Starting phenix.real_space_refine
on Wed Aug  5 21:17:16 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9qdq_53032/08_2026/9qdq_53032.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9qdq_53032/08_2026/9qdq_53032.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9qdq_53032/08_2026/9qdq_53032.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9qdq_53032/08_2026/9qdq_53032.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9qdq_53032/08_2026/9qdq_53032.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9qdq_53032/08_2026/9qdq_53032.cif"
  }
  resolution = 3.6
  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=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       9      5.49       5
     S      49      5.16       5
     C    7231      2.51       5
     N    1942      2.21       5
     O    2151      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 11382
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6299
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 797, 6299
          Classifications: {'peptide': 797}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 36, 'TRANS': 759}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 3
    Chain: "B"
      Number of atoms: 4494
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 558, 4494
          Classifications: {'peptide': 558}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 18, 'TRANS': 539}
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 35
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 409
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 409
          Classifications: {'peptide': 50}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 48}
    Chain: "D"
      Number of atoms: 180
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 180
          Classifications: {'RNA': 9}
          Modifications used: {'rna2p_pyr': 2, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 2, 'rna3p': 6}
  Time building chain proxies: 2.46, per 1000 atoms: 0.22
  Number of scatterers: 11382
  At special positions: 0
  Unit cell: (91.9296, 107.251, 160.877, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P       9     15.00
     O    2151      8.00
     N    1942      7.00
     C    7231      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 499.8 milliseconds
  

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2672

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 8 sheets defined
      55.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 93 through 102
    Processing helix  chain 'A' and resid 161 through 165
      removed outlier: 4.009A  pdb=" N   GLN A 164 " --> pdb=" O   ASP A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 190
    Processing helix  chain 'A' and resid 194 through 203
    Processing helix  chain 'A' and resid 212 through 217
      removed outlier: 3.629A  pdb=" N   ILE A 216 " --> pdb=" O   THR A 212 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   ASP A 217 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 212 through 217'
    Processing helix  chain 'A' and resid 234 through 259
      Proline residue:  A 244  - end of helix
    Processing helix  chain 'A' and resid 284 through 291
    Processing helix  chain 'A' and resid 355 through 371
      removed outlier: 3.936A  pdb=" N   MET A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 375
      removed outlier: 4.139A  pdb=" N   ILE A 375 " --> pdb=" O   LYS A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 372 through 375'
    Processing helix  chain 'A' and resid 376 through 384
    Processing helix  chain 'A' and resid 410 through 421
      removed outlier: 3.792A  pdb=" N   LEU A 421 " --> pdb=" O   VAL A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 435 through 452
      removed outlier: 3.977A  pdb=" N   THR A 439 " --> pdb=" O   GLY A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 461 through 475
    Processing helix  chain 'A' and resid 494 through 497
    Processing helix  chain 'A' and resid 498 through 506
    Processing helix  chain 'A' and resid 509 through 522
      removed outlier: 3.639A  pdb=" N   ASN A 513 " --> pdb=" O   GLY A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 547
    Processing helix  chain 'A' and resid 555 through 559
    Processing helix  chain 'A' and resid 573 through 577
    Processing helix  chain 'A' and resid 578 through 584
    Processing helix  chain 'A' and resid 608 through 615
    Processing helix  chain 'A' and resid 619 through 628
    Processing helix  chain 'A' and resid 641 through 653
      removed outlier: 4.846A  pdb=" N   PHE A 647 " --> pdb=" O   TYR A 643 " (cutoff:3.500A)
      Proline residue:  A 648  - end of helix
    Processing helix  chain 'A' and resid 702 through 719
    Processing helix  chain 'A' and resid 722 through 724
      No H-bonds generated for 'chain 'A' and resid 722 through 724'
    Processing helix  chain 'A' and resid 732 through 746
    Processing helix  chain 'A' and resid 750 through 756
      removed outlier: 3.737A  pdb=" N   TYR A 754 " --> pdb=" O   ASP A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 763 through 766
      removed outlier: 3.765A  pdb=" N   GLN A 766 " --> pdb=" O   ASP A 763 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 763 through 766'
    Processing helix  chain 'A' and resid 787 through 790
      removed outlier: 3.979A  pdb=" N   ARG A 790 " --> pdb=" O   GLY A 787 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 787 through 790'
    Processing helix  chain 'A' and resid 791 through 800
      removed outlier: 3.982A  pdb=" N   LEU A 795 " --> pdb=" O   ASP A 791 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   THR A 800 " --> pdb=" O   ASN A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 811 through 816
      removed outlier: 3.677A  pdb=" N   LEU A 815 " --> pdb=" O   ASN A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 831
      removed outlier: 3.548A  pdb=" N   LYS A 831 " --> pdb=" O   HIS A 827 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 15 through 29
    Processing helix  chain 'B' and resid 30 through 33
    Processing helix  chain 'B' and resid 34 through 63
      removed outlier: 4.104A  pdb=" N   LEU B  38 " --> pdb=" O   ASP B  34 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LYS B  63 " --> pdb=" O   SER B  59 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 68 through 72
    Processing helix  chain 'B' and resid 74 through 88
      removed outlier: 4.420A  pdb=" N   SER B  78 " --> pdb=" O   GLN B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 105
    Processing helix  chain 'B' and resid 111 through 148
      removed outlier: 3.776A  pdb=" N   LYS B 115 " --> pdb=" O   LYS B 111 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR B 148 " --> pdb=" O   VAL B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 162
    Processing helix  chain 'B' and resid 187 through 215
      removed outlier: 4.001A  pdb=" N   LEU B 191 " --> pdb=" O   PRO B 187 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ILE B 192 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
      Proline residue:  B 193  - end of helix
      removed outlier: 3.511A  pdb=" N   GLU B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 224
    Processing helix  chain 'B' and resid 225 through 239
    Processing helix  chain 'B' and resid 242 through 256
      removed outlier: 4.092A  pdb=" N   TYR B 246 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   THR B 256 " --> pdb=" O   ILE B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 259 through 271
    Processing helix  chain 'B' and resid 276 through 288
    Processing helix  chain 'B' and resid 292 through 312
    Processing helix  chain 'B' and resid 316 through 334
      removed outlier: 3.875A  pdb=" N   PHE B 325 " --> pdb=" O   LEU B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 4.201A  pdb=" N   TRP B 338 " --> pdb=" O   SER B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 352 through 368
    Processing helix  chain 'B' and resid 371 through 393
      removed outlier: 3.984A  pdb=" N   PHE B 386 " --> pdb=" O   THR B 382 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   HIS B 387 " --> pdb=" O   ILE B 383 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ARG B 393 " --> pdb=" O   LEU B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 426
    Processing helix  chain 'B' and resid 426 through 431
    Processing helix  chain 'B' and resid 438 through 454
      removed outlier: 3.969A  pdb=" N   VAL B 444 " --> pdb=" O   ILE B 440 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN B 454 " --> pdb=" O   TRP B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 463
      removed outlier: 3.777A  pdb=" N   SER B 463 " --> pdb=" O   GLN B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 482
    Processing helix  chain 'B' and resid 500 through 506
    Processing helix  chain 'B' and resid 509 through 513
    Processing helix  chain 'B' and resid 521 through 528
      removed outlier: 3.645A  pdb=" N   MET B 528 " --> pdb=" O   LYS B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 536
    Processing helix  chain 'B' and resid 540 through 544
    Processing helix  chain 'B' and resid 546 through 567
    Processing helix  chain 'C' and resid 170 through 186
    Processing sheet with id=AA1, first strand: chain 'A' and resid 81 through 83
      removed outlier: 3.595A  pdb=" N   LYS A  81 " --> pdb=" O   CYS A  76 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 148
      removed outlier: 3.565A  pdb=" N   PHE A 135 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   GLN A 166 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 271
      removed outlier: 4.593A  pdb=" N   SER A 266 " --> pdb=" O   THR A 282 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   HIS A 277 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   THR A 329 " --> pdb=" O   VAL A 318 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   TYR A 303 " --> pdb=" O   TRP A 311 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLY A 315 " --> pdb=" O   MET A 299 " (cutoff:3.500A)
      removed outlier: 5.803A  pdb=" N   PHE A 347 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 391 through 393
      removed outlier: 3.723A  pdb=" N   THR C 200 " --> pdb=" O   SER A 392 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 479 through 481
      removed outlier: 6.493A  pdb=" N   VAL A 480 " --> pdb=" O   CYS A 551 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   ILE A 455 " --> pdb=" O   VAL A 550 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   VAL A 569 " --> pdb=" O   ILE A 594 " (cutoff:3.500A)
      removed outlier: 8.014A  pdb=" N   VAL A 596 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   ILE A 571 " --> pdb=" O   VAL A 596 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   LEU A 427 " --> pdb=" O   ILE A 632 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 636 through 637
    Processing sheet with id=AA8, first strand: chain 'A' and resid 758 through 761
      removed outlier: 7.339A  pdb=" N   ILE A 726 " --> pdb=" O   GLU A 758 " (cutoff:3.500A)
      removed outlier: 9.016A  pdb=" N   ALA A 760 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
      removed outlier: 6.155A  pdb=" N   VAL A 728 " --> pdb=" O   ALA A 760 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   SER A 776 " --> pdb=" O   ILE A 729 " (cutoff:3.500A)
      removed outlier: 7.098A  pdb=" N   ASP A 771 " --> pdb=" O   LYS A 803 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ILE A 773 " --> pdb=" O   GLY A 805 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL A 807 " --> pdb=" O   ILE A 773 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   MET A 683 " --> pdb=" O   LEU A 806 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   GLY A 810 " --> pdb=" O   TRP A 685 " (cutoff:3.500A)
      removed outlier: 7.981A  pdb=" N   VAL A 835 " --> pdb=" O   MET A 682 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   PHE A 684 " --> pdb=" O   VAL A 835 " (cutoff:3.500A)

    552 hydrogen bonds defined for protein.
    1596 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: 1.73

  Time building geometry restraints manager: 1.24 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: 3582
        1.34 -     1.46: 1709
        1.46 -     1.58: 6250
        1.58 -     1.69: 17
        1.69 -     1.81: 75
  Bond restraints: 11633
  Sorted by residual:
  bond pdb=" CG  LYS A 512 "
       pdb=" CD  LYS A 512 "
    ideal  model  delta    sigma   weight residual
    1.520  1.476  0.044 3.00e-02 1.11e+03 2.17e+00
  bond pdb=" CB  TRP B 450 "
       pdb=" CG  TRP B 450 "
    ideal  model  delta    sigma   weight residual
    1.498  1.459  0.039 3.10e-02 1.04e+03 1.62e+00
  bond pdb=" CB  LEU B 360 "
       pdb=" CG  LEU B 360 "
    ideal  model  delta    sigma   weight residual
    1.530  1.505  0.025 2.00e-02 2.50e+03 1.54e+00
  bond pdb=" N   PRO B 275 "
       pdb=" CA  PRO B 275 "
    ideal  model  delta    sigma   weight residual
    1.467  1.452  0.015 1.19e-02 7.06e+03 1.53e+00
  bond pdb=" CB  ASN A  60 "
       pdb=" CG  ASN A  60 "
    ideal  model  delta    sigma   weight residual
    1.516  1.544 -0.028 2.50e-02 1.60e+03 1.29e+00
  ... (remaining 11628 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.11: 15400
        2.11 -     4.21: 278
        4.21 -     6.32: 63
        6.32 -     8.42: 22
        8.42 -    10.53: 10
  Bond angle restraints: 15773
  Sorted by residual:
  angle pdb=" C   ILE B 302 "
        pdb=" N   MET B 303 "
        pdb=" CA  MET B 303 "
      ideal   model   delta    sigma   weight residual
     121.14  112.86    8.28 1.75e+00 3.27e-01 2.24e+01
  angle pdb=" C   MET B 270 "
        pdb=" N   MET B 271 "
        pdb=" CA  MET B 271 "
      ideal   model   delta    sigma   weight residual
     122.56  114.76    7.80 1.72e+00 3.38e-01 2.06e+01
  angle pdb=" N   PRO B 275 "
        pdb=" CA  PRO B 275 "
        pdb=" C   PRO B 275 "
      ideal   model   delta    sigma   weight residual
     111.32  118.04   -6.72 1.71e+00 3.42e-01 1.54e+01
  angle pdb=" CA  MET B 303 "
        pdb=" CB  MET B 303 "
        pdb=" CG  MET B 303 "
      ideal   model   delta    sigma   weight residual
     114.10  121.74   -7.64 2.00e+00 2.50e-01 1.46e+01
  angle pdb=" CA  MET B 126 "
        pdb=" CB  MET B 126 "
        pdb=" CG  MET B 126 "
      ideal   model   delta    sigma   weight residual
     114.10  121.45   -7.35 2.00e+00 2.50e-01 1.35e+01
  ... (remaining 15768 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 6231
       17.98 -    35.97: 662
       35.97 -    53.95: 148
       53.95 -    71.94: 31
       71.94 -    89.92: 6
  Dihedral angle restraints: 7078
    sinusoidal: 2959
      harmonic: 4119
  Sorted by residual:
  dihedral pdb=" CA  MET B 528 "
           pdb=" C   MET B 528 "
           pdb=" N   ASP B 529 "
           pdb=" CA  ASP B 529 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.23  -24.77     0      5.00e+00 4.00e-02 2.45e+01
  dihedral pdb=" CA  LEU A 842 "
           pdb=" C   LEU A 842 "
           pdb=" N   GLN A 843 "
           pdb=" CA  GLN A 843 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.48   20.52     0      5.00e+00 4.00e-02 1.68e+01
  dihedral pdb=" CA  LEU A 634 "
           pdb=" C   LEU A 634 "
           pdb=" N   GLU A 635 "
           pdb=" CA  GLU A 635 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.55  -17.45     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 7075 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.064: 1533
       0.064 -    0.129: 229
       0.129 -    0.193: 19
       0.193 -    0.257: 0
       0.257 -    0.322: 3
  Chirality restraints: 1784
  Sorted by residual:
  chirality pdb=" CG  LEU B 360 "
            pdb=" CB  LEU B 360 "
            pdb=" CD1 LEU B 360 "
            pdb=" CD2 LEU B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.91    0.32 2.00e-01 2.50e+01 2.59e+00
  chirality pdb=" CG  LEU B 552 "
            pdb=" CB  LEU B 552 "
            pdb=" CD1 LEU B 552 "
            pdb=" CD2 LEU B 552 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.31   -0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CA  PRO B 275 "
            pdb=" N   PRO B 275 "
            pdb=" C   PRO B 275 "
            pdb=" CB  PRO B 275 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.44    0.28 2.00e-01 2.50e+01 1.96e+00
  ... (remaining 1781 not shown)

  Planarity restraints: 1984
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 266 "    0.020 2.00e-02 2.50e+03   2.31e-02 9.34e+00
        pdb=" CG  PHE B 266 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 266 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 266 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 266 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 266 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 266 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 431 "   -0.020 2.00e-02 2.50e+03   1.91e-02 9.11e+00
        pdb=" CG  TRP B 431 "    0.051 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 431 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 431 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 431 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 431 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 431 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 431 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 431 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 431 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 165 "   -0.017 2.00e-02 2.50e+03   1.58e-02 6.28e+00
        pdb=" CG  TRP A 165 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 165 "   -0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 165 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 165 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 165 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 165 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 165 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 165 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 165 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1981 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2799
        2.79 -     3.32: 11428
        3.32 -     3.84: 19047
        3.84 -     4.37: 21808
        4.37 -     4.90: 35993
  Nonbonded interactions: 91075
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN B 413 "
            pdb=" OH  TYR B 460 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O   ILE B 261 "
            pdb=" ND2 ASN B 265 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" O   ASN A 746 "
            pdb=" ND2 ASN A 746 "
     model   vdw
     2.282 3.120
  nonbonded pdb=" O   ILE B 426 "
            pdb=" OG  SER B 430 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" ND2 ASN A 781 "
            pdb=" O   ALA A 785 "
     model   vdw
     2.309 3.120
  ... (remaining 91070 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
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:             5.440
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.710
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5944
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      :  0.003   0.044  11633  Z= 0.146
  Angle     :  0.758  10.530  15773  Z= 0.388
  Chirality :  0.046   0.322   1784
  Planarity :  0.005   0.069   1984
  Dihedral  : 15.454  89.921   4406
  Min Nonbonded Distance : 2.262

Molprobity Statistics.
  All-atom Clashscore : 15.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 23.02 %
    Favored  : 76.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.78 (0.23), residues: 1399
  helix:  0.84 (0.20), residues: 691
  sheet:  0.36 (0.53), residues: 107
  loop :  0.36 (0.26), residues: 601

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 531 
 TYR   0.022   0.001   TYR B 207 
 PHE   0.054   0.002   PHE B 266 
 TRP   0.051   0.003   TRP B 431 
 HIS   0.004   0.001   HIS A 104 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00320 /  0.15 (11633)
  covalent geometry    : angle       0.75790 /  0.39 (15773)
  hydrogen bonds       : bond        0.16970 / 11.33 (  552)
  hydrogen bonds       : angle       6.59891 /  4.70 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
REVERT: A  743 MET cc_start: 0.6896 (mmt) cc_final: 0.6537 (mmt)
REVERT: A  849 LEU cc_start: 0.8540 (pt) cc_final: 0.8083 (mt)
REVERT: B   22 LEU cc_start: 0.7204 (tp) cc_final: 0.6915 (tp)
REVERT: B  443 MET cc_start: 0.7495 (ppp) cc_final: 0.7115 (ppp)
  outliers start: 5
  outliers final: 4
  residues processed: 107
  average time/residue: 0.0863
  time to fit residues: 13.9089
Evaluate side-chains
  94 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 90
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  844 LEU
Chi-restraints excluded: chain B residue  487 PHE
Chi-restraints excluded: chain C residue  181 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    6.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    0.7980
   overall best weight:    1.1382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
A 422 GLN
B 101 ASN
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 ASN
B 448 ASN
** C 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.134245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.106167 restraints weight = 47094.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.109152 restraints weight = 26400.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.111248 restraints weight = 18369.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.112570 restraints weight = 14541.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.113459 restraints weight = 12483.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5971
moved from start:          0.1276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11633  Z= 0.141
  Angle     :  0.613   8.382  15773  Z= 0.318
  Chirality :  0.042   0.178   1784
  Planarity :  0.004   0.045   1984
  Dihedral  :  8.734  74.170   1663
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 19.17 %
    Favored  : 78.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.90 (0.23), residues: 1399
  helix:  1.01 (0.20), residues: 692
  sheet: -0.06 (0.47), residues: 125
  loop :  0.44 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 296 
 TYR   0.018   0.001   TYR B 207 
 PHE   0.035   0.002   PHE B 266 
 TRP   0.017   0.001   TRP A 165 
 HIS   0.004   0.001   HIS B 387 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00306 /  0.14 (11633)
  covalent geometry    : angle       0.61348 /  0.32 (15773)
  hydrogen bonds       : bond        0.04411 /  3.00 (  552)
  hydrogen bonds       : angle       5.16991 /  3.65 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 103
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  743 MET cc_start: 0.7005 (mmt) cc_final: 0.6528 (mmt)
REVERT: A  849 LEU cc_start: 0.8555 (pt) cc_final: 0.8039 (mt)
REVERT: B  270 MET cc_start: 0.6055 (ptp) cc_final: 0.5853 (ptp)
REVERT: B  377 HIS cc_start: 0.7892 (m170) cc_final: 0.7670 (m90)
REVERT: B  443 MET cc_start: 0.7529 (ppp) cc_final: 0.7243 (ppp)
REVERT: B  551 MET cc_start: -0.1634 (ptm) cc_final: -0.1849 (ptm)
  outliers start: 27
  outliers final: 12
  residues processed: 123
  average time/residue: 0.0719
  time to fit residues: 14.1633
Evaluate side-chains
  97 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  683 MET
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  360 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 34 optimal weight:    0.0050
   chunk 135 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 106 optimal weight:   10.0000
   chunk 115 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 77 optimal weight:    4.9990
   chunk 121 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0570
   chunk 113 optimal weight:   20.0000
   chunk 109 optimal weight:    2.9990
   overall best weight:    0.7714

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 154 GLN
A 181 GLN
A 796 ASN
B 421 HIS
C 201 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.131157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4075 r_free = 0.4075 target = 0.104448 restraints weight = 52075.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4130 r_free = 0.4130 target = 0.107565 restraints weight = 28428.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4166 r_free = 0.4166 target = 0.109595 restraints weight = 19366.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.110852 restraints weight = 15128.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.111427 restraints weight = 12958.620|
|-----------------------------------------------------------------------------|
r_work (final): 0.4158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6037
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11633  Z= 0.113
  Angle     :  0.573  10.566  15773  Z= 0.290
  Chirality :  0.041   0.174   1784
  Planarity :  0.004   0.043   1984
  Dihedral  :  8.126  65.317   1653
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.96 %
    Favored  : 79.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  1.02 (0.23), residues: 1399
  helix:  1.18 (0.20), residues: 693
  sheet: -0.23 (0.46), residues: 123
  loop :  0.45 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 537 
 TYR   0.013   0.001   TYR B 207 
 PHE   0.024   0.002   PHE B 266 
 TRP   0.024   0.002   TRP B 431 
 HIS   0.002   0.001   HIS A 451 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 (11633)
  covalent geometry    : angle       0.57331 /  0.29 (15773)
  hydrogen bonds       : bond        0.04009 /  2.72 (  552)
  hydrogen bonds       : angle       4.86882 /  3.42 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 95
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  743 MET cc_start: 0.7086 (mmt) cc_final: 0.6718 (mmt)
REVERT: A  849 LEU cc_start: 0.8425 (pt) cc_final: 0.8004 (mt)
REVERT: B   99 TRP cc_start: 0.8020 (t60) cc_final: 0.7597 (t60)
REVERT: B  274 MET cc_start: 0.7583 (tmm) cc_final: 0.6772 (mmm)
REVERT: B  443 MET cc_start: 0.7417 (ppp) cc_final: 0.7190 (ppp)
  outliers start: 29
  outliers final: 12
  residues processed: 116
  average time/residue: 0.0652
  time to fit residues: 12.1945
Evaluate side-chains
  96 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  178 VAL
Chi-restraints excluded: chain A residue  181 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  360 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 73 optimal weight:    7.9990
   chunk 26 optimal weight:    0.0770
   chunk 84 optimal weight:    9.9990
   chunk 1 optimal weight:   10.0000
   chunk 7 optimal weight:    2.9990
   chunk 118 optimal weight:   10.0000
   chunk 13 optimal weight:    6.9990
   chunk 120 optimal weight:    9.9990
   chunk 67 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    2.9344

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 181 GLN
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 843 GLN
B  21 GLN
B 112 GLN
** B 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 454 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4482 r_free = 0.4482 target = 0.124918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.097933 restraints weight = 53005.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.100684 restraints weight = 29634.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.102470 restraints weight = 20647.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.103633 restraints weight = 16420.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.104308 restraints weight = 14193.244|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6362
moved from start:          0.3153

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.104  11633  Z= 0.232
  Angle     :  0.729  10.916  15773  Z= 0.379
  Chirality :  0.045   0.195   1784
  Planarity :  0.005   0.078   1984
  Dihedral  :  8.763  66.711   1653
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 17.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 18.52 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.29 (0.22), residues: 1399
  helix:  0.55 (0.19), residues: 694
  sheet: -0.90 (0.45), residues: 121
  loop :  0.23 (0.27), residues: 584

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 567 
 TYR   0.025   0.003   TYR B 148 
 PHE   0.022   0.002   PHE B 264 
 TRP   0.022   0.002   TRP A 353 
 HIS   0.006   0.002   HIS A  94 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00518 /  0.23 (11633)
  covalent geometry    : angle       0.72941 /  0.38 (15773)
  hydrogen bonds       : bond        0.04849 /  3.25 (  552)
  hydrogen bonds       : angle       5.22515 /  3.67 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 95
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.8272 (t0) cc_final: 0.8064 (t0)
REVERT: A  427 LEU cc_start: 0.7093 (mt) cc_final: 0.6731 (mt)
REVERT: A  827 HIS cc_start: 0.7374 (OUTLIER) cc_final: 0.6264 (t-90)
REVERT: A  849 LEU cc_start: 0.8905 (pt) cc_final: 0.8276 (mp)
REVERT: B  274 MET cc_start: 0.7883 (tmm) cc_final: 0.6915 (mmm)
REVERT: B  443 MET cc_start: 0.7677 (ppp) cc_final: 0.7301 (ppp)
  outliers start: 44
  outliers final: 24
  residues processed: 129
  average time/residue: 0.0734
  time to fit residues: 15.1776
Evaluate side-chains
  112 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 87
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  318 VAL
Chi-restraints excluded: chain A residue  575 THR
Chi-restraints excluded: chain A residue  693 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  804 TYR
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain A residue  828 PHE
Chi-restraints excluded: chain B residue   41 PHE
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  383 ILE
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  551 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 129 optimal weight:    0.7980
   chunk 73 optimal weight:    0.3980
   chunk 47 optimal weight:    9.9990
   chunk 97 optimal weight:    0.7980
   chunk 87 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 115 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0170
   chunk 84 optimal weight:   20.0000
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.5618

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
** A 410 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 513 ASN
** A 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 766 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 371 ASN
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4528 r_free = 0.4528 target = 0.127748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.100731 restraints weight = 51359.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.103641 restraints weight = 28227.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.105561 restraints weight = 19352.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.106784 restraints weight = 15227.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.107472 restraints weight = 13088.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.4101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6220
moved from start:          0.3187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.052  11633  Z= 0.111
  Angle     :  0.590  12.923  15773  Z= 0.295
  Chirality :  0.041   0.178   1784
  Planarity :  0.004   0.058   1984
  Dihedral  :  8.442  69.396   1653
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.73 %
    Favored  : 78.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.78 (0.23), residues: 1399
  helix:  1.02 (0.20), residues: 694
  sheet: -0.62 (0.46), residues: 123
  loop :  0.35 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 210 
 TYR   0.010   0.001   TYR A 381 
 PHE   0.016   0.001   PHE B 266 
 TRP   0.013   0.002   TRP A 177 
 HIS   0.003   0.001   HIS B 387 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00238 /  0.11 (11633)
  covalent geometry    : angle       0.59048 /  0.29 (15773)
  hydrogen bonds       : bond        0.03802 /  2.57 (  552)
  hydrogen bonds       : angle       4.74045 /  3.32 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 93
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.8035 (t0) cc_final: 0.7775 (t0)
REVERT: A  827 HIS cc_start: 0.7205 (OUTLIER) cc_final: 0.6225 (t-90)
REVERT: A  828 PHE cc_start: 0.6684 (OUTLIER) cc_final: 0.6341 (t80)
REVERT: A  849 LEU cc_start: 0.8685 (pt) cc_final: 0.8057 (mt)
REVERT: B  274 MET cc_start: 0.7906 (tmm) cc_final: 0.7168 (mmp)
REVERT: B  443 MET cc_start: 0.7519 (ppp) cc_final: 0.7233 (ppp)
  outliers start: 26
  outliers final: 16
  residues processed: 112
  average time/residue: 0.0679
  time to fit residues: 12.5763
Evaluate side-chains
  103 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain A residue  828 PHE
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  532 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    0.0980
   chunk 89 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 18 optimal weight:    1.9990
   chunk 122 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
A 601 GLN
A 766 GLN
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 469 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.131575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.103668 restraints weight = 49659.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.106537 restraints weight = 27386.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.108545 restraints weight = 18951.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.109745 restraints weight = 14932.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.110343 restraints weight = 12843.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6212
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11633  Z= 0.117
  Angle     :  0.598  13.011  15773  Z= 0.296
  Chirality :  0.041   0.211   1784
  Planarity :  0.004   0.057   1984
  Dihedral  :  8.313  68.598   1653
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 11.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 20.13 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.88 (0.23), residues: 1399
  helix:  1.17 (0.20), residues: 693
  sheet: -0.52 (0.47), residues: 123
  loop :  0.29 (0.27), residues: 583

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 210 
 TYR   0.012   0.001   TYR B 148 
 PHE   0.023   0.001   PHE A 717 
 TRP   0.021   0.002   TRP A 165 
 HIS   0.003   0.001   HIS B 387 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00257 /  0.12 (11633)
  covalent geometry    : angle       0.59776 /  0.30 (15773)
  hydrogen bonds       : bond        0.03723 /  2.53 (  552)
  hydrogen bonds       : angle       4.69146 /  3.29 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 87
  time to evaluate  : 0.440 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.8127 (t0) cc_final: 0.7873 (t0)
REVERT: A  361 MET cc_start: 0.8055 (tmm) cc_final: 0.7664 (tmm)
REVERT: A  413 GLN cc_start: 0.6975 (mp10) cc_final: 0.6155 (pm20)
REVERT: A  827 HIS cc_start: 0.7075 (OUTLIER) cc_final: 0.6139 (t-90)
REVERT: A  828 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6399 (t80)
REVERT: A  849 LEU cc_start: 0.8708 (pt) cc_final: 0.8061 (mt)
REVERT: B  274 MET cc_start: 0.7927 (tmm) cc_final: 0.7237 (mmp)
REVERT: B  443 MET cc_start: 0.7705 (ppp) cc_final: 0.7429 (ppp)
REVERT: B  505 MET cc_start: 0.6382 (ttp) cc_final: 0.6145 (tmm)
  outliers start: 26
  outliers final: 18
  residues processed: 107
  average time/residue: 0.0763
  time to fit residues: 13.3114
Evaluate side-chains
  104 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 84
  time to evaluate  : 0.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  260 GLN
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  425 LEU
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  656 SER
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain A residue  828 PHE
Chi-restraints excluded: chain B residue  171 THR
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain C residue  181 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 29 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 57 optimal weight:    0.8980
   chunk 116 optimal weight:    5.9990
   chunk 118 optimal weight:    5.9990
   chunk 9 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0370
   chunk 121 optimal weight:    0.9990
   overall best weight:    2.1864

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
B 387 HIS
B 454 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.123431 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.096284 restraints weight = 52837.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.098909 restraints weight = 29324.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.100737 restraints weight = 20473.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.101891 restraints weight = 16222.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.102534 restraints weight = 13998.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6413
moved from start:          0.4231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  11633  Z= 0.175
  Angle     :  0.671  11.367  15773  Z= 0.337
  Chirality :  0.043   0.210   1784
  Planarity :  0.005   0.067   1984
  Dihedral  :  8.560  67.885   1653
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 14.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.73 %
    Allowed  : 20.29 %
    Favored  : 76.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.59 (0.23), residues: 1399
  helix:  0.92 (0.20), residues: 694
  sheet: -0.82 (0.46), residues: 123
  loop :  0.20 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 210 
 TYR   0.020   0.002   TYR B 148 
 PHE   0.023   0.002   PHE A 717 
 TRP   0.026   0.003   TRP B 333 
 HIS   0.004   0.001   HIS A 629 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00390 /  0.17 (11633)
  covalent geometry    : angle       0.67128 /  0.34 (15773)
  hydrogen bonds       : bond        0.04322 /  2.91 (  552)
  hydrogen bonds       : angle       4.95399 /  3.49 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 87
  time to evaluate  : 0.423 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.8137 (t0) cc_final: 0.7899 (t0)
REVERT: A  361 MET cc_start: 0.8037 (tmm) cc_final: 0.7575 (tmm)
REVERT: A  427 LEU cc_start: 0.6978 (mt) cc_final: 0.6598 (mt)
REVERT: A  608 GLU cc_start: 0.7706 (tm-30) cc_final: 0.6911 (mm-30)
REVERT: A  609 ARG cc_start: 0.8230 (ttp80) cc_final: 0.7837 (ttm170)
REVERT: A  827 HIS cc_start: 0.7407 (OUTLIER) cc_final: 0.6347 (t-90)
REVERT: A  849 LEU cc_start: 0.8872 (pt) cc_final: 0.8261 (mt)
REVERT: B  274 MET cc_start: 0.8080 (tmm) cc_final: 0.7198 (mmm)
REVERT: B  443 MET cc_start: 0.7744 (ppp) cc_final: 0.7412 (ppp)
  outliers start: 34
  outliers final: 27
  residues processed: 114
  average time/residue: 0.0876
  time to fit residues: 15.5445
Evaluate side-chains
  107 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ASN
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  249 GLU
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  728 VAL
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain A residue  828 PHE
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain B residue  548 SER
Chi-restraints excluded: chain C residue  181 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 84 optimal weight:   20.0000
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 0 optimal weight:   10.0000
   chunk 52 optimal weight:    0.0770
   chunk 127 optimal weight:   10.0000
   chunk 37 optimal weight:    0.5980
   chunk 96 optimal weight:    0.1980
   chunk 76 optimal weight:    4.9990
   chunk 121 optimal weight:    0.9980
   chunk 86 optimal weight:    0.9980
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4499 r_free = 0.4499 target = 0.125476 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.098579 restraints weight = 50914.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.101255 restraints weight = 28041.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.102767 restraints weight = 19328.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.104191 restraints weight = 15513.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.104933 restraints weight = 13288.699|
|-----------------------------------------------------------------------------|
r_work (final): 0.4053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6304
moved from start:          0.4299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  11633  Z= 0.112
  Angle     :  0.622  15.360  15773  Z= 0.304
  Chirality :  0.042   0.218   1784
  Planarity :  0.004   0.055   1984
  Dihedral  :  8.391  68.765   1653
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 12.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 20.77 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.80 (0.23), residues: 1399
  helix:  1.11 (0.20), residues: 692
  sheet: -0.59 (0.47), residues: 125
  loop :  0.25 (0.27), residues: 582

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 210 
 TYR   0.014   0.001   TYR A 381 
 PHE   0.021   0.002   PHE A 717 
 TRP   0.017   0.002   TRP B 450 
 HIS   0.012   0.001   HIS B 387 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.11 (11633)
  covalent geometry    : angle       0.62246 /  0.30 (15773)
  hydrogen bonds       : bond        0.03784 /  2.56 (  552)
  hydrogen bonds       : angle       4.71139 /  3.30 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 ASP cc_start: 0.8092 (t0) cc_final: 0.7862 (t0)
REVERT: A  361 MET cc_start: 0.7911 (tmm) cc_final: 0.7457 (tmm)
REVERT: A  608 GLU cc_start: 0.7684 (tm-30) cc_final: 0.7433 (mm-30)
REVERT: A  827 HIS cc_start: 0.7307 (OUTLIER) cc_final: 0.6289 (t-90)
REVERT: A  828 PHE cc_start: 0.6870 (OUTLIER) cc_final: 0.6532 (t80)
REVERT: A  849 LEU cc_start: 0.8745 (pt) cc_final: 0.8113 (mt)
REVERT: B  101 ASN cc_start: 0.8642 (m110) cc_final: 0.8333 (p0)
REVERT: B  274 MET cc_start: 0.8067 (tmm) cc_final: 0.7237 (mmm)
REVERT: B  418 TYR cc_start: 0.5794 (m-80) cc_final: 0.5326 (m-80)
REVERT: B  443 MET cc_start: 0.7631 (ppp) cc_final: 0.7417 (ppp)
  outliers start: 24
  outliers final: 17
  residues processed: 109
  average time/residue: 0.0915
  time to fit residues: 15.7286
Evaluate side-chains
  106 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 87
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain A residue  828 PHE
Chi-restraints excluded: chain B residue  360 LEU
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  532 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 24 optimal weight:    7.9990
   chunk 22 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 2 optimal weight:    0.8980
   chunk 132 optimal weight:   20.0000
   chunk 128 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 44 optimal weight:   10.0000
   chunk 34 optimal weight:    0.0970
   chunk 117 optimal weight:    9.9990
   overall best weight:    3.5984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
A 462 ASN
** A 687 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 265 ASN
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 413 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.125449 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.097509 restraints weight = 49939.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.100035 restraints weight = 29072.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.101776 restraints weight = 20812.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.102858 restraints weight = 16761.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.103415 restraints weight = 14611.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6536
moved from start:          0.5546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  11633  Z= 0.261
  Angle     :  0.817  12.011  15773  Z= 0.416
  Chirality :  0.048   0.247   1784
  Planarity :  0.005   0.073   1984
  Dihedral  :  8.987  65.919   1653
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 17.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 20.21 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.08 (0.22), residues: 1399
  helix:  0.49 (0.19), residues: 689
  sheet: -1.07 (0.46), residues: 120
  loop : -0.02 (0.27), residues: 590

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG C 210 
 TYR   0.026   0.003   TYR A 252 
 PHE   0.028   0.003   PHE A 621 
 TRP   0.041   0.003   TRP B 338 
 HIS   0.009   0.002   HIS A 629 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00579 /  0.26 (11633)
  covalent geometry    : angle       0.81691 /  0.42 (15773)
  hydrogen bonds       : bond        0.05185 /  3.48 (  552)
  hydrogen bonds       : angle       5.42663 /  3.80 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 86
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  608 GLU cc_start: 0.7997 (tm-30) cc_final: 0.6710 (mm-30)
REVERT: A  609 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.7534 (ttm170)
REVERT: A  743 MET cc_start: 0.7442 (mmt) cc_final: 0.6884 (mmt)
REVERT: A  765 PHE cc_start: 0.4562 (OUTLIER) cc_final: 0.3543 (t80)
REVERT: A  827 HIS cc_start: 0.7542 (OUTLIER) cc_final: 0.6520 (t-90)
REVERT: A  849 LEU cc_start: 0.9087 (pt) cc_final: 0.8369 (mt)
REVERT: B  125 LYS cc_start: 0.8831 (mttt) cc_final: 0.8362 (mttt)
REVERT: B  274 MET cc_start: 0.8162 (tmm) cc_final: 0.7396 (mmm)
REVERT: B  443 MET cc_start: 0.7940 (ppp) cc_final: 0.7568 (ppp)
  outliers start: 43
  outliers final: 32
  residues processed: 120
  average time/residue: 0.0975
  time to fit residues: 17.7607
Evaluate side-chains
  112 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 77
  time to evaluate  : 0.487 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  112 ASP
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  130 VAL
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain A residue  173 GLN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  213 ILE
Chi-restraints excluded: chain A residue  245 LEU
Chi-restraints excluded: chain A residue  308 HIS
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain A residue  596 VAL
Chi-restraints excluded: chain A residue  609 ARG
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  651 MET
Chi-restraints excluded: chain A residue  704 ILE
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  739 ILE
Chi-restraints excluded: chain A residue  765 PHE
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain A residue  828 PHE
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  120 ARG
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain C residue  181 MET
Chi-restraints excluded: chain C residue  197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 21 optimal weight:   30.0000
   chunk 133 optimal weight:    8.9990
   chunk 73 optimal weight:    0.7980
   chunk 134 optimal weight:    9.9990
   chunk 76 optimal weight:    0.9980
   chunk 120 optimal weight:    4.9990
   chunk 89 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
A 462 ASN
B 265 ASN
** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 387 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.126895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.098797 restraints weight = 50191.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.101476 restraints weight = 28584.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.103361 restraints weight = 20114.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.104348 restraints weight = 16103.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.105181 restraints weight = 14062.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.4019
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6385
moved from start:          0.5500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11633  Z= 0.122
  Angle     :  0.671  13.248  15773  Z= 0.331
  Chirality :  0.043   0.266   1784
  Planarity :  0.004   0.060   1984
  Dihedral  :  8.555  67.171   1653
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 21.89 %
    Favored  : 76.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.48 (0.23), residues: 1399
  helix:  0.89 (0.19), residues: 690
  sheet: -0.73 (0.47), residues: 120
  loop :  0.02 (0.27), residues: 589

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 240 
 TYR   0.022   0.001   TYR A 252 
 PHE   0.018   0.001   PHE A 717 
 TRP   0.031   0.002   TRP B 338 
 HIS   0.006   0.001   HIS B 377 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 (11633)
  covalent geometry    : angle       0.67133 /  0.33 (15773)
  hydrogen bonds       : bond        0.04068 /  2.75 (  552)
  hydrogen bonds       : angle       4.88193 /  3.42 ( 1596)

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

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

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2798 Ramachandran restraints generated.
    1399 Oldfield, 0 Emsley, 1399 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 88
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  608 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7057 (mm-30)
REVERT: A  827 HIS cc_start: 0.7396 (OUTLIER) cc_final: 0.6422 (t-90)
REVERT: A  828 PHE cc_start: 0.7147 (OUTLIER) cc_final: 0.6731 (t80)
REVERT: A  849 LEU cc_start: 0.8876 (pt) cc_final: 0.8200 (mt)
REVERT: B  101 ASN cc_start: 0.8755 (m110) cc_final: 0.8401 (p0)
REVERT: B  274 MET cc_start: 0.8118 (tmm) cc_final: 0.7408 (mmm)
  outliers start: 23
  outliers final: 17
  residues processed: 104
  average time/residue: 0.0901
  time to fit residues: 14.7848
Evaluate side-chains
  101 residues out of total 1257 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  103 HIS
Chi-restraints excluded: chain A residue  120 LEU
Chi-restraints excluded: chain A residue  136 VAL
Chi-restraints excluded: chain A residue  157 ASN
Chi-restraints excluded: chain A residue  204 LYS
Chi-restraints excluded: chain A residue  406 PHE
Chi-restraints excluded: chain A residue  449 LYS
Chi-restraints excluded: chain A residue  624 LEU
Chi-restraints excluded: chain A residue  713 ILE
Chi-restraints excluded: chain A residue  774 ILE
Chi-restraints excluded: chain A residue  786 ILE
Chi-restraints excluded: chain A residue  827 HIS
Chi-restraints excluded: chain A residue  828 PHE
Chi-restraints excluded: chain B residue  119 PHE
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  506 VAL
Chi-restraints excluded: chain B residue  532 LEU
Chi-restraints excluded: chain C residue  181 MET
Chi-restraints excluded: chain C residue  197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 134 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 12 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 42 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 115 optimal weight:    0.9990
   chunk 119 optimal weight:    9.9990
   chunk 49 optimal weight:    0.4980
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  85 ASN
A 746 ASN
** B 349 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4477 r_free = 0.4477 target = 0.123392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.096421 restraints weight = 51969.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.099070 restraints weight = 28747.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.100852 restraints weight = 19958.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.102012 restraints weight = 15880.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.102457 restraints weight = 13687.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6416
moved from start:          0.5597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  11633  Z= 0.112
  Angle     :  0.650  13.688  15773  Z= 0.316
  Chirality :  0.042   0.346   1784
  Planarity :  0.004   0.055   1984
  Dihedral  :  8.245  65.168   1653
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 22.37 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.79 %
    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:  0.72 (0.23), residues: 1399
  helix:  1.12 (0.20), residues: 686
  sheet: -0.65 (0.46), residues: 132
  loop :  0.14 (0.28), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 354 
 TYR   0.015   0.001   TYR A 381 
 PHE   0.018   0.001   PHE B 376 
 TRP   0.033   0.002   TRP B 338 
 HIS   0.004   0.001   HIS A 629 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00241 /  0.11 (11633)
  covalent geometry    : angle       0.64978 /  0.32 (15773)
  hydrogen bonds       : bond        0.03784 /  2.56 (  552)
  hydrogen bonds       : angle       4.73609 /  3.32 ( 1596)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2249.59 seconds
wall clock time: 39 minutes 39.40 seconds (2379.40 seconds total)