Starting phenix.real_space_refine
on Wed Apr 30 22:28:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vpp_43412/04_2025/8vpp_43412_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vpp_43412/04_2025/8vpp_43412.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vpp_43412/04_2025/8vpp_43412.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vpp_43412/04_2025/8vpp_43412.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vpp_43412/04_2025/8vpp_43412_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vpp_43412/04_2025/8vpp_43412_trim.cif"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.036
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      55      5.16       5
     Cl      1      4.86       5
     C    6418      2.51       5
     N    1698      2.21       5
     O    1755      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9930
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 6896
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 892, 6896
          Classifications: {'peptide': 892}
          Incomplete info: {'truncation_to_alanine': 31}
          Link IDs: {'PTRANS': 41, 'TRANS': 850}
          Chain breaks: 2
          Unresolved chain link angles: 3
          Unresolved non-hydrogen bonds: 118
          Unresolved non-hydrogen angles: 143
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 3, 'TPO:plan-1': 2, 'ASP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 58
    Chain: "B"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 3010
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 354}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 24
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 24
          Unusual residues: {'KLT': 1}
          Classifications: {'undetermined': 1, 'water': 2}
          Link IDs: {None: 2}
  Time building chain proxies: 6.72, per 1000 atoms: 0.68
  Number of scatterers: 9930
  At special positions: 0
  Unit cell: (156.87, 86.32, 113.71, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      55     16.00
     P       3     15.00
     O    1755      8.00
     N    1698      7.00
     C    6418      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 420 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 429 " - pdb=" SG  CYS A 435 " distance=2.03

  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: 2.65
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2336

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 2 sheets defined
      60.5% alpha, 6.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 66 through 71
      removed outlier: 4.228A  pdb=" N   TYR A  70 " --> pdb=" O   THR A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 90
    Processing helix  chain 'A' and resid 136 through 141
    Processing helix  chain 'A' and resid 141 through 150
    Processing helix  chain 'A' and resid 151 through 157
      removed outlier: 3.950A  pdb=" N   TYR A 155 " --> pdb=" O   GLY A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 166
    Processing helix  chain 'A' and resid 166 through 194
      removed outlier: 3.699A  pdb=" N   ASN A 194 " --> pdb=" O   ALA A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 210
    Processing helix  chain 'A' and resid 211 through 247
      removed outlier: 3.554A  pdb=" N   SER A 217 " --> pdb=" O   GLU A 213 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ALA A 231 " --> pdb=" O   ALA A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 258 through 277
      removed outlier: 3.738A  pdb=" N   GLY A 277 " --> pdb=" O   ILE A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 304
      removed outlier: 3.593A  pdb=" N   LEU A 304 " --> pdb=" O   LEU A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 314
    Processing helix  chain 'A' and resid 320 through 327
    Processing helix  chain 'A' and resid 338 through 347
    Processing helix  chain 'A' and resid 348 through 351
      removed outlier: 3.579A  pdb=" N   THR A 351 " --> pdb=" O   PRO A 348 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 348 through 351'
    Processing helix  chain 'A' and resid 356 through 363
      removed outlier: 5.476A  pdb=" N   GLY A 361 " --> pdb=" O   ASN A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 394
      Proline residue:  A 371  - end of helix
    Processing helix  chain 'A' and resid 403 through 407
    Processing helix  chain 'A' and resid 418 through 423
    Processing helix  chain 'A' and resid 426 through 431
    Processing helix  chain 'A' and resid 444 through 450
    Processing helix  chain 'A' and resid 452 through 486
      removed outlier: 3.513A  pdb=" N   ILE A 456 " --> pdb=" O   PHE A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 491 through 496
      removed outlier: 3.504A  pdb=" N   GLY A 495 " --> pdb=" O   ILE A 491 " (cutoff:3.500A)
      removed outlier: 4.076A  pdb=" N   LYS A 496 " --> pdb=" O   GLY A 492 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 491 through 496'
    Processing helix  chain 'A' and resid 504 through 522
      removed outlier: 3.948A  pdb=" N   ILE A 521 " --> pdb=" O   ALA A 517 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA A 522 " --> pdb=" O   PHE A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 553
    Processing helix  chain 'A' and resid 565 through 584
      removed outlier: 3.675A  pdb=" N   THR A 584 " --> pdb=" O   MET A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 606
    Processing helix  chain 'A' and resid 613 through 633
    Processing helix  chain 'A' and resid 650 through 653
    Processing helix  chain 'A' and resid 654 through 666
      removed outlier: 3.672A  pdb=" N   VAL A 658 " --> pdb=" O   ARG A 654 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE A 664 " --> pdb=" O   PHE A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 684 through 702
      removed outlier: 3.666A  pdb=" N   LEU A 688 " --> pdb=" O   ARG A 684 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 727
    Processing helix  chain 'A' and resid 749 through 766
      removed outlier: 3.932A  pdb=" N   VAL A 753 " --> pdb=" O   HIS A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 851
      Proline residue:  A 846  - end of helix
    Processing helix  chain 'A' and resid 852 through 856
    Processing helix  chain 'A' and resid 867 through 871
    Processing helix  chain 'A' and resid 872 through 878
    Processing helix  chain 'A' and resid 880 through 885
    Processing helix  chain 'A' and resid 895 through 899
      removed outlier: 3.597A  pdb=" N   ILE A 898 " --> pdb=" O   LEU A 895 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   ASN A 899 " --> pdb=" O   PRO A 896 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 895 through 899'
    Processing helix  chain 'A' and resid 903 through 915
    Processing helix  chain 'A' and resid 925 through 933
      removed outlier: 3.724A  pdb=" N   ARG A 933 " --> pdb=" O   VAL A 929 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 941 through 948
      removed outlier: 3.542A  pdb=" N   ILE A 945 " --> pdb=" O   SER A 941 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 948 through 966
      removed outlier: 3.597A  pdb=" N   ASP A 964 " --> pdb=" O   GLU A 960 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 997
    Processing helix  chain 'B' and resid 616 through 630
    Processing helix  chain 'B' and resid 636 through 640
    Processing helix  chain 'B' and resid 654 through 666
      removed outlier: 3.841A  pdb=" N   VAL B 658 " --> pdb=" O   ARG B 654 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 702
      Proline residue:  B 686  - end of helix
      removed outlier: 3.915A  pdb=" N   ASN B 693 " --> pdb=" O   GLN B 689 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   GLY B 694 " --> pdb=" O   LEU B 690 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 715 through 727
    Processing helix  chain 'B' and resid 749 through 766
      removed outlier: 3.596A  pdb=" N   VAL B 753 " --> pdb=" O   HIS B 749 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 819 through 823
    Processing helix  chain 'B' and resid 840 through 851
      Proline residue:  B 846  - end of helix
    Processing helix  chain 'B' and resid 870 through 886
      removed outlier: 3.734A  pdb=" N   SER B 883 " --> pdb=" O   ILE B 879 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 896 through 899
      removed outlier: 4.248A  pdb=" N   ASN B 899 " --> pdb=" O   PRO B 896 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 896 through 899'
    Processing helix  chain 'B' and resid 903 through 914
      removed outlier: 3.851A  pdb=" N   LYS B 908 " --> pdb=" O   ALA B 904 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 925 through 929
    Processing helix  chain 'B' and resid 930 through 934
      removed outlier: 3.631A  pdb=" N   ARG B 934 " --> pdb=" O   GLU B 931 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 941 through 948
      removed outlier: 3.539A  pdb=" N   LYS B 947 " --> pdb=" O   GLU B 943 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 948 through 964
    Processing helix  chain 'B' and resid 985 through 997
    Processing sheet with id=AA1, first strand: chain 'A' and resid 707 through 712
      removed outlier: 6.956A  pdb=" N   MET A 671 " --> pdb=" O   PHE A 707 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   SER A 709 " --> pdb=" O   MET A 671 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   CYS A 673 " --> pdb=" O   SER A 709 " (cutoff:3.500A)
      removed outlier: 7.599A  pdb=" N   VAL A 711 " --> pdb=" O   CYS A 673 " (cutoff:3.500A)
      removed outlier: 6.324A  pdb=" N   HIS A 675 " --> pdb=" O   VAL A 711 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   GLY A 740 " --> pdb=" O   LEU A 647 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ILE A 972 " --> pdb=" O   ILE A1005 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   ILE A1007 " --> pdb=" O   ILE A 972 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   ILE A 974 " --> pdb=" O   ILE A1007 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 971 " --> pdb=" O   THR A 829 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 707 through 712
      removed outlier: 6.617A  pdb=" N   CYS B 644 " --> pdb=" O   ILE B 672 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   GLY B 674 " --> pdb=" O   CYS B 644 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   VAL B 646 " --> pdb=" O   GLY B 674 " (cutoff:3.500A)
      removed outlier: 8.424A  pdb=" N   VAL B 676 " --> pdb=" O   VAL B 646 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   LEU B 737 " --> pdb=" O   CYS B 771 " (cutoff:3.500A)
      removed outlier: 7.470A  pdb=" N   MET B 773 " --> pdb=" O   LEU B 737 " (cutoff:3.500A)
      removed outlier: 6.876A  pdb=" N   VAL B 739 " --> pdb=" O   MET B 773 " (cutoff:3.500A)
      removed outlier: 8.488A  pdb=" N   MET B 775 " --> pdb=" O   VAL B 739 " (cutoff:3.500A)
      removed outlier: 6.530A  pdb=" N   ILE B 972 " --> pdb=" O   ILE B1005 " (cutoff:3.500A)
      removed outlier: 7.072A  pdb=" N   ILE B1007 " --> pdb=" O   ILE B 972 " (cutoff:3.500A)
      removed outlier: 5.868A  pdb=" N   ILE B 974 " --> pdb=" O   ILE B1007 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   LEU B 971 " --> pdb=" O   THR B 829 " (cutoff:3.500A)
      removed outlier: 5.916A  pdb=" N   ILE B 830 " --> pdb=" O   ARG B 861 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   PHE B 863 " --> pdb=" O   ILE B 830 " (cutoff:3.500A)
      removed outlier: 6.289A  pdb=" N   ILE B 832 " --> pdb=" O   PHE B 863 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   GLU B 891 " --> pdb=" O   ILE B 860 " (cutoff:3.500A)

    537 hydrogen bonds defined for protein.
    1542 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: 3.02

  Time building geometry restraints manager: 3.09 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2850
        1.33 -     1.45: 1666
        1.45 -     1.57: 5550
        1.57 -     1.69: 12
        1.69 -     1.82: 85
  Bond restraints: 10163
  Sorted by residual:
  bond pdb=" OG1 TPO A  55 "
       pdb=" P   TPO A  55 "
    ideal  model  delta    sigma   weight residual
    1.717  1.608  0.109 2.00e-02 2.50e+03 2.99e+01
  bond pdb=" OG1 TPO A  60 "
       pdb=" P   TPO A  60 "
    ideal  model  delta    sigma   weight residual
    1.717  1.611  0.106 2.00e-02 2.50e+03 2.79e+01
  bond pdb=" O3P TPO A  60 "
       pdb=" P   TPO A  60 "
    ideal  model  delta    sigma   weight residual
    1.528  1.611 -0.083 2.00e-02 2.50e+03 1.72e+01
  bond pdb=" O2P TPO A  55 "
       pdb=" P   TPO A  55 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" O3P TPO A  55 "
       pdb=" P   TPO A  55 "
    ideal  model  delta    sigma   weight residual
    1.528  1.610 -0.082 2.00e-02 2.50e+03 1.69e+01
  ... (remaining 10158 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 13704
        2.83 -     5.66: 86
        5.66 -     8.49: 10
        8.49 -    11.32: 5
       11.32 -    14.15: 3
  Bond angle restraints: 13808
  Sorted by residual:
  angle pdb=" CA  PRO A 985 "
        pdb=" N   PRO A 985 "
        pdb=" CD  PRO A 985 "
      ideal   model   delta    sigma   weight residual
     112.00   97.85   14.15 1.40e+00 5.10e-01 1.02e+02
  angle pdb=" N   PRO A 985 "
        pdb=" CD  PRO A 985 "
        pdb=" CG  PRO A 985 "
      ideal   model   delta    sigma   weight residual
     103.20   94.17    9.03 1.50e+00 4.44e-01 3.63e+01
  angle pdb=" O1  KLT A1101 "
        pdb=" S1  KLT A1101 "
        pdb=" O2  KLT A1101 "
      ideal   model   delta    sigma   weight residual
     120.26  107.51   12.75 3.00e+00 1.11e-01 1.81e+01
  angle pdb=" CB  TPO A  55 "
        pdb=" OG1 TPO A  55 "
        pdb=" P   TPO A  55 "
      ideal   model   delta    sigma   weight residual
     119.31  106.80   12.51 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" N   ILE A 491 "
        pdb=" CA  ILE A 491 "
        pdb=" C   ILE A 491 "
      ideal   model   delta    sigma   weight residual
     113.20  109.83    3.37 9.60e-01 1.09e+00 1.23e+01
  ... (remaining 13803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    25.15: 5392
       25.15 -    50.30: 528
       50.30 -    75.45: 67
       75.45 -   100.60: 10
      100.60 -   125.75: 6
  Dihedral angle restraints: 6003
    sinusoidal: 2365
      harmonic: 3638
  Sorted by residual:
  dihedral pdb=" CA  PRO B1002 "
           pdb=" C   PRO B1002 "
           pdb=" N   PRO B1003 "
           pdb=" CA  PRO B1003 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.23   35.77     0      5.00e+00 4.00e-02 5.12e+01
  dihedral pdb=" CB  CYS A 429 "
           pdb=" SG  CYS A 429 "
           pdb=" SG  CYS A 435 "
           pdb=" CB  CYS A 435 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  151.70  -58.70     1      1.00e+01 1.00e-02 4.61e+01
  dihedral pdb=" CA  GLY A 679 "
           pdb=" C   GLY A 679 "
           pdb=" N   PRO A 680 "
           pdb=" CA  PRO A 680 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.41   32.59     0      5.00e+00 4.00e-02 4.25e+01
  ... (remaining 6000 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.064: 1555
       1.064 -    2.128: 0
       2.128 -    3.192: 0
       3.192 -    4.256: 0
       4.256 -    5.319: 1
  Chirality restraints: 1556
  Sorted by residual:
  chirality pdb=" C7  KLT A1101 "
            pdb=" C6  KLT A1101 "
            pdb=" C9  KLT A1101 "
            pdb=" N2  KLT A1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.70   -2.62    5.32 2.00e-01 2.50e+01 7.07e+02
  chirality pdb=" CA  ILE A 832 "
            pdb=" N   ILE A 832 "
            pdb=" C   ILE A 832 "
            pdb=" CB  ILE A 832 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.80e-01
  chirality pdb=" CA  ILE B1005 "
            pdb=" N   ILE B1005 "
            pdb=" C   ILE B1005 "
            pdb=" CB  ILE B1005 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.42e-01
  ... (remaining 1553 not shown)

  Planarity restraints: 1741
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 984 "   -0.073 5.00e-02 4.00e+02   1.02e-01 1.67e+01
        pdb=" N   PRO A 985 "    0.176 5.00e-02 4.00e+02
        pdb=" CA  PRO A 985 "   -0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A 985 "   -0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 488 "    0.053 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO A 489 "   -0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO A 489 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO A 489 "    0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 938 "   -0.022 2.00e-02 2.50e+03   1.59e-02 6.29e+00
        pdb=" CG  TRP A 938 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 938 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 938 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 938 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 938 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 938 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 938 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 938 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 938 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1738 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.45: 69
        2.45 -     3.06: 7463
        3.06 -     3.67: 15678
        3.67 -     4.29: 22977
        4.29 -     4.90: 37700
  Nonbonded interactions: 83887
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 155 "
            pdb=" OG  SER A 295 "
     model   vdw
     1.832 3.040
  nonbonded pdb=" O   THR A 351 "
            pdb=" OH  TYR A 539 "
     model   vdw
     1.869 3.040
  nonbonded pdb=" O   SER A 880 "
            pdb=" OG  SER A 883 "
     model   vdw
     1.971 3.040
  nonbonded pdb=" O   ILE A 878 "
            pdb=" N   LEU A 882 "
     model   vdw
     2.003 3.120
  nonbonded pdb=" O   GLY A 740 "
            pdb=" OH  TYR A 756 "
     model   vdw
     2.014 3.040
  ... (remaining 83882 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.010
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     26.230
  Find NCS groups from input model:        0.090
  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:             0.000
  Load rotamer database and sin/cos tables:11.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   42.300
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.109  10165  Z= 0.204
  Angle     :  0.655  14.154  13812  Z= 0.344
  Chirality :  0.141   5.319   1556
  Planarity :  0.006   0.102   1741
  Dihedral  : 19.235 125.751   3661
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 47.41
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.90 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 37.19 %
    Favored  : 58.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1245
  helix:  1.49 (0.21), residues: 669
  sheet: -1.72 (0.47), residues: 122
  loop : -0.92 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP A 938 
 HIS   0.006   0.001   HIS A  90 
 PHE   0.013   0.001   PHE A 535 
 TYR   0.012   0.001   TYR B 756 
 ARG   0.004   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17545 (  537)
  hydrogen bonds       : angle       5.97997 ( 1542)
  SS BOND              : bond        0.00384 (    2)
  SS BOND              : angle       1.82094 (    4)
  covalent geometry    : bond        0.00440 (10163)
  covalent geometry    : angle       0.65400 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  294 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 249
  time to evaluate  : 1.073 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  142 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8550 (ttt)
REVERT: A  239 GLU cc_start: 0.7283 (tm-30) cc_final: 0.6217 (mp0)
REVERT: A  344 SER cc_start: 0.8589 (OUTLIER) cc_final: 0.8181 (p)
REVERT: A  365 ASP cc_start: 0.8052 (t70) cc_final: 0.7612 (p0)
REVERT: A  527 ILE cc_start: 0.7707 (mm) cc_final: 0.7222 (pp)
REVERT: A  550 SER cc_start: 0.9124 (t) cc_final: 0.8907 (m)
REVERT: A  597 PHE cc_start: 0.6858 (t80) cc_final: 0.6583 (t80)
REVERT: A  714 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7358 (pm20)
REVERT: A  776 ARG cc_start: 0.6994 (ptm-80) cc_final: 0.6460 (ttp-110)
REVERT: A  965 TYR cc_start: 0.7052 (m-10) cc_final: 0.6787 (m-10)
REVERT: A  998 GLN cc_start: 0.7779 (pt0) cc_final: 0.7548 (pt0)
REVERT: B  731 ARG cc_start: 0.8490 (mtt-85) cc_final: 0.8146 (mtt-85)
REVERT: B  875 ARG cc_start: 0.7349 (tmm160) cc_final: 0.6995 (ttt-90)
REVERT: B 1012 GLU cc_start: 0.7770 (tp30) cc_final: 0.7440 (mt-10)
  outliers start: 45
  outliers final: 13
  residues processed: 283
  average time/residue: 1.0202
  time to fit residues: 314.3645
Evaluate side-chains
  175 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 159
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 PHE
Chi-restraints excluded: chain A residue  142 MET
Chi-restraints excluded: chain A residue  246 GLN
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  344 SER
Chi-restraints excluded: chain A residue  362 ASP
Chi-restraints excluded: chain A residue  394 SER
Chi-restraints excluded: chain A residue  441 ASN
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  648 THR
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  714 GLU
Chi-restraints excluded: chain A residue  956 VAL
Chi-restraints excluded: chain B residue  818 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 95 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    0.3980
   chunk 64 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 73 optimal weight:    5.9990
   chunk 114 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 725 GLN
A 816 GLN
A 825 GLN
A 906 HIS
A 930 ASN
A1010 ASN
B 890 HIS
B 899 ASN
B 900 GLN
B 930 ASN
B 955 GLN
** B 998 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1010 ASN
B1011 GLN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.155623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.121253 restraints weight = 13190.821|
|-----------------------------------------------------------------------------|
r_work (start): 0.3405 rms_B_bonded: 2.22
r_work: 0.3304 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3187 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10165  Z= 0.171
  Angle     :  0.802  22.846  13812  Z= 0.376
  Chirality :  0.079   2.498   1556
  Planarity :  0.005   0.060   1741
  Dihedral  : 10.504 146.140   1419
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 11.83
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  4.18 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  7.46 %
    Allowed  : 29.64 %
    Favored  : 62.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.34 (0.24), residues: 1245
  helix:  1.39 (0.20), residues: 675
  sheet: -1.83 (0.43), residues: 129
  loop : -0.88 (0.30), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 938 
 HIS   0.007   0.001   HIS B 761 
 PHE   0.025   0.002   PHE B 664 
 TYR   0.023   0.002   TYR A 847 
 ARG   0.007   0.001   ARG B 980 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05164 (  537)
  hydrogen bonds       : angle       4.83882 ( 1542)
  SS BOND              : bond        0.00377 (    2)
  SS BOND              : angle       2.02521 (    4)
  covalent geometry    : bond        0.00401 (10163)
  covalent geometry    : angle       0.80163 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 171
  time to evaluate  : 1.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  209 SER cc_start: 0.8380 (t) cc_final: 0.8147 (m)
REVERT: A  344 SER cc_start: 0.8776 (p) cc_final: 0.8454 (p)
REVERT: A  345 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7943 (pt)
REVERT: A  368 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8312 (tt)
REVERT: A  383 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8770 (mp)
REVERT: A  446 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8539 (tpp)
REVERT: A  590 ILE cc_start: 0.8507 (OUTLIER) cc_final: 0.8294 (mp)
REVERT: A  597 PHE cc_start: 0.7476 (t80) cc_final: 0.7204 (t80)
REVERT: A  632 GLU cc_start: 0.7137 (pp20) cc_final: 0.6623 (pp20)
REVERT: A  776 ARG cc_start: 0.7148 (ptm-80) cc_final: 0.6530 (ttp-110)
REVERT: A  825 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.6800 (pm20)
REVERT: A  874 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5717 (mm-30)
REVERT: A  957 ARG cc_start: 0.7891 (tpt170) cc_final: 0.7559 (tpt170)
REVERT: B  731 ARG cc_start: 0.8663 (mtt-85) cc_final: 0.8372 (mtt-85)
REVERT: B  909 ARG cc_start: 0.7539 (tmm-80) cc_final: 0.7238 (tmm-80)
REVERT: B  932 MET cc_start: 0.7838 (OUTLIER) cc_final: 0.7370 (pmm)
  outliers start: 78
  outliers final: 19
  residues processed: 225
  average time/residue: 0.8244
  time to fit residues: 205.4264
Evaluate side-chains
  169 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 142
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  345 ILE
Chi-restraints excluded: chain A residue  368 ILE
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  446 MET
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  818 THR
Chi-restraints excluded: chain A residue  825 GLN
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  932 MET
Chi-restraints excluded: chain B residue  986 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9990
   chunk 69 optimal weight:    0.8980
   chunk 30 optimal weight:    0.9980
   chunk 87 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0670
   chunk 14 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 1 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 869 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.152537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.117743 restraints weight = 13591.819|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 2.28
r_work: 0.3269 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3151 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8179
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  10165  Z= 0.156
  Angle     :  0.747  24.435  13812  Z= 0.347
  Chirality :  0.073   2.273   1556
  Planarity :  0.005   0.047   1741
  Dihedral  :  9.957 147.737   1398
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.45 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  6.60 %
    Allowed  : 28.11 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.24), residues: 1245
  helix:  1.42 (0.20), residues: 676
  sheet: -1.59 (0.44), residues: 128
  loop : -0.88 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 938 
 HIS   0.005   0.001   HIS B 761 
 PHE   0.022   0.002   PHE B 664 
 TYR   0.016   0.002   TYR B 756 
 ARG   0.007   0.001   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04751 (  537)
  hydrogen bonds       : angle       4.63619 ( 1542)
  SS BOND              : bond        0.00437 (    2)
  SS BOND              : angle       1.57256 (    4)
  covalent geometry    : bond        0.00366 (10163)
  covalent geometry    : angle       0.74640 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 159
  time to evaluate  : 1.392 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7113 (pt0)
REVERT: A  293 MET cc_start: 0.8977 (mmm) cc_final: 0.8702 (mmp)
REVERT: A  336 ASP cc_start: 0.7894 (m-30) cc_final: 0.7473 (t0)
REVERT: A  344 SER cc_start: 0.8806 (p) cc_final: 0.8468 (p)
REVERT: A  345 ILE cc_start: 0.8408 (tt) cc_final: 0.7935 (pt)
REVERT: A  365 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8213 (p0)
REVERT: A  383 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8716 (mp)
REVERT: A  446 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8500 (ttt)
REVERT: A  590 ILE cc_start: 0.8440 (OUTLIER) cc_final: 0.8149 (mp)
REVERT: A  597 PHE cc_start: 0.7492 (t80) cc_final: 0.7193 (t80)
REVERT: A  776 ARG cc_start: 0.7073 (ptm-80) cc_final: 0.6508 (ttp-110)
REVERT: A  874 GLU cc_start: 0.6067 (OUTLIER) cc_final: 0.5635 (mm-30)
REVERT: A  875 ARG cc_start: 0.5805 (OUTLIER) cc_final: 0.5454 (mtt90)
REVERT: A  880 SER cc_start: 0.5640 (OUTLIER) cc_final: 0.5432 (p)
REVERT: A  957 ARG cc_start: 0.7912 (tpt170) cc_final: 0.7693 (tpt170)
REVERT: B  681 HIS cc_start: 0.2805 (OUTLIER) cc_final: 0.2457 (m-70)
REVERT: B  731 ARG cc_start: 0.8657 (mtt-85) cc_final: 0.8418 (mtt-85)
REVERT: B  776 ARG cc_start: 0.7939 (ttm-80) cc_final: 0.7689 (mtt-85)
REVERT: B  859 LYS cc_start: 0.8588 (ttpp) cc_final: 0.8271 (tmmm)
REVERT: B  932 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7310 (pmm)
  outliers start: 69
  outliers final: 18
  residues processed: 205
  average time/residue: 1.0206
  time to fit residues: 230.2012
Evaluate side-chains
  170 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 143
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  365 ASP
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  446 MET
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  818 THR
Chi-restraints excluded: chain A residue  874 GLU
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  681 HIS
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  932 MET
Chi-restraints excluded: chain B residue  986 SER
Chi-restraints excluded: chain B residue 1020 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 14 optimal weight:    0.5980
   chunk 121 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 84 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 80 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0000
   chunk 103 optimal weight:    3.9990
   overall best weight:    0.5984

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1010 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.152882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.117850 restraints weight = 13430.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3369 rms_B_bonded: 2.32
r_work: 0.3273 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3159 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.3159
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.3258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10165  Z= 0.140
  Angle     :  0.721  24.709  13812  Z= 0.336
  Chirality :  0.071   2.192   1556
  Planarity :  0.005   0.046   1741
  Dihedral  :  9.873 148.986   1397
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.45 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  5.93 %
    Allowed  : 28.49 %
    Favored  : 65.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.24), residues: 1245
  helix:  1.39 (0.20), residues: 684
  sheet: -1.34 (0.44), residues: 129
  loop : -0.90 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP A 938 
 HIS   0.006   0.001   HIS A 636 
 PHE   0.020   0.001   PHE B 664 
 TYR   0.020   0.001   TYR A 601 
 ARG   0.010   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04347 (  537)
  hydrogen bonds       : angle       4.49306 ( 1542)
  SS BOND              : bond        0.00299 (    2)
  SS BOND              : angle       1.01634 (    4)
  covalent geometry    : bond        0.00325 (10163)
  covalent geometry    : angle       0.72100 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 157
  time to evaluate  : 1.184 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 GLU cc_start: 0.7648 (tm-30) cc_final: 0.7036 (pt0)
REVERT: A  336 ASP cc_start: 0.7884 (m-30) cc_final: 0.7385 (t0)
REVERT: A  344 SER cc_start: 0.8714 (p) cc_final: 0.8398 (p)
REVERT: A  345 ILE cc_start: 0.8342 (tt) cc_final: 0.7813 (pt)
REVERT: A  383 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8702 (mp)
REVERT: A  590 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8168 (mp)
REVERT: A  597 PHE cc_start: 0.7555 (t80) cc_final: 0.7206 (t80)
REVERT: A  621 ASN cc_start: 0.8957 (m110) cc_final: 0.8753 (m110)
REVERT: A  666 ARG cc_start: 0.8560 (ttt90) cc_final: 0.8317 (ttt180)
REVERT: A  776 ARG cc_start: 0.6996 (ptm-80) cc_final: 0.6470 (ttp-110)
REVERT: A  874 GLU cc_start: 0.6023 (pm20) cc_final: 0.5502 (mm-30)
REVERT: A  875 ARG cc_start: 0.5863 (OUTLIER) cc_final: 0.5484 (mtt90)
REVERT: A  880 SER cc_start: 0.5727 (OUTLIER) cc_final: 0.5495 (p)
REVERT: A  900 GLN cc_start: 0.6923 (pp30) cc_final: 0.6666 (pp30)
REVERT: B  681 HIS cc_start: 0.2888 (OUTLIER) cc_final: 0.2524 (m-70)
REVERT: B  731 ARG cc_start: 0.8651 (mtt-85) cc_final: 0.8389 (mtt-85)
REVERT: B  859 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8319 (tmmm)
REVERT: B  867 GLN cc_start: 0.6978 (OUTLIER) cc_final: 0.6072 (tt0)
REVERT: B  871 MET cc_start: 0.6851 (OUTLIER) cc_final: 0.6532 (mmm)
REVERT: B  879 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8857 (mt)
REVERT: B  909 ARG cc_start: 0.7533 (tmm-80) cc_final: 0.7141 (tmm-80)
REVERT: B  932 MET cc_start: 0.7969 (OUTLIER) cc_final: 0.7314 (pmm)
REVERT: B  934 ARG cc_start: 0.8058 (mtm180) cc_final: 0.7674 (ptt-90)
REVERT: B  941 SER cc_start: 0.6147 (OUTLIER) cc_final: 0.5871 (p)
  outliers start: 62
  outliers final: 23
  residues processed: 200
  average time/residue: 1.2329
  time to fit residues: 268.8931
Evaluate side-chains
  173 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 140
  time to evaluate  : 1.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  520 ILE
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  818 THR
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  681 HIS
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue  879 ILE
Chi-restraints excluded: chain B residue  882 LEU
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  913 MET
Chi-restraints excluded: chain B residue  932 MET
Chi-restraints excluded: chain B residue  941 SER
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  986 SER
Chi-restraints excluded: chain B residue 1020 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 6 optimal weight:    0.5980
   chunk 75 optimal weight:    5.9990
   chunk 51 optimal weight:    0.8980
   chunk 110 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 16 optimal weight:    6.9990
   chunk 44 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    5.9990
   overall best weight:    2.2986

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 358 ASN
A1013 ASN
B 890 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.145556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.110518 restraints weight = 13570.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3266 rms_B_bonded: 2.22
r_work: 0.3168 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3053 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.086  10165  Z= 0.302
  Angle     :  0.816  22.360  13812  Z= 0.395
  Chirality :  0.085   2.682   1556
  Planarity :  0.006   0.050   1741
  Dihedral  : 10.009 141.984   1397
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 10.17
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.10 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 28.01 %
    Favored  : 65.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.04 (0.23), residues: 1245
  helix:  0.83 (0.20), residues: 683
  sheet: -1.30 (0.43), residues: 125
  loop : -0.87 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 938 
 HIS   0.006   0.001   HIS A 636 
 PHE   0.028   0.002   PHE B 664 
 TYR   0.021   0.002   TYR B 756 
 ARG   0.007   0.001   ARG A 208 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05934 (  537)
  hydrogen bonds       : angle       4.78016 ( 1542)
  SS BOND              : bond        0.00598 (    2)
  SS BOND              : angle       1.90644 (    4)
  covalent geometry    : bond        0.00747 (10163)
  covalent geometry    : angle       0.81592 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 140
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 CYS cc_start: 0.6910 (t) cc_final: 0.6248 (m)
REVERT: A   92 PHE cc_start: 0.7069 (OUTLIER) cc_final: 0.6577 (p90)
REVERT: A  239 GLU cc_start: 0.7702 (tm-30) cc_final: 0.7284 (tm-30)
REVERT: A  336 ASP cc_start: 0.7878 (m-30) cc_final: 0.7365 (t0)
REVERT: A  344 SER cc_start: 0.8802 (p) cc_final: 0.8481 (p)
REVERT: A  345 ILE cc_start: 0.8457 (tt) cc_final: 0.7907 (pt)
REVERT: A  383 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8649 (mp)
REVERT: A  590 ILE cc_start: 0.8417 (OUTLIER) cc_final: 0.8083 (mp)
REVERT: A  597 PHE cc_start: 0.7631 (t80) cc_final: 0.7298 (t80)
REVERT: A  678 ILE cc_start: 0.7980 (mp) cc_final: 0.7710 (mm)
REVERT: A  859 LYS cc_start: 0.7828 (OUTLIER) cc_final: 0.7549 (ttmm)
REVERT: A  875 ARG cc_start: 0.5813 (OUTLIER) cc_final: 0.5288 (mtt90)
REVERT: A  880 SER cc_start: 0.5832 (OUTLIER) cc_final: 0.5503 (p)
REVERT: A  900 GLN cc_start: 0.7211 (OUTLIER) cc_final: 0.6997 (pp30)
REVERT: A  998 GLN cc_start: 0.7911 (pt0) cc_final: 0.7555 (pt0)
REVERT: B  681 HIS cc_start: 0.3276 (OUTLIER) cc_final: 0.2804 (m-70)
REVERT: B  773 MET cc_start: 0.8892 (OUTLIER) cc_final: 0.7854 (tpt)
REVERT: B  775 MET cc_start: 0.8660 (mtm) cc_final: 0.8249 (mtt)
REVERT: B  859 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8322 (tmmm)
REVERT: B  867 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.6179 (tt0)
REVERT: B  871 MET cc_start: 0.6983 (OUTLIER) cc_final: 0.6716 (mmm)
REVERT: B  879 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9004 (mt)
REVERT: B  909 ARG cc_start: 0.7622 (tmm-80) cc_final: 0.7202 (tmm-80)
REVERT: B  934 ARG cc_start: 0.8230 (mtm180) cc_final: 0.7828 (ptt-90)
  outliers start: 66
  outliers final: 28
  residues processed: 185
  average time/residue: 0.9431
  time to fit residues: 191.6587
Evaluate side-chains
  173 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 132
  time to evaluate  : 1.045 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue   92 PHE
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  516 VAL
Chi-restraints excluded: chain A residue  518 PHE
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  818 THR
Chi-restraints excluded: chain A residue  859 LYS
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain A residue  878 ILE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  900 GLN
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  975 THR
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  681 HIS
Chi-restraints excluded: chain B residue  747 SER
Chi-restraints excluded: chain B residue  773 MET
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  859 LYS
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue  879 ILE
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  986 SER
Chi-restraints excluded: chain B residue 1020 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 79 optimal weight:    5.9990
   chunk 108 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0970
   chunk 121 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 20 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.150546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.115394 restraints weight = 13395.676|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.31
r_work: 0.3235 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10165  Z= 0.138
  Angle     :  0.720  24.883  13812  Z= 0.336
  Chirality :  0.070   2.198   1556
  Planarity :  0.005   0.046   1741
  Dihedral  :  9.754 149.227   1395
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 9.31
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.53 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  5.07 %
    Allowed  : 29.54 %
    Favored  : 65.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.24), residues: 1245
  helix:  1.20 (0.20), residues: 683
  sheet: -1.14 (0.43), residues: 128
  loop : -0.87 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 938 
 HIS   0.005   0.001   HIS B 761 
 PHE   0.021   0.001   PHE B 664 
 TYR   0.019   0.001   TYR A 847 
 ARG   0.007   0.000   ARG B 875 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  537)
  hydrogen bonds       : angle       4.43897 ( 1542)
  SS BOND              : bond        0.00372 (    2)
  SS BOND              : angle       0.90706 (    4)
  covalent geometry    : bond        0.00322 (10163)
  covalent geometry    : angle       0.71960 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 144
  time to evaluate  : 1.118 
Fit side-chains
REVERT: A  239 GLU cc_start: 0.7664 (tm-30) cc_final: 0.6968 (mt-10)
REVERT: A  257 ASN cc_start: 0.7797 (p0) cc_final: 0.7545 (t0)
REVERT: A  336 ASP cc_start: 0.7881 (m-30) cc_final: 0.7377 (t0)
REVERT: A  344 SER cc_start: 0.8800 (p) cc_final: 0.8509 (p)
REVERT: A  383 ILE cc_start: 0.9039 (OUTLIER) cc_final: 0.8662 (mp)
REVERT: A  590 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8132 (mp)
REVERT: A  597 PHE cc_start: 0.7561 (t80) cc_final: 0.7282 (t80)
REVERT: A  621 ASN cc_start: 0.8962 (m110) cc_final: 0.8733 (m110)
REVERT: A  677 LEU cc_start: 0.8667 (OUTLIER) cc_final: 0.8407 (mt)
REVERT: A  859 LYS cc_start: 0.7791 (OUTLIER) cc_final: 0.7520 (ttmm)
REVERT: A  875 ARG cc_start: 0.6121 (OUTLIER) cc_final: 0.5553 (mtt90)
REVERT: A  880 SER cc_start: 0.5891 (OUTLIER) cc_final: 0.5652 (p)
REVERT: A  998 GLN cc_start: 0.7663 (pt0) cc_final: 0.7333 (pt0)
REVERT: B  681 HIS cc_start: 0.3232 (OUTLIER) cc_final: 0.2825 (m-70)
REVERT: B  731 ARG cc_start: 0.8679 (mtt-85) cc_final: 0.8401 (mtt-85)
REVERT: B  867 GLN cc_start: 0.6912 (OUTLIER) cc_final: 0.5736 (tt0)
REVERT: B  871 MET cc_start: 0.6865 (mmm) cc_final: 0.6420 (mmm)
REVERT: B  909 ARG cc_start: 0.7506 (tmm-80) cc_final: 0.7125 (tmm-80)
REVERT: B  914 ILE cc_start: 0.7634 (tt) cc_final: 0.7345 (tp)
REVERT: B  934 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7819 (ptt-90)
  outliers start: 53
  outliers final: 20
  residues processed: 185
  average time/residue: 1.0269
  time to fit residues: 208.9471
Evaluate side-chains
  162 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 1.011 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  859 LYS
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1013 ASN
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  681 HIS
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  986 SER
Chi-restraints excluded: chain B residue 1020 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 13 optimal weight:    0.6980
   chunk 123 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 117 optimal weight:    0.0980
   chunk 67 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 2 optimal weight:   10.0000
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.150999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.116058 restraints weight = 13651.624|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 2.34
r_work: 0.3245 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8168
moved from start:          0.3999

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10165  Z= 0.137
  Angle     :  0.717  25.045  13812  Z= 0.332
  Chirality :  0.070   2.172   1556
  Planarity :  0.005   0.045   1741
  Dihedral  :  9.684 149.474   1395
  Min Nonbonded Distance : 2.170

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.61 %
    Favored  : 96.14 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 30.40 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1245
  helix:  1.39 (0.20), residues: 683
  sheet: -0.87 (0.43), residues: 126
  loop : -0.81 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP A 938 
 HIS   0.004   0.001   HIS B 761 
 PHE   0.024   0.001   PHE B 664 
 TYR   0.021   0.001   TYR A 601 
 ARG   0.007   0.000   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04318 (  537)
  hydrogen bonds       : angle       4.32611 ( 1542)
  SS BOND              : bond        0.00529 (    2)
  SS BOND              : angle       1.39772 (    4)
  covalent geometry    : bond        0.00322 (10163)
  covalent geometry    : angle       0.71663 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 143
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A   52 CYS cc_start: 0.6750 (t) cc_final: 0.6036 (m)
REVERT: A  239 GLU cc_start: 0.7696 (tm-30) cc_final: 0.6990 (mt-10)
REVERT: A  336 ASP cc_start: 0.7812 (m-30) cc_final: 0.7333 (t0)
REVERT: A  344 SER cc_start: 0.8784 (p) cc_final: 0.8480 (p)
REVERT: A  345 ILE cc_start: 0.8363 (tt) cc_final: 0.7859 (pt)
REVERT: A  383 ILE cc_start: 0.9053 (OUTLIER) cc_final: 0.8694 (mp)
REVERT: A  571 PHE cc_start: 0.8435 (t80) cc_final: 0.8172 (t80)
REVERT: A  590 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8096 (mp)
REVERT: A  597 PHE cc_start: 0.7562 (t80) cc_final: 0.7238 (t80)
REVERT: A  606 LYS cc_start: 0.8860 (tppp) cc_final: 0.8633 (tppt)
REVERT: A  621 ASN cc_start: 0.8976 (m110) cc_final: 0.8749 (m110)
REVERT: A  677 LEU cc_start: 0.8654 (OUTLIER) cc_final: 0.8360 (mt)
REVERT: A  859 LYS cc_start: 0.7728 (mmtm) cc_final: 0.7527 (ttmm)
REVERT: A  875 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.5543 (mtt90)
REVERT: A  880 SER cc_start: 0.5874 (OUTLIER) cc_final: 0.5653 (p)
REVERT: A  889 PHE cc_start: 0.6321 (m-80) cc_final: 0.5992 (m-80)
REVERT: A  967 ARG cc_start: 0.7049 (OUTLIER) cc_final: 0.6785 (mtp85)
REVERT: A  998 GLN cc_start: 0.7645 (pt0) cc_final: 0.7356 (pt0)
REVERT: B  628 VAL cc_start: 0.8224 (t) cc_final: 0.8024 (m)
REVERT: B  681 HIS cc_start: 0.3264 (OUTLIER) cc_final: 0.2820 (m-70)
REVERT: B  731 ARG cc_start: 0.8648 (mtt-85) cc_final: 0.8388 (mtt-85)
REVERT: B  867 GLN cc_start: 0.6768 (OUTLIER) cc_final: 0.6363 (tm-30)
REVERT: B  871 MET cc_start: 0.6892 (OUTLIER) cc_final: 0.6393 (mmm)
REVERT: B  909 ARG cc_start: 0.7499 (tmm-80) cc_final: 0.7129 (tmm-80)
REVERT: B  914 ILE cc_start: 0.7652 (tt) cc_final: 0.7371 (tp)
REVERT: B  932 MET cc_start: 0.7867 (OUTLIER) cc_final: 0.7233 (pmm)
REVERT: B  934 ARG cc_start: 0.8191 (mtm180) cc_final: 0.7812 (ptt-90)
  outliers start: 45
  outliers final: 22
  residues processed: 177
  average time/residue: 1.1360
  time to fit residues: 220.8060
Evaluate side-chains
  169 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 137
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  590 ILE
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1013 ASN
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  681 HIS
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  932 MET
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  986 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 18 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 108 optimal weight:    0.9980
   chunk 12 optimal weight:    3.9990
   chunk 33 optimal weight:    7.9990
   chunk 21 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   chunk 98 optimal weight:    0.4980
   chunk 101 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.150430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.115373 restraints weight = 13536.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.33
r_work: 0.3233 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.3116 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3116
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  10165  Z= 0.153
  Angle     :  0.725  24.911  13812  Z= 0.340
  Chirality :  0.071   2.207   1556
  Planarity :  0.005   0.045   1741
  Dihedral  :  9.678 148.982   1395
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.86 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 29.92 %
    Favored  : 65.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.24), residues: 1245
  helix:  1.42 (0.20), residues: 684
  sheet: -0.69 (0.44), residues: 126
  loop : -0.76 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 938 
 HIS   0.004   0.001   HIS B 761 
 PHE   0.025   0.001   PHE B 664 
 TYR   0.019   0.001   TYR A 847 
 ARG   0.007   0.001   ARG B 875 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04434 (  537)
  hydrogen bonds       : angle       4.32827 ( 1542)
  SS BOND              : bond        0.00335 (    2)
  SS BOND              : angle       1.34414 (    4)
  covalent geometry    : bond        0.00369 (10163)
  covalent geometry    : angle       0.72515 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 138
  time to evaluate  : 1.041 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 GLU cc_start: 0.7694 (tm-30) cc_final: 0.6989 (mt-10)
REVERT: A  336 ASP cc_start: 0.7819 (m-30) cc_final: 0.7275 (t0)
REVERT: A  344 SER cc_start: 0.8803 (p) cc_final: 0.8519 (p)
REVERT: A  383 ILE cc_start: 0.9046 (OUTLIER) cc_final: 0.8665 (mp)
REVERT: A  597 PHE cc_start: 0.7622 (t80) cc_final: 0.7277 (t80)
REVERT: A  606 LYS cc_start: 0.8858 (tppp) cc_final: 0.8658 (tppt)
REVERT: A  621 ASN cc_start: 0.8995 (m110) cc_final: 0.8769 (m110)
REVERT: A  632 GLU cc_start: 0.7514 (tm-30) cc_final: 0.7312 (tm-30)
REVERT: A  677 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8395 (mt)
REVERT: A  743 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7209 (ptmm)
REVERT: A  875 ARG cc_start: 0.6350 (OUTLIER) cc_final: 0.5585 (tpp80)
REVERT: A  880 SER cc_start: 0.5824 (OUTLIER) cc_final: 0.5623 (p)
REVERT: A  900 GLN cc_start: 0.6774 (pp30) cc_final: 0.6231 (pp30)
REVERT: A  932 MET cc_start: 0.6170 (mmm) cc_final: 0.5954 (mtm)
REVERT: A  960 GLU cc_start: 0.7137 (tt0) cc_final: 0.6864 (tp30)
REVERT: A  967 ARG cc_start: 0.7079 (OUTLIER) cc_final: 0.6826 (mtp85)
REVERT: A  998 GLN cc_start: 0.7740 (pt0) cc_final: 0.7491 (pt0)
REVERT: B  681 HIS cc_start: 0.3347 (OUTLIER) cc_final: 0.2904 (m-70)
REVERT: B  731 ARG cc_start: 0.8645 (mtt-85) cc_final: 0.8380 (mtt-85)
REVERT: B  867 GLN cc_start: 0.6799 (OUTLIER) cc_final: 0.6432 (tm-30)
REVERT: B  871 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6419 (mmm)
REVERT: B  909 ARG cc_start: 0.7513 (tmm-80) cc_final: 0.7136 (tmm-80)
REVERT: B  914 ILE cc_start: 0.7662 (tt) cc_final: 0.7381 (tp)
REVERT: B  932 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.7217 (pmm)
REVERT: B  934 ARG cc_start: 0.8139 (mtm180) cc_final: 0.7780 (ptt-90)
  outliers start: 49
  outliers final: 26
  residues processed: 176
  average time/residue: 0.9469
  time to fit residues: 182.9871
Evaluate side-chains
  170 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 134
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  486 GLN
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  538 SER
Chi-restraints excluded: chain A residue  575 ILE
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  743 LYS
Chi-restraints excluded: chain A residue  818 THR
Chi-restraints excluded: chain A residue  820 ILE
Chi-restraints excluded: chain A residue  875 ARG
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  681 HIS
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  932 MET
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  986 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 15 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 122 optimal weight:    0.7980
   chunk 107 optimal weight:    0.5980
   chunk 27 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.150855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.115841 restraints weight = 13528.376|
|-----------------------------------------------------------------------------|
r_work (start): 0.3337 rms_B_bonded: 2.34
r_work: 0.3235 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3119 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.4182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  10165  Z= 0.147
  Angle     :  0.727  24.917  13812  Z= 0.342
  Chirality :  0.071   2.197   1556
  Planarity :  0.005   0.045   1741
  Dihedral  :  9.645 149.117   1395
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.94 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 31.07 %
    Favored  : 64.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.24), residues: 1245
  helix:  1.45 (0.20), residues: 684
  sheet: -0.59 (0.44), residues: 126
  loop : -0.74 (0.30), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP A 938 
 HIS   0.004   0.001   HIS A 636 
 PHE   0.025   0.001   PHE B 664 
 TYR   0.019   0.001   TYR A 847 
 ARG   0.007   0.001   ARG B 875 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04377 (  537)
  hydrogen bonds       : angle       4.32470 ( 1542)
  SS BOND              : bond        0.00410 (    2)
  SS BOND              : angle       1.51703 (    4)
  covalent geometry    : bond        0.00351 (10163)
  covalent geometry    : angle       0.72649 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 139
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
REVERT: A   52 CYS cc_start: 0.6632 (t) cc_final: 0.5929 (m)
REVERT: A  239 GLU cc_start: 0.7715 (tm-30) cc_final: 0.7022 (mt-10)
REVERT: A  336 ASP cc_start: 0.7794 (m-30) cc_final: 0.7308 (t0)
REVERT: A  344 SER cc_start: 0.8813 (p) cc_final: 0.8546 (p)
REVERT: A  383 ILE cc_start: 0.9044 (OUTLIER) cc_final: 0.8706 (mp)
REVERT: A  597 PHE cc_start: 0.7561 (t80) cc_final: 0.7267 (t80)
REVERT: A  606 LYS cc_start: 0.8842 (tppp) cc_final: 0.7701 (mppt)
REVERT: A  621 ASN cc_start: 0.8989 (m110) cc_final: 0.8732 (m110)
REVERT: A  677 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8422 (mt)
REVERT: A  743 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7232 (ptmm)
REVERT: A  880 SER cc_start: 0.5787 (OUTLIER) cc_final: 0.5583 (p)
REVERT: A  900 GLN cc_start: 0.6736 (pp30) cc_final: 0.6216 (pp30)
REVERT: A  960 GLU cc_start: 0.7125 (tt0) cc_final: 0.6816 (tp30)
REVERT: A  967 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6905 (mtp85)
REVERT: A  986 SER cc_start: 0.7723 (OUTLIER) cc_final: 0.7316 (t)
REVERT: A  998 GLN cc_start: 0.7780 (pt0) cc_final: 0.7515 (pt0)
REVERT: B  628 VAL cc_start: 0.8156 (t) cc_final: 0.7954 (m)
REVERT: B  681 HIS cc_start: 0.3368 (OUTLIER) cc_final: 0.3146 (m-70)
REVERT: B  731 ARG cc_start: 0.8615 (mtt-85) cc_final: 0.8355 (mtt-85)
REVERT: B  867 GLN cc_start: 0.6804 (OUTLIER) cc_final: 0.6443 (tm-30)
REVERT: B  871 MET cc_start: 0.6841 (OUTLIER) cc_final: 0.6408 (mmm)
REVERT: B  909 ARG cc_start: 0.7507 (tmm-80) cc_final: 0.7190 (tmm-80)
REVERT: B  914 ILE cc_start: 0.7667 (OUTLIER) cc_final: 0.7391 (tp)
REVERT: B  924 LYS cc_start: 0.5800 (mptt) cc_final: 0.5226 (mppt)
REVERT: B  932 MET cc_start: 0.7790 (OUTLIER) cc_final: 0.7148 (pmm)
REVERT: B  934 ARG cc_start: 0.8153 (mtm180) cc_final: 0.7797 (ptt-90)
  outliers start: 42
  outliers final: 25
  residues processed: 168
  average time/residue: 0.9265
  time to fit residues: 170.8811
Evaluate side-chains
  169 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 133
  time to evaluate  : 1.008 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  152 VAL
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  486 GLN
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  677 LEU
Chi-restraints excluded: chain A residue  743 LYS
Chi-restraints excluded: chain A residue  818 THR
Chi-restraints excluded: chain A residue  820 ILE
Chi-restraints excluded: chain A residue  880 SER
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  681 HIS
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  932 MET
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  986 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 2 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1013 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.150562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.115762 restraints weight = 13564.805|
|-----------------------------------------------------------------------------|
r_work (start): 0.3338 rms_B_bonded: 2.26
r_work: 0.3240 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3125 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  10165  Z= 0.157
  Angle     :  0.742  24.910  13812  Z= 0.349
  Chirality :  0.072   2.217   1556
  Planarity :  0.005   0.046   1741
  Dihedral  :  9.653 148.874   1395
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.78 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 30.59 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.24), residues: 1245
  helix:  1.45 (0.20), residues: 683
  sheet: -0.59 (0.44), residues: 126
  loop : -0.74 (0.30), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.001   TRP A 938 
 HIS   0.004   0.001   HIS A 636 
 PHE   0.025   0.001   PHE B 664 
 TYR   0.018   0.002   TYR A 847 
 ARG   0.006   0.001   ARG A1008 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04475 (  537)
  hydrogen bonds       : angle       4.34801 ( 1542)
  SS BOND              : bond        0.00365 (    2)
  SS BOND              : angle       1.17731 (    4)
  covalent geometry    : bond        0.00382 (10163)
  covalent geometry    : angle       0.74162 (13808)

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

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

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2490 Ramachandran restraints generated.
    1245 Oldfield, 0 Emsley, 1245 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 133
  time to evaluate  : 1.102 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 GLU cc_start: 0.7721 (tm-30) cc_final: 0.7039 (mt-10)
REVERT: A  336 ASP cc_start: 0.7758 (m-30) cc_final: 0.7272 (t0)
REVERT: A  344 SER cc_start: 0.8817 (p) cc_final: 0.8558 (p)
REVERT: A  383 ILE cc_start: 0.9054 (OUTLIER) cc_final: 0.8670 (mp)
REVERT: A  539 TYR cc_start: 0.7908 (m-10) cc_final: 0.7304 (m-10)
REVERT: A  590 ILE cc_start: 0.8291 (mp) cc_final: 0.7984 (mp)
REVERT: A  597 PHE cc_start: 0.7541 (t80) cc_final: 0.7268 (t80)
REVERT: A  606 LYS cc_start: 0.8842 (tppp) cc_final: 0.7701 (mppt)
REVERT: A  621 ASN cc_start: 0.9002 (m110) cc_final: 0.8763 (m110)
REVERT: A  743 LYS cc_start: 0.7981 (OUTLIER) cc_final: 0.7292 (ptmm)
REVERT: A  900 GLN cc_start: 0.6807 (pp30) cc_final: 0.6336 (pp30)
REVERT: A  967 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6714 (mtp85)
REVERT: A  986 SER cc_start: 0.7717 (OUTLIER) cc_final: 0.7335 (t)
REVERT: A  998 GLN cc_start: 0.7797 (pt0) cc_final: 0.7526 (pt0)
REVERT: B  731 ARG cc_start: 0.8633 (mtt-85) cc_final: 0.8362 (mtt-85)
REVERT: B  867 GLN cc_start: 0.6812 (OUTLIER) cc_final: 0.6484 (tm-30)
REVERT: B  871 MET cc_start: 0.6780 (OUTLIER) cc_final: 0.6428 (mmm)
REVERT: B  909 ARG cc_start: 0.7518 (tmm-80) cc_final: 0.7204 (tmm-80)
REVERT: B  914 ILE cc_start: 0.7676 (OUTLIER) cc_final: 0.7411 (tp)
REVERT: B  924 LYS cc_start: 0.5801 (mptt) cc_final: 0.5392 (mppt)
REVERT: B  932 MET cc_start: 0.7795 (OUTLIER) cc_final: 0.7174 (pmm)
REVERT: B  934 ARG cc_start: 0.8129 (mtm180) cc_final: 0.7667 (ptt-90)
  outliers start: 43
  outliers final: 27
  residues processed: 163
  average time/residue: 1.1426
  time to fit residues: 203.4563
Evaluate side-chains
  165 residues out of total 1077 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 130
  time to evaluate  : 1.675 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 VAL
Chi-restraints excluded: chain A residue   82 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  235 VAL
Chi-restraints excluded: chain A residue  262 ILE
Chi-restraints excluded: chain A residue  281 GLU
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  383 ILE
Chi-restraints excluded: chain A residue  389 SER
Chi-restraints excluded: chain A residue  399 ASP
Chi-restraints excluded: chain A residue  486 GLN
Chi-restraints excluded: chain A residue  526 THR
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  743 LYS
Chi-restraints excluded: chain A residue  818 THR
Chi-restraints excluded: chain A residue  820 ILE
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  967 ARG
Chi-restraints excluded: chain A residue  978 ILE
Chi-restraints excluded: chain A residue  986 SER
Chi-restraints excluded: chain A residue 1013 ASN
Chi-restraints excluded: chain A residue 1015 LEU
Chi-restraints excluded: chain B residue  658 VAL
Chi-restraints excluded: chain B residue  677 LEU
Chi-restraints excluded: chain B residue  818 THR
Chi-restraints excluded: chain B residue  867 GLN
Chi-restraints excluded: chain B residue  871 MET
Chi-restraints excluded: chain B residue  895 LEU
Chi-restraints excluded: chain B residue  914 ILE
Chi-restraints excluded: chain B residue  925 ASP
Chi-restraints excluded: chain B residue  932 MET
Chi-restraints excluded: chain B residue  963 LEU
Chi-restraints excluded: chain B residue  965 TYR
Chi-restraints excluded: chain B residue  986 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    0.5980
   chunk 79 optimal weight:    0.9980
   chunk 117 optimal weight:    0.8980
   chunk 111 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 77 optimal weight:    5.9990
   chunk 53 optimal weight:    0.5980
   chunk 87 optimal weight:    0.7980
   chunk 56 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 80 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 148 ASN
** A 285 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.150109 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.115207 restraints weight = 13494.794|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.31
r_work: 0.3232 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3117 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8185
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.126  10165  Z= 0.222
  Angle     :  1.020  59.199  13812  Z= 0.543
  Chirality :  0.075   2.216   1556
  Planarity :  0.005   0.050   1741
  Dihedral  :  9.675 148.918   1395
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.78 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 31.17 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 3.51 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.70 (0.24), residues: 1245
  helix:  1.46 (0.20), residues: 683
  sheet: -0.56 (0.44), residues: 125
  loop : -0.75 (0.30), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 938 
 HIS   0.004   0.001   HIS A 636 
 PHE   0.025   0.001   PHE B 664 
 TYR   0.072   0.002   TYR A 498 
 ARG   0.020   0.001   ARG A 506 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04454 (  537)
  hydrogen bonds       : angle       4.34946 ( 1542)
  SS BOND              : bond        0.01073 (    2)
  SS BOND              : angle      12.25936 (    4)
  covalent geometry    : bond        0.00477 (10163)
  covalent geometry    : angle       0.99892 (13808)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8104.30 seconds
wall clock time: 142 minutes 3.46 seconds (8523.46 seconds total)