Starting phenix.real_space_refine
on Wed Mar  4 03:49:31 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dcp_27327/03_2026/8dcp_27327.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dcp_27327/03_2026/8dcp_27327.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dcp_27327/03_2026/8dcp_27327.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dcp_27327/03_2026/8dcp_27327.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dcp_27327/03_2026/8dcp_27327.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dcp_27327/03_2026/8dcp_27327.map"
  }
  resolution = 2.41
  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
-------------------------------------------------------------------------------
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=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      75      5.16       5
     C    6724      2.51       5
     N    1835      2.21       5
     O    1961      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10595
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8233
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1005, 8222
          Classifications: {'peptide': 1005}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959}
          Chain breaks: 4
      Conformer: "B"
        Number of residues, atoms: 1005, 8222
          Classifications: {'peptide': 1005}
          Link IDs: {'PCIS': 1, 'PTRANS': 44, 'TRANS': 959}
          Chain breaks: 4
          bond proxies already assigned to first conformer: 8389
    Chain: "B"
      Number of atoms: 2341
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2341
          Classifications: {'peptide': 276}
          Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 271}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 20
          Classifications: {'water': 20}
          Link IDs: {None: 19}
    Chain: "B"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 704 " occ=0.50
      ... (20 atoms not shown)
      pdb=" NH2BARG A 704 " occ=0.50
  Time building chain proxies: 3.62, per 1000 atoms: 0.34
  Number of scatterers: 10595
  At special positions: 0
  Unit cell: (89.88, 130.54, 119.84, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      75     16.00
     O    1961      8.00
     N    1835      7.00
     C    6724      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: 0.79
  Conformation dependent library (CDL) restraints added in 693.7 milliseconds
  

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2454

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 11 sheets defined
      52.1% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.33
  Creating SS restraints...
    Processing helix  chain 'A' and resid 41 through 52
    Processing helix  chain 'A' and resid 64 through 68
      removed outlier: 3.705A  pdb=" N   SER A  67 " --> pdb=" O   ASP A  64 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   TYR A  68 " --> pdb=" O   GLU A  65 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 64 through 68'
    Processing helix  chain 'A' and resid 89 through 93
      removed outlier: 3.564A  pdb=" N   LEU A  92 " --> pdb=" O   LEU A  89 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG A  93 " --> pdb=" O   CYS A  90 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 89 through 93'
    Processing helix  chain 'A' and resid 107 through 122
      removed outlier: 3.509A  pdb=" N   LYS A 111 " --> pdb=" O   ASN A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.684A  pdb=" N   ASP A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 155
      removed outlier: 4.309A  pdb=" N   LEU A 144 " --> pdb=" O   ARG A 140 " (cutoff:3.500A)
      removed outlier: 4.760A  pdb=" N   ASN A 145 " --> pdb=" O   ARG A 141 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   VAL A 146 " --> pdb=" O   ASN A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 178 through 183
      removed outlier: 3.544A  pdb=" N   ASN A 183 " --> pdb=" O   LYS A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 232
      removed outlier: 3.866A  pdb=" N   SER A 231 " --> pdb=" O   LYS A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 296
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.538A  pdb=" N   SER A 308 " --> pdb=" O   PRO A 305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 496
    Processing helix  chain 'A' and resid 498 through 503
      removed outlier: 3.683A  pdb=" N   ARG A 502 " --> pdb=" O   TRP A 498 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   GLU A 503 " --> pdb=" O   SER A 499 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 498 through 503'
    Processing helix  chain 'A' and resid 524 through 536
      removed outlier: 3.517A  pdb=" N   GLN A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
    Processing helix  chain 'A' and resid 557 through 563
      Proline residue:  A 562  - end of helix
    Processing helix  chain 'A' and resid 564 through 571
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 4.045A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 599
    Processing helix  chain 'A' and resid 600 through 603
    Processing helix  chain 'A' and resid 608 through 623
    Processing helix  chain 'A' and resid 624 through 631
    Processing helix  chain 'A' and resid 631 through 638
    Processing helix  chain 'A' and resid 639 through 642
    Processing helix  chain 'A' and resid 647 through 660
    Processing helix  chain 'A' and resid 660 through 674
      removed outlier: 3.690A  pdb=" N   PHE A 666 " --> pdb=" O   ARG A 662 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   GLU A 674 " --> pdb=" O   HIS A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 695
    Processing helix  chain 'A' and resid 697 through 722
      removed outlier: 4.058A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 739
    Processing helix  chain 'A' and resid 741 through 748
    Processing helix  chain 'A' and resid 765 through 769
    Processing helix  chain 'A' and resid 789 through 794
      removed outlier: 4.330A  pdb=" N   LEU A 793 " --> pdb=" O   MET A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 807 through 828
    Processing helix  chain 'A' and resid 857 through 864
    Processing helix  chain 'A' and resid 871 through 874
    Processing helix  chain 'A' and resid 875 through 885
    Processing helix  chain 'A' and resid 888 through 912
      removed outlier: 4.245A  pdb=" N   ALA A 892 " --> pdb=" O   GLU A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 957 through 965
      removed outlier: 3.541A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 993
    Processing helix  chain 'A' and resid 994 through 1004
      removed outlier: 3.787A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1026
      removed outlier: 3.889A  pdb=" N   ILE A1019 " --> pdb=" O   SER A1015 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   TYR A1021 " --> pdb=" O   ASP A1017 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ILE A1022 " --> pdb=" O   ASP A1018 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1048
      removed outlier: 3.561A  pdb=" N   ALA A1046 " --> pdb=" O   GLN A1042 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 347
    Processing helix  chain 'B' and resid 400 through 411
      removed outlier: 3.815A  pdb=" N   LEU B 404 " --> pdb=" O   SER B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 416
      removed outlier: 3.550A  pdb=" N   GLN B 415 " --> pdb=" O   SER B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 442 through 509
      removed outlier: 3.858A  pdb=" N   LYS B 506 " --> pdb=" O   GLU B 502 " (cutoff:3.500A)
      removed outlier: 5.040A  pdb=" N   GLU B 507 " --> pdb=" O   ARG B 503 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   TYR B 508 " --> pdb=" O   TYR B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 514
      removed outlier: 3.863A  pdb=" N   LYS B 513 " --> pdb=" O   GLU B 510 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   ARG B 514 " --> pdb=" O   LYS B 511 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 510 through 514'
    Processing helix  chain 'B' and resid 517 through 588
      removed outlier: 4.136A  pdb=" N   ILE B 521 " --> pdb=" O   ASN B 517 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ASN B 527 " --> pdb=" O   ARG B 523 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR B 528 " --> pdb=" O   ILE B 524 " (cutoff:3.500A)
      Proline residue:  B 568  - end of helix
      removed outlier: 3.999A  pdb=" N   GLY B 588 " --> pdb=" O   LEU B 584 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 590 through 596
      removed outlier: 4.054A  pdb=" N   LEU B 594 " --> pdb=" O   ARG B 590 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 35
      removed outlier: 3.601A  pdb=" N   VAL A  22 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
      removed outlier: 8.421A  pdb=" N   LEU A  99 " --> pdb=" O   LEU A  21 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   GLU A  23 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      removed outlier: 8.369A  pdb=" N   VAL A 101 " --> pdb=" O   GLU A  23 " (cutoff:3.500A)
      removed outlier: 7.112A  pdb=" N   LEU A  25 " --> pdb=" O   VAL A 101 " (cutoff:3.500A)
      removed outlier: 6.898A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  73 " (cutoff:3.500A)
      removed outlier: 5.405A  pdb=" N   VAL A  73 " --> pdb=" O   PHE A  98 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   PHE A  70 " --> pdb=" O   PHE A  82 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   SER A  72 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212
      removed outlier: 4.457A  pdb=" N   LEU A 252 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326
      removed outlier: 6.751A  pdb=" N   LYS A 325 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.788A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 7.250A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.582A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLY A 439 " --> pdb=" O   PHE A 477 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366
    Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 372
      removed outlier: 3.794A  pdb=" N   LYS A 353 " --> pdb=" O   VAL A 409 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752
    Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771
      removed outlier: 6.924A  pdb=" N   VAL A 845 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856
    Processing sheet with id=AB1, first strand: chain 'B' and resid 377 through 382
      removed outlier: 4.434A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 373 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 384 through 386

    521 hydrogen bonds defined for protein.
    1492 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: 1.92

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3480
        1.34 -     1.46: 2355
        1.46 -     1.58: 4841
        1.58 -     1.70: 0
        1.70 -     1.82: 117
  Bond restraints: 10793
  Sorted by residual:
  bond pdb=" CG1 ILE A 121 "
       pdb=" CD1 ILE A 121 "
    ideal  model  delta    sigma   weight residual
    1.513  1.445  0.068 3.90e-02 6.57e+02 3.07e+00
  bond pdb=" CG1 ILE A 894 "
       pdb=" CD1 ILE A 894 "
    ideal  model  delta    sigma   weight residual
    1.513  1.450  0.063 3.90e-02 6.57e+02 2.58e+00
  bond pdb=" CG  LYS A 132 "
       pdb=" CD  LYS A 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.02e+00
  bond pdb=" CB  LYS A 132 "
       pdb=" CG  LYS A 132 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.75e+00
  bond pdb=" CB  MET B 322 "
       pdb=" CG  MET B 322 "
    ideal  model  delta    sigma   weight residual
    1.520  1.559 -0.039 3.00e-02 1.11e+03 1.70e+00
  ... (remaining 10788 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.09: 14311
        2.09 -     4.17: 188
        4.17 -     6.26: 30
        6.26 -     8.35: 13
        8.35 -    10.44: 6
  Bond angle restraints: 14548
  Sorted by residual:
  angle pdb=" CB  LYS A 132 "
        pdb=" CG  LYS A 132 "
        pdb=" CD  LYS A 132 "
      ideal   model   delta    sigma   weight residual
     111.30  121.47  -10.17 2.30e+00 1.89e-01 1.96e+01
  angle pdb=" CA  MET B 322 "
        pdb=" CB  MET B 322 "
        pdb=" CG  MET B 322 "
      ideal   model   delta    sigma   weight residual
     114.10  122.17   -8.07 2.00e+00 2.50e-01 1.63e+01
  angle pdb=" CB  MET B 563 "
        pdb=" CG  MET B 563 "
        pdb=" SD  MET B 563 "
      ideal   model   delta    sigma   weight residual
     112.70  102.26   10.44 3.00e+00 1.11e-01 1.21e+01
  angle pdb=" CB  MET A 299 "
        pdb=" CG  MET A 299 "
        pdb=" SD  MET A 299 "
      ideal   model   delta    sigma   weight residual
     112.70  123.07  -10.37 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" CA  GLU A 493 "
        pdb=" CB  GLU A 493 "
        pdb=" CG  GLU A 493 "
      ideal   model   delta    sigma   weight residual
     114.10  120.77   -6.67 2.00e+00 2.50e-01 1.11e+01
  ... (remaining 14543 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 5413
       17.83 -    35.66: 823
       35.66 -    53.48: 284
       53.48 -    71.31: 63
       71.31 -    89.14: 29
  Dihedral angle restraints: 6612
    sinusoidal: 2829
      harmonic: 3783
  Sorted by residual:
  dihedral pdb=" CA  PRO A 200 "
           pdb=" C   PRO A 200 "
           pdb=" N   ASN A 201 "
           pdb=" CA  ASN A 201 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.75   18.25     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  HIS A 940 "
           pdb=" C   HIS A 940 "
           pdb=" N   LYS A 941 "
           pdb=" CA  LYS A 941 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.02   17.98     0      5.00e+00 4.00e-02 1.29e+01
  dihedral pdb=" CA  SER A 199 "
           pdb=" C   SER A 199 "
           pdb=" N   PRO A 200 "
           pdb=" CA  PRO A 200 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  ... (remaining 6609 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 971
       0.031 -    0.061: 392
       0.061 -    0.092: 128
       0.092 -    0.123: 71
       0.123 -    0.154: 8
  Chirality restraints: 1570
  Sorted by residual:
  chirality pdb=" CB  ILE A 197 "
            pdb=" CA  ILE A 197 "
            pdb=" CG1 ILE A 197 "
            pdb=" CG2 ILE A 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.15 2.00e-01 2.50e+01 5.90e-01
  chirality pdb=" CA  ILE A 191 "
            pdb=" N   ILE A 191 "
            pdb=" C   ILE A 191 "
            pdb=" CB  ILE A 191 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.81e-01
  chirality pdb=" CA  ILE A 561 "
            pdb=" N   ILE A 561 "
            pdb=" C   ILE A 561 "
            pdb=" CB  ILE A 561 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.52e-01
  ... (remaining 1567 not shown)

  Planarity restraints: 1871
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 282 "    0.029 5.00e-02 4.00e+02   4.38e-02 3.07e+00
        pdb=" N   PRO A 283 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 420 "    0.024 5.00e-02 4.00e+02   3.65e-02 2.14e+00
        pdb=" N   PRO A 421 "   -0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A 421 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 421 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 216 "   -0.022 5.00e-02 4.00e+02   3.28e-02 1.73e+00
        pdb=" N   PRO A 217 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 217 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 217 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 1868 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2293
        2.78 -     3.31: 9871
        3.31 -     3.84: 18197
        3.84 -     4.37: 20893
        4.37 -     4.90: 35063
  Nonbonded interactions: 86317
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 884 "
            pdb=" OD1 ASP A 925 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   GLY B 321 "
            pdb=" ND2 ASN B 323 "
     model   vdw
     2.263 3.120
  nonbonded pdb=" N   ASN B 319 "
            pdb=" ND2 ASN B 319 "
     model   vdw
     2.293 3.200
  nonbonded pdb=" ND2 ASN A 782 "
            pdb=" OD1 ASN A 796 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" NH2 ARG A 398 "
            pdb=" OD1 ASP A 434 "
     model   vdw
     2.296 3.120
  ... (remaining 86312 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.500
  Check model and map are aligned:         0.040
  Set scattering table:                    0.020
  Process input model:                     12.260
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  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:6.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
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   0.068  10793  Z= 0.133
  Angle     :  0.641  10.437  14548  Z= 0.317
  Chirality :  0.041   0.154   1570
  Planarity :  0.004   0.047   1871
  Dihedral  : 20.067  89.140   4158
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.06 %
    Allowed  : 33.73 %
    Favored  : 63.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.79 (0.24), residues: 1270
  helix:  1.62 (0.22), residues: 575
  sheet: -0.03 (0.42), residues: 162
  loop : -0.47 (0.27), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 543 
 TYR   0.017   0.001   TYR B 470 
 PHE   0.021   0.002   PHE A 744 
 TRP   0.011   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A1047 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (10793)
  covalent geometry    : angle       0.64110 (14548)
  hydrogen bonds       : bond        0.15001 (  521)
  hydrogen bonds       : angle       5.56483 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  274 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 239
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  347 ASN cc_start: 0.7096 (t0) cc_final: 0.6637 (t0)
REVERT: A 1041 LYS cc_start: 0.7197 (tttm) cc_final: 0.6896 (tppp)
REVERT: B  326 MET cc_start: 0.5247 (mpp) cc_final: 0.4113 (ttp)
  outliers start: 35
  outliers final: 30
  residues processed: 272
  average time/residue: 0.6138
  time to fit residues: 178.2872
Evaluate side-chains
  259 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 229
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  573 LYS
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  690 SER
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  782 ASN
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  942 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  972 THR
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1053 THR
Chi-restraints excluded: chain B residue  330 ASP
Chi-restraints excluded: chain B residue  393 SER
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  416 TYR
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  533 SER
Chi-restraints excluded: chain B residue  576 THR
Chi-restraints excluded: chain B residue  578 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    9.9990
   chunk 33 optimal weight:    0.0050
   chunk 123 optimal weight:   10.0000
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    1.3400

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
B 478 GLN
B 552 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.189651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.147733 restraints weight = 21731.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 2.66
r_work: 0.3462 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.3333 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.122         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.0735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10793  Z= 0.121
  Angle     :  0.562   8.825  14548  Z= 0.286
  Chirality :  0.041   0.151   1570
  Planarity :  0.004   0.037   1871
  Dihedral  :  7.356  59.322   1465
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 30.16 %
    Favored  : 64.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.00 (0.24), residues: 1270
  helix:  1.83 (0.22), residues: 590
  sheet: -0.03 (0.40), residues: 162
  loop : -0.44 (0.27), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 557 
 TYR   0.017   0.001   TYR B 470 
 PHE   0.021   0.001   PHE A 744 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10793)
  covalent geometry    : angle       0.56162 (14548)
  hydrogen bonds       : bond        0.04734 (  521)
  hydrogen bonds       : angle       4.36346 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 251
  time to evaluate  : 0.332 
Fit side-chains
REVERT: A  107 ASN cc_start: 0.7660 (t0) cc_final: 0.7426 (t0)
REVERT: A  278 MET cc_start: 0.7564 (mmm) cc_final: 0.7163 (mpp)
REVERT: A  739 MET cc_start: 0.8057 (mtt) cc_final: 0.7610 (mtt)
REVERT: A  772 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.6395 (mtp)
REVERT: A  843 ASP cc_start: 0.8224 (t70) cc_final: 0.8016 (t70)
REVERT: A  861 GLN cc_start: 0.8213 (OUTLIER) cc_final: 0.7797 (mt0)
REVERT: A 1041 LYS cc_start: 0.7512 (OUTLIER) cc_final: 0.7111 (tppp)
REVERT: B  326 MET cc_start: 0.5344 (mpp) cc_final: 0.3941 (ttp)
REVERT: B  364 MET cc_start: 0.6758 (mpt) cc_final: 0.6057 (mpt)
REVERT: B  469 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6714 (tp30)
REVERT: B  532 LYS cc_start: 0.5573 (OUTLIER) cc_final: 0.5202 (mmmm)
REVERT: B  542 ARG cc_start: 0.7448 (OUTLIER) cc_final: 0.6022 (ttm170)
  outliers start: 66
  outliers final: 26
  residues processed: 289
  average time/residue: 0.6201
  time to fit residues: 191.5856
Evaluate side-chains
  268 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 236
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  572 VAL
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  941 LYS
Chi-restraints excluded: chain A residue  942 LYS
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  466 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  524 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 33 optimal weight:    0.0370
   chunk 124 optimal weight:    9.9990
   chunk 78 optimal weight:   10.0000
   chunk 116 optimal weight:    6.9990
   chunk 115 optimal weight:   10.0000
   chunk 101 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0870
   chunk 73 optimal weight:    3.9990
   chunk 58 optimal weight:    8.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   overall best weight:    1.4240

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

Flipped N/Q/H residues before XYZ refinement:
A  47 HIS
A  59 HIS
A 822 ASN
A 826 ASN
A 958 GLN
A1047 HIS
B 319 ASN
B 323 ASN
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.189877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.149954 restraints weight = 15609.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3658 rms_B_bonded: 2.10
r_work: 0.3510 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3390 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3390
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.0931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  10793  Z= 0.118
  Angle     :  0.548   7.969  14548  Z= 0.277
  Chirality :  0.040   0.153   1570
  Planarity :  0.003   0.045   1871
  Dihedral  :  6.446  58.842   1445
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 31.86 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.10 (0.24), residues: 1270
  helix:  1.89 (0.21), residues: 598
  sheet: -0.03 (0.40), residues: 160
  loop : -0.36 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 557 
 TYR   0.018   0.001   TYR B 470 
 PHE   0.016   0.001   PHE A 128 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10793)
  covalent geometry    : angle       0.54812 (14548)
  hydrogen bonds       : bond        0.04414 (  521)
  hydrogen bonds       : angle       4.13057 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 242
  time to evaluate  : 0.434 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7303 (mt-10)
REVERT: A  211 ILE cc_start: 0.8800 (OUTLIER) cc_final: 0.8376 (pp)
REVERT: A  278 MET cc_start: 0.7438 (mmm) cc_final: 0.7089 (mpp)
REVERT: A  347 ASN cc_start: 0.7296 (OUTLIER) cc_final: 0.6914 (t0)
REVERT: A  772 MET cc_start: 0.8074 (OUTLIER) cc_final: 0.6271 (mtp)
REVERT: A  843 ASP cc_start: 0.8111 (t70) cc_final: 0.7909 (t70)
REVERT: A  861 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7749 (mt0)
REVERT: A 1041 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.7075 (tppp)
REVERT: B  326 MET cc_start: 0.5336 (mpp) cc_final: 0.4023 (ttm)
REVERT: B  364 MET cc_start: 0.6621 (mpt) cc_final: 0.5759 (mpt)
REVERT: B  469 GLU cc_start: 0.6880 (OUTLIER) cc_final: 0.6661 (tp30)
REVERT: B  478 GLN cc_start: 0.7541 (tp40) cc_final: 0.6840 (tm-30)
REVERT: B  479 MET cc_start: 0.7565 (mtm) cc_final: 0.7011 (mpp)
REVERT: B  542 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.5921 (ttm170)
REVERT: B  575 LYS cc_start: 0.6957 (ttmt) cc_final: 0.6685 (ptmm)
  outliers start: 52
  outliers final: 24
  residues processed: 269
  average time/residue: 0.6281
  time to fit residues: 180.7132
Evaluate side-chains
  266 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 234
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  550 LYS
Chi-restraints excluded: chain B residue  551 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 39 optimal weight:    0.7980
   chunk 120 optimal weight:   20.0000
   chunk 11 optimal weight:    4.9990
   chunk 49 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   chunk 2 optimal weight:   10.0000
   chunk 83 optimal weight:    4.9990
   chunk 91 optimal weight:    0.8980
   chunk 31 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    2.5386

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 107 ASN
A 826 ASN
A 958 GLN
A1047 HIS
B 319 ASN
B 552 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.188004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.147253 restraints weight = 18049.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.3623 rms_B_bonded: 2.21
r_work: 0.3475 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.3348 rms_B_bonded: 4.05 restraints_weight: 0.2500
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
moved from start:          0.0992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.068  10793  Z= 0.152
  Angle     :  0.587  11.778  14548  Z= 0.296
  Chirality :  0.042   0.169   1570
  Planarity :  0.004   0.043   1871
  Dihedral  :  5.700  58.871   1425
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  5.69 %
    Allowed  : 30.84 %
    Favored  : 63.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.08 (0.24), residues: 1270
  helix:  1.86 (0.21), residues: 598
  sheet:  0.05 (0.40), residues: 160
  loop : -0.39 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 557 
 TYR   0.022   0.001   TYR B 470 
 PHE   0.014   0.002   PHE A 128 
 TRP   0.009   0.001   TRP A 574 
 HIS   0.004   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (10793)
  covalent geometry    : angle       0.58744 (14548)
  hydrogen bonds       : bond        0.04782 (  521)
  hydrogen bonds       : angle       4.16646 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  304 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 238
  time to evaluate  : 0.479 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7983 (OUTLIER) cc_final: 0.7293 (mt-10)
REVERT: A  211 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8419 (pp)
REVERT: A  263 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7731 (mm-30)
REVERT: A  297 LEU cc_start: 0.7908 (OUTLIER) cc_final: 0.7682 (pp)
REVERT: A  347 ASN cc_start: 0.7338 (OUTLIER) cc_final: 0.6949 (t0)
REVERT: A  741 ARG cc_start: 0.7032 (mpp-170) cc_final: 0.6782 (mpp-170)
REVERT: A  772 MET cc_start: 0.8070 (OUTLIER) cc_final: 0.6555 (mtp)
REVERT: A  777 ARG cc_start: 0.6049 (OUTLIER) cc_final: 0.4590 (mpt90)
REVERT: A  857 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8290 (mm)
REVERT: A  861 GLN cc_start: 0.8168 (OUTLIER) cc_final: 0.7794 (mt0)
REVERT: A 1041 LYS cc_start: 0.7524 (OUTLIER) cc_final: 0.7137 (tppp)
REVERT: B  326 MET cc_start: 0.5374 (mpp) cc_final: 0.3830 (ttp)
REVERT: B  364 MET cc_start: 0.6664 (mpt) cc_final: 0.5724 (mpt)
REVERT: B  404 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8284 (tp)
REVERT: B  469 GLU cc_start: 0.6899 (OUTLIER) cc_final: 0.6683 (tp30)
REVERT: B  478 GLN cc_start: 0.7567 (tp40) cc_final: 0.7110 (tp-100)
REVERT: B  532 LYS cc_start: 0.5580 (OUTLIER) cc_final: 0.5230 (mmmm)
REVERT: B  542 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.5933 (ttm170)
REVERT: B  562 ARG cc_start: 0.7404 (mtp-110) cc_final: 0.7103 (mtp180)
REVERT: B  572 GLN cc_start: 0.6431 (mm110) cc_final: 0.5763 (tp-100)
REVERT: B  575 LYS cc_start: 0.6930 (ttmt) cc_final: 0.5965 (ptpt)
  outliers start: 66
  outliers final: 28
  residues processed: 274
  average time/residue: 0.6347
  time to fit residues: 185.3996
Evaluate side-chains
  273 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 231
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  352 ASP
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  404 LEU
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 22 optimal weight:    8.9990
   chunk 117 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 75 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0470
   chunk 9 optimal weight:    1.9990
   chunk 29 optimal weight:    6.9990
   chunk 95 optimal weight:    1.9990
   chunk 125 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.4084

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

Flipped N/Q/H residues before XYZ refinement:
A  59 HIS
A 107 ASN
A 822 ASN
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 319 ASN
** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.188845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.151394 restraints weight = 15434.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 1.83
r_work: 0.3482 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3348
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3348 r_free = 0.3348    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3348
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.1051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10793  Z= 0.117
  Angle     :  0.558  10.956  14548  Z= 0.279
  Chirality :  0.040   0.152   1570
  Planarity :  0.003   0.046   1871
  Dihedral  :  5.586  59.888   1425
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  5.10 %
    Allowed  : 31.61 %
    Favored  : 63.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.18 (0.24), residues: 1270
  helix:  1.96 (0.21), residues: 599
  sheet:  0.02 (0.40), residues: 160
  loop : -0.33 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 557 
 TYR   0.017   0.001   TYR B 470 
 PHE   0.015   0.001   PHE A 937 
 TRP   0.010   0.001   TRP A 669 
 HIS   0.002   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (10793)
  covalent geometry    : angle       0.55844 (14548)
  hydrogen bonds       : bond        0.04290 (  521)
  hydrogen bonds       : angle       4.05871 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 240
  time to evaluate  : 0.415 
Fit side-chains
REVERT: A  172 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7391 (mt-10)
REVERT: A  211 ILE cc_start: 0.8839 (OUTLIER) cc_final: 0.8456 (pp)
REVERT: A  263 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7696 (mm-30)
REVERT: A  278 MET cc_start: 0.7499 (mmm) cc_final: 0.6947 (mpp)
REVERT: A  297 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7655 (pp)
REVERT: A  768 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7543 (mm-30)
REVERT: A  772 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.6449 (mtp)
REVERT: A  777 ARG cc_start: 0.6065 (OUTLIER) cc_final: 0.4911 (mpt90)
REVERT: A  857 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8224 (mm)
REVERT: A  861 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7810 (mt0)
REVERT: A 1041 LYS cc_start: 0.7493 (tttm) cc_final: 0.7095 (tppp)
REVERT: B  326 MET cc_start: 0.5426 (mpp) cc_final: 0.3859 (ttp)
REVERT: B  364 MET cc_start: 0.6656 (mpt) cc_final: 0.5790 (mpt)
REVERT: B  433 GLN cc_start: 0.5705 (OUTLIER) cc_final: 0.5450 (mt0)
REVERT: B  469 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6699 (tp30)
REVERT: B  478 GLN cc_start: 0.7536 (tp40) cc_final: 0.6812 (tm-30)
REVERT: B  479 MET cc_start: 0.7581 (mtm) cc_final: 0.6981 (mpp)
REVERT: B  532 LYS cc_start: 0.5590 (OUTLIER) cc_final: 0.5226 (mmmm)
REVERT: B  542 ARG cc_start: 0.7463 (OUTLIER) cc_final: 0.6007 (ttm170)
REVERT: B  575 LYS cc_start: 0.6924 (ttmt) cc_final: 0.6674 (ptmm)
  outliers start: 59
  outliers final: 25
  residues processed: 271
  average time/residue: 0.6349
  time to fit residues: 183.5080
Evaluate side-chains
  272 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 235
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  449 LEU
Chi-restraints excluded: chain B residue  469 GLU
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 102 optimal weight:    3.9990
   chunk 47 optimal weight:   40.0000
   chunk 12 optimal weight:    9.9990
   chunk 31 optimal weight:    7.9990
   chunk 104 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0070
   chunk 117 optimal weight:   10.0000
   chunk 83 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    3.4004

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** 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 = 0.4055 r_free = 0.4055 target = 0.186239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.145041 restraints weight = 23521.140|
|-----------------------------------------------------------------------------|
r_work (start): 0.3586 rms_B_bonded: 2.65
r_work: 0.3424 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3285
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3285 r_free = 0.3285    target_work(ls_wunit_k1) = 0.119         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3285
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8277
moved from start:          0.1099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078  10793  Z= 0.184
  Angle     :  0.633  10.380  14548  Z= 0.315
  Chirality :  0.044   0.186   1570
  Planarity :  0.004   0.055   1871
  Dihedral  :  5.706  59.220   1423
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  5.18 %
    Allowed  : 31.35 %
    Favored  : 63.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.98 (0.24), residues: 1270
  helix:  1.79 (0.21), residues: 597
  sheet:  0.00 (0.39), residues: 166
  loop : -0.46 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 557 
 TYR   0.028   0.002   TYR A 622 
 PHE   0.015   0.002   PHE A 128 
 TRP   0.009   0.001   TRP A 574 
 HIS   0.005   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (10793)
  covalent geometry    : angle       0.63307 (14548)
  hydrogen bonds       : bond        0.05029 (  521)
  hydrogen bonds       : angle       4.19736 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 234
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7996 (tppt)
REVERT: A  172 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7361 (mt-10)
REVERT: A  211 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8494 (pp)
REVERT: A  263 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7780 (mm-30)
REVERT: A  297 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7706 (pp)
REVERT: A  772 MET cc_start: 0.8133 (OUTLIER) cc_final: 0.6743 (mtp)
REVERT: A  777 ARG cc_start: 0.6140 (OUTLIER) cc_final: 0.5026 (mpt90)
REVERT: A  857 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8520 (mp)
REVERT: A  861 GLN cc_start: 0.8250 (OUTLIER) cc_final: 0.7873 (mt0)
REVERT: A 1041 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7171 (tppp)
REVERT: B  326 MET cc_start: 0.5431 (mpp) cc_final: 0.3781 (ttp)
REVERT: B  364 MET cc_start: 0.6689 (mpt) cc_final: 0.5801 (mpt)
REVERT: B  433 GLN cc_start: 0.5744 (OUTLIER) cc_final: 0.5483 (mt0)
REVERT: B  478 GLN cc_start: 0.7569 (tp40) cc_final: 0.7099 (tp-100)
REVERT: B  479 MET cc_start: 0.7633 (mtm) cc_final: 0.7047 (mpp)
REVERT: B  532 LYS cc_start: 0.5649 (OUTLIER) cc_final: 0.5279 (mmmm)
REVERT: B  542 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.5929 (ttm170)
REVERT: B  551 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7375 (mttp)
REVERT: B  575 LYS cc_start: 0.6899 (ttmt) cc_final: 0.6660 (ptmm)
  outliers start: 60
  outliers final: 28
  residues processed: 260
  average time/residue: 0.6609
  time to fit residues: 183.1199
Evaluate side-chains
  272 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 230
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 16 optimal weight:    0.2980
   chunk 76 optimal weight:    5.9990
   chunk 31 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 118 optimal weight:    3.9990
   chunk 48 optimal weight:    8.9990
   chunk 123 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    1.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 552 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.188117 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.149386 restraints weight = 17089.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3653 rms_B_bonded: 2.01
r_work: 0.3422 rms_B_bonded: 3.12 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3416
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3416 r_free = 0.3416    target_work(ls_wunit_k1) = 0.129         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3416
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8146
moved from start:          0.1131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10793  Z= 0.127
  Angle     :  0.594  10.557  14548  Z= 0.293
  Chirality :  0.041   0.180   1570
  Planarity :  0.003   0.045   1871
  Dihedral  :  5.598  59.876   1423
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 32.03 %
    Favored  : 63.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.08 (0.24), residues: 1270
  helix:  1.88 (0.21), residues: 598
  sheet: -0.02 (0.39), residues: 166
  loop : -0.39 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 557 
 TYR   0.028   0.001   TYR A 622 
 PHE   0.013   0.001   PHE A 128 
 TRP   0.010   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10793)
  covalent geometry    : angle       0.59434 (14548)
  hydrogen bonds       : bond        0.04434 (  521)
  hydrogen bonds       : angle       4.08249 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 236
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8387 (OUTLIER) cc_final: 0.7881 (tppt)
REVERT: A  172 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7298 (mt-10)
REVERT: A  211 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8431 (pp)
REVERT: A  263 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7532 (mm-30)
REVERT: A  297 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7681 (pp)
REVERT: A  347 ASN cc_start: 0.7311 (OUTLIER) cc_final: 0.6970 (t0)
REVERT: A  741 ARG cc_start: 0.6909 (mpp-170) cc_final: 0.6677 (mpp-170)
REVERT: A  768 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7491 (mm-30)
REVERT: A  772 MET cc_start: 0.7994 (OUTLIER) cc_final: 0.6398 (mtp)
REVERT: A  777 ARG cc_start: 0.6005 (OUTLIER) cc_final: 0.4886 (mpt90)
REVERT: A  857 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8222 (mm)
REVERT: A  861 GLN cc_start: 0.8132 (OUTLIER) cc_final: 0.7762 (mt0)
REVERT: A 1041 LYS cc_start: 0.7439 (OUTLIER) cc_final: 0.7076 (tppp)
REVERT: B  326 MET cc_start: 0.5397 (mpp) cc_final: 0.3832 (ttp)
REVERT: B  364 MET cc_start: 0.6609 (mpt) cc_final: 0.5767 (mpt)
REVERT: B  433 GLN cc_start: 0.5731 (OUTLIER) cc_final: 0.5461 (mt0)
REVERT: B  478 GLN cc_start: 0.7453 (tp40) cc_final: 0.6779 (tm-30)
REVERT: B  479 MET cc_start: 0.7368 (mtm) cc_final: 0.6822 (mpp)
REVERT: B  532 LYS cc_start: 0.5556 (OUTLIER) cc_final: 0.5228 (mmmm)
REVERT: B  542 ARG cc_start: 0.7392 (OUTLIER) cc_final: 0.5952 (ttm170)
REVERT: B  551 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.7250 (mttp)
REVERT: B  575 LYS cc_start: 0.6861 (ttmt) cc_final: 0.6634 (ptmm)
  outliers start: 51
  outliers final: 25
  residues processed: 260
  average time/residue: 0.6609
  time to fit residues: 182.9729
Evaluate side-chains
  273 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 233
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  529 ASP
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  571 ILE
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 8 optimal weight:    6.9990
   chunk 26 optimal weight:    0.8980
   chunk 98 optimal weight:    7.9990
   chunk 0 optimal weight:   20.0000
   chunk 118 optimal weight:    9.9990
   chunk 115 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 66 optimal weight:    9.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** 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 = 0.4060 r_free = 0.4060 target = 0.186786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.145710 restraints weight = 20378.271|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 2.42
r_work: 0.3445 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.20 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3314
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3314 r_free = 0.3314    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3314
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070  10793  Z= 0.156
  Angle     :  0.629  11.061  14548  Z= 0.310
  Chirality :  0.043   0.179   1570
  Planarity :  0.004   0.050   1871
  Dihedral  :  5.496  59.827   1421
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 32.03 %
    Favored  : 63.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.99 (0.24), residues: 1270
  helix:  1.79 (0.21), residues: 598
  sheet: -0.02 (0.39), residues: 166
  loop : -0.43 (0.28), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 557 
 TYR   0.021   0.002   TYR B 470 
 PHE   0.012   0.002   PHE A 980 
 TRP   0.009   0.001   TRP A 574 
 HIS   0.004   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 (10793)
  covalent geometry    : angle       0.62896 (14548)
  hydrogen bonds       : bond        0.04785 (  521)
  hydrogen bonds       : angle       4.13902 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  286 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 235
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8475 (OUTLIER) cc_final: 0.7968 (tppt)
REVERT: A  172 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7394 (mt-10)
REVERT: A  179 LYS cc_start: 0.7390 (OUTLIER) cc_final: 0.6917 (tppt)
REVERT: A  211 ILE cc_start: 0.8901 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: A  263 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7676 (mm-30)
REVERT: A  297 LEU cc_start: 0.7912 (OUTLIER) cc_final: 0.7693 (pp)
REVERT: A  347 ASN cc_start: 0.7347 (OUTLIER) cc_final: 0.7009 (t0)
REVERT: A  768 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7559 (mm-30)
REVERT: A  772 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.6669 (mtp)
REVERT: A  777 ARG cc_start: 0.6101 (OUTLIER) cc_final: 0.5021 (mpt90)
REVERT: A  857 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8277 (mm)
REVERT: A  861 GLN cc_start: 0.8225 (OUTLIER) cc_final: 0.7864 (mt0)
REVERT: A 1041 LYS cc_start: 0.7556 (OUTLIER) cc_final: 0.7134 (tppp)
REVERT: B  364 MET cc_start: 0.6643 (mpt) cc_final: 0.5780 (mpt)
REVERT: B  433 GLN cc_start: 0.5746 (OUTLIER) cc_final: 0.5483 (mt0)
REVERT: B  478 GLN cc_start: 0.7565 (tp40) cc_final: 0.6814 (tm-30)
REVERT: B  479 MET cc_start: 0.7572 (mtm) cc_final: 0.6967 (mpp)
REVERT: B  532 LYS cc_start: 0.5616 (OUTLIER) cc_final: 0.5244 (mmmm)
REVERT: B  542 ARG cc_start: 0.7473 (OUTLIER) cc_final: 0.5908 (ttm170)
REVERT: B  551 LYS cc_start: 0.7577 (OUTLIER) cc_final: 0.7331 (mttp)
REVERT: B  562 ARG cc_start: 0.7476 (mtp180) cc_final: 0.7049 (mtp-110)
  outliers start: 51
  outliers final: 26
  residues processed: 259
  average time/residue: 0.6746
  time to fit residues: 185.8311
Evaluate side-chains
  275 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 233
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  172 GLU
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  782 ASN
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  576 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 121 optimal weight:    1.9990
   chunk 85 optimal weight:    7.9990
   chunk 79 optimal weight:    8.9990
   chunk 16 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 27 optimal weight:    5.9990
   chunk 115 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 108 optimal weight:   10.0000
   chunk 117 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    1.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** 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 = 0.4070 r_free = 0.4070 target = 0.187825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.148661 restraints weight = 17943.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 2.47
r_work: 0.3446 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3318 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3310
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3310 r_free = 0.3310    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3310
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.1206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10793  Z= 0.135
  Angle     :  0.618  11.038  14548  Z= 0.304
  Chirality :  0.042   0.170   1570
  Planarity :  0.004   0.047   1871
  Dihedral  :  5.277  59.921   1419
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 31.78 %
    Favored  : 63.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.12 (0.24), residues: 1270
  helix:  1.89 (0.21), residues: 592
  sheet: -0.04 (0.39), residues: 166
  loop : -0.30 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 557 
 TYR   0.019   0.001   TYR B 470 
 PHE   0.014   0.001   PHE A 977 
 TRP   0.010   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10793)
  covalent geometry    : angle       0.61805 (14548)
  hydrogen bonds       : bond        0.04523 (  521)
  hydrogen bonds       : angle       4.07937 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 234
  time to evaluate  : 0.412 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7938 (tppt)
REVERT: A  179 LYS cc_start: 0.7360 (OUTLIER) cc_final: 0.6900 (tppt)
REVERT: A  211 ILE cc_start: 0.8915 (OUTLIER) cc_final: 0.8531 (pp)
REVERT: A  263 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7747 (mm-30)
REVERT: A  278 MET cc_start: 0.7703 (mmm) cc_final: 0.7185 (mpp)
REVERT: A  347 ASN cc_start: 0.7329 (OUTLIER) cc_final: 0.6968 (t0)
REVERT: A  768 GLU cc_start: 0.7808 (mm-30) cc_final: 0.7600 (mm-30)
REVERT: A  772 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.6630 (mtp)
REVERT: A  777 ARG cc_start: 0.6120 (OUTLIER) cc_final: 0.4979 (mpt90)
REVERT: A  857 ILE cc_start: 0.8782 (OUTLIER) cc_final: 0.8244 (mm)
REVERT: A  861 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7876 (mt0)
REVERT: A 1041 LYS cc_start: 0.7543 (OUTLIER) cc_final: 0.7128 (tppp)
REVERT: B  364 MET cc_start: 0.6665 (mpt) cc_final: 0.5831 (mpt)
REVERT: B  433 GLN cc_start: 0.5730 (OUTLIER) cc_final: 0.5463 (mt0)
REVERT: B  478 GLN cc_start: 0.7578 (tp40) cc_final: 0.6821 (tm-30)
REVERT: B  479 MET cc_start: 0.7558 (mtm) cc_final: 0.6953 (mpp)
REVERT: B  532 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5244 (mmmm)
REVERT: B  542 ARG cc_start: 0.7474 (OUTLIER) cc_final: 0.5941 (ttm170)
REVERT: B  551 LYS cc_start: 0.7560 (OUTLIER) cc_final: 0.7340 (mttp)
REVERT: B  562 ARG cc_start: 0.7478 (mtp180) cc_final: 0.7055 (mtp-110)
  outliers start: 53
  outliers final: 28
  residues processed: 260
  average time/residue: 0.6548
  time to fit residues: 181.4336
Evaluate side-chains
  272 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 230
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  347 ASN
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  782 ASN
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  964 ILE
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  576 THR
Chi-restraints excluded: chain B residue  578 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 16 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 116 optimal weight:    9.9990
   chunk 92 optimal weight:    5.9990
   chunk 41 optimal weight:   10.0000
   chunk 68 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 87 optimal weight:    0.5980
   chunk 102 optimal weight:    3.9990
   chunk 122 optimal weight:    4.9990
   overall best weight:    2.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** 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 = 0.4056 r_free = 0.4056 target = 0.186343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.146387 restraints weight = 14234.586|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 2.01
r_work: 0.3444 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3315
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3315 r_free = 0.3315    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3315
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.1217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077  10793  Z= 0.169
  Angle     :  0.665  12.134  14548  Z= 0.326
  Chirality :  0.044   0.182   1570
  Planarity :  0.004   0.051   1871
  Dihedral  :  5.390  59.715   1419
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.34 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 32.63 %
    Favored  : 63.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  0.94 (0.24), residues: 1270
  helix:  1.70 (0.21), residues: 599
  sheet: -0.01 (0.40), residues: 160
  loop : -0.41 (0.28), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 557 
 TYR   0.022   0.002   TYR B 470 
 PHE   0.013   0.002   PHE A 980 
 TRP   0.009   0.001   TRP A 574 
 HIS   0.004   0.001   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10793)
  covalent geometry    : angle       0.66494 (14548)
  hydrogen bonds       : bond        0.04908 (  521)
  hydrogen bonds       : angle       4.16951 ( 1492)

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

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

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2540 Ramachandran restraints generated.
    1270 Oldfield, 0 Emsley, 1270 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 232
  time to evaluate  : 0.445 
Fit side-chains
REVERT: A  148 LYS cc_start: 0.8482 (OUTLIER) cc_final: 0.7959 (tppt)
REVERT: A  211 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8499 (pp)
REVERT: A  263 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7669 (mm-30)
REVERT: A  768 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7562 (mm-30)
REVERT: A  772 MET cc_start: 0.8082 (OUTLIER) cc_final: 0.6680 (mtp)
REVERT: A  777 ARG cc_start: 0.6105 (OUTLIER) cc_final: 0.5021 (mpt90)
REVERT: A  861 GLN cc_start: 0.8232 (OUTLIER) cc_final: 0.7848 (mt0)
REVERT: A 1041 LYS cc_start: 0.7575 (OUTLIER) cc_final: 0.7160 (tppp)
REVERT: B  364 MET cc_start: 0.6670 (mpt) cc_final: 0.5846 (mpt)
REVERT: B  433 GLN cc_start: 0.5745 (OUTLIER) cc_final: 0.5477 (mt0)
REVERT: B  478 GLN cc_start: 0.7529 (tp40) cc_final: 0.6790 (tm-30)
REVERT: B  479 MET cc_start: 0.7543 (mtm) cc_final: 0.6934 (mpp)
REVERT: B  532 LYS cc_start: 0.5598 (OUTLIER) cc_final: 0.5232 (mmmm)
REVERT: B  542 ARG cc_start: 0.7443 (OUTLIER) cc_final: 0.5873 (ttm170)
REVERT: B  551 LYS cc_start: 0.7559 (OUTLIER) cc_final: 0.7303 (mttp)
REVERT: B  562 ARG cc_start: 0.7448 (mtp180) cc_final: 0.7023 (mtp-110)
  outliers start: 46
  outliers final: 29
  residues processed: 256
  average time/residue: 0.6344
  time to fit residues: 173.1436
Evaluate side-chains
  270 residues out of total 1175 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 230
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 LEU
Chi-restraints excluded: chain A residue   30 MET
Chi-restraints excluded: chain A residue   33 THR
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  148 LYS
Chi-restraints excluded: chain A residue  179 LYS
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  211 ILE
Chi-restraints excluded: chain A residue  228 LYS
Chi-restraints excluded: chain A residue  263 GLU
Chi-restraints excluded: chain A residue  303 THR
Chi-restraints excluded: chain A residue  378 CYS
Chi-restraints excluded: chain A residue  418 GLU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  490 SER
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  577 ARG
Chi-restraints excluded: chain A residue  578 ASP
Chi-restraints excluded: chain A residue  650 VAL
Chi-restraints excluded: chain A residue  772 MET
Chi-restraints excluded: chain A residue  777 ARG
Chi-restraints excluded: chain A residue  782 ASN
Chi-restraints excluded: chain A residue  845 VAL
Chi-restraints excluded: chain A residue  861 GLN
Chi-restraints excluded: chain A residue  947 TYR
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1017 ASP
Chi-restraints excluded: chain A residue 1025 THR
Chi-restraints excluded: chain A residue 1034 GLU
Chi-restraints excluded: chain A residue 1041 LYS
Chi-restraints excluded: chain B residue  343 VAL
Chi-restraints excluded: chain B residue  370 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  433 GLN
Chi-restraints excluded: chain B residue  484 ILE
Chi-restraints excluded: chain B residue  532 LYS
Chi-restraints excluded: chain B residue  542 ARG
Chi-restraints excluded: chain B residue  551 LYS
Chi-restraints excluded: chain B residue  576 THR
Chi-restraints excluded: chain B residue  578 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 22 optimal weight:    0.0030
   chunk 64 optimal weight:   10.0000
   chunk 86 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0670
   chunk 43 optimal weight:    9.9990
   chunk 40 optimal weight:    2.9990
   chunk 125 optimal weight:   10.0000
   chunk 92 optimal weight:    4.9990
   chunk 107 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   overall best weight:    1.7932

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

Flipped N/Q/H residues before XYZ refinement:
A 826 ASN
A 958 GLN
** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 552 GLN ** 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 = 0.4075 r_free = 0.4075 target = 0.188267 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.147221 restraints weight = 23056.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 2.62
r_work: 0.3455 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3324 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3316
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3316 r_free = 0.3316    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3316
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.1232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10793  Z= 0.134
  Angle     :  0.646  11.974  14548  Z= 0.313
  Chirality :  0.042   0.204   1570
  Planarity :  0.004   0.048   1871
  Dihedral  :  5.282  59.883   1419
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 33.05 %
    Favored  : 63.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.08 %
    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:  1.08 (0.24), residues: 1270
  helix:  1.85 (0.21), residues: 592
  sheet: -0.05 (0.39), residues: 166
  loop : -0.31 (0.28), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 557 
 TYR   0.019   0.001   TYR B 470 
 PHE   0.011   0.001   PHE A 667 
 TRP   0.010   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 676 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 (10793)
  covalent geometry    : angle       0.64587 (14548)
  hydrogen bonds       : bond        0.04504 (  521)
  hydrogen bonds       : angle       4.09656 ( 1492)

===============================================================================
Job complete
usr+sys time: 5986.33 seconds
wall clock time: 102 minutes 4.02 seconds (6124.02 seconds total)