg_67288/05_2026/9xvg_67288.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xvg_67288/05_2026/9xvg_67288.map"
  }
  resolution = 2.49
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      67      5.16       5
     C    6705      2.51       5
     N    1793      2.21       5
     O    1947      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10512
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 653, 5300
          Classifications: {'peptide': 653}
          Link IDs: {'PCIS': 2, 'PTRANS': 30, 'TRANS': 620}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 5212
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 642, 5212
          Classifications: {'peptide': 642}
          Link IDs: {'PCIS': 2, 'PTRANS': 29, 'TRANS': 610}
          Chain breaks: 4
  Time building chain proxies: 2.50, per 1000 atoms: 0.24
  Number of scatterers: 10512
  At special positions: 0
  Unit cell: (71.04, 70.08, 195.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      67     16.00
     O    1947      8.00
     N    1793      7.00
     C    6705      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.89
  Conformation dependent library (CDL) restraints added in 379.9 milliseconds
  

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2406

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 13 sheets defined
      29.2% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 67
    Processing helix  chain 'A' and resid 110 through 113
    Processing helix  chain 'A' and resid 181 through 187
      removed outlier: 4.536A  pdb=" N   THR A 186 " --> pdb=" O   VAL A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 192
      removed outlier: 3.661A  pdb=" N   LYS A 192 " --> pdb=" O   GLU A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 205
    Processing helix  chain 'A' and resid 205 through 213
      removed outlier: 3.987A  pdb=" N   LEU A 209 " --> pdb=" O   LYS A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 260
      removed outlier: 3.595A  pdb=" N   ALA A 260 " --> pdb=" O   ILE A 257 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 257 through 260'
    Processing helix  chain 'A' and resid 269 through 285
      removed outlier: 3.870A  pdb=" N   ASN A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 310 through 319
      removed outlier: 8.564A  pdb=" N   SER A 316 " --> pdb=" O   GLY A 312 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   VAL A 317 " --> pdb=" O   VAL A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 341 through 359
      removed outlier: 3.503A  pdb=" N   ARG A 345 " --> pdb=" O   HIS A 341 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   MET A 359 " --> pdb=" O   TRP A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 411
    Processing helix  chain 'A' and resid 446 through 458
      removed outlier: 3.607A  pdb=" N   ARG A 450 " --> pdb=" O   ASN A 446 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN A 455 " --> pdb=" O   ASP A 451 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A 458 " --> pdb=" O   ARG A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 472
    Processing helix  chain 'A' and resid 483 through 485
      No H-bonds generated for 'chain 'A' and resid 483 through 485'
    Processing helix  chain 'A' and resid 498 through 503
      removed outlier: 3.901A  pdb=" N   VAL A 503 " --> pdb=" O   LEU A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 556
      removed outlier: 3.850A  pdb=" N   ARG A 549 " --> pdb=" O   LYS A 545 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ASN A 550 " --> pdb=" O   ARG A 546 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE A 551 " --> pdb=" O   GLN A 547 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   PHE A 552 " --> pdb=" O   MET A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 589
    Processing helix  chain 'A' and resid 591 through 598
    Processing helix  chain 'A' and resid 602 through 616
    Processing helix  chain 'A' and resid 705 through 712
      removed outlier: 3.604A  pdb=" N   ALA A 709 " --> pdb=" O   GLU A 705 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   GLN A 712 " --> pdb=" O   THR A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 719
    Processing helix  chain 'B' and resid 62 through 67
    Processing helix  chain 'B' and resid 110 through 113
    Processing helix  chain 'B' and resid 181 through 186
      removed outlier: 4.624A  pdb=" N   THR B 186 " --> pdb=" O   VAL B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 187 through 192
      removed outlier: 5.873A  pdb=" N   SER B 190 " --> pdb=" O   ARG B 187 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS B 192 " --> pdb=" O   GLU B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 198 through 203
    Processing helix  chain 'B' and resid 205 through 213
      removed outlier: 3.659A  pdb=" N   LEU B 209 " --> pdb=" O   LYS B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 256 through 260
    Processing helix  chain 'B' and resid 269 through 285
      removed outlier: 3.704A  pdb=" N   ASN B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG B 285 " --> pdb=" O   GLU B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 319
      removed outlier: 8.090A  pdb=" N   SER B 316 " --> pdb=" O   GLY B 312 " (cutoff:3.500A)
      removed outlier: 7.368A  pdb=" N   VAL B 317 " --> pdb=" O   VAL B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 359
    Processing helix  chain 'B' and resid 406 through 411
      removed outlier: 4.027A  pdb=" N   SER B 410 " --> pdb=" O   ILE B 406 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 446 through 458
      removed outlier: 3.913A  pdb=" N   ARG B 450 " --> pdb=" O   ASN B 446 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ASP B 451 " --> pdb=" O   GLY B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 463 through 472
      removed outlier: 3.502A  pdb=" N   PHE B 467 " --> pdb=" O   PHE B 463 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ALA B 468 " --> pdb=" O   SER B 464 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   GLU B 469 " --> pdb=" O   GLY B 465 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   CYS B 470 " --> pdb=" O   ALA B 466 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   CYS B 472 " --> pdb=" O   ALA B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 483 through 485
      No H-bonds generated for 'chain 'B' and resid 483 through 485'
    Processing helix  chain 'B' and resid 498 through 503
      removed outlier: 4.025A  pdb=" N   VAL B 503 " --> pdb=" O   LEU B 499 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 537 through 557
      removed outlier: 3.505A  pdb=" N   LEU B 543 " --> pdb=" O   SER B 539 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   ARG B 549 " --> pdb=" O   LYS B 545 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   PHE B 551 " --> pdb=" O   GLN B 547 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 585 through 589
    Processing helix  chain 'B' and resid 591 through 598
      removed outlier: 3.606A  pdb=" N   GLU B 596 " --> pdb=" O   TRP B 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 602 through 616
    Processing helix  chain 'B' and resid 705 through 712
      removed outlier: 3.738A  pdb=" N   ALA B 709 " --> pdb=" O   GLU B 705 " (cutoff:3.500A)
      removed outlier: 3.925A  pdb=" N   GLN B 712 " --> pdb=" O   THR B 708 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 713 through 718
      removed outlier: 3.566A  pdb=" N   LEU B 717 " --> pdb=" O   TYR B 713 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 27
    Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75
      removed outlier: 3.809A  pdb=" N   SER A  54 " --> pdb=" O   ASP A 105 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   ARG A 103 " --> pdb=" O   THR A  56 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   CYS A  58 " --> pdb=" O   GLY A 101 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A 150 " --> pdb=" O   ILE A 131 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 108 through 109
    Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 488
      removed outlier: 8.515A  pdb=" N   ILE A 488 " --> pdb=" O   TRP A 442 " (cutoff:3.500A)
      removed outlier: 6.977A  pdb=" N   GLU A 444 " --> pdb=" O   ILE A 488 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   LEU A 420 " --> pdb=" O   SER A 443 " (cutoff:3.500A)
      removed outlier: 7.935A  pdb=" N   TRP A 445 " --> pdb=" O   LEU A 420 " (cutoff:3.500A)
      removed outlier: 7.499A  pdb=" N   ALA A 422 " --> pdb=" O   TRP A 445 " (cutoff:3.500A)
      removed outlier: 6.460A  pdb=" N   PHE A 364 " --> pdb=" O   ILE A 421 " (cutoff:3.500A)
      removed outlier: 6.959A  pdb=" N   VAL A 289 " --> pdb=" O   GLY A 363 " (cutoff:3.500A)
      removed outlier: 8.308A  pdb=" N   ARG A 365 " --> pdb=" O   VAL A 289 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   MET A 291 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225
      removed outlier: 6.829A  pdb=" N   GLU A 224 " --> pdb=" O   ILE A 250 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 633
      removed outlier: 5.047A  pdb=" N   GLU A 660 " --> pdb=" O   LEU A 734 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   SER A 729 " --> pdb=" O   ASP A 689 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ASP A 689 " --> pdb=" O   SER A 729 " (cutoff:3.500A)
      removed outlier: 6.438A  pdb=" N   ILE A 731 " --> pdb=" O   PHE A 687 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 672 through 675
    Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 27
    Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 76
      removed outlier: 4.289A  pdb=" N   ALA B  55 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   SER B  54 " --> pdb=" O   ASP B 105 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASP B 105 " --> pdb=" O   SER B  54 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 108 through 109
    Processing sheet with id=AB2, first strand: chain 'B' and resid 177 through 180
      removed outlier: 6.287A  pdb=" N   ILE B 217 " --> pdb=" O   ILE B 290 " (cutoff:3.500A)
      removed outlier: 7.338A  pdb=" N   ASP B 292 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
      removed outlier: 7.194A  pdb=" N   LEU B 219 " --> pdb=" O   ASP B 292 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLY B 363 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU B 420 " --> pdb=" O   SER B 443 " (cutoff:3.500A)
      removed outlier: 7.958A  pdb=" N   TRP B 445 " --> pdb=" O   LEU B 420 " (cutoff:3.500A)
      removed outlier: 7.661A  pdb=" N   ALA B 422 " --> pdb=" O   TRP B 445 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   GLU B 444 " --> pdb=" O   ILE B 488 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 630 through 633
      removed outlier: 4.190A  pdb=" N   ALA B 650 " --> pdb=" O   HIS B 633 " (cutoff:3.500A)
      removed outlier: 4.938A  pdb=" N   GLU B 660 " --> pdb=" O   LEU B 734 " (cutoff:3.500A)
      removed outlier: 6.981A  pdb=" N   SER B 729 " --> pdb=" O   ASP B 689 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ASP B 689 " --> pdb=" O   SER B 729 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ILE B 731 " --> pdb=" O   PHE B 687 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 672 through 675

    305 hydrogen bonds defined for protein.
    840 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: 1.65

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3434
        1.34 -     1.46: 2499
        1.46 -     1.58: 4771
        1.58 -     1.70: 0
        1.70 -     1.82: 103
  Bond restraints: 10807
  Sorted by residual:
  bond pdb=" CB  ASN B  51 "
       pdb=" CG  ASN B  51 "
    ideal  model  delta    sigma   weight residual
    1.516  1.555 -0.039 2.50e-02 1.60e+03 2.39e+00
  bond pdb=" C   MET A 220 "
       pdb=" N   PRO A 221 "
    ideal  model  delta    sigma   weight residual
    1.334  1.361 -0.027 2.34e-02 1.83e+03 1.38e+00
  bond pdb=" CA  ASN B  51 "
       pdb=" CB  ASN B  51 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.015 1.30e-02 5.92e+03 1.37e+00
  bond pdb=" CB  ASN B  68 "
       pdb=" CG  ASN B  68 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.36e+00
  bond pdb=" C   ALA A 322 "
       pdb=" N   PRO A 323 "
    ideal  model  delta    sigma   weight residual
    1.334  1.358 -0.024 2.34e-02 1.83e+03 1.06e+00
  ... (remaining 10802 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 14367
        1.89 -     3.77: 225
        3.77 -     5.66: 31
        5.66 -     7.55: 1
        7.55 -     9.43: 3
  Bond angle restraints: 14627
  Sorted by residual:
  angle pdb=" N   GLY A 334 "
        pdb=" CA  GLY A 334 "
        pdb=" C   GLY A 334 "
      ideal   model   delta    sigma   weight residual
     113.18  121.14   -7.96 2.37e+00 1.78e-01 1.13e+01
  angle pdb=" N   ASP A 584 "
        pdb=" CA  ASP A 584 "
        pdb=" C   ASP A 584 "
      ideal   model   delta    sigma   weight residual
     110.44  106.43    4.01 1.20e+00 6.94e-01 1.12e+01
  angle pdb=" N   SER A 331 "
        pdb=" CA  SER A 331 "
        pdb=" C   SER A 331 "
      ideal   model   delta    sigma   weight residual
     114.75  110.61    4.14 1.26e+00 6.30e-01 1.08e+01
  angle pdb=" CA  ASN B  51 "
        pdb=" CB  ASN B  51 "
        pdb=" CG  ASN B  51 "
      ideal   model   delta    sigma   weight residual
     112.60  115.88   -3.28 1.00e+00 1.00e+00 1.08e+01
  angle pdb=" C   PRO A 323 "
        pdb=" N   LYS A 324 "
        pdb=" CA  LYS A 324 "
      ideal   model   delta    sigma   weight residual
     121.54  127.79   -6.25 1.91e+00 2.74e-01 1.07e+01
  ... (remaining 14622 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.44: 5283
       17.44 -    34.87: 742
       34.87 -    52.31: 240
       52.31 -    69.74: 56
       69.74 -    87.18: 21
  Dihedral angle restraints: 6342
    sinusoidal: 2590
      harmonic: 3752
  Sorted by residual:
  dihedral pdb=" CA  CYS A 333 "
           pdb=" C   CYS A 333 "
           pdb=" N   GLY A 334 "
           pdb=" CA  GLY A 334 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  dihedral pdb=" CA  LEU B 175 "
           pdb=" C   LEU B 175 "
           pdb=" N   VAL B 176 "
           pdb=" CA  VAL B 176 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.07   19.93     0      5.00e+00 4.00e-02 1.59e+01
  dihedral pdb=" CA  SER A 331 "
           pdb=" C   SER A 331 "
           pdb=" N   GLY A 332 "
           pdb=" CA  GLY A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.45  -18.55     0      5.00e+00 4.00e-02 1.38e+01
  ... (remaining 6339 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 811
       0.032 -    0.064: 465
       0.064 -    0.096: 140
       0.096 -    0.128: 70
       0.128 -    0.160: 11
  Chirality restraints: 1497
  Sorted by residual:
  chirality pdb=" CG  LEU B 321 "
            pdb=" CB  LEU B 321 "
            pdb=" CD1 LEU B 321 "
            pdb=" CD2 LEU B 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.43   -0.16 2.00e-01 2.50e+01 6.37e-01
  chirality pdb=" CA  ASN B  68 "
            pdb=" N   ASN B  68 "
            pdb=" C   ASN B  68 "
            pdb=" CB  ASN B  68 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CB  VAL B 503 "
            pdb=" CA  VAL B 503 "
            pdb=" CG1 VAL B 503 "
            pdb=" CG2 VAL B 503 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.78    0.15 2.00e-01 2.50e+01 5.70e-01
  ... (remaining 1494 not shown)

  Planarity restraints: 1916
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B  51 "    0.015 2.00e-02 2.50e+03   2.99e-02 8.93e+00
        pdb=" C   ASN B  51 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   ASN B  51 "    0.019 2.00e-02 2.50e+03
        pdb=" N   SER B  52 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 170 "   -0.029 5.00e-02 4.00e+02   4.45e-02 3.17e+00
        pdb=" N   PRO B 171 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO B 171 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 171 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 227 "    0.008 2.00e-02 2.50e+03   1.59e-02 2.51e+00
        pdb=" C   GLU A 227 "   -0.027 2.00e-02 2.50e+03
        pdb=" O   GLU A 227 "    0.010 2.00e-02 2.50e+03
        pdb=" N   LEU A 228 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1913 not shown)

  Histogram of nonbonded interaction distances:
        2.34 -     2.85: 3650
        2.85 -     3.36: 8719
        3.36 -     3.88: 16915
        3.88 -     4.39: 19969
        4.39 -     4.90: 34039
  Nonbonded interactions: 83292
  Sorted by model distance:
  nonbonded pdb=" O   ASN B  51 "
            pdb=" OD1 ASN B  51 "
     model   vdw
     2.340 3.040
  nonbonded pdb=" CG  LYS A 595 "
            pdb=" NZ  LYS A 595 "
     model   vdw
     2.465 2.816
  nonbonded pdb=" O   ASN A 678 "
            pdb=" OD1 ASN A 678 "
     model   vdw
     2.494 3.040
  nonbonded pdb=" O   ASP A 584 "
            pdb=" OD1 ASP A 584 "
     model   vdw
     2.511 3.040
  nonbonded pdb=" O   ASP B 461 "
            pdb=" OD1 ASP B 461 "
     model   vdw
     2.559 3.040
  ... (remaining 83287 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 25 through 322 or resid 334 through 738))
  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:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.500
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.570
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6812
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      :  0.004   0.039  10807  Z= 0.167
  Angle     :  0.601   9.434  14627  Z= 0.326
  Chirality :  0.046   0.160   1497
  Planarity :  0.004   0.044   1916
  Dihedral  : 18.691  87.179   3936
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.03 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 28.25 %
    Favored  : 68.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.22), residues: 1277
  helix: -0.88 (0.29), residues: 286
  sheet: -0.42 (0.33), residues: 252
  loop : -1.46 (0.21), residues: 739

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 285 
 TYR   0.012   0.002   TYR B 116 
 PHE   0.026   0.002   PHE A 603 
 TRP   0.016   0.001   TRP B 355 
 HIS   0.007   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10807)
  covalent geometry    : angle       0.60133 (14627)
  hydrogen bonds       : bond        0.25986 (  305)
  hydrogen bonds       : angle       8.99188 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 165
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A   73 GLU cc_start: 0.6918 (tp30) cc_final: 0.6561 (tt0)
REVERT: A   96 LYS cc_start: 0.6879 (OUTLIER) cc_final: 0.6651 (tppt)
REVERT: A  119 SER cc_start: 0.8200 (m) cc_final: 0.7823 (t)
REVERT: A  187 ARG cc_start: 0.7985 (tpt90) cc_final: 0.7772 (tpm170)
REVERT: A  192 LYS cc_start: 0.7800 (mttt) cc_final: 0.7552 (mmtp)
REVERT: A  194 GLU cc_start: 0.7734 (tt0) cc_final: 0.7330 (tt0)
REVERT: A  295 LEU cc_start: 0.6561 (OUTLIER) cc_final: 0.5853 (mp)
REVERT: A  361 VAL cc_start: 0.7090 (OUTLIER) cc_final: 0.6657 (t)
REVERT: A  408 MET cc_start: 0.2641 (ttp) cc_final: 0.0681 (mtp)
REVERT: A  469 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7067 (mm-30)
REVERT: A  491 ILE cc_start: 0.7110 (OUTLIER) cc_final: 0.6794 (mt)
REVERT: A  552 PHE cc_start: 0.7175 (t80) cc_final: 0.6640 (t80)
REVERT: A  594 LYS cc_start: 0.7937 (mmtp) cc_final: 0.7407 (mtmt)
REVERT: A  647 ARG cc_start: 0.7267 (OUTLIER) cc_final: 0.6892 (mmt90)
REVERT: A  685 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7874 (mm-30)
REVERT: B  166 MET cc_start: 0.6952 (ptm) cc_final: 0.6630 (mtt)
REVERT: B  200 GLN cc_start: 0.7083 (mt0) cc_final: 0.6387 (mm-40)
REVERT: B  291 MET cc_start: 0.8399 (mtp) cc_final: 0.7931 (mtp)
REVERT: B  320 MET cc_start: 0.4737 (pp-130) cc_final: 0.3503 (mtt)
REVERT: B  587 MET cc_start: 0.7492 (mtm) cc_final: 0.7245 (ttp)
REVERT: B  630 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8149 (tt)
REVERT: B  638 GLU cc_start: 0.7441 (mt-10) cc_final: 0.7006 (mp0)
REVERT: B  683 ARG cc_start: 0.7067 (ttm170) cc_final: 0.5862 (tpm170)
  outliers start: 37
  outliers final: 14
  residues processed: 195
  average time/residue: 0.4911
  time to fit residues: 103.9244
Evaluate side-chains
  143 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   96 LYS
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  333 CYS
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  469 GLU
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  685 GLU
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  609 LEU
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  721 VAL
Chi-restraints excluded: chain B residue  735 SER
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.0070
   chunk 124 optimal weight:    0.4980
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    0.6980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    0.0000
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    5.9990
   overall best weight:    0.3802

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

Flipped N/Q/H residues before XYZ refinement:
A  51 ASN
A 188 HIS
A 715 HIS
B  44 ASN
B 341 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.204503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.175385 restraints weight = 11845.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.4135 rms_B_bonded: 1.95
r_work: 0.4038 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3926 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7017
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10807  Z= 0.103
  Angle     :  0.521   7.978  14627  Z= 0.277
  Chirality :  0.043   0.144   1497
  Planarity :  0.004   0.036   1916
  Dihedral  :  7.055  83.380   1460
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.03 %
    Favored  : 93.89 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 25.72 %
    Favored  : 69.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.28 (0.22), residues: 1277
  helix: -0.03 (0.29), residues: 312
  sheet: -0.37 (0.32), residues: 254
  loop : -1.42 (0.21), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 285 
 TYR   0.011   0.001   TYR B 116 
 PHE   0.013   0.001   PHE B 195 
 TRP   0.006   0.001   TRP A 485 
 HIS   0.003   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 (10807)
  covalent geometry    : angle       0.52094 (14627)
  hydrogen bonds       : bond        0.04554 (  305)
  hydrogen bonds       : angle       6.01877 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 133
  time to evaluate  : 0.294 
Fit side-chains
REVERT: A   67 GLN cc_start: 0.6975 (mm-40) cc_final: 0.6292 (pt0)
REVERT: A   77 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.7110 (p0)
REVERT: A  194 GLU cc_start: 0.7552 (tt0) cc_final: 0.7342 (tt0)
REVERT: A  284 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6820 (mtpt)
REVERT: A  295 LEU cc_start: 0.6742 (OUTLIER) cc_final: 0.5977 (mp)
REVERT: A  349 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6775 (mp)
REVERT: A  408 MET cc_start: 0.2306 (ttp) cc_final: 0.0394 (mtp)
REVERT: A  552 PHE cc_start: 0.7233 (OUTLIER) cc_final: 0.6783 (t80)
REVERT: A  594 LYS cc_start: 0.7959 (mmtp) cc_final: 0.7670 (mtmt)
REVERT: A  613 ARG cc_start: 0.7986 (OUTLIER) cc_final: 0.5385 (ttt90)
REVERT: A  618 SER cc_start: 0.7206 (OUTLIER) cc_final: 0.6890 (p)
REVERT: A  647 ARG cc_start: 0.7144 (OUTLIER) cc_final: 0.5423 (mmt90)
REVERT: B   62 LEU cc_start: 0.7894 (mt) cc_final: 0.7672 (mt)
REVERT: B   98 MET cc_start: 0.6221 (mmt) cc_final: 0.5939 (mmt)
REVERT: B  134 ASP cc_start: 0.7162 (OUTLIER) cc_final: 0.6400 (t0)
REVERT: B  166 MET cc_start: 0.7134 (ptm) cc_final: 0.6861 (mtt)
REVERT: B  200 GLN cc_start: 0.7167 (mt0) cc_final: 0.6568 (mm-40)
REVERT: B  256 MET cc_start: 0.6638 (OUTLIER) cc_final: 0.5287 (tpt)
REVERT: B  320 MET cc_start: 0.4877 (pp-130) cc_final: 0.3737 (mtt)
REVERT: B  353 ARG cc_start: 0.8098 (mtm-85) cc_final: 0.7890 (mtm180)
REVERT: B  444 GLU cc_start: 0.6898 (OUTLIER) cc_final: 0.6646 (pp20)
REVERT: B  660 GLU cc_start: 0.7641 (OUTLIER) cc_final: 0.7424 (tt0)
  outliers start: 58
  outliers final: 16
  residues processed: 174
  average time/residue: 0.5671
  time to fit residues: 106.1077
Evaluate side-chains
  141 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 113
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   74 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  161 ASP
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  284 LYS
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  552 PHE
Chi-restraints excluded: chain A residue  613 ARG
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  444 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  660 GLU
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 68 optimal weight:    8.9990
   chunk 30 optimal weight:    5.9990
   chunk 106 optimal weight:    0.9990
   chunk 22 optimal weight:    4.9990
   chunk 89 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 123 optimal weight:    4.9990
   chunk 75 optimal weight:    4.9990
   chunk 99 optimal weight:    5.9990
   chunk 113 optimal weight:    7.9990
   chunk 126 optimal weight:    3.9990
   overall best weight:    3.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 712 GLN
B  44 ASN
** B  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 GLN
B 360 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.194041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.164135 restraints weight = 12026.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.4010 rms_B_bonded: 1.97
r_work: 0.3912 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.3801 rms_B_bonded: 4.10 restraints_weight: 0.2500
r_work (final): 0.3801
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.2311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.106  10807  Z= 0.366
  Angle     :  0.890  11.656  14627  Z= 0.477
  Chirality :  0.058   0.251   1497
  Planarity :  0.007   0.060   1916
  Dihedral  :  7.093  78.669   1437
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.01 %
    Favored  : 90.92 %
  Rotamer:
    Outliers :  7.06 %
    Allowed  : 22.49 %
    Favored  : 70.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.08 (0.21), residues: 1277
  helix: -0.95 (0.27), residues: 310
  sheet: -0.45 (0.32), residues: 230
  loop : -1.94 (0.20), residues: 737

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 544 
 TYR   0.024   0.003   TYR A  48 
 PHE   0.045   0.004   PHE B 337 
 TRP   0.021   0.003   TRP B 146 
 HIS   0.012   0.002   HIS B 360 

Details of bonding type rmsd
  covalent geometry    : bond        0.00868 (10807)
  covalent geometry    : angle       0.89001 (14627)
  hydrogen bonds       : bond        0.07734 (  305)
  hydrogen bonds       : angle       6.71788 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 81
    poor density    : 121
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
REVERT: A   67 GLN cc_start: 0.6804 (mm-40) cc_final: 0.6599 (mm110)
REVERT: A   77 ASP cc_start: 0.7455 (OUTLIER) cc_final: 0.7048 (t70)
REVERT: A  107 LYS cc_start: 0.4562 (OUTLIER) cc_final: 0.3789 (mppt)
REVERT: A  173 LYS cc_start: 0.7287 (pttp) cc_final: 0.6889 (pttp)
REVERT: A  194 GLU cc_start: 0.7618 (tt0) cc_final: 0.7319 (tt0)
REVERT: A  295 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6462 (mp)
REVERT: A  361 VAL cc_start: 0.7225 (OUTLIER) cc_final: 0.6579 (p)
REVERT: A  365 ARG cc_start: 0.6752 (ttp80) cc_final: 0.5735 (ttt90)
REVERT: A  491 ILE cc_start: 0.7520 (OUTLIER) cc_final: 0.7290 (mt)
REVERT: A  552 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7123 (t80)
REVERT: A  594 LYS cc_start: 0.8083 (mmtp) cc_final: 0.7719 (mtmt)
REVERT: A  613 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.4499 (ttt90)
REVERT: A  618 SER cc_start: 0.7297 (OUTLIER) cc_final: 0.6911 (p)
REVERT: B   96 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7472 (mtpt)
REVERT: B  134 ASP cc_start: 0.7527 (OUTLIER) cc_final: 0.6651 (t0)
REVERT: B  200 GLN cc_start: 0.7512 (mt0) cc_final: 0.6884 (mm-40)
REVERT: B  273 ASN cc_start: 0.6461 (OUTLIER) cc_final: 0.6178 (m-40)
REVERT: B  291 MET cc_start: 0.8556 (mtp) cc_final: 0.8064 (mtp)
REVERT: B  295 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7577 (pp)
REVERT: B  320 MET cc_start: 0.5025 (pp-130) cc_final: 0.3594 (mtt)
REVERT: B  337 PHE cc_start: 0.7605 (OUTLIER) cc_final: 0.6314 (m-10)
REVERT: B  521 GLU cc_start: 0.5704 (OUTLIER) cc_final: 0.5377 (mp0)
  outliers start: 81
  outliers final: 34
  residues processed: 187
  average time/residue: 0.6109
  time to fit residues: 122.6280
Evaluate side-chains
  157 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 109
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  261 SER
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  278 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  491 ILE
Chi-restraints excluded: chain A residue  508 LYS
Chi-restraints excluded: chain A residue  552 PHE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  581 TYR
Chi-restraints excluded: chain A residue  613 ARG
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  726 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   96 LYS
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  273 ASN
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  411 ASN
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  443 SER
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  521 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  660 GLU
Chi-restraints excluded: chain B residue  710 MET
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 96 optimal weight:    0.7980
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 66 optimal weight:    0.0170
   chunk 65 optimal weight:    4.9990
   chunk 5 optimal weight:    0.4980
   chunk 18 optimal weight:    0.7980
   chunk 93 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.6218

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

Flipped N/Q/H residues before XYZ refinement:
A 455 GLN
** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 ASN
B  44 ASN
B 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.200479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.171479 restraints weight = 12070.135|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 1.97
r_work: 0.3995 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3885 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7083
moved from start:          0.2378

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10807  Z= 0.112
  Angle     :  0.560   8.094  14627  Z= 0.300
  Chirality :  0.044   0.141   1497
  Planarity :  0.004   0.047   1916
  Dihedral  :  6.008  61.524   1431
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.79 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 25.37 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.57 (0.22), residues: 1277
  helix: -0.13 (0.29), residues: 311
  sheet: -0.56 (0.30), residues: 260
  loop : -1.69 (0.21), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.017   0.001   TYR B 589 
 PHE   0.022   0.002   PHE A 337 
 TRP   0.014   0.001   TRP A 442 
 HIS   0.004   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10807)
  covalent geometry    : angle       0.55982 (14627)
  hydrogen bonds       : bond        0.04083 (  305)
  hydrogen bonds       : angle       5.70179 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 115
  time to evaluate  : 0.403 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7563 (OUTLIER) cc_final: 0.7102 (t70)
REVERT: A  169 LYS cc_start: 0.6602 (mtmt) cc_final: 0.6288 (mtpp)
REVERT: A  194 GLU cc_start: 0.7630 (tt0) cc_final: 0.7321 (tt0)
REVERT: A  295 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6080 (mp)
REVERT: A  469 GLU cc_start: 0.7658 (OUTLIER) cc_final: 0.7296 (mm-30)
REVERT: A  594 LYS cc_start: 0.7970 (mmtp) cc_final: 0.7603 (mtmt)
REVERT: A  618 SER cc_start: 0.6954 (OUTLIER) cc_final: 0.6583 (p)
REVERT: A  647 ARG cc_start: 0.7406 (OUTLIER) cc_final: 0.6860 (mmt90)
REVERT: B  134 ASP cc_start: 0.7423 (OUTLIER) cc_final: 0.6580 (t0)
REVERT: B  200 GLN cc_start: 0.7223 (mt0) cc_final: 0.6590 (mm-40)
REVERT: B  256 MET cc_start: 0.6740 (OUTLIER) cc_final: 0.5345 (tpt)
REVERT: B  320 MET cc_start: 0.5089 (pp-130) cc_final: 0.3718 (mtt)
REVERT: B  337 PHE cc_start: 0.7402 (OUTLIER) cc_final: 0.6206 (m-10)
REVERT: B  350 ASP cc_start: 0.7809 (OUTLIER) cc_final: 0.7550 (t70)
REVERT: B  683 ARG cc_start: 0.7326 (ptm160) cc_final: 0.6135 (tpm170)
  outliers start: 52
  outliers final: 23
  residues processed: 154
  average time/residue: 0.5853
  time to fit residues: 97.3509
Evaluate side-chains
  145 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 113
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  469 GLU
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  694 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  545 LYS
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 85 optimal weight:    0.0970
   chunk 4 optimal weight:    4.9990
   chunk 121 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9980
   chunk 54 optimal weight:    0.0010
   chunk 18 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 ASN
A 599 HIS
B  44 ASN
B 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.199303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.170170 restraints weight = 12012.549|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 1.96
r_work: 0.3978 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3870 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7111
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10807  Z= 0.135
  Angle     :  0.578   8.499  14627  Z= 0.308
  Chirality :  0.045   0.150   1497
  Planarity :  0.004   0.046   1916
  Dihedral  :  5.850  57.923   1431
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.36 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  5.23 %
    Allowed  : 24.50 %
    Favored  : 70.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.45 (0.22), residues: 1277
  helix:  0.03 (0.29), residues: 312
  sheet: -0.48 (0.31), residues: 257
  loop : -1.64 (0.21), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.014   0.002   TYR B 589 
 PHE   0.029   0.002   PHE A 185 
 TRP   0.012   0.001   TRP A 442 
 HIS   0.004   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10807)
  covalent geometry    : angle       0.57755 (14627)
  hydrogen bonds       : bond        0.04442 (  305)
  hydrogen bonds       : angle       5.65244 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  177 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 117
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7575 (OUTLIER) cc_final: 0.7031 (t70)
REVERT: A  169 LYS cc_start: 0.6530 (mtmt) cc_final: 0.6229 (mtpp)
REVERT: A  194 GLU cc_start: 0.7597 (tt0) cc_final: 0.7289 (tt0)
REVERT: A  295 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6064 (mp)
REVERT: A  594 LYS cc_start: 0.7974 (mmtp) cc_final: 0.7651 (mtmt)
REVERT: A  618 SER cc_start: 0.7017 (OUTLIER) cc_final: 0.6653 (p)
REVERT: A  647 ARG cc_start: 0.7503 (OUTLIER) cc_final: 0.6061 (mmt90)
REVERT: B  134 ASP cc_start: 0.7370 (OUTLIER) cc_final: 0.6625 (t0)
REVERT: B  157 GLU cc_start: 0.5103 (OUTLIER) cc_final: 0.3801 (mp0)
REVERT: B  169 LYS cc_start: 0.7307 (OUTLIER) cc_final: 0.6884 (mtpt)
REVERT: B  200 GLN cc_start: 0.7218 (mt0) cc_final: 0.6570 (mm-40)
REVERT: B  256 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.5254 (tpt)
REVERT: B  273 ASN cc_start: 0.6343 (OUTLIER) cc_final: 0.6136 (t0)
REVERT: B  320 MET cc_start: 0.5096 (pp-130) cc_final: 0.3714 (mtt)
REVERT: B  337 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6525 (m-10)
REVERT: B  350 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7649 (t70)
REVERT: B  683 ARG cc_start: 0.7365 (ptm160) cc_final: 0.7071 (ttm170)
  outliers start: 60
  outliers final: 28
  residues processed: 160
  average time/residue: 0.5741
  time to fit residues: 99.0906
Evaluate side-chains
  153 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 114
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 ASP
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  694 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  273 ASN
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 123 optimal weight:    5.9990
   chunk 100 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 127 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 106 optimal weight:    4.9990
   chunk 124 optimal weight:    1.9990
   chunk 92 optimal weight:    0.0030
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.9396

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

Flipped N/Q/H residues before XYZ refinement:
** A 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 509 ASN
A 599 HIS
B  44 ASN
B 346 GLN
B 518 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.199326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.169504 restraints weight = 12031.548|
|-----------------------------------------------------------------------------|
r_work (start): 0.4067 rms_B_bonded: 2.00
r_work: 0.3972 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3861 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7084
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10807  Z= 0.128
  Angle     :  0.561   8.155  14627  Z= 0.300
  Chirality :  0.045   0.145   1497
  Planarity :  0.004   0.050   1916
  Dihedral  :  5.767  59.056   1431
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.50 %
    Favored  : 93.42 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 23.19 %
    Favored  : 70.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.36 (0.22), residues: 1277
  helix:  0.16 (0.30), residues: 314
  sheet: -0.51 (0.31), residues: 260
  loop : -1.57 (0.22), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  39 
 TYR   0.014   0.002   TYR B 589 
 PHE   0.016   0.002   PHE B 337 
 TRP   0.011   0.001   TRP B 355 
 HIS   0.003   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10807)
  covalent geometry    : angle       0.56141 (14627)
  hydrogen bonds       : bond        0.04205 (  305)
  hydrogen bonds       : angle       5.52595 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 117
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7581 (OUTLIER) cc_final: 0.6983 (t70)
REVERT: A  169 LYS cc_start: 0.6479 (mtmt) cc_final: 0.6229 (mtpp)
REVERT: A  194 GLU cc_start: 0.7503 (tt0) cc_final: 0.7233 (tt0)
REVERT: A  295 LEU cc_start: 0.6815 (OUTLIER) cc_final: 0.6109 (mp)
REVERT: A  594 LYS cc_start: 0.7901 (mmtp) cc_final: 0.7520 (mtmt)
REVERT: A  618 SER cc_start: 0.6907 (OUTLIER) cc_final: 0.6531 (p)
REVERT: A  647 ARG cc_start: 0.7492 (OUTLIER) cc_final: 0.6202 (mmt90)
REVERT: B  134 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.6712 (t0)
REVERT: B  157 GLU cc_start: 0.4973 (OUTLIER) cc_final: 0.3638 (mp0)
REVERT: B  169 LYS cc_start: 0.7326 (OUTLIER) cc_final: 0.6921 (mtpt)
REVERT: B  200 GLN cc_start: 0.7189 (mt0) cc_final: 0.6482 (mm-40)
REVERT: B  230 TYR cc_start: 0.4218 (OUTLIER) cc_final: 0.3334 (m-80)
REVERT: B  256 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.5239 (tpt)
REVERT: B  320 MET cc_start: 0.5058 (pp-130) cc_final: 0.3673 (mtt)
REVERT: B  337 PHE cc_start: 0.7312 (OUTLIER) cc_final: 0.6500 (m-10)
REVERT: B  350 ASP cc_start: 0.7874 (OUTLIER) cc_final: 0.7642 (t70)
REVERT: B  516 GLU cc_start: 0.5944 (OUTLIER) cc_final: 0.5514 (tm-30)
  outliers start: 69
  outliers final: 31
  residues processed: 169
  average time/residue: 0.5677
  time to fit residues: 103.7669
Evaluate side-chains
  156 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 113
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  726 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  149 MET
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  406 ILE
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  516 GLU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 57 optimal weight:    0.9980
   chunk 126 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   chunk 110 optimal weight:    3.9990
   chunk 127 optimal weight:    2.9990
   chunk 81 optimal weight:    3.9990
   chunk 118 optimal weight:    5.9990
   chunk 55 optimal weight:    7.9990
   chunk 84 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A 509 ASN
A 599 HIS
B  44 ASN
B 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.196636 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.166666 restraints weight = 11966.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 1.98
r_work: 0.3941 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3829 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7135
moved from start:          0.2691

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  10807  Z= 0.179
  Angle     :  0.637   9.123  14627  Z= 0.341
  Chirality :  0.047   0.164   1497
  Planarity :  0.005   0.050   1916
  Dihedral  :  5.928  57.963   1431
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.75 %
    Favored  : 92.17 %
  Rotamer:
    Outliers :  6.02 %
    Allowed  : 23.80 %
    Favored  : 70.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.22), residues: 1277
  helix: -0.03 (0.29), residues: 312
  sheet: -0.52 (0.31), residues: 256
  loop : -1.67 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 454 
 TYR   0.016   0.002   TYR A 696 
 PHE   0.031   0.002   PHE A 185 
 TRP   0.012   0.002   TRP B 355 
 HIS   0.005   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 (10807)
  covalent geometry    : angle       0.63736 (14627)
  hydrogen bonds       : bond        0.05156 (  305)
  hydrogen bonds       : angle       5.78743 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 111
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A   69 LYS cc_start: 0.5339 (OUTLIER) cc_final: 0.5062 (tmtt)
REVERT: A   77 ASP cc_start: 0.7411 (OUTLIER) cc_final: 0.6653 (t70)
REVERT: A  107 LYS cc_start: 0.4205 (OUTLIER) cc_final: 0.3562 (mppt)
REVERT: A  169 LYS cc_start: 0.6575 (mtmt) cc_final: 0.6312 (mtpp)
REVERT: A  194 GLU cc_start: 0.7531 (tt0) cc_final: 0.7240 (tt0)
REVERT: A  295 LEU cc_start: 0.6788 (OUTLIER) cc_final: 0.6072 (mp)
REVERT: A  361 VAL cc_start: 0.7210 (OUTLIER) cc_final: 0.6732 (t)
REVERT: A  594 LYS cc_start: 0.7913 (mmtp) cc_final: 0.7535 (mtmt)
REVERT: A  618 SER cc_start: 0.6974 (OUTLIER) cc_final: 0.6602 (p)
REVERT: A  647 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.6208 (mmt90)
REVERT: B   96 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7224 (mmpt)
REVERT: B  134 ASP cc_start: 0.7402 (OUTLIER) cc_final: 0.6662 (t0)
REVERT: B  157 GLU cc_start: 0.4966 (OUTLIER) cc_final: 0.3638 (mp0)
REVERT: B  169 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6918 (mtpt)
REVERT: B  200 GLN cc_start: 0.7377 (mt0) cc_final: 0.6624 (mm-40)
REVERT: B  256 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.5117 (tpt)
REVERT: B  273 ASN cc_start: 0.6275 (OUTLIER) cc_final: 0.6044 (t0)
REVERT: B  320 MET cc_start: 0.5023 (pp-130) cc_final: 0.3554 (mtt)
REVERT: B  337 PHE cc_start: 0.7464 (OUTLIER) cc_final: 0.6464 (m-10)
REVERT: B  350 ASP cc_start: 0.7912 (OUTLIER) cc_final: 0.7688 (t70)
REVERT: B  630 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8231 (tt)
REVERT: B  683 ARG cc_start: 0.7277 (ptm160) cc_final: 0.7060 (ttp-170)
  outliers start: 69
  outliers final: 32
  residues processed: 167
  average time/residue: 0.5828
  time to fit residues: 105.0109
Evaluate side-chains
  160 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 112
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   69 LYS
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  585 ASN
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  694 SER
Chi-restraints excluded: chain A residue  726 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   96 LYS
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  174 ASP
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  273 ASN
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  661 ILE
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 109 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 32 optimal weight:    2.9990
   chunk 65 optimal weight:    6.9990
   chunk 66 optimal weight:    0.6980
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 120 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
A 509 ASN
A 599 HIS
B  44 ASN
B 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.195348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.165634 restraints weight = 11841.796|
|-----------------------------------------------------------------------------|
r_work (start): 0.4023 rms_B_bonded: 1.95
r_work: 0.3927 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3818 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.2844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064  10807  Z= 0.208
  Angle     :  0.680   9.443  14627  Z= 0.365
  Chirality :  0.049   0.182   1497
  Planarity :  0.005   0.051   1916
  Dihedral  :  5.921  56.853   1429
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.07 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  5.58 %
    Allowed  : 24.32 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.69 (0.22), residues: 1277
  helix: -0.23 (0.29), residues: 311
  sheet: -0.50 (0.31), residues: 251
  loop : -1.81 (0.21), residues: 715

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 454 
 TYR   0.020   0.002   TYR B 589 
 PHE   0.028   0.002   PHE B 337 
 TRP   0.016   0.002   TRP B 355 
 HIS   0.006   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (10807)
  covalent geometry    : angle       0.67995 (14627)
  hydrogen bonds       : bond        0.05543 (  305)
  hydrogen bonds       : angle       5.93937 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 116
  time to evaluate  : 0.430 
Fit side-chains
REVERT: A   77 ASP cc_start: 0.7297 (OUTLIER) cc_final: 0.6397 (t70)
REVERT: A   96 LYS cc_start: 0.7373 (ttpt) cc_final: 0.7026 (tptt)
REVERT: A  107 LYS cc_start: 0.4321 (OUTLIER) cc_final: 0.3593 (mppt)
REVERT: A  169 LYS cc_start: 0.6613 (mtmt) cc_final: 0.6122 (ttmm)
REVERT: A  185 PHE cc_start: 0.7474 (t80) cc_final: 0.7227 (t80)
REVERT: A  194 GLU cc_start: 0.7452 (tt0) cc_final: 0.7188 (tt0)
REVERT: A  295 LEU cc_start: 0.6963 (OUTLIER) cc_final: 0.6183 (mp)
REVERT: A  350 ASP cc_start: 0.7191 (m-30) cc_final: 0.6983 (m-30)
REVERT: A  361 VAL cc_start: 0.7268 (OUTLIER) cc_final: 0.6701 (p)
REVERT: A  594 LYS cc_start: 0.7960 (mmtp) cc_final: 0.7591 (mtmt)
REVERT: A  613 ARG cc_start: 0.7984 (OUTLIER) cc_final: 0.4743 (ttt90)
REVERT: A  618 SER cc_start: 0.6956 (OUTLIER) cc_final: 0.6566 (p)
REVERT: A  647 ARG cc_start: 0.7584 (OUTLIER) cc_final: 0.6231 (mmt90)
REVERT: B   96 LYS cc_start: 0.8147 (OUTLIER) cc_final: 0.7140 (mmpt)
REVERT: B   98 MET cc_start: 0.6141 (mmt) cc_final: 0.5833 (mmp)
REVERT: B  134 ASP cc_start: 0.7508 (OUTLIER) cc_final: 0.6704 (t0)
REVERT: B  157 GLU cc_start: 0.4944 (OUTLIER) cc_final: 0.3658 (mp0)
REVERT: B  169 LYS cc_start: 0.7379 (OUTLIER) cc_final: 0.6915 (mtpt)
REVERT: B  200 GLN cc_start: 0.7433 (mt0) cc_final: 0.6677 (mm-40)
REVERT: B  230 TYR cc_start: 0.5177 (OUTLIER) cc_final: 0.4545 (m-80)
REVERT: B  256 MET cc_start: 0.6822 (OUTLIER) cc_final: 0.5197 (tpt)
REVERT: B  320 MET cc_start: 0.5029 (pp-130) cc_final: 0.3484 (mtt)
REVERT: B  337 PHE cc_start: 0.7587 (OUTLIER) cc_final: 0.6389 (m-10)
REVERT: B  350 ASP cc_start: 0.7919 (OUTLIER) cc_final: 0.7678 (t70)
REVERT: B  448 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7281 (ttmm)
REVERT: B  630 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8297 (tt)
REVERT: B  683 ARG cc_start: 0.7344 (ptm160) cc_final: 0.6261 (tpm-80)
  outliers start: 64
  outliers final: 31
  residues processed: 168
  average time/residue: 0.5765
  time to fit residues: 104.5484
Evaluate side-chains
  162 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 114
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   77 ASP
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  361 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  613 ARG
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  694 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   96 LYS
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  169 LYS
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  350 ASP
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  414 ILE
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  448 LYS
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  630 LEU
Chi-restraints excluded: chain B residue  642 TRP
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  647 ARG
Chi-restraints excluded: chain B residue  661 ILE
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 63 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 74 optimal weight:    8.9990
   chunk 84 optimal weight:    1.9990
   chunk 3 optimal weight:   10.0000
   chunk 92 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 70 optimal weight:    0.0570
   chunk 80 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   overall best weight:    0.8500

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

Flipped N/Q/H residues before XYZ refinement:
A 509 ASN
A 599 HIS
B  44 ASN
** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.198558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.169024 restraints weight = 11948.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.4061 rms_B_bonded: 1.98
r_work: 0.3967 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3857 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.2861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10807  Z= 0.125
  Angle     :  0.569   8.340  14627  Z= 0.303
  Chirality :  0.045   0.195   1497
  Planarity :  0.004   0.048   1916
  Dihedral  :  5.522  58.786   1429
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.73 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 25.63 %
    Favored  : 70.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.46 (0.22), residues: 1277
  helix:  0.14 (0.30), residues: 312
  sheet: -0.51 (0.31), residues: 256
  loop : -1.70 (0.21), residues: 709

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  39 
 TYR   0.016   0.001   TYR B 589 
 PHE   0.014   0.002   PHE B 337 
 TRP   0.011   0.001   TRP B 355 
 HIS   0.004   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (10807)
  covalent geometry    : angle       0.56855 (14627)
  hydrogen bonds       : bond        0.04136 (  305)
  hydrogen bonds       : angle       5.54019 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 114
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   69 LYS cc_start: 0.5283 (OUTLIER) cc_final: 0.5028 (tmtt)
REVERT: A   77 ASP cc_start: 0.7202 (m-30) cc_final: 0.6392 (t70)
REVERT: A   96 LYS cc_start: 0.7348 (ttpt) cc_final: 0.7007 (tptt)
REVERT: A  107 LYS cc_start: 0.4051 (OUTLIER) cc_final: 0.3495 (mppt)
REVERT: A  115 TYR cc_start: 0.7459 (m-80) cc_final: 0.6372 (m-80)
REVERT: A  169 LYS cc_start: 0.6439 (mtmt) cc_final: 0.6024 (ttmm)
REVERT: A  194 GLU cc_start: 0.7477 (tt0) cc_final: 0.7202 (tt0)
REVERT: A  295 LEU cc_start: 0.6688 (OUTLIER) cc_final: 0.6001 (mp)
REVERT: A  594 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7536 (mtmt)
REVERT: A  618 SER cc_start: 0.6941 (OUTLIER) cc_final: 0.6600 (p)
REVERT: A  647 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.5729 (mmt90)
REVERT: B   98 MET cc_start: 0.6044 (mmt) cc_final: 0.5772 (mmp)
REVERT: B  134 ASP cc_start: 0.7516 (OUTLIER) cc_final: 0.6743 (t0)
REVERT: B  157 GLU cc_start: 0.4902 (OUTLIER) cc_final: 0.3638 (mp0)
REVERT: B  200 GLN cc_start: 0.7273 (mt0) cc_final: 0.6541 (mm-40)
REVERT: B  230 TYR cc_start: 0.4691 (OUTLIER) cc_final: 0.4022 (m-80)
REVERT: B  256 MET cc_start: 0.6708 (OUTLIER) cc_final: 0.5281 (tpt)
REVERT: B  320 MET cc_start: 0.5067 (pp-130) cc_final: 0.3626 (mtt)
REVERT: B  337 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6285 (m-10)
  outliers start: 49
  outliers final: 25
  residues processed: 155
  average time/residue: 0.6013
  time to fit residues: 100.1905
Evaluate side-chains
  149 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 114
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   69 LYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  694 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 91 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 89 optimal weight:    0.8980
   chunk 95 optimal weight:    5.9990
   chunk 112 optimal weight:    0.8980
   chunk 122 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 69 optimal weight:    2.9990
   chunk 65 optimal weight:    7.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 509 ASN
A 599 HIS
B  44 ASN
** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.196910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.167258 restraints weight = 11919.631|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 1.98
r_work: 0.3946 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3836 rms_B_bonded: 4.24 restraints_weight: 0.2500
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  10807  Z= 0.162
  Angle     :  0.622   9.109  14627  Z= 0.333
  Chirality :  0.047   0.210   1497
  Planarity :  0.005   0.050   1916
  Dihedral  :  5.620  57.803   1427
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.67 %
    Favored  : 92.25 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 26.24 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.54 (0.22), residues: 1277
  helix:  0.04 (0.29), residues: 311
  sheet: -0.55 (0.31), residues: 256
  loop : -1.73 (0.21), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 454 
 TYR   0.015   0.002   TYR B 589 
 PHE   0.032   0.002   PHE A 185 
 TRP   0.014   0.001   TRP B 355 
 HIS   0.004   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 (10807)
  covalent geometry    : angle       0.62241 (14627)
  hydrogen bonds       : bond        0.04862 (  305)
  hydrogen bonds       : angle       5.70264 (  840)

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

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

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2554 Ramachandran restraints generated.
    1277 Oldfield, 0 Emsley, 1277 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 115
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A   69 LYS cc_start: 0.5409 (OUTLIER) cc_final: 0.5122 (tmtt)
REVERT: A   77 ASP cc_start: 0.7095 (m-30) cc_final: 0.6426 (t70)
REVERT: A   96 LYS cc_start: 0.7338 (ttpt) cc_final: 0.7017 (tptt)
REVERT: A  107 LYS cc_start: 0.4280 (OUTLIER) cc_final: 0.3565 (mppt)
REVERT: A  169 LYS cc_start: 0.6523 (mtmt) cc_final: 0.6071 (ttmm)
REVERT: A  295 LEU cc_start: 0.6795 (OUTLIER) cc_final: 0.6108 (mp)
REVERT: A  594 LYS cc_start: 0.7918 (mmtp) cc_final: 0.7600 (mtmt)
REVERT: A  618 SER cc_start: 0.6926 (OUTLIER) cc_final: 0.6572 (p)
REVERT: A  647 ARG cc_start: 0.7512 (OUTLIER) cc_final: 0.6226 (mmt90)
REVERT: B   96 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7109 (mmpt)
REVERT: B  134 ASP cc_start: 0.7436 (OUTLIER) cc_final: 0.6698 (t0)
REVERT: B  157 GLU cc_start: 0.4965 (OUTLIER) cc_final: 0.3599 (mp0)
REVERT: B  200 GLN cc_start: 0.7386 (mt0) cc_final: 0.6633 (mm-40)
REVERT: B  230 TYR cc_start: 0.4911 (OUTLIER) cc_final: 0.4159 (m-80)
REVERT: B  256 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.5131 (tpt)
REVERT: B  320 MET cc_start: 0.5040 (pp-130) cc_final: 0.3564 (mtt)
REVERT: B  337 PHE cc_start: 0.7414 (OUTLIER) cc_final: 0.6123 (m-10)
REVERT: B  683 ARG cc_start: 0.7205 (ttm170) cc_final: 0.6037 (tpm170)
  outliers start: 44
  outliers final: 28
  residues processed: 152
  average time/residue: 0.5836
  time to fit residues: 95.7413
Evaluate side-chains
  153 residues out of total 1147 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 114
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   56 THR
Chi-restraints excluded: chain A residue   57 ILE
Chi-restraints excluded: chain A residue   60 ILE
Chi-restraints excluded: chain A residue   69 LYS
Chi-restraints excluded: chain A residue   89 VAL
Chi-restraints excluded: chain A residue  107 LYS
Chi-restraints excluded: chain A residue  119 SER
Chi-restraints excluded: chain A residue  151 CYS
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  272 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  317 VAL
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  356 VAL
Chi-restraints excluded: chain A residue  443 SER
Chi-restraints excluded: chain A residue  545 LYS
Chi-restraints excluded: chain A residue  618 SER
Chi-restraints excluded: chain A residue  647 ARG
Chi-restraints excluded: chain A residue  694 SER
Chi-restraints excluded: chain B residue   49 SER
Chi-restraints excluded: chain B residue   56 THR
Chi-restraints excluded: chain B residue   60 ILE
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue   89 VAL
Chi-restraints excluded: chain B residue   96 LYS
Chi-restraints excluded: chain B residue  134 ASP
Chi-restraints excluded: chain B residue  157 GLU
Chi-restraints excluded: chain B residue  230 TYR
Chi-restraints excluded: chain B residue  256 MET
Chi-restraints excluded: chain B residue  294 VAL
Chi-restraints excluded: chain B residue  295 LEU
Chi-restraints excluded: chain B residue  337 PHE
Chi-restraints excluded: chain B residue  361 VAL
Chi-restraints excluded: chain B residue  445 TRP
Chi-restraints excluded: chain B residue  464 SER
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  545 LYS
Chi-restraints excluded: chain B residue  646 SER
Chi-restraints excluded: chain B residue  721 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 81 optimal weight:    2.9990
   chunk 113 optimal weight:    4.9990
   chunk 84 optimal weight:    2.9990
   chunk 15 optimal weight:    0.4980
   chunk 20 optimal weight:    2.9990
   chunk 105 optimal weight:    0.8980
   chunk 70 optimal weight:    2.9990
   chunk 111 optimal weight:    3.9990
   chunk 127 optimal weight:    0.0980
   chunk 124 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 509 ASN
A 599 HIS
B  44 ASN
** B 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 346 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.198684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.169062 restraints weight = 12108.198|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.00
r_work: 0.3969 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3859 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7093
moved from start:          0.2942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10807  Z= 0.127
  Angle     :  0.574   9.466  14627  Z= 0.307
  Chirality :  0.045   0.212   1497
  Planarity :  0.004   0.047   1916
  Dihedral  :  5.435  59.110   1427
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  6.73 %
    Favored  : 93.19 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 26.07 %
    Favored  : 70.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.44 (0.22), residues: 1277
  helix:  0.16 (0.30), residues: 313
  sheet: -0.50 (0.31), residues: 256
  loop : -1.69 (0.21), residues: 708

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  39 
 TYR   0.011   0.001   TYR A 696 
 PHE   0.015   0.002   PHE B 337 
 TRP   0.014   0.001   TRP B 355 
 HIS   0.004   0.001   HIS A 715 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10807)
  covalent geometry    : angle       0.57428 (14627)
  hydrogen bonds       : bond        0.04202 (  305)
  hydrogen bonds       : angle       5.51546 (  840)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4357.64 seconds
wall clock time: 74 minutes 59.29 seconds (4499.29 seconds total)