Starting phenix.real_space_refine
on Wed Sep 17 22:29:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gy0_51680/09_2025/9gy0_51680.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gy0_51680/09_2025/9gy0_51680.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gy0_51680/09_2025/9gy0_51680.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gy0_51680/09_2025/9gy0_51680.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gy0_51680/09_2025/9gy0_51680.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gy0_51680/09_2025/9gy0_51680.cif"
  }
  resolution = 3.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.058
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
     Ca      1      9.91       5
     P      64      5.49       5
     S      72      5.16       5
     C    7297      2.51       5
     N    2042      2.21       5
     O    2390      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11866
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 596, 4816
          Classifications: {'peptide': 596}
          Link IDs: {'PTRANS': 21, 'TRANS': 574}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 605
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "C"
      Number of atoms: 471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 471
          Classifications: {'DNA': 23}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 22}
    Chain: "D"
      Number of atoms: 251
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 251
          Classifications: {'DNA': 12}
          Modifications used: {'p5*END': 1}
          Link IDs: {'rna3p': 11}
    Chain: "E"
      Number of atoms: 1964
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 256, 1964
          Classifications: {'peptide': 256}
          Link IDs: {'PTRANS': 7, 'TRANS': 248}
          Unresolved chain link angles: 1
          Unresolved chain link dihedrals: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 9
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "F"
      Number of atoms: 1812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 235, 1812
          Classifications: {'peptide': 235}
          Link IDs: {'PTRANS': 7, 'TRANS': 227}
          Chain breaks: 3
    Chain: "G"
      Number of atoms: 1946
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 1946
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 7, 'TRANS': 245}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' CA': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" P    DG B  21 " occ=0.00
      ... (20 atoms not shown)
      pdb=" C4   DG B  21 " occ=0.00
  Time building chain proxies: 2.90, per 1000 atoms: 0.24
  Number of scatterers: 11866
  At special positions: 0
  Unit cell: (105.133, 104.219, 144.444, 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)
     Ca      1     19.99
     S      72     16.00
     P      64     15.00
     O    2390      8.00
     N    2042      7.00
     C    7297      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS G 135 " - pdb=" SG  CYS G 162 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.05
  Conformation dependent library (CDL) restraints added in 460.5 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2544

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 14 sheets defined
      40.9% alpha, 19.8% beta
      27 base pairs and 53 stacking pairs defined.
    Time for finding SS restraints: 1.41
  Creating SS restraints...
    Processing helix  chain 'A' and resid 373 through 389
    Processing helix  chain 'A' and resid 389 through 394
      removed outlier: 3.512A  pdb=" N   LEU A 394 " --> pdb=" O   GLU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 409
    Processing helix  chain 'A' and resid 411 through 424
      removed outlier: 3.755A  pdb=" N   ARG A 424 " --> pdb=" O   ARG A 420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 454
    Processing helix  chain 'A' and resid 458 through 462
    Processing helix  chain 'A' and resid 464 through 472
      removed outlier: 3.678A  pdb=" N   GLU A 470 " --> pdb=" O   SER A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 484
    Processing helix  chain 'A' and resid 492 through 506
      removed outlier: 3.932A  pdb=" N   GLN A 506 " --> pdb=" O   LYS A 502 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 532
      removed outlier: 3.546A  pdb=" N   VAL A 522 " --> pdb=" O   GLY A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 555
      removed outlier: 4.552A  pdb=" N   THR A 555 " --> pdb=" O   LEU A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 577
    Processing helix  chain 'A' and resid 598 through 622
    Processing helix  chain 'A' and resid 623 through 642
    Processing helix  chain 'A' and resid 646 through 651
      removed outlier: 3.592A  pdb=" N   HIS A 650 " --> pdb=" O   SER A 646 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 661 through 681
    Processing helix  chain 'A' and resid 682 through 695
      removed outlier: 3.533A  pdb=" N   SER A 695 " --> pdb=" O   GLU A 691 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 717
    Processing helix  chain 'A' and resid 722 through 735
    Processing helix  chain 'A' and resid 740 through 755
      removed outlier: 3.865A  pdb=" N   LEU A 746 " --> pdb=" O   HIS A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 756 through 760
    Processing helix  chain 'A' and resid 813 through 825
    Processing helix  chain 'A' and resid 834 through 851
      removed outlier: 4.063A  pdb=" N   PHE A 838 " --> pdb=" O   GLU A 834 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   ASP A 848 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
      removed outlier: 6.215A  pdb=" N   ILE A 849 " --> pdb=" O   LEU A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 874 through 879
      removed outlier: 3.801A  pdb=" N   ARG A 879 " --> pdb=" O   PHE A 875 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 879 through 892
      removed outlier: 3.678A  pdb=" N   ASP A 892 " --> pdb=" O   GLN A 888 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 894 through 909
    Processing helix  chain 'A' and resid 924 through 949
      removed outlier: 6.172A  pdb=" N   GLY A 937 " --> pdb=" O   SER A 933 " (cutoff:3.500A)
      Proline residue:  A 938  - end of helix
    Processing helix  chain 'A' and resid 950 through 955
    Processing helix  chain 'A' and resid 984 through 997
    Processing helix  chain 'E' and resid 9 through 23
      removed outlier: 3.564A  pdb=" N   LYS E  20 " --> pdb=" O   LEU E  16 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   ASP E  21 " --> pdb=" O   GLU E  17 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   LEU E  22 " --> pdb=" O   ALA E  18 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 72 through 80
    Processing helix  chain 'E' and resid 141 through 153
    Processing helix  chain 'E' and resid 209 through 216
    Processing helix  chain 'E' and resid 217 through 222
      Proline residue:  E 220  - end of helix
      No H-bonds generated for 'chain 'E' and resid 217 through 222'
    Processing helix  chain 'F' and resid 8 through 19
      removed outlier: 3.837A  pdb=" N   LEU F  12 " --> pdb=" O   GLN F   8 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 72 through 80
    Processing helix  chain 'F' and resid 141 through 155
    Processing helix  chain 'F' and resid 209 through 215
    Processing helix  chain 'G' and resid 9 through 19
      removed outlier: 3.570A  pdb=" N   LYS G  13 " --> pdb=" O   GLY G   9 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 54 through 57
    Processing helix  chain 'G' and resid 71 through 80
    Processing helix  chain 'G' and resid 94 through 96
      No H-bonds generated for 'chain 'G' and resid 94 through 96'
    Processing helix  chain 'G' and resid 141 through 155
    Processing helix  chain 'G' and resid 209 through 217
    Processing helix  chain 'G' and resid 218 through 222
    Processing sheet with id=AA1, first strand: chain 'A' and resid 429 through 430
    Processing sheet with id=AA2, first strand: chain 'A' and resid 778 through 783
      removed outlier: 4.156A  pdb=" N   LYS A 778 " --> pdb=" O   VAL A1001 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   HIS A 970 " --> pdb=" O   ASN A 965 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 972 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'E' and resid 58 through 62
      removed outlier: 5.496A  pdb=" N   THR E  59 " --> pdb=" O   ARG E   5 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   ARG E   5 " --> pdb=" O   THR E  59 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ARG E  61 " --> pdb=" O   GLU E   3 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASN G 177 " --> pdb=" O   GLU E 115 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 25 through 26
    Processing sheet with id=AA5, first strand: chain 'E' and resid 34 through 36
    Processing sheet with id=AA6, first strand: chain 'E' and resid 34 through 36
      removed outlier: 4.430A  pdb=" N   LYS E 240 " --> pdb=" O   THR E 224 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   THR E 224 " --> pdb=" O   LYS E 240 " (cutoff:3.500A)
      removed outlier: 4.771A  pdb=" N   MET E 229 " --> pdb=" O   CYS E 135 " (cutoff:3.500A)
      removed outlier: 4.285A  pdb=" N   CYS E 135 " --> pdb=" O   MET E 229 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 204 through 208
      removed outlier: 5.747A  pdb=" N   ALA E 157 " --> pdb=" O   SER E 172 " (cutoff:3.500A)
      removed outlier: 4.815A  pdb=" N   SER E 172 " --> pdb=" O   ALA E 157 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'F' and resid 25 through 27
      removed outlier: 3.540A  pdb=" N   ALA F  26 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'F' and resid 29 through 30
    Processing sheet with id=AB1, first strand: chain 'F' and resid 196 through 197
      removed outlier: 3.563A  pdb=" N   THR F 196 " --> pdb=" O   LYS F 138 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'F' and resid 177 through 181
      removed outlier: 3.704A  pdb=" N   ALA F 157 " --> pdb=" O   SER F 172 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'G' and resid 2 through 6
      removed outlier: 3.930A  pdb=" N   PHE G   2 " --> pdb=" O   ALA G  92 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'G' and resid 35 through 40
      removed outlier: 4.580A  pdb=" N   LYS G 240 " --> pdb=" O   THR G 224 " (cutoff:3.500A)
      removed outlier: 6.261A  pdb=" N   THR G 224 " --> pdb=" O   LYS G 240 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 159

    552 hydrogen bonds defined for protein.
    1572 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      72 hydrogen bonds
      140 hydrogen bond angles
      0 basepair planarities
      27 basepair parallelities
      53 stacking parallelities
  Total time for adding SS restraints: 2.49

  Time building geometry restraints manager: 1.34 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 2023
        1.32 -     1.45: 3279
        1.45 -     1.57: 6662
        1.57 -     1.69: 126
        1.69 -     1.81: 111
  Bond restraints: 12201
  Sorted by residual:
  bond pdb=" C   MET F  68 "
       pdb=" N   GLY F  69 "
    ideal  model  delta    sigma   weight residual
    1.331  1.409 -0.079 1.46e-02 4.69e+03 2.90e+01
  bond pdb=" C   ALA F  67 "
       pdb=" N   MET F  68 "
    ideal  model  delta    sigma   weight residual
    1.333  1.262  0.070 1.42e-02 4.96e+03 2.46e+01
  bond pdb=" CA  SER A 825 "
       pdb=" CB  SER A 825 "
    ideal  model  delta    sigma   weight residual
    1.531  1.463  0.068 1.69e-02 3.50e+03 1.60e+01
  bond pdb=" C   VAL G 236 "
       pdb=" N   VAL G 237 "
    ideal  model  delta    sigma   weight residual
    1.331  1.285  0.046 1.27e-02 6.20e+03 1.29e+01
  bond pdb=" C   TRP A 707 "
       pdb=" O   TRP A 707 "
    ideal  model  delta    sigma   weight residual
    1.237  1.201  0.036 1.19e-02 7.06e+03 9.04e+00
  ... (remaining 12196 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 16248
        1.64 -     3.27: 421
        3.27 -     4.91: 76
        4.91 -     6.55: 16
        6.55 -     8.19: 6
  Bond angle restraints: 16767
  Sorted by residual:
  angle pdb=" C   ALA G  67 "
        pdb=" N   MET G  68 "
        pdb=" CA  MET G  68 "
      ideal   model   delta    sigma   weight residual
     122.36  114.17    8.19 1.42e+00 4.96e-01 3.32e+01
  angle pdb=" N   LEU A 713 "
        pdb=" CA  LEU A 713 "
        pdb=" C   LEU A 713 "
      ideal   model   delta    sigma   weight residual
     111.69  106.58    5.11 1.23e+00 6.61e-01 1.73e+01
  angle pdb=" CA  TRP A 707 "
        pdb=" C   TRP A 707 "
        pdb=" O   TRP A 707 "
      ideal   model   delta    sigma   weight residual
     120.42  116.03    4.39 1.06e+00 8.90e-01 1.71e+01
  angle pdb=" N   MET G  68 "
        pdb=" CA  MET G  68 "
        pdb=" C   MET G  68 "
      ideal   model   delta    sigma   weight residual
     111.39  105.75    5.64 1.38e+00 5.25e-01 1.67e+01
  angle pdb=" N   VAL G 237 "
        pdb=" CA  VAL G 237 "
        pdb=" C   VAL G 237 "
      ideal   model   delta    sigma   weight residual
     108.11  102.45    5.66 1.40e+00 5.10e-01 1.64e+01
  ... (remaining 16762 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.64: 5862
       17.64 -    35.28: 858
       35.28 -    52.93: 394
       52.93 -    70.57: 92
       70.57 -    88.21: 11
  Dihedral angle restraints: 7217
    sinusoidal: 3310
      harmonic: 3907
  Sorted by residual:
  dihedral pdb=" CB  CYS G 135 "
           pdb=" SG  CYS G 135 "
           pdb=" SG  CYS G 162 "
           pdb=" CB  CYS G 162 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.21   47.79     1      1.00e+01 1.00e-02 3.15e+01
  dihedral pdb=" CA  HIS A 681 "
           pdb=" C   HIS A 681 "
           pdb=" N   MET A 682 "
           pdb=" CA  MET A 682 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.58   23.42     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" C   LEU G 118 "
           pdb=" N   LEU G 118 "
           pdb=" CA  LEU G 118 "
           pdb=" CB  LEU G 118 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.86   -9.74     0      2.50e+00 1.60e-01 1.52e+01
  ... (remaining 7214 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1868
       0.104 -    0.208: 58
       0.208 -    0.313: 2
       0.313 -    0.417: 0
       0.417 -    0.521: 3
  Chirality restraints: 1931
  Sorted by residual:
  chirality pdb=" P    DT C  22 "
            pdb=" OP1  DT C  22 "
            pdb=" OP2  DT C  22 "
            pdb=" O5'  DT C  22 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.87   -0.52 2.00e-01 2.50e+01 6.79e+00
  chirality pdb=" P    DT C  21 "
            pdb=" OP1  DT C  21 "
            pdb=" OP2  DT C  21 "
            pdb=" O5'  DT C  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.86   -0.51 2.00e-01 2.50e+01 6.63e+00
  chirality pdb=" CA  LEU G 118 "
            pdb=" N   LEU G 118 "
            pdb=" C   LEU G 118 "
            pdb=" CB  LEU G 118 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.94   -0.43 2.00e-01 2.50e+01 4.65e+00
  ... (remaining 1928 not shown)

  Planarity restraints: 1913
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 706 "    0.218 9.50e-02 1.11e+02   9.80e-02 5.91e+00
        pdb=" NE  ARG A 706 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 706 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 706 "   -0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 706 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR G 114 "   -0.011 2.00e-02 2.50e+03   2.28e-02 5.20e+00
        pdb=" C   TYR G 114 "    0.039 2.00e-02 2.50e+03
        pdb=" O   TYR G 114 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLU G 115 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 704 "   -0.169 9.50e-02 1.11e+02   7.57e-02 3.52e+00
        pdb=" NE  ARG A 704 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 704 "    0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 704 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 704 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1910 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 348
        2.70 -     3.25: 11421
        3.25 -     3.80: 19621
        3.80 -     4.35: 24494
        4.35 -     4.90: 39917
  Nonbonded interactions: 95801
  Sorted by model distance:
  nonbonded pdb=" O2   DC B  36 "
            pdb=" N2   DG C   5 "
     model   vdw
     2.148 2.496
  nonbonded pdb=" OG  SER G  46 "
            pdb=" O   TYR G 250 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" NE2 HIS A 718 "
            pdb=" OP1  DC B  17 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" OG  SER G 222 "
            pdb=" O   THR G 224 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   PHE A 396 "
            pdb=" NZ  LYS A 401 "
     model   vdw
     2.251 3.120
  ... (remaining 95796 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'E' and (resid 1 through 119 or resid 128 through 162 or resid 167 throug \ 
h 185 or resid 193 through 253))
  selection = (chain 'F' and resid 1 through 253)
  selection = (chain 'G' and (resid 1 through 119 or resid 128 through 162 or resid 167 throug \ 
h 185 or resid 193 through 253))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 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:             1.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.460
  Find NCS groups from input model:        0.140
  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:1.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.890
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
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   0.079  12202  Z= 0.218
  Angle     :  0.635   8.187  16769  Z= 0.379
  Chirality :  0.046   0.521   1931
  Planarity :  0.004   0.098   1913
  Dihedral  : 19.963  88.211   4670
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 28.09 %
    Favored  : 69.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.20 (0.24), residues: 1319
  helix:  1.32 (0.25), residues: 481
  sheet:  0.15 (0.28), residues: 341
  loop : -1.00 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 149 
 TYR   0.009   0.001   TYR A 418 
 PHE   0.024   0.001   PHE F 144 
 TRP   0.016   0.001   TRP A 708 
 HIS   0.007   0.001   HIS A 970 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 (12201)
  covalent geometry    : angle       0.63448 (16767)
  SS BOND              : bond        0.00590 (    1)
  SS BOND              : angle       0.88712 (    2)
  hydrogen bonds       : bond        0.13478 (  622)
  hydrogen bonds       : angle       5.60268 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 153
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  581 ARG cc_start: 0.7973 (mtm110) cc_final: 0.7720 (mtm110)
REVERT: A  648 ARG cc_start: 0.7539 (mpt180) cc_final: 0.6777 (mmt180)
REVERT: A  670 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7723 (mp)
REVERT: A  764 HIS cc_start: 0.7376 (OUTLIER) cc_final: 0.6981 (m170)
REVERT: A  950 ASP cc_start: 0.8229 (t70) cc_final: 0.7810 (t70)
REVERT: E  116 MET cc_start: 0.7687 (mtp) cc_final: 0.7391 (mtp)
REVERT: E  151 LEU cc_start: 0.7423 (OUTLIER) cc_final: 0.7160 (mp)
REVERT: E  240 LYS cc_start: 0.8173 (mttt) cc_final: 0.7620 (mmtm)
REVERT: F    1 MET cc_start: 0.7663 (ppp) cc_final: 0.7311 (tmm)
REVERT: F   30 ILE cc_start: 0.6765 (tp) cc_final: 0.6401 (mm)
REVERT: F   49 GLN cc_start: 0.6182 (tp40) cc_final: 0.4782 (tm-30)
REVERT: F  146 ARG cc_start: 0.8058 (mtt-85) cc_final: 0.7714 (mmm160)
REVERT: F  168 LYS cc_start: 0.8279 (mttt) cc_final: 0.7940 (mptt)
REVERT: F  199 MET cc_start: 0.5196 (ptp) cc_final: 0.4943 (mmm)
REVERT: F  215 PHE cc_start: 0.6758 (m-10) cc_final: 0.6000 (m-80)
REVERT: F  248 LYS cc_start: 0.5975 (mttt) cc_final: 0.5053 (tttm)
REVERT: G  151 LEU cc_start: 0.7538 (OUTLIER) cc_final: 0.7171 (mm)
REVERT: G  229 MET cc_start: 0.4954 (mpp) cc_final: 0.4176 (mpp)
  outliers start: 26
  outliers final: 19
  residues processed: 173
  average time/residue: 0.1315
  time to fit residues: 31.2829
Evaluate side-chains
  162 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 139
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  759 CYS
Chi-restraints excluded: chain A residue  764 HIS
Chi-restraints excluded: chain A residue  781 THR
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain F residue   19 LEU
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue  109 GLU
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  206 THR
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue  151 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.0470
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.7478

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

Flipped N/Q/H residues before XYZ refinement:
A 861 ASN
E  71 ASN
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 153 HIS
G 184 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.181998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.142427 restraints weight = 18486.095|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 3.57
r_work: 0.3434 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.0843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12202  Z= 0.130
  Angle     :  0.533   8.388  16769  Z= 0.282
  Chirality :  0.040   0.163   1931
  Planarity :  0.003   0.036   1913
  Dihedral  : 18.675  70.593   2143
  Min Nonbonded Distance : 2.119

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 25.02 %
    Favored  : 70.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.24), residues: 1319
  helix:  1.63 (0.24), residues: 497
  sheet:  0.23 (0.28), residues: 337
  loop : -1.06 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 149 
 TYR   0.015   0.001   TYR E 211 
 PHE   0.017   0.001   PHE F 144 
 TRP   0.011   0.001   TRP A 707 
 HIS   0.005   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (12201)
  covalent geometry    : angle       0.53265 (16767)
  SS BOND              : bond        0.00506 (    1)
  SS BOND              : angle       1.09441 (    2)
  hydrogen bonds       : bond        0.04016 (  622)
  hydrogen bonds       : angle       4.56351 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 164
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7898 (mtmm)
REVERT: A  498 ASP cc_start: 0.8700 (m-30) cc_final: 0.8384 (m-30)
REVERT: A  648 ARG cc_start: 0.7530 (mpt180) cc_final: 0.6995 (mmt180)
REVERT: A  649 CYS cc_start: 0.8944 (t) cc_final: 0.8721 (t)
REVERT: A  765 LEU cc_start: 0.7253 (OUTLIER) cc_final: 0.6677 (tp)
REVERT: A  869 ASP cc_start: 0.8688 (m-30) cc_final: 0.8419 (m-30)
REVERT: A  910 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7310 (tp30)
REVERT: A  950 ASP cc_start: 0.8325 (t0) cc_final: 0.7997 (t70)
REVERT: E    2 PHE cc_start: 0.7358 (OUTLIER) cc_final: 0.5780 (p90)
REVERT: E  116 MET cc_start: 0.7783 (mtp) cc_final: 0.7475 (mtp)
REVERT: E  151 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.7164 (mp)
REVERT: E  179 ASN cc_start: 0.7014 (p0) cc_final: 0.6755 (p0)
REVERT: E  240 LYS cc_start: 0.8123 (mttt) cc_final: 0.7567 (mmtm)
REVERT: F    1 MET cc_start: 0.7709 (ppp) cc_final: 0.7346 (tmm)
REVERT: F   30 ILE cc_start: 0.6648 (tp) cc_final: 0.6325 (mm)
REVERT: F   49 GLN cc_start: 0.6117 (tp40) cc_final: 0.4715 (tm-30)
REVERT: F  146 ARG cc_start: 0.8050 (mtt-85) cc_final: 0.7689 (mmm-85)
REVERT: F  168 LYS cc_start: 0.8202 (mttt) cc_final: 0.7865 (mptt)
REVERT: F  199 MET cc_start: 0.5183 (ptp) cc_final: 0.4909 (mmm)
REVERT: F  215 PHE cc_start: 0.6664 (m-10) cc_final: 0.5859 (m-80)
REVERT: F  248 LYS cc_start: 0.5948 (mttt) cc_final: 0.5039 (tttm)
REVERT: G   75 MET cc_start: 0.6949 (ttt) cc_final: 0.5890 (mmp)
REVERT: G  151 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.6956 (mm)
REVERT: G  229 MET cc_start: 0.4748 (mpp) cc_final: 0.4119 (mpp)
REVERT: G  249 TYR cc_start: 0.5193 (m-80) cc_final: 0.4984 (m-80)
  outliers start: 54
  outliers final: 22
  residues processed: 206
  average time/residue: 0.1253
  time to fit residues: 35.5101
Evaluate side-chains
  173 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 145
  time to evaluate  : 0.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  910 GLU
Chi-restraints excluded: chain A residue  966 SER
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue  109 GLU
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 9 optimal weight:    0.9990
   chunk 103 optimal weight:    0.7980
   chunk 81 optimal weight:    6.9990
   chunk 99 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 125 optimal weight:   10.0000
   chunk 137 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 95 optimal weight:    5.9990
   chunk 120 optimal weight:    0.6980
   overall best weight:    1.2986

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

Flipped N/Q/H residues before XYZ refinement:
F 184 GLN
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 153 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.180024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.140950 restraints weight = 18670.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3804 rms_B_bonded: 3.87
r_work: 0.3380 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12202  Z= 0.170
  Angle     :  0.564   8.413  16769  Z= 0.294
  Chirality :  0.041   0.160   1931
  Planarity :  0.003   0.038   1913
  Dihedral  : 18.679  70.701   2120
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 10.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 25.36 %
    Favored  : 69.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.23), residues: 1319
  helix:  1.55 (0.24), residues: 496
  sheet:  0.28 (0.28), residues: 331
  loop : -1.12 (0.27), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 880 
 TYR   0.017   0.002   TYR E 211 
 PHE   0.011   0.001   PHE A 422 
 TRP   0.008   0.001   TRP A 638 
 HIS   0.005   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12201)
  covalent geometry    : angle       0.56392 (16767)
  SS BOND              : bond        0.00555 (    1)
  SS BOND              : angle       0.97518 (    2)
  hydrogen bonds       : bond        0.03996 (  622)
  hydrogen bonds       : angle       4.57625 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 154
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 LEU cc_start: 0.8737 (tt) cc_final: 0.8536 (mt)
REVERT: A  401 LYS cc_start: 0.8436 (OUTLIER) cc_final: 0.7998 (mtmm)
REVERT: A  498 ASP cc_start: 0.8745 (m-30) cc_final: 0.8402 (m-30)
REVERT: A  581 ARG cc_start: 0.8165 (mtm110) cc_final: 0.7942 (mtm110)
REVERT: A  592 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8434 (mmtt)
REVERT: A  648 ARG cc_start: 0.7670 (mpt180) cc_final: 0.7012 (mmt180)
REVERT: A  715 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8267 (mp)
REVERT: A  869 ASP cc_start: 0.8753 (m-30) cc_final: 0.8468 (m-30)
REVERT: A  910 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7289 (tp30)
REVERT: A  982 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8427 (mtm110)
REVERT: E    2 PHE cc_start: 0.7509 (OUTLIER) cc_final: 0.5908 (p90)
REVERT: E  116 MET cc_start: 0.7822 (mtp) cc_final: 0.7408 (mtp)
REVERT: E  179 ASN cc_start: 0.7103 (p0) cc_final: 0.6867 (p0)
REVERT: E  240 LYS cc_start: 0.8174 (mttt) cc_final: 0.7610 (mmtm)
REVERT: F    1 MET cc_start: 0.7768 (ppp) cc_final: 0.7368 (tmm)
REVERT: F   30 ILE cc_start: 0.6658 (tp) cc_final: 0.6342 (mm)
REVERT: F  146 ARG cc_start: 0.8080 (mtt-85) cc_final: 0.7727 (mmm160)
REVERT: F  168 LYS cc_start: 0.8147 (mttt) cc_final: 0.7797 (mptt)
REVERT: F  199 MET cc_start: 0.5234 (ptp) cc_final: 0.4778 (mmm)
REVERT: F  215 PHE cc_start: 0.6723 (m-10) cc_final: 0.5948 (m-80)
REVERT: F  248 LYS cc_start: 0.6005 (mttt) cc_final: 0.5265 (tttm)
REVERT: G   75 MET cc_start: 0.6874 (ttt) cc_final: 0.5735 (mmp)
REVERT: G  229 MET cc_start: 0.4797 (mpp) cc_final: 0.4222 (mpp)
  outliers start: 63
  outliers final: 42
  residues processed: 202
  average time/residue: 0.1287
  time to fit residues: 35.7665
Evaluate side-chains
  191 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 145
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  577 VAL
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  598 ASP
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  910 GLU
Chi-restraints excluded: chain A residue  924 SER
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain A residue 1006 VAL
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  167 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  209 LEU
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain G residue   16 LEU
Chi-restraints excluded: chain G residue   51 THR
Chi-restraints excluded: chain G residue  109 GLU
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 59 optimal weight:    5.9990
   chunk 24 optimal weight:    0.8980
   chunk 51 optimal weight:    0.0470
   chunk 93 optimal weight:    5.9990
   chunk 120 optimal weight:    0.9990
   chunk 133 optimal weight:    8.9990
   chunk 25 optimal weight:    0.8980
   chunk 54 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9980
   chunk 65 optimal weight:   20.0000
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 153 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.181935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.135430 restraints weight = 18688.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3708 rms_B_bonded: 2.26
r_work: 0.3533 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12202  Z= 0.119
  Angle     :  0.523   7.439  16769  Z= 0.274
  Chirality :  0.040   0.158   1931
  Planarity :  0.003   0.036   1913
  Dihedral  : 18.567  69.863   2114
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  4.68 %
    Allowed  : 26.64 %
    Favored  : 68.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.23), residues: 1319
  helix:  1.76 (0.24), residues: 496
  sheet:  0.25 (0.28), residues: 333
  loop : -1.10 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG F   5 
 TYR   0.014   0.001   TYR E 211 
 PHE   0.021   0.001   PHE F 144 
 TRP   0.007   0.001   TRP A 708 
 HIS   0.006   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (12201)
  covalent geometry    : angle       0.52263 (16767)
  SS BOND              : bond        0.00414 (    1)
  SS BOND              : angle       0.65742 (    2)
  hydrogen bonds       : bond        0.03602 (  622)
  hydrogen bonds       : angle       4.39847 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 159
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 LEU cc_start: 0.8770 (tt) cc_final: 0.8530 (mt)
REVERT: A  498 ASP cc_start: 0.8780 (m-30) cc_final: 0.8426 (m-30)
REVERT: A  592 LYS cc_start: 0.8695 (mmtt) cc_final: 0.8418 (mmtt)
REVERT: A  648 ARG cc_start: 0.7625 (mpt180) cc_final: 0.7004 (mmt180)
REVERT: A  670 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7683 (mp)
REVERT: A  715 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8303 (mp)
REVERT: A  765 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.6835 (tp)
REVERT: A  869 ASP cc_start: 0.8774 (m-30) cc_final: 0.8448 (m-30)
REVERT: E    2 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.5901 (p90)
REVERT: E  116 MET cc_start: 0.7761 (mtp) cc_final: 0.7433 (mtp)
REVERT: E  151 LEU cc_start: 0.7329 (OUTLIER) cc_final: 0.6949 (mp)
REVERT: E  179 ASN cc_start: 0.7105 (p0) cc_final: 0.6844 (p0)
REVERT: E  240 LYS cc_start: 0.8206 (mttt) cc_final: 0.7587 (mmtm)
REVERT: F   30 ILE cc_start: 0.6664 (tp) cc_final: 0.6395 (mm)
REVERT: F   49 GLN cc_start: 0.6265 (tp40) cc_final: 0.4818 (tm-30)
REVERT: F  146 ARG cc_start: 0.8089 (mtt-85) cc_final: 0.7719 (mmm160)
REVERT: F  168 LYS cc_start: 0.8117 (mttt) cc_final: 0.7720 (mptt)
REVERT: F  199 MET cc_start: 0.5266 (ptp) cc_final: 0.4811 (mmm)
REVERT: F  248 LYS cc_start: 0.5953 (mttt) cc_final: 0.5088 (tttm)
REVERT: G   75 MET cc_start: 0.6940 (ttt) cc_final: 0.5770 (mmp)
REVERT: G  199 MET cc_start: 0.3869 (mmp) cc_final: 0.0847 (tmm)
  outliers start: 55
  outliers final: 34
  residues processed: 199
  average time/residue: 0.1302
  time to fit residues: 36.4685
Evaluate side-chains
  185 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 146
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  153 HIS
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain G residue   11 ILE
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Chi-restraints excluded: chain G residue  251 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 117 optimal weight:    6.9990
   chunk 131 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 120 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 112 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 597 GLN
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 153 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.180420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.141032 restraints weight = 18641.650|
|-----------------------------------------------------------------------------|
r_work (start): 0.3795 rms_B_bonded: 3.49
r_work: 0.3407 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12202  Z= 0.134
  Angle     :  0.533   6.875  16769  Z= 0.280
  Chirality :  0.040   0.222   1931
  Planarity :  0.003   0.036   1913
  Dihedral  : 18.566  69.381   2114
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 26.13 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.50 (0.23), residues: 1319
  helix:  1.78 (0.24), residues: 496
  sheet:  0.24 (0.28), residues: 333
  loop : -1.11 (0.27), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F   5 
 TYR   0.015   0.002   TYR E 211 
 PHE   0.009   0.001   PHE F 169 
 TRP   0.007   0.001   TRP A 638 
 HIS   0.006   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (12201)
  covalent geometry    : angle       0.53330 (16767)
  SS BOND              : bond        0.00470 (    1)
  SS BOND              : angle       0.78060 (    2)
  hydrogen bonds       : bond        0.03666 (  622)
  hydrogen bonds       : angle       4.40814 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 152
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
REVERT: A  394 LEU cc_start: 0.8766 (tt) cc_final: 0.8526 (mt)
REVERT: A  401 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.8075 (mtmt)
REVERT: A  498 ASP cc_start: 0.8743 (m-30) cc_final: 0.8391 (m-30)
REVERT: A  592 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8402 (mmtt)
REVERT: A  648 ARG cc_start: 0.7611 (mpt180) cc_final: 0.7002 (mmt180)
REVERT: A  670 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7739 (mp)
REVERT: A  715 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8152 (mp)
REVERT: A  765 LEU cc_start: 0.7310 (OUTLIER) cc_final: 0.6809 (tp)
REVERT: A  869 ASP cc_start: 0.8742 (m-30) cc_final: 0.8433 (m-30)
REVERT: A  982 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8430 (mtm110)
REVERT: E    2 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.5995 (p90)
REVERT: E   16 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8430 (mm)
REVERT: E  116 MET cc_start: 0.7735 (mtp) cc_final: 0.7356 (mtp)
REVERT: E  179 ASN cc_start: 0.7119 (p0) cc_final: 0.6842 (p0)
REVERT: E  198 GLU cc_start: 0.6108 (OUTLIER) cc_final: 0.5782 (pp20)
REVERT: E  199 MET cc_start: 0.5567 (mmm) cc_final: 0.5193 (mmm)
REVERT: E  240 LYS cc_start: 0.8195 (mttt) cc_final: 0.7600 (mmtm)
REVERT: F    5 ARG cc_start: 0.6628 (ttm-80) cc_final: 0.6370 (ttm-80)
REVERT: F   30 ILE cc_start: 0.6685 (tp) cc_final: 0.6406 (mm)
REVERT: F   49 GLN cc_start: 0.6262 (tp40) cc_final: 0.4793 (tm-30)
REVERT: F  146 ARG cc_start: 0.8040 (mtt-85) cc_final: 0.7705 (mmm160)
REVERT: F  168 LYS cc_start: 0.8099 (mttt) cc_final: 0.7666 (mptt)
REVERT: F  199 MET cc_start: 0.5267 (ptp) cc_final: 0.4824 (mmm)
REVERT: F  215 PHE cc_start: 0.6559 (m-10) cc_final: 0.5755 (m-80)
REVERT: F  248 LYS cc_start: 0.5853 (mttt) cc_final: 0.5031 (tttm)
REVERT: G  229 MET cc_start: 0.4524 (mpp) cc_final: 0.3744 (mpp)
  outliers start: 63
  outliers final: 45
  residues processed: 201
  average time/residue: 0.1307
  time to fit residues: 36.7307
Evaluate side-chains
  196 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 144
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  380 LEU
Chi-restraints excluded: chain A residue  395 LEU
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  597 GLN
Chi-restraints excluded: chain A residue  600 ASP
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  153 HIS
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  198 GLU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain G residue   11 ILE
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue  109 GLU
Chi-restraints excluded: chain G residue  143 GLU
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Chi-restraints excluded: chain G residue  251 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 91 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 11 optimal weight:    0.6980
   chunk 89 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 113 optimal weight:    0.6980
   chunk 13 optimal weight:    0.5980
   chunk 108 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0060
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A 597 GLN
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G 153 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.181908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.142193 restraints weight = 18625.770|
|-----------------------------------------------------------------------------|
r_work (start): 0.3821 rms_B_bonded: 3.45
r_work: 0.3443 rms_B_bonded: 4.33 restraints_weight: 0.5000
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  12202  Z= 0.117
  Angle     :  0.520   6.997  16769  Z= 0.272
  Chirality :  0.040   0.155   1931
  Planarity :  0.003   0.035   1913
  Dihedral  : 18.533  68.734   2114
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 26.72 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.24), residues: 1319
  helix:  1.90 (0.24), residues: 497
  sheet:  0.28 (0.28), residues: 334
  loop : -1.08 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 149 
 TYR   0.015   0.001   TYR E 211 
 PHE   0.012   0.001   PHE A 596 
 TRP   0.007   0.001   TRP A 638 
 HIS   0.002   0.001   HIS A1005 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (12201)
  covalent geometry    : angle       0.51952 (16767)
  SS BOND              : bond        0.00427 (    1)
  SS BOND              : angle       0.64156 (    2)
  hydrogen bonds       : bond        0.03541 (  622)
  hydrogen bonds       : angle       4.31639 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 149
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 LEU cc_start: 0.8791 (tt) cc_final: 0.8541 (mt)
REVERT: A  401 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.8064 (mtmt)
REVERT: A  464 GLU cc_start: 0.8306 (tp30) cc_final: 0.7981 (mm-30)
REVERT: A  498 ASP cc_start: 0.8750 (m-30) cc_final: 0.8404 (m-30)
REVERT: A  592 LYS cc_start: 0.8652 (mmtt) cc_final: 0.8424 (mmtt)
REVERT: A  648 ARG cc_start: 0.7621 (mpt180) cc_final: 0.7064 (mmt180)
REVERT: A  670 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.7675 (mp)
REVERT: A  715 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8130 (mp)
REVERT: A  765 LEU cc_start: 0.7361 (OUTLIER) cc_final: 0.6887 (tp)
REVERT: A  869 ASP cc_start: 0.8701 (m-30) cc_final: 0.8387 (m-30)
REVERT: E    2 PHE cc_start: 0.7598 (OUTLIER) cc_final: 0.6061 (p90)
REVERT: E   16 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8422 (mm)
REVERT: E  116 MET cc_start: 0.7682 (mtp) cc_final: 0.7416 (mtp)
REVERT: E  151 LEU cc_start: 0.7366 (OUTLIER) cc_final: 0.6970 (mp)
REVERT: E  179 ASN cc_start: 0.7102 (p0) cc_final: 0.6828 (p0)
REVERT: E  198 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5855 (pp20)
REVERT: E  240 LYS cc_start: 0.8209 (mttt) cc_final: 0.7638 (mmtm)
REVERT: F   30 ILE cc_start: 0.6675 (tp) cc_final: 0.6409 (mm)
REVERT: F   49 GLN cc_start: 0.6320 (tp40) cc_final: 0.4874 (tm-30)
REVERT: F  146 ARG cc_start: 0.8017 (mtt-85) cc_final: 0.7669 (mmm-85)
REVERT: F  168 LYS cc_start: 0.8097 (mttt) cc_final: 0.7678 (mptt)
REVERT: F  199 MET cc_start: 0.5265 (ptp) cc_final: 0.4829 (mmm)
REVERT: F  221 LEU cc_start: 0.5852 (OUTLIER) cc_final: 0.5440 (tt)
REVERT: F  248 LYS cc_start: 0.5899 (mttt) cc_final: 0.5072 (tttm)
REVERT: G   75 MET cc_start: 0.6982 (ttt) cc_final: 0.5883 (mmp)
  outliers start: 60
  outliers final: 43
  residues processed: 193
  average time/residue: 0.1389
  time to fit residues: 36.8185
Evaluate side-chains
  194 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 142
  time to evaluate  : 0.437 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  597 GLN
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 PHE
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  153 HIS
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  198 GLU
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  221 LEU
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain G residue   11 ILE
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue  109 GLU
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Chi-restraints excluded: chain G residue  251 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 0 optimal weight:    1.9990
   chunk 67 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 66 optimal weight:    0.8980
   chunk 93 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 103 optimal weight:    0.8980
   chunk 15 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
F 184 GLN
G  71 ASN
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4274 r_free = 0.4274 target = 0.180374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.140301 restraints weight = 18604.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3793 rms_B_bonded: 3.42
r_work: 0.3414 rms_B_bonded: 4.30 restraints_weight: 0.5000
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12202  Z= 0.148
  Angle     :  0.539   6.960  16769  Z= 0.282
  Chirality :  0.040   0.157   1931
  Planarity :  0.003   0.035   1913
  Dihedral  : 18.577  68.642   2114
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.70 %
    Allowed  : 26.04 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.52 (0.23), residues: 1319
  helix:  1.79 (0.24), residues: 498
  sheet:  0.28 (0.28), residues: 334
  loop : -1.13 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG F   5 
 TYR   0.015   0.002   TYR E 211 
 PHE   0.012   0.001   PHE A 596 
 TRP   0.007   0.001   TRP A 638 
 HIS   0.003   0.001   HIS A1005 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 (12201)
  covalent geometry    : angle       0.53868 (16767)
  SS BOND              : bond        0.00478 (    1)
  SS BOND              : angle       0.72739 (    2)
  hydrogen bonds       : bond        0.03684 (  622)
  hydrogen bonds       : angle       4.40440 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 67
    poor density    : 147
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.8097 (mtmt)
REVERT: A  464 GLU cc_start: 0.8324 (tp30) cc_final: 0.7997 (mm-30)
REVERT: A  498 ASP cc_start: 0.8748 (m-30) cc_final: 0.8385 (m-30)
REVERT: A  592 LYS cc_start: 0.8660 (mmtt) cc_final: 0.8432 (mmtt)
REVERT: A  648 ARG cc_start: 0.7626 (mpt180) cc_final: 0.7008 (mmt180)
REVERT: A  670 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.7767 (mp)
REVERT: A  715 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.8179 (mp)
REVERT: A  765 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.6998 (tp)
REVERT: A  880 ARG cc_start: 0.7802 (ttp-110) cc_final: 0.7497 (ttp-110)
REVERT: A  950 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8229 (t70)
REVERT: E    2 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.6062 (p90)
REVERT: E   16 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8452 (mm)
REVERT: E   99 LEU cc_start: 0.6438 (tp) cc_final: 0.6125 (tp)
REVERT: E  116 MET cc_start: 0.7682 (mtp) cc_final: 0.7290 (mtp)
REVERT: E  151 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6933 (mp)
REVERT: E  179 ASN cc_start: 0.7076 (p0) cc_final: 0.6814 (p0)
REVERT: E  198 GLU cc_start: 0.6151 (OUTLIER) cc_final: 0.5845 (pp20)
REVERT: E  240 LYS cc_start: 0.8228 (mttt) cc_final: 0.7654 (mmtm)
REVERT: F   30 ILE cc_start: 0.6699 (tp) cc_final: 0.6431 (mm)
REVERT: F   49 GLN cc_start: 0.6313 (tp40) cc_final: 0.4829 (tm-30)
REVERT: F  146 ARG cc_start: 0.8026 (mtt-85) cc_final: 0.7677 (mmm-85)
REVERT: F  168 LYS cc_start: 0.7991 (mttt) cc_final: 0.7585 (mptt)
REVERT: F  199 MET cc_start: 0.5301 (ptp) cc_final: 0.4861 (mmm)
REVERT: F  215 PHE cc_start: 0.6566 (m-10) cc_final: 0.5732 (m-80)
REVERT: F  221 LEU cc_start: 0.5973 (OUTLIER) cc_final: 0.5500 (tt)
REVERT: F  238 GLU cc_start: 0.3933 (OUTLIER) cc_final: 0.3602 (tm-30)
REVERT: F  248 LYS cc_start: 0.5915 (mttt) cc_final: 0.5129 (tttm)
REVERT: G   75 MET cc_start: 0.6965 (ttt) cc_final: 0.5838 (mmp)
REVERT: G  229 MET cc_start: 0.4511 (mpp) cc_final: 0.3370 (mpp)
  outliers start: 67
  outliers final: 48
  residues processed: 200
  average time/residue: 0.1344
  time to fit residues: 37.2566
Evaluate side-chains
  201 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 142
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  404 VAL
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  597 GLN
Chi-restraints excluded: chain A residue  598 ASP
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  950 ASP
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 PHE
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  153 HIS
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  198 GLU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  198 GLU
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  221 LEU
Chi-restraints excluded: chain F residue  238 GLU
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain G residue   11 ILE
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue  109 GLU
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0870
   chunk 66 optimal weight:    0.9980
   chunk 135 optimal weight:    3.9990
   chunk 123 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 10 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 130 optimal weight:    9.9990
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.181421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.135295 restraints weight = 18541.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.30
r_work: 0.3532 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3391 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12202  Z= 0.123
  Angle     :  0.527   7.165  16769  Z= 0.276
  Chirality :  0.040   0.157   1931
  Planarity :  0.003   0.035   1913
  Dihedral  : 18.550  67.927   2114
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 26.38 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.57 (0.23), residues: 1319
  helix:  1.88 (0.24), residues: 498
  sheet:  0.24 (0.28), residues: 332
  loop : -1.08 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 149 
 TYR   0.015   0.001   TYR E 211 
 PHE   0.009   0.001   PHE F 169 
 TRP   0.007   0.001   TRP A 638 
 HIS   0.002   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (12201)
  covalent geometry    : angle       0.52693 (16767)
  SS BOND              : bond        0.00402 (    1)
  SS BOND              : angle       0.60618 (    2)
  hydrogen bonds       : bond        0.03556 (  622)
  hydrogen bonds       : angle       4.33773 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 148
  time to evaluate  : 0.462 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8064 (mtpt)
REVERT: A  464 GLU cc_start: 0.8342 (tp30) cc_final: 0.8013 (mm-30)
REVERT: A  498 ASP cc_start: 0.8801 (m-30) cc_final: 0.8427 (m-30)
REVERT: A  592 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8427 (mmtt)
REVERT: A  648 ARG cc_start: 0.7674 (mpt180) cc_final: 0.7090 (mmt180)
REVERT: A  670 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7689 (mp)
REVERT: A  715 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8172 (mp)
REVERT: A  765 LEU cc_start: 0.7469 (OUTLIER) cc_final: 0.7020 (tp)
REVERT: A  880 ARG cc_start: 0.7823 (ttp-110) cc_final: 0.7533 (ttp-110)
REVERT: A  950 ASP cc_start: 0.8524 (OUTLIER) cc_final: 0.8260 (t70)
REVERT: E    2 PHE cc_start: 0.7540 (OUTLIER) cc_final: 0.6019 (p90)
REVERT: E   16 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8414 (mm)
REVERT: E   91 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7717 (mtp180)
REVERT: E  116 MET cc_start: 0.7657 (mtp) cc_final: 0.7265 (mtp)
REVERT: E  151 LEU cc_start: 0.7385 (OUTLIER) cc_final: 0.6971 (mp)
REVERT: E  179 ASN cc_start: 0.7048 (p0) cc_final: 0.6796 (p0)
REVERT: E  198 GLU cc_start: 0.6161 (OUTLIER) cc_final: 0.5840 (pp20)
REVERT: E  240 LYS cc_start: 0.8299 (mttt) cc_final: 0.7669 (mmtm)
REVERT: F   30 ILE cc_start: 0.6711 (tp) cc_final: 0.6478 (mm)
REVERT: F   49 GLN cc_start: 0.6311 (tp40) cc_final: 0.4850 (tm-30)
REVERT: F  146 ARG cc_start: 0.8120 (mtt-85) cc_final: 0.7706 (mmm-85)
REVERT: F  168 LYS cc_start: 0.7976 (mttt) cc_final: 0.7378 (mppt)
REVERT: F  199 MET cc_start: 0.5279 (ptp) cc_final: 0.4826 (mmm)
REVERT: F  215 PHE cc_start: 0.6529 (m-10) cc_final: 0.5702 (m-80)
REVERT: F  221 LEU cc_start: 0.5823 (OUTLIER) cc_final: 0.5392 (tt)
REVERT: F  238 GLU cc_start: 0.3873 (OUTLIER) cc_final: 0.3569 (tm-30)
REVERT: F  248 LYS cc_start: 0.5856 (mttt) cc_final: 0.5127 (tttm)
REVERT: G   75 MET cc_start: 0.7010 (ttt) cc_final: 0.5886 (mmp)
REVERT: G  201 GLU cc_start: 0.5719 (pp20) cc_final: 0.4329 (pm20)
REVERT: G  214 PHE cc_start: 0.7045 (m-80) cc_final: 0.6774 (m-10)
REVERT: G  229 MET cc_start: 0.4581 (mpp) cc_final: 0.3459 (mpp)
  outliers start: 63
  outliers final: 43
  residues processed: 194
  average time/residue: 0.1386
  time to fit residues: 37.0950
Evaluate side-chains
  197 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 143
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  950 ASP
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 PHE
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  153 HIS
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  198 GLU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  221 LEU
Chi-restraints excluded: chain F residue  238 GLU
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain G residue   11 ILE
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Chi-restraints excluded: chain G residue  251 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 10 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   chunk 134 optimal weight:    0.8980
   chunk 80 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 6 optimal weight:    0.1980
   chunk 44 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0050
   chunk 9 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 597 GLN
** G 107 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 = 0.4300 r_free = 0.4300 target = 0.182587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.142739 restraints weight = 18388.122|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 3.22
r_work: 0.3461 rms_B_bonded: 4.17 restraints_weight: 0.5000
r_work (final): 0.3461
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12202  Z= 0.111
  Angle     :  0.520   7.917  16769  Z= 0.271
  Chirality :  0.039   0.147   1931
  Planarity :  0.003   0.034   1913
  Dihedral  : 18.471  66.938   2114
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  5.11 %
    Allowed  : 26.72 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.63 (0.23), residues: 1319
  helix:  1.98 (0.24), residues: 498
  sheet:  0.20 (0.28), residues: 333
  loop : -1.05 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 149 
 TYR   0.014   0.001   TYR E 211 
 PHE   0.008   0.001   PHE F 169 
 TRP   0.007   0.001   TRP A 638 
 HIS   0.003   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 (12201)
  covalent geometry    : angle       0.52005 (16767)
  SS BOND              : bond        0.00392 (    1)
  SS BOND              : angle       0.55322 (    2)
  hydrogen bonds       : bond        0.03448 (  622)
  hydrogen bonds       : angle       4.25170 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 152
  time to evaluate  : 0.495 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.8002 (mtpt)
REVERT: A  464 GLU cc_start: 0.8235 (tp30) cc_final: 0.7894 (mm-30)
REVERT: A  498 ASP cc_start: 0.8739 (m-30) cc_final: 0.8379 (m-30)
REVERT: A  512 TRP cc_start: 0.5809 (p90) cc_final: 0.3873 (m-90)
REVERT: A  592 LYS cc_start: 0.8642 (mmtt) cc_final: 0.8397 (mmtt)
REVERT: A  648 ARG cc_start: 0.7668 (mpt180) cc_final: 0.7015 (mmt180)
REVERT: A  670 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.7652 (mp)
REVERT: A  715 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8107 (mp)
REVERT: A  869 ASP cc_start: 0.8673 (m-30) cc_final: 0.8334 (m-30)
REVERT: A  880 ARG cc_start: 0.7731 (ttp-110) cc_final: 0.7443 (ttp-110)
REVERT: A  950 ASP cc_start: 0.8452 (OUTLIER) cc_final: 0.8156 (t70)
REVERT: E    2 PHE cc_start: 0.7466 (OUTLIER) cc_final: 0.5846 (p90)
REVERT: E   16 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8351 (mm)
REVERT: E   91 ARG cc_start: 0.8003 (mtp180) cc_final: 0.7739 (mtp180)
REVERT: E  116 MET cc_start: 0.7627 (mtp) cc_final: 0.7287 (mtp)
REVERT: E  151 LEU cc_start: 0.7306 (OUTLIER) cc_final: 0.6905 (mp)
REVERT: E  179 ASN cc_start: 0.6944 (p0) cc_final: 0.6734 (p0)
REVERT: E  198 GLU cc_start: 0.6136 (OUTLIER) cc_final: 0.5781 (pp20)
REVERT: E  199 MET cc_start: 0.5360 (mmm) cc_final: 0.5037 (mmm)
REVERT: E  240 LYS cc_start: 0.8309 (mttt) cc_final: 0.7695 (mmtm)
REVERT: F   30 ILE cc_start: 0.6610 (tp) cc_final: 0.6395 (mm)
REVERT: F   49 GLN cc_start: 0.6291 (tp40) cc_final: 0.4860 (tm-30)
REVERT: F  146 ARG cc_start: 0.8048 (mtt-85) cc_final: 0.7733 (mmm-85)
REVERT: F  168 LYS cc_start: 0.7956 (mttt) cc_final: 0.7456 (mmtm)
REVERT: F  199 MET cc_start: 0.5161 (ptp) cc_final: 0.4740 (mmm)
REVERT: F  215 PHE cc_start: 0.6572 (m-10) cc_final: 0.5768 (m-80)
REVERT: F  238 GLU cc_start: 0.3856 (OUTLIER) cc_final: 0.3572 (tm-30)
REVERT: F  248 LYS cc_start: 0.5901 (mttt) cc_final: 0.5135 (tttm)
REVERT: G   75 MET cc_start: 0.6932 (ttt) cc_final: 0.5826 (mmp)
REVERT: G  201 GLU cc_start: 0.5555 (pp20) cc_final: 0.4222 (pm20)
REVERT: G  214 PHE cc_start: 0.7078 (m-80) cc_final: 0.6785 (m-10)
REVERT: G  229 MET cc_start: 0.4525 (mpp) cc_final: 0.3555 (mpp)
  outliers start: 60
  outliers final: 43
  residues processed: 194
  average time/residue: 0.1390
  time to fit residues: 37.0628
Evaluate side-chains
  199 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 147
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  597 GLN
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  932 VAL
Chi-restraints excluded: chain A residue  950 ASP
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   43 SER
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  103 PHE
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  153 HIS
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  198 GLU
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  238 GLU
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain G residue   11 ILE
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Chi-restraints excluded: chain G residue  235 LEU
Chi-restraints excluded: chain G residue  251 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 99 optimal weight:    6.9990
   chunk 8 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 93 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    4.9990
   chunk 54 optimal weight:    0.0870
   chunk 90 optimal weight:    5.9990
   chunk 137 optimal weight:    4.9990
   chunk 36 optimal weight:    0.4980
   overall best weight:    1.5162

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

Flipped N/Q/H residues before XYZ refinement:
** G 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.179041 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.139898 restraints weight = 18591.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.3789 rms_B_bonded: 3.74
r_work: 0.3370 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  12202  Z= 0.189
  Angle     :  0.591   9.137  16769  Z= 0.309
  Chirality :  0.042   0.179   1931
  Planarity :  0.004   0.036   1913
  Dihedral  : 18.627  67.323   2114
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 27.15 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.23), residues: 1319
  helix:  1.64 (0.24), residues: 499
  sheet:  0.10 (0.28), residues: 333
  loop : -1.15 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 149 
 TYR   0.019   0.002   TYR G 249 
 PHE   0.018   0.002   PHE A 762 
 TRP   0.008   0.001   TRP A 638 
 HIS   0.004   0.001   HIS A1005 

Details of bonding type rmsd
  covalent geometry    : bond        0.00450 (12201)
  covalent geometry    : angle       0.59107 (16767)
  SS BOND              : bond        0.00490 (    1)
  SS BOND              : angle       0.84849 (    2)
  hydrogen bonds       : bond        0.03953 (  622)
  hydrogen bonds       : angle       4.54141 ( 1712)

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

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

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2638 Ramachandran restraints generated.
    1319 Oldfield, 0 Emsley, 1319 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 149
  time to evaluate  : 0.461 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  401 LYS cc_start: 0.8412 (OUTLIER) cc_final: 0.8159 (mtpt)
REVERT: A  464 GLU cc_start: 0.8428 (tp30) cc_final: 0.8152 (mm-30)
REVERT: A  498 ASP cc_start: 0.8766 (m-30) cc_final: 0.8373 (m-30)
REVERT: A  648 ARG cc_start: 0.7768 (mpt180) cc_final: 0.7447 (mpt180)
REVERT: A  670 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7811 (mp)
REVERT: A  715 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8214 (mp)
REVERT: A  880 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.7600 (ttp-110)
REVERT: A  982 ARG cc_start: 0.8749 (ttm110) cc_final: 0.8482 (mtm110)
REVERT: E    2 PHE cc_start: 0.7465 (OUTLIER) cc_final: 0.5853 (p90)
REVERT: E   91 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7717 (mtp180)
REVERT: E  116 MET cc_start: 0.7524 (mtp) cc_final: 0.7213 (mtp)
REVERT: E  151 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7073 (mp)
REVERT: E  179 ASN cc_start: 0.7181 (p0) cc_final: 0.6909 (p0)
REVERT: E  198 GLU cc_start: 0.6267 (OUTLIER) cc_final: 0.5917 (pp20)
REVERT: E  240 LYS cc_start: 0.8261 (mttt) cc_final: 0.7683 (mmtm)
REVERT: F   30 ILE cc_start: 0.6693 (tp) cc_final: 0.6443 (mm)
REVERT: F  146 ARG cc_start: 0.8110 (mtt-85) cc_final: 0.7746 (mmm160)
REVERT: F  168 LYS cc_start: 0.8008 (mttt) cc_final: 0.7499 (mmtm)
REVERT: F  199 MET cc_start: 0.5318 (ptp) cc_final: 0.4875 (mmm)
REVERT: F  215 PHE cc_start: 0.6542 (m-10) cc_final: 0.5711 (m-80)
REVERT: F  238 GLU cc_start: 0.4021 (OUTLIER) cc_final: 0.3703 (tm-30)
REVERT: F  248 LYS cc_start: 0.6062 (mttt) cc_final: 0.5431 (tttm)
REVERT: G   75 MET cc_start: 0.6917 (ttt) cc_final: 0.5722 (mmp)
REVERT: G  199 MET cc_start: 0.3108 (mmp) cc_final: 0.0300 (tmm)
REVERT: G  214 PHE cc_start: 0.7185 (m-80) cc_final: 0.6866 (m-10)
REVERT: G  229 MET cc_start: 0.4556 (mpp) cc_final: 0.3469 (mpp)
  outliers start: 56
  outliers final: 44
  residues processed: 190
  average time/residue: 0.1443
  time to fit residues: 37.5855
Evaluate side-chains
  196 residues out of total 1176 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 145
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  401 LYS
Chi-restraints excluded: chain A residue  447 ILE
Chi-restraints excluded: chain A residue  458 THR
Chi-restraints excluded: chain A residue  466 SER
Chi-restraints excluded: chain A residue  495 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  548 ILE
Chi-restraints excluded: chain A residue  571 LEU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  595 ILE
Chi-restraints excluded: chain A residue  669 ILE
Chi-restraints excluded: chain A residue  670 LEU
Chi-restraints excluded: chain A residue  680 LEU
Chi-restraints excluded: chain A residue  695 SER
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  715 LEU
Chi-restraints excluded: chain A residue  898 LEU
Chi-restraints excluded: chain A residue  961 LEU
Chi-restraints excluded: chain E residue    2 PHE
Chi-restraints excluded: chain E residue   16 LEU
Chi-restraints excluded: chain E residue   24 ASN
Chi-restraints excluded: chain E residue   46 SER
Chi-restraints excluded: chain E residue   48 VAL
Chi-restraints excluded: chain E residue   76 SER
Chi-restraints excluded: chain E residue   90 LEU
Chi-restraints excluded: chain E residue  101 LEU
Chi-restraints excluded: chain E residue  151 LEU
Chi-restraints excluded: chain E residue  156 ASP
Chi-restraints excluded: chain E residue  198 GLU
Chi-restraints excluded: chain E residue  203 VAL
Chi-restraints excluded: chain E residue  219 THR
Chi-restraints excluded: chain E residue  222 SER
Chi-restraints excluded: chain F residue   27 CYS
Chi-restraints excluded: chain F residue   66 LEU
Chi-restraints excluded: chain F residue  107 ASN
Chi-restraints excluded: chain F residue  111 VAL
Chi-restraints excluded: chain F residue  119 MET
Chi-restraints excluded: chain F residue  137 VAL
Chi-restraints excluded: chain F residue  159 VAL
Chi-restraints excluded: chain F residue  179 ASN
Chi-restraints excluded: chain F residue  196 THR
Chi-restraints excluded: chain F residue  198 GLU
Chi-restraints excluded: chain F residue  216 THR
Chi-restraints excluded: chain F residue  238 GLU
Chi-restraints excluded: chain F residue  247 LEU
Chi-restraints excluded: chain G residue   11 ILE
Chi-restraints excluded: chain G residue   52 LEU
Chi-restraints excluded: chain G residue  151 LEU
Chi-restraints excluded: chain G residue  158 VAL
Chi-restraints excluded: chain G residue  160 ILE
Chi-restraints excluded: chain G residue  235 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 138
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 61 optimal weight:    8.9990
   chunk 62 optimal weight:    7.9990
   chunk 87 optimal weight:    0.6980
   chunk 102 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 103 optimal weight:    0.0050
   chunk 83 optimal weight:    0.3980
   chunk 90 optimal weight:    3.9990
   chunk 98 optimal weight:    1.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 821 HIS
** G 107 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 = 0.4286 r_free = 0.4286 target = 0.181244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.134692 restraints weight = 18415.851|
|-----------------------------------------------------------------------------|
r_work (start): 0.3731 rms_B_bonded: 2.44
r_work: 0.3506 rms_B_bonded: 3.34 restraints_weight: 0.5000
r_work (final): 0.3506
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.1874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12202  Z= 0.118
  Angle     :  0.539   9.173  16769  Z= 0.280
  Chirality :  0.040   0.158   1931
  Planarity :  0.003   0.035   1913
  Dihedral  : 18.513  66.294   2114
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.71 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 27.66 %
    Favored  : 68.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.51 (0.23), residues: 1319
  helix:  1.88 (0.24), residues: 498
  sheet:  0.09 (0.28), residues: 325
  loop : -1.08 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 149 
 TYR   0.016   0.001   TYR G 249 
 PHE   0.025   0.001   PHE A 762 
 TRP   0.007   0.001   TRP A 638 
 HIS   0.003   0.001   HIS E  44 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 (12201)
  covalent geometry    : angle       0.53880 (16767)
  SS BOND              : bond        0.00432 (    1)
  SS BOND              : angle       0.74821 (    2)
  hydrogen bonds       : bond        0.03518 (  622)
  hydrogen bonds       : angle       4.33292 ( 1712)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3205.42 seconds
wall clock time: 55 minutes 49.41 seconds (3349.41 seconds total)