Starting phenix.real_space_refine
on Sat Jun 14 18:31:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hai_34591/06_2025/8hai_34591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hai_34591/06_2025/8hai_34591.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hai_34591/06_2025/8hai_34591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hai_34591/06_2025/8hai_34591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hai_34591/06_2025/8hai_34591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hai_34591/06_2025/8hai_34591.cif"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      47      5.16       5
     C    9542      2.51       5
     N    3017      2.21       5
     O    3647      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 115 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 16547
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 819
          Classifications: {'peptide': 99}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 714
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 714
          Classifications: {'peptide': 91}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 24
          Unresolved non-hydrogen dihedrals: 16
          Planarities with less than four sites: {'HIS:plan': 1, 'ALY:plan-2': 2, 'ALY:plan-1': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 801
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      Number of atoms: 668
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 83, 668
          Classifications: {'peptide': 83}
          Link IDs: {'PTRANS': 1, 'TRANS': 81}
    Chain: "G"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 810
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "H"
      Number of atoms: 784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 784
          Classifications: {'peptide': 103}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 2, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 32
          Unresolved non-hydrogen dihedrals: 26
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "K"
      Number of atoms: 4381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 533, 4381
          Classifications: {'peptide': 533}
          Link IDs: {'PCIS': 3, 'PTRANS': 32, 'TRANS': 497}
          Chain breaks: 2
    Chain: "J"
      Number of atoms: 3012
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3012
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "I"
      Number of atoms: 3015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3015
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N   ALA C  14 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA C  14 " occ=0.00
  Time building chain proxies: 9.42, per 1000 atoms: 0.57
  Number of scatterers: 16547
  At special positions: 0
  Unit cell: (107.31, 167.58, 138.18, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      47     16.00
     P     294     15.00
     O    3647      8.00
     N    3017      7.00
     C    9542      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.26
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2468

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 14 sheets defined
      61.3% alpha, 7.2% beta
      112 base pairs and 219 stacking pairs defined.
    Time for finding SS restraints: 6.91
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 77
      removed outlier: 3.540A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.594A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.766A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   GLU B  63 " --> pdb=" O   LYS B  59 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 5.102A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 92
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.637A  pdb=" N   ALA C  21 " --> pdb=" O   ARG C  17 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.394A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.582A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
    Processing helix  chain 'D' and resid 37 through 49
    Processing helix  chain 'D' and resid 55 through 84
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.560A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 123
    Processing helix  chain 'E' and resid 44 through 57
    Processing helix  chain 'E' and resid 63 through 79
    Processing helix  chain 'E' and resid 85 through 114
    Processing helix  chain 'E' and resid 120 through 131
      removed outlier: 3.587A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.677A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
    Processing helix  chain 'G' and resid 16 through 21
    Processing helix  chain 'G' and resid 26 through 37
    Processing helix  chain 'G' and resid 45 through 73
      removed outlier: 4.407A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 89
    Processing helix  chain 'G' and resid 90 through 97
    Processing helix  chain 'H' and resid 26 through 30
    Processing helix  chain 'H' and resid 37 through 49
    Processing helix  chain 'H' and resid 55 through 84
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.658A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 1052 through 1067
      Proline residue:  K1060  - end of helix
    Processing helix  chain 'K' and resid 1072 through 1076
    Processing helix  chain 'K' and resid 1080 through 1085
    Processing helix  chain 'K' and resid 1088 through 1093
    Processing helix  chain 'K' and resid 1098 through 1108
    Processing helix  chain 'K' and resid 1113 through 1132
      removed outlier: 4.212A  pdb=" N   TYR K1117 " --> pdb=" O   GLU K1113 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1136 through 1160
      removed outlier: 3.543A  pdb=" N   LYS K1140 " --> pdb=" O   SER K1136 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ASP K1154 " --> pdb=" O   GLU K1150 " (cutoff:3.500A)
      Proline residue:  K1155  - end of helix
    Processing helix  chain 'K' and resid 1256 through 1260
    Processing helix  chain 'K' and resid 1272 through 1279
    Processing helix  chain 'K' and resid 1296 through 1314
    Processing helix  chain 'K' and resid 1336 through 1343
    Processing helix  chain 'K' and resid 1406 through 1429
      removed outlier: 4.225A  pdb=" N   THR K1411 " --> pdb=" O   LYS K1407 " (cutoff:3.500A)
      removed outlier: 4.829A  pdb=" N   ALA K1412 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   GLY K1420 " --> pdb=" O   GLU K1416 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LYS K1426 " --> pdb=" O   LEU K1422 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1459 through 1477
    Processing helix  chain 'K' and resid 1486 through 1493
    Processing helix  chain 'K' and resid 1497 through 1501
      removed outlier: 3.582A  pdb=" N   LEU K1501 " --> pdb=" O   ALA K1498 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1507 through 1523
      removed outlier: 3.963A  pdb=" N   ASN K1511 " --> pdb=" O   ASP K1507 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1579 through 1591
    Processing helix  chain 'K' and resid 1602 through 1607
      removed outlier: 4.200A  pdb=" N   ALA K1605 " --> pdb=" O   ALA K1602 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1621 through 1625
    Processing helix  chain 'K' and resid 1627 through 1638
    Processing helix  chain 'K' and resid 1643 through 1663
      removed outlier: 3.588A  pdb=" N   GLN K1663 " --> pdb=" O   HIS K1659 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.644A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.588A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98
      removed outlier: 6.510A  pdb=" N   THR B  96 " --> pdb=" O   THR G 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 7.188A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 101
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.849A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119
    Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43
      removed outlier: 7.194A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AB2, first strand: chain 'K' and resid 1169 through 1170
      removed outlier: 3.736A  pdb=" N   ASP K1240 " --> pdb=" O   PHE K1170 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1198 through 1200
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1244 through 1246
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1321 through 1334
      removed outlier: 6.465A  pdb=" N   ALA K1359 " --> pdb=" O   VAL K1326 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ALA K1328 " --> pdb=" O   THR K1357 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   THR K1357 " --> pdb=" O   ALA K1328 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   ASP K1330 " --> pdb=" O   TYR K1355 " (cutoff:3.500A)
      removed outlier: 6.690A  pdb=" N   TYR K1355 " --> pdb=" O   ASP K1330 " (cutoff:3.500A)
      removed outlier: 4.612A  pdb=" N   THR K1332 " --> pdb=" O   PHE K1353 " (cutoff:3.500A)
      removed outlier: 6.306A  pdb=" N   PHE K1353 " --> pdb=" O   THR K1332 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU K1360 " --> pdb=" O   MET K1376 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE K1374 " --> pdb=" O   ALA K1362 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   GLU K1364 " --> pdb=" O   CYS K1372 " (cutoff:3.500A)
      removed outlier: 5.424A  pdb=" N   CYS K1372 " --> pdb=" O   GLU K1364 " (cutoff:3.500A)
      removed outlier: 6.195A  pdb=" N   ILE K1366 " --> pdb=" O   ASP K1370 " (cutoff:3.500A)
      removed outlier: 5.080A  pdb=" N   ASP K1370 " --> pdb=" O   ILE K1366 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   GLN K1379 " --> pdb=" O   ILE K1395 " (cutoff:3.500A)
      removed outlier: 5.584A  pdb=" N   ILE K1395 " --> pdb=" O   GLN K1379 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   TYR K1381 " --> pdb=" O   VAL K1393 " (cutoff:3.500A)
      removed outlier: 5.409A  pdb=" N   VAL K1393 " --> pdb=" O   TYR K1381 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   TRP K1436 " --> pdb=" O   ILE K1395 " (cutoff:3.500A)
      removed outlier: 7.107A  pdb=" N   TYR K1397 " --> pdb=" O   TRP K1436 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ASP K1482 " --> pdb=" O   ARG K1599 " (cutoff:3.500A)

    594 hydrogen bonds defined for protein.
    1746 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      266 hydrogen bonds
      532 hydrogen bond angles
      0 basepair planarities
      112 basepair parallelities
      219 stacking parallelities
  Total time for adding SS restraints: 7.91

  Time building geometry restraints manager: 4.84 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3938
        1.34 -     1.46: 4891
        1.46 -     1.58: 7993
        1.58 -     1.70: 586
        1.70 -     1.82: 70
  Bond restraints: 17478
  Sorted by residual:
  bond pdb=" NZ  ALY B  16 "
       pdb=" CH  ALY B  16 "
    ideal  model  delta    sigma   weight residual
    1.343  1.385 -0.042 2.00e-02 2.50e+03 4.46e+00
  bond pdb=" C3'  DA J  59 "
       pdb=" O3'  DA J  59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.463 -0.041 3.00e-02 1.11e+03 1.89e+00
  bond pdb=" C   LEU D 101 "
       pdb=" N   LEU D 102 "
    ideal  model  delta    sigma   weight residual
    1.326  1.351 -0.024 1.84e-02 2.95e+03 1.76e+00
  bond pdb=" C3'  DT I 136 "
       pdb=" O3'  DT I 136 "
    ideal  model  delta    sigma   weight residual
    1.422  1.458 -0.036 3.00e-02 1.11e+03 1.43e+00
  bond pdb=" CH  ALY B  16 "
       pdb=" OH  ALY B  16 "
    ideal  model  delta    sigma   weight residual
    1.225  1.247 -0.022 2.00e-02 2.50e+03 1.23e+00
  ... (remaining 17473 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 24227
        1.64 -     3.28: 596
        3.28 -     4.92: 32
        4.92 -     6.56: 11
        6.56 -     8.20: 3
  Bond angle restraints: 24869
  Sorted by residual:
  angle pdb=" C   ASN B  64 "
        pdb=" N   VAL B  65 "
        pdb=" CA  VAL B  65 "
      ideal   model   delta    sigma   weight residual
     122.97  119.57    3.40 9.80e-01 1.04e+00 1.20e+01
  angle pdb=" N   ILE K1479 "
        pdb=" CA  ILE K1479 "
        pdb=" C   ILE K1479 "
      ideal   model   delta    sigma   weight residual
     111.45  108.33    3.12 9.30e-01 1.16e+00 1.12e+01
  angle pdb=" CB  MET H  62 "
        pdb=" CG  MET H  62 "
        pdb=" SD  MET H  62 "
      ideal   model   delta    sigma   weight residual
     112.70  120.90   -8.20 3.00e+00 1.11e-01 7.47e+00
  angle pdb=" CA  ARG K1494 "
        pdb=" CB  ARG K1494 "
        pdb=" CG  ARG K1494 "
      ideal   model   delta    sigma   weight residual
     114.10  119.37   -5.27 2.00e+00 2.50e-01 6.93e+00
  angle pdb=" CB  ARG E  52 "
        pdb=" CG  ARG E  52 "
        pdb=" CD  ARG E  52 "
      ideal   model   delta    sigma   weight residual
     111.30  117.32   -6.02 2.30e+00 1.89e-01 6.85e+00
  ... (remaining 24864 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.34: 8559
       35.34 -    70.67: 1299
       70.67 -   106.01: 22
      106.01 -   141.34: 0
      141.34 -   176.68: 2
  Dihedral angle restraints: 9882
    sinusoidal: 6059
      harmonic: 3823
  Sorted by residual:
  dihedral pdb=" C4'  DT I 136 "
           pdb=" C3'  DT I 136 "
           pdb=" O3'  DT I 136 "
           pdb=" P    DT I 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   36.68 -176.68     1      3.50e+01 8.16e-04 1.57e+01
  dihedral pdb=" C4'  DA J  59 "
           pdb=" C3'  DA J  59 "
           pdb=" O3'  DA J  59 "
           pdb=" P    DA J  60 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   53.71  166.29     1      3.50e+01 8.16e-04 1.55e+01
  dihedral pdb=" CA  ILE B  50 "
           pdb=" C   ILE B  50 "
           pdb=" N   TYR B  51 "
           pdb=" CA  TYR B  51 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.72  -16.28     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 9879 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1895
       0.028 -    0.055: 612
       0.055 -    0.082: 168
       0.082 -    0.110: 70
       0.110 -    0.137: 27
  Chirality restraints: 2772
  Sorted by residual:
  chirality pdb=" CA  TYR B  88 "
            pdb=" N   TYR B  88 "
            pdb=" C   TYR B  88 "
            pdb=" CB  TYR B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.73e-01
  chirality pdb=" CA  ILE K1598 "
            pdb=" N   ILE K1598 "
            pdb=" C   ILE K1598 "
            pdb=" CB  ILE K1598 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.68e-01
  chirality pdb=" CA  ILE F  46 "
            pdb=" N   ILE F  46 "
            pdb=" C   ILE F  46 "
            pdb=" CB  ILE F  46 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-01
  ... (remaining 2769 not shown)

  Planarity restraints: 2150
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  88 "    0.020 2.00e-02 2.50e+03   1.63e-02 5.31e+00
        pdb=" CG  TYR B  88 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  88 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  88 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  88 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  88 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  88 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B  88 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B  59 "    0.009 2.00e-02 2.50e+03   1.73e-02 2.99e+00
        pdb=" C   LYS B  59 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   LYS B  59 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL B  60 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "    0.026 5.00e-02 4.00e+02   3.95e-02 2.49e+00
        pdb=" N   PRO D 103 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2147 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2774
        2.78 -     3.31: 16057
        3.31 -     3.84: 32438
        3.84 -     4.37: 36547
        4.37 -     4.90: 53996
  Nonbonded interactions: 141812
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG C  29 "
            pdb=" O   SER D  36 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" N   GLN G  24 "
            pdb=" OE2 GLU G  56 "
     model   vdw
     2.264 3.120
  nonbonded pdb=" N   THR H  90 "
            pdb=" OE2 GLU H  93 "
     model   vdw
     2.277 3.120
  nonbonded pdb=" NE2 HIS A 113 "
            pdb=" OD1 ASP E 123 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" O   TYR B  51 "
            pdb=" OG1 THR B  54 "
     model   vdw
     2.309 3.040
  ... (remaining 141807 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = (chain 'E' and resid 38 through 134)
}
ncs_group {
  reference = (chain 'B' and resid 19 through 101)
  selection = (chain 'F' and (resid 19 or (resid 20 and (name N or name CA or name C or name O \ 
 or name CB )) or resid 21 through 101))
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 14 through 117)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 31 through 124)
}
ncs_group {
  reference = (chain 'I' and resid 18 through 163)
  selection = (chain 'J' and resid 18 through 163)
}

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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.140
  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:             0.020
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.120
  Set scattering table:                    0.170
  Process input model:                     43.670
  Find NCS groups from input model:        0.450
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.610
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  17478  Z= 0.146
  Angle     :  0.578   8.197  24869  Z= 0.359
  Chirality :  0.033   0.137   2772
  Planarity :  0.004   0.039   2150
  Dihedral  : 24.523 176.680   7414
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.74 (0.24), residues: 1283
  helix:  1.61 (0.19), residues: 777
  sheet:  0.55 (0.65), residues: 68
  loop :  0.60 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K1509 
 HIS   0.004   0.000   HIS A  39 
 PHE   0.011   0.001   PHE G  25 
 TYR   0.039   0.001   TYR B  88 
 ARG   0.006   0.001   ARG E  53 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12563 (  860)
  hydrogen bonds       : angle       5.03596 ( 2278)
  covalent geometry    : bond        0.00282 (17478)
  covalent geometry    : angle       0.57781 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   68 ASP cc_start: 0.9049 (m-30) cc_final: 0.8814 (m-30)
REVERT: D  100 LEU cc_start: 0.9459 (mt) cc_final: 0.9232 (mt)
REVERT: G   73 ASN cc_start: 0.8705 (t0) cc_final: 0.8365 (t0)
REVERT: K 1094 LYS cc_start: 0.7492 (mtpt) cc_final: 0.6648 (mmmt)
REVERT: K 1097 MET cc_start: 0.3272 (ppp) cc_final: 0.2525 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 0.2745
  time to fit residues: 43.7929
Evaluate side-chains
  67 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 1.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 130 optimal weight:    7.9990
   chunk 117 optimal weight:    4.9990
   chunk 65 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   chunk 47 optimal weight:    7.9990
   chunk 73 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 140 optimal weight:   10.0000
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
B  64 ASN
C 104 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
K1112 GLN
K1255 HIS
K1379 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.055557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.039767 restraints weight = 175666.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.040165 restraints weight = 108146.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.040412 restraints weight = 98817.372|
|-----------------------------------------------------------------------------|
r_work (final): 0.3060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.081  17478  Z= 0.250
  Angle     :  0.674   8.086  24869  Z= 0.381
  Chirality :  0.039   0.144   2772
  Planarity :  0.006   0.053   2150
  Dihedral  : 28.776 169.666   4768
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 13.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.38 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.23), residues: 1283
  helix:  1.79 (0.18), residues: 774
  sheet:  0.43 (0.68), residues: 64
  loop :  0.55 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K1509 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.018   0.002   PHE G  25 
 TYR   0.035   0.002   TYR B  88 
 ARG   0.008   0.001   ARG B  67 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07073 (  860)
  hydrogen bonds       : angle       3.63854 ( 2278)
  covalent geometry    : bond        0.00540 (17478)
  covalent geometry    : angle       0.67374 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 89
  time to evaluate  : 1.409 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8311 (mpp) cc_final: 0.7939 (mpp)
REVERT: B   68 ASP cc_start: 0.9412 (m-30) cc_final: 0.9017 (m-30)
REVERT: B   88 TYR cc_start: 0.8467 (m-80) cc_final: 0.8216 (m-80)
REVERT: D   45 LEU cc_start: 0.8965 (tp) cc_final: 0.8757 (tp)
REVERT: D   54 ILE cc_start: 0.8818 (pt) cc_final: 0.8568 (mm)
REVERT: D  100 LEU cc_start: 0.9256 (mt) cc_final: 0.9036 (mt)
REVERT: E   73 GLU cc_start: 0.8612 (tt0) cc_final: 0.8264 (mt-10)
REVERT: E  120 MET cc_start: 0.8527 (mtm) cc_final: 0.8092 (ptp)
REVERT: G   38 ASN cc_start: 0.8434 (m-40) cc_final: 0.7589 (m-40)
REVERT: G   41 GLU cc_start: 0.8337 (tm-30) cc_final: 0.8039 (tm-30)
REVERT: G   73 ASN cc_start: 0.8927 (t0) cc_final: 0.8515 (t0)
REVERT: H   46 LYS cc_start: 0.9139 (mmpt) cc_final: 0.8522 (pttm)
REVERT: H   69 ILE cc_start: 0.9199 (mm) cc_final: 0.8958 (mm)
REVERT: K 1090 PHE cc_start: 0.8493 (m-10) cc_final: 0.7811 (m-80)
REVERT: K 1094 LYS cc_start: 0.7617 (mtpt) cc_final: 0.7101 (mmmt)
REVERT: K 1097 MET cc_start: 0.2880 (ppp) cc_final: 0.2388 (ppp)
REVERT: K 1349 MET cc_start: 0.0521 (mmt) cc_final: 0.0156 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 90
  average time/residue: 0.2574
  time to fit residues: 37.1194
Evaluate side-chains
  63 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 1.526 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 123 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9990
   chunk 59 optimal weight:    8.9990
   chunk 107 optimal weight:    2.9990
   chunk 122 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 25 optimal weight:    4.9990
   chunk 112 optimal weight:    0.0970
   chunk 82 optimal weight:    0.0030
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A 108 ASN
B  64 ASN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  67 ASN
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.058950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.043011 restraints weight = 185491.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.044094 restraints weight = 106863.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.044785 restraints weight = 74432.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.2323

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.079  17478  Z= 0.136
  Angle     :  0.540   7.683  24869  Z= 0.314
  Chirality :  0.034   0.180   2772
  Planarity :  0.004   0.039   2150
  Dihedral  : 28.782 179.647   4768
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.23), residues: 1283
  helix:  2.11 (0.18), residues: 777
  sheet:  0.43 (0.68), residues: 64
  loop :  0.56 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1509 
 HIS   0.004   0.001   HIS F  75 
 PHE   0.011   0.001   PHE G  25 
 TYR   0.017   0.001   TYR G  50 
 ARG   0.007   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03983 (  860)
  hydrogen bonds       : angle       3.13992 ( 2278)
  covalent geometry    : bond        0.00290 (17478)
  covalent geometry    : angle       0.54038 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.438 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8880 (tt0) cc_final: 0.8288 (pt0)
REVERT: A  105 GLU cc_start: 0.8969 (tp30) cc_final: 0.8622 (tp30)
REVERT: A  120 MET cc_start: 0.8268 (mpp) cc_final: 0.7871 (mpp)
REVERT: B   68 ASP cc_start: 0.9232 (m-30) cc_final: 0.8771 (m-30)
REVERT: B   88 TYR cc_start: 0.8552 (m-10) cc_final: 0.8282 (m-80)
REVERT: E   73 GLU cc_start: 0.8736 (tt0) cc_final: 0.8360 (tt0)
REVERT: G   41 GLU cc_start: 0.8255 (tm-30) cc_final: 0.8025 (tm-30)
REVERT: G   73 ASN cc_start: 0.8904 (t0) cc_final: 0.8559 (t0)
REVERT: H   46 LYS cc_start: 0.9172 (mmpt) cc_final: 0.8442 (pttm)
REVERT: H   69 ILE cc_start: 0.9189 (mm) cc_final: 0.8930 (mm)
REVERT: K 1090 PHE cc_start: 0.8500 (m-10) cc_final: 0.7836 (m-80)
REVERT: K 1094 LYS cc_start: 0.7826 (mtpt) cc_final: 0.7201 (mmmt)
REVERT: K 1349 MET cc_start: 0.1749 (mmt) cc_final: 0.1347 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 96
  average time/residue: 0.2707
  time to fit residues: 41.0885
Evaluate side-chains
  66 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 132 optimal weight:    6.9990
   chunk 129 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 47 optimal weight:    5.9990
   chunk 14 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 152 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 111 optimal weight:   20.0000
   overall best weight:    2.5388

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  24 GLN
K1262 HIS
K1451 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.055465 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.039617 restraints weight = 188054.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.040730 restraints weight = 104475.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3085 r_free = 0.3085 target = 0.041410 restraints weight = 71008.827|
|-----------------------------------------------------------------------------|
r_work (final): 0.3024
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056  17478  Z= 0.210
  Angle     :  0.609   6.610  24869  Z= 0.349
  Chirality :  0.036   0.168   2772
  Planarity :  0.005   0.058   2150
  Dihedral  : 29.063 176.647   4768
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.23), residues: 1283
  helix:  2.06 (0.18), residues: 777
  sheet:  0.83 (0.72), residues: 62
  loop :  0.52 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1509 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.010   0.001   PHE D  65 
 TYR   0.020   0.002   TYR F  88 
 ARG   0.011   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06057 (  860)
  hydrogen bonds       : angle       3.34306 ( 2278)
  covalent geometry    : bond        0.00455 (17478)
  covalent geometry    : angle       0.60949 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 1.551 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8357 (mpp) cc_final: 0.8019 (mpp)
REVERT: B   68 ASP cc_start: 0.9381 (m-30) cc_final: 0.8826 (m-30)
REVERT: D   93 GLU cc_start: 0.9096 (mp0) cc_final: 0.8467 (mp0)
REVERT: E   73 GLU cc_start: 0.8748 (tt0) cc_final: 0.8440 (mt-10)
REVERT: E  120 MET cc_start: 0.8698 (mtm) cc_final: 0.7929 (mtp)
REVERT: G   73 ASN cc_start: 0.8924 (t0) cc_final: 0.8592 (t0)
REVERT: H   69 ILE cc_start: 0.9219 (mm) cc_final: 0.8957 (mm)
REVERT: K 1090 PHE cc_start: 0.8520 (m-10) cc_final: 0.7865 (m-80)
REVERT: K 1094 LYS cc_start: 0.7918 (mtpt) cc_final: 0.7382 (mmmt)
REVERT: K 1349 MET cc_start: 0.2208 (mmt) cc_final: 0.1411 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.2781
  time to fit residues: 35.7566
Evaluate side-chains
  55 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 1.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 5 optimal weight:    7.9990
   chunk 151 optimal weight:    6.9990
   chunk 78 optimal weight:    3.9990
   chunk 89 optimal weight:   10.0000
   chunk 66 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 55 optimal weight:    7.9990
   chunk 141 optimal weight:   10.0000
   chunk 8 optimal weight:    3.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
C  38 ASN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 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 = 0.3501 r_free = 0.3501 target = 0.054871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.039133 restraints weight = 189747.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.040239 restraints weight = 104862.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.040907 restraints weight = 71022.243|
|-----------------------------------------------------------------------------|
r_work (final): 0.3010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.4011

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  17478  Z= 0.177
  Angle     :  0.581   6.575  24869  Z= 0.335
  Chirality :  0.035   0.155   2772
  Planarity :  0.004   0.037   2150
  Dihedral  : 29.291 179.629   4768
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.78 %
    Favored  : 98.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.23), residues: 1283
  helix:  1.97 (0.18), residues: 783
  sheet:  0.94 (0.76), residues: 58
  loop :  0.47 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1509 
 HIS   0.004   0.001   HIS H  82 
 PHE   0.009   0.001   PHE G  25 
 TYR   0.030   0.002   TYR F  88 
 ARG   0.013   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04407 (  860)
  hydrogen bonds       : angle       3.28524 ( 2278)
  covalent geometry    : bond        0.00382 (17478)
  covalent geometry    : angle       0.58074 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 82
  time to evaluate  : 1.424 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8946 (tp30) cc_final: 0.8491 (tp30)
REVERT: A  120 MET cc_start: 0.8399 (mpp) cc_final: 0.8013 (mpp)
REVERT: B   68 ASP cc_start: 0.9455 (m-30) cc_final: 0.8954 (m-30)
REVERT: D  100 LEU cc_start: 0.8908 (mt) cc_final: 0.8705 (mt)
REVERT: E   73 GLU cc_start: 0.8785 (tt0) cc_final: 0.8482 (mt-10)
REVERT: E  120 MET cc_start: 0.8784 (mtm) cc_final: 0.7964 (mtp)
REVERT: F   88 TYR cc_start: 0.8087 (m-80) cc_final: 0.7849 (m-10)
REVERT: G   38 ASN cc_start: 0.8045 (m-40) cc_final: 0.7706 (m-40)
REVERT: G   73 ASN cc_start: 0.9002 (t0) cc_final: 0.8764 (t0)
REVERT: H   69 ILE cc_start: 0.9295 (mm) cc_final: 0.8972 (mm)
REVERT: K 1090 PHE cc_start: 0.8586 (m-10) cc_final: 0.8023 (m-80)
REVERT: K 1094 LYS cc_start: 0.7960 (mtpt) cc_final: 0.7564 (mmmt)
REVERT: K 1349 MET cc_start: 0.2595 (mmt) cc_final: 0.1952 (mtt)
  outliers start: 1
  outliers final: 0
  residues processed: 83
  average time/residue: 0.2603
  time to fit residues: 35.0577
Evaluate side-chains
  57 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 122 optimal weight:    7.9990
   chunk 153 optimal weight:    8.9990
   chunk 93 optimal weight:    6.9990
   chunk 135 optimal weight:    7.9990
   chunk 116 optimal weight:    0.1980
   chunk 154 optimal weight:   10.0000
   chunk 11 optimal weight:    0.6980
   chunk 118 optimal weight:    9.9990
   chunk 67 optimal weight:    2.9990
   chunk 13 optimal weight:    0.5980
   chunk 62 optimal weight:    7.9990
   overall best weight:    2.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1489 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.052196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.036003 restraints weight = 183472.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 66)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.036956 restraints weight = 108259.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.037562 restraints weight = 76981.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.2962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7888
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  17478  Z= 0.187
  Angle     :  0.584   6.326  24869  Z= 0.338
  Chirality :  0.035   0.153   2772
  Planarity :  0.004   0.043   2150
  Dihedral  : 29.320 177.722   4768
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.23), residues: 1283
  helix:  1.98 (0.18), residues: 788
  sheet:  0.77 (0.73), residues: 62
  loop :  0.43 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K1509 
 HIS   0.005   0.001   HIS B  75 
 PHE   0.010   0.001   PHE B  61 
 TYR   0.031   0.002   TYR F  88 
 ARG   0.015   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05423 (  860)
  hydrogen bonds       : angle       3.25670 ( 2278)
  covalent geometry    : bond        0.00403 (17478)
  covalent geometry    : angle       0.58394 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 1.935 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8848 (tp30) cc_final: 0.8511 (tp30)
REVERT: A  120 MET cc_start: 0.8505 (mpp) cc_final: 0.8065 (mpp)
REVERT: B   68 ASP cc_start: 0.9491 (m-30) cc_final: 0.8993 (m-30)
REVERT: B   88 TYR cc_start: 0.8299 (m-80) cc_final: 0.8083 (m-80)
REVERT: D   93 GLU cc_start: 0.9155 (mp0) cc_final: 0.8590 (mp0)
REVERT: E   73 GLU cc_start: 0.8755 (tt0) cc_final: 0.8518 (mt-10)
REVERT: E  120 MET cc_start: 0.8834 (mtm) cc_final: 0.8058 (mtp)
REVERT: G   73 ASN cc_start: 0.8878 (t0) cc_final: 0.8612 (t0)
REVERT: H   69 ILE cc_start: 0.9332 (mm) cc_final: 0.9114 (mm)
REVERT: K 1090 PHE cc_start: 0.8607 (m-10) cc_final: 0.8075 (m-80)
REVERT: K 1094 LYS cc_start: 0.8144 (mtpt) cc_final: 0.7875 (mmmt)
REVERT: K 1349 MET cc_start: 0.2648 (mmt) cc_final: 0.1841 (mtt)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2676
  time to fit residues: 37.6541
Evaluate side-chains
  58 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.441 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 154 optimal weight:   10.0000
   chunk 73 optimal weight:    0.9980
   chunk 119 optimal weight:   20.0000
   chunk 0 optimal weight:   20.0000
   chunk 9 optimal weight:   40.0000
   chunk 82 optimal weight:    0.0870
   chunk 141 optimal weight:   10.0000
   chunk 149 optimal weight:    6.9990
   chunk 116 optimal weight:    0.0050
   overall best weight:    0.5774

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.054998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.039373 restraints weight = 186648.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.040493 restraints weight = 103054.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.041156 restraints weight = 69762.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.4484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  17478  Z= 0.136
  Angle     :  0.552   6.903  24869  Z= 0.319
  Chirality :  0.035   0.153   2772
  Planarity :  0.004   0.036   2150
  Dihedral  : 29.204 179.655   4768
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.20 (0.23), residues: 1283
  helix:  2.11 (0.18), residues: 788
  sheet:  0.80 (0.74), residues: 62
  loop :  0.45 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP K1122 
 HIS   0.003   0.001   HIS F  75 
 PHE   0.009   0.001   PHE E  67 
 TYR   0.025   0.001   TYR F  88 
 ARG   0.007   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03881 (  860)
  hydrogen bonds       : angle       3.03604 ( 2278)
  covalent geometry    : bond        0.00288 (17478)
  covalent geometry    : angle       0.55183 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8943 (tp30) cc_final: 0.8543 (tp30)
REVERT: A  120 MET cc_start: 0.8450 (mpp) cc_final: 0.7927 (mpp)
REVERT: B   68 ASP cc_start: 0.9385 (m-30) cc_final: 0.8928 (m-30)
REVERT: C   90 ASP cc_start: 0.8926 (t0) cc_final: 0.8626 (t0)
REVERT: D   93 GLU cc_start: 0.9104 (mp0) cc_final: 0.8592 (mp0)
REVERT: E   81 ASP cc_start: 0.8556 (t70) cc_final: 0.8222 (t0)
REVERT: E  120 MET cc_start: 0.8729 (mtm) cc_final: 0.7896 (mtp)
REVERT: F   88 TYR cc_start: 0.7897 (m-80) cc_final: 0.7397 (m-10)
REVERT: G   38 ASN cc_start: 0.8454 (m-40) cc_final: 0.7937 (m-40)
REVERT: G   73 ASN cc_start: 0.8796 (t0) cc_final: 0.8517 (t0)
REVERT: H   69 ILE cc_start: 0.9305 (mm) cc_final: 0.9033 (mm)
REVERT: K 1090 PHE cc_start: 0.8542 (m-10) cc_final: 0.8020 (m-80)
REVERT: K 1094 LYS cc_start: 0.7993 (mtpt) cc_final: 0.7674 (mmmt)
REVERT: K 1349 MET cc_start: 0.2846 (mmt) cc_final: 0.2265 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.3435
  time to fit residues: 47.7820
Evaluate side-chains
  61 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 1.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 132 optimal weight:    8.9990
   chunk 23 optimal weight:    4.9990
   chunk 25 optimal weight:    1.9990
   chunk 115 optimal weight:    2.9990
   chunk 126 optimal weight:   30.0000
   chunk 76 optimal weight:    9.9990
   chunk 68 optimal weight:    7.9990
   chunk 35 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 148 optimal weight:    7.9990
   chunk 73 optimal weight:    0.0270
   overall best weight:    3.2046

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  39 HIS
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1415 HIS
K1449 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.050797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.034914 restraints weight = 182545.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.035849 restraints weight = 106459.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.036435 restraints weight = 75435.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7952
moved from start:          0.5211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  17478  Z= 0.229
  Angle     :  0.624   6.631  24869  Z= 0.357
  Chirality :  0.036   0.143   2772
  Planarity :  0.005   0.042   2150
  Dihedral  : 29.509 178.342   4768
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 14.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.80 %
    Favored  : 99.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.23), residues: 1283
  helix:  1.97 (0.18), residues: 780
  sheet:  0.88 (0.77), residues: 57
  loop :  0.28 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP K1509 
 HIS   0.005   0.001   HIS K1255 
 PHE   0.012   0.002   PHE B  61 
 TYR   0.029   0.002   TYR F  88 
 ARG   0.016   0.001   ARG E  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06348 (  860)
  hydrogen bonds       : angle       3.44590 ( 2278)
  covalent geometry    : bond        0.00492 (17478)
  covalent geometry    : angle       0.62353 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 1.663 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8846 (tp30) cc_final: 0.8505 (tp30)
REVERT: B   53 GLU cc_start: 0.8892 (tp30) cc_final: 0.8645 (tm-30)
REVERT: B   68 ASP cc_start: 0.9553 (m-30) cc_final: 0.9019 (m-30)
REVERT: C   90 ASP cc_start: 0.9108 (t0) cc_final: 0.8847 (t0)
REVERT: D   93 GLU cc_start: 0.9174 (mp0) cc_final: 0.8750 (mp0)
REVERT: D  100 LEU cc_start: 0.8841 (mt) cc_final: 0.8597 (mt)
REVERT: E  120 MET cc_start: 0.9021 (mtm) cc_final: 0.8140 (mtp)
REVERT: G   61 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8641 (tm-30)
REVERT: G   73 ASN cc_start: 0.8963 (t0) cc_final: 0.8730 (t0)
REVERT: H   69 ILE cc_start: 0.9336 (mm) cc_final: 0.9060 (mm)
REVERT: K 1349 MET cc_start: 0.3218 (mmt) cc_final: 0.2194 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.2979
  time to fit residues: 36.2970
Evaluate side-chains
  54 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 2.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 116 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 128 optimal weight:   10.0000
   chunk 24 optimal weight:    0.8980
   chunk 117 optimal weight:    5.9990
   chunk 126 optimal weight:   20.0000
   chunk 88 optimal weight:    8.9990
   chunk 113 optimal weight:    5.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1659 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.053658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.038203 restraints weight = 189538.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.039287 restraints weight = 104388.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.039957 restraints weight = 70512.465|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.5216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  17478  Z= 0.148
  Angle     :  0.572   7.218  24869  Z= 0.328
  Chirality :  0.035   0.171   2772
  Planarity :  0.004   0.036   2150
  Dihedral  : 29.441 178.024   4768
  Min Nonbonded Distance : 2.364

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.23), residues: 1283
  helix:  2.04 (0.18), residues: 786
  sheet:  0.76 (0.75), residues: 61
  loop :  0.31 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1509 
 HIS   0.010   0.001   HIS K1415 
 PHE   0.031   0.001   PHE K1075 
 TYR   0.045   0.002   TYR B  88 
 ARG   0.009   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04140 (  860)
  hydrogen bonds       : angle       3.20640 ( 2278)
  covalent geometry    : bond        0.00319 (17478)
  covalent geometry    : angle       0.57166 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.765 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8887 (tp30) cc_final: 0.8392 (tp30)
REVERT: B   53 GLU cc_start: 0.8812 (tp30) cc_final: 0.8559 (tm-30)
REVERT: B   68 ASP cc_start: 0.9470 (m-30) cc_final: 0.9011 (m-30)
REVERT: C   90 ASP cc_start: 0.9001 (t0) cc_final: 0.8615 (t0)
REVERT: D   93 GLU cc_start: 0.9179 (mp0) cc_final: 0.8643 (mp0)
REVERT: E   81 ASP cc_start: 0.8573 (t70) cc_final: 0.8240 (t0)
REVERT: E  120 MET cc_start: 0.8862 (mtm) cc_final: 0.8029 (mtp)
REVERT: G   61 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8695 (tm-30)
REVERT: G   73 ASN cc_start: 0.8813 (t0) cc_final: 0.8536 (t0)
REVERT: H   69 ILE cc_start: 0.9342 (mm) cc_final: 0.9080 (mm)
REVERT: K 1097 MET cc_start: 0.1037 (ppp) cc_final: 0.0761 (ppp)
REVERT: K 1314 ASN cc_start: 0.7619 (t0) cc_final: 0.7241 (m110)
REVERT: K 1349 MET cc_start: 0.3800 (mmt) cc_final: 0.3129 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2745
  time to fit residues: 37.2720
Evaluate side-chains
  57 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 1.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   chunk 153 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 110 optimal weight:    0.7980
   chunk 15 optimal weight:    8.9990
   chunk 19 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 89 optimal weight:    7.9990
   chunk 36 optimal weight:    4.9990
   chunk 67 optimal weight:    5.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E 108 ASN
F  25 ASN
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.053332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2976 r_free = 0.2976 target = 0.037874 restraints weight = 198295.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.3013 r_free = 0.3013 target = 0.038923 restraints weight = 111202.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.039588 restraints weight = 76190.797|
|-----------------------------------------------------------------------------|
r_work (final): 0.2978
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.5380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  17478  Z= 0.157
  Angle     :  0.569   7.542  24869  Z= 0.327
  Chirality :  0.035   0.147   2772
  Planarity :  0.004   0.034   2150
  Dihedral  : 29.340 179.656   4768
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 11.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.23), residues: 1283
  helix:  2.09 (0.18), residues: 786
  sheet:  0.76 (0.76), residues: 61
  loop :  0.31 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1509 
 HIS   0.010   0.001   HIS K1415 
 PHE   0.019   0.001   PHE K1075 
 TYR   0.034   0.002   TYR F  88 
 ARG   0.008   0.000   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04500 (  860)
  hydrogen bonds       : angle       3.18997 ( 2278)
  covalent geometry    : bond        0.00338 (17478)
  covalent geometry    : angle       0.56941 (24869)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 GLU cc_start: 0.8543 (tp30) cc_final: 0.8066 (tp30)
REVERT: A  105 GLU cc_start: 0.8817 (tp30) cc_final: 0.8414 (tp30)
REVERT: B   53 GLU cc_start: 0.8783 (tp30) cc_final: 0.8549 (tm-30)
REVERT: B   68 ASP cc_start: 0.9514 (m-30) cc_final: 0.9051 (m-30)
REVERT: C   90 ASP cc_start: 0.9014 (t0) cc_final: 0.8661 (t0)
REVERT: D   93 GLU cc_start: 0.9158 (mp0) cc_final: 0.8667 (mp0)
REVERT: E  120 MET cc_start: 0.8877 (mtm) cc_final: 0.8070 (mtp)
REVERT: G   61 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8669 (tm-30)
REVERT: G   73 ASN cc_start: 0.8798 (t0) cc_final: 0.8534 (t0)
REVERT: H   69 ILE cc_start: 0.9340 (mm) cc_final: 0.9070 (mm)
REVERT: H   71 GLU cc_start: 0.9185 (tp30) cc_final: 0.8800 (tp30)
REVERT: K 1075 PHE cc_start: 0.9426 (t80) cc_final: 0.9178 (t80)
REVERT: K 1349 MET cc_start: 0.4340 (mmt) cc_final: 0.3584 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.2289
  time to fit residues: 30.0542
Evaluate side-chains
  54 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 120 optimal weight:   30.0000
   chunk 113 optimal weight:    0.0070
   chunk 67 optimal weight:    5.9990
   chunk 27 optimal weight:    7.9990
   chunk 127 optimal weight:   10.0000
   chunk 15 optimal weight:    0.8980
   chunk 107 optimal weight:   40.0000
   chunk 30 optimal weight:    5.9990
   chunk 151 optimal weight:    6.9990
   chunk 48 optimal weight:    0.4980
   chunk 99 optimal weight:   30.0000
   overall best weight:    2.6802

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
D  82 HIS
** E  55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
E 108 ASN
G  38 ASN
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.050397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2929 r_free = 0.2929 target = 0.035197 restraints weight = 185424.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2951 r_free = 0.2951 target = 0.035685 restraints weight = 110778.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.035996 restraints weight = 87653.919|
|-----------------------------------------------------------------------------|
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7961
moved from start:          0.5841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  17478  Z= 0.200
  Angle     :  0.605   7.570  24869  Z= 0.346
  Chirality :  0.036   0.145   2772
  Planarity :  0.004   0.038   2150
  Dihedral  : 29.538 178.433   4768
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 13.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.23), residues: 1283
  helix:  2.02 (0.18), residues: 777
  sheet:  0.89 (0.78), residues: 55
  loop :  0.12 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K1509 
 HIS   0.009   0.001   HIS K1415 
 PHE   0.013   0.001   PHE E  67 
 TYR   0.049   0.002   TYR B  88 
 ARG   0.007   0.001   ARG E  52 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05545 (  860)
  hydrogen bonds       : angle       3.44346 ( 2278)
  covalent geometry    : bond        0.00432 (17478)
  covalent geometry    : angle       0.60471 (24869)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5418.77 seconds
wall clock time: 97 minutes 31.28 seconds (5851.28 seconds total)