Starting phenix.real_space_refine
on Thu Sep 18 11:36:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hai_34591/09_2025/8hai_34591.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hai_34591/09_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_34591/09_2025/8hai_34591.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hai_34591/09_2025/8hai_34591.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hai_34591/09_2025/8hai_34591.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hai_34591/09_2025/8hai_34591.cif"
  }
  resolution = 4.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: {'ALY:plan-1': 1, 'ALY:plan-2': 2, 'HIS:plan': 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, 'ASP:plan': 1, 'ARG: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: 3.93, per 1000 atoms: 0.24
  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: 1.27
  Conformation dependent library (CDL) restraints added in 477.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 2.24
  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: 3.96

  Time building geometry restraints manager: 1.73 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:               0.010
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     17.510
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.400
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.400
-------------------------------------------------------------------------------
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 : 10.76
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  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
 ARG   0.006   0.001   ARG E  53 
 TYR   0.039   0.001   TYR B  88 
 PHE   0.011   0.001   PHE G  25 
 TRP   0.009   0.001   TRP K1509 
 HIS   0.004   0.000   HIS A  39 

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

*********************** 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  : 0.544 
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: 0.1134
  time to fit residues: 18.4622
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  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    7.9990
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    8.9990
   chunk 91 optimal weight:   10.0000
   chunk 149 optimal weight:    7.9990
   overall best weight:    4.3188

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
C 104 GLN
** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1112 GLN
K1255 HIS
K1379 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.054244 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3014 r_free = 0.3014 target = 0.037904 restraints weight = 178474.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.038811 restraints weight = 110168.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 61)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.039365 restraints weight = 80700.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.039701 restraints weight = 66921.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.039851 restraints weight = 60227.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3039
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.130  17478  Z= 0.311
  Angle     :  0.742   9.848  24869  Z= 0.417
  Chirality :  0.041   0.150   2772
  Planarity :  0.006   0.060   2150
  Dihedral  : 28.936 170.411   4768
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.47 %
    Favored  : 96.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.66 (0.23), residues: 1283
  helix:  1.61 (0.18), residues: 776
  sheet:  0.40 (0.68), residues: 64
  loop :  0.46 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B  67 
 TYR   0.033   0.002   TYR B  88 
 PHE   0.017   0.002   PHE G  25 
 TRP   0.012   0.002   TRP K1509 
 HIS   0.011   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00671 (17478)
  covalent geometry    : angle       0.74245 (24869)
  hydrogen bonds       : bond        0.08028 (  860)
  hydrogen bonds       : angle       3.88042 ( 2278)

*********************** 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
  84 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 82
  time to evaluate  : 0.540 
Fit side-chains
REVERT: A  120 MET cc_start: 0.8232 (mpp) cc_final: 0.7826 (mpp)
REVERT: B   68 ASP cc_start: 0.9467 (m-30) cc_final: 0.9144 (m-30)
REVERT: D   45 LEU cc_start: 0.8994 (tp) cc_final: 0.8793 (tp)
REVERT: D   54 ILE cc_start: 0.8802 (pt) cc_final: 0.8586 (mm)
REVERT: E   73 GLU cc_start: 0.8679 (tt0) cc_final: 0.8390 (mt-10)
REVERT: E  120 MET cc_start: 0.8712 (mtm) cc_final: 0.8132 (ptp)
REVERT: G   73 ASN cc_start: 0.8903 (t0) cc_final: 0.8518 (t0)
REVERT: H   69 ILE cc_start: 0.9165 (mm) cc_final: 0.8930 (mm)
REVERT: K 1090 PHE cc_start: 0.8396 (m-10) cc_final: 0.7756 (m-80)
REVERT: K 1094 LYS cc_start: 0.7658 (mtpt) cc_final: 0.7140 (mmmt)
REVERT: K 1349 MET cc_start: 0.1418 (mmt) cc_final: 0.1085 (mtt)
  outliers start: 2
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1286
  time to fit residues: 17.5314
Evaluate side-chains
  56 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 60 optimal weight:    5.9990
   chunk 22 optimal weight:    0.8980
   chunk 88 optimal weight:    0.3980
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 154 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   chunk 140 optimal weight:   10.0000
   chunk 117 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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
E 108 ASN
** F  25 ASN ** 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 = 0.3573 r_free = 0.3573 target = 0.057547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.041652 restraints weight = 184098.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.042763 restraints weight = 102516.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.043460 restraints weight = 69968.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.043773 restraints weight = 55279.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.044091 restraints weight = 48705.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.2707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  17478  Z= 0.142
  Angle     :  0.551   6.271  24869  Z= 0.320
  Chirality :  0.035   0.180   2772
  Planarity :  0.004   0.039   2150
  Dihedral  : 28.961 179.649   4768
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.22
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.23), residues: 1283
  helix:  2.03 (0.18), residues: 777
  sheet:  0.68 (0.70), residues: 62
  loop :  0.58 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG E  52 
 TYR   0.039   0.001   TYR B  88 
 PHE   0.012   0.001   PHE G  25 
 TRP   0.007   0.001   TRP K1509 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (17478)
  covalent geometry    : angle       0.55123 (24869)
  hydrogen bonds       : bond        0.04092 (  860)
  hydrogen bonds       : angle       3.20452 ( 2278)

*********************** 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
  92 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A   50 GLU cc_start: 0.8889 (tt0) cc_final: 0.8284 (pt0)
REVERT: A  105 GLU cc_start: 0.9009 (tp30) cc_final: 0.8600 (tp30)
REVERT: A  110 CYS cc_start: 0.9278 (m) cc_final: 0.8863 (t)
REVERT: A  120 MET cc_start: 0.8282 (mpp) cc_final: 0.7888 (mpp)
REVERT: B   68 ASP cc_start: 0.9303 (m-30) cc_final: 0.8884 (m-30)
REVERT: B   84 MET cc_start: 0.8943 (tpp) cc_final: 0.8696 (tpp)
REVERT: D  100 LEU cc_start: 0.8864 (mt) cc_final: 0.8598 (mt)
REVERT: E   73 GLU cc_start: 0.8751 (tt0) cc_final: 0.8405 (tt0)
REVERT: G   73 ASN cc_start: 0.8923 (t0) cc_final: 0.8577 (t0)
REVERT: H   69 ILE cc_start: 0.9184 (mm) cc_final: 0.8963 (mm)
REVERT: K 1090 PHE cc_start: 0.8507 (m-10) cc_final: 0.7836 (m-80)
REVERT: K 1094 LYS cc_start: 0.7583 (mtpt) cc_final: 0.7077 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1309
  time to fit residues: 19.0770
Evaluate side-chains
  62 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 84 optimal weight:    3.9990
   chunk 94 optimal weight:    6.9990
   chunk 143 optimal weight:    5.9990
   chunk 80 optimal weight:    9.9990
   chunk 128 optimal weight:   10.0000
   chunk 17 optimal weight:    9.9990
   chunk 149 optimal weight:    7.9990
   chunk 127 optimal weight:   10.0000
   chunk 137 optimal weight:    8.9990
   chunk 93 optimal weight:   10.0000
   chunk 132 optimal weight:    5.9990
   overall best weight:    6.1990

-------------------------------------------------------------------------------
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
C  73 ASN
E  39 HIS
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1132 ASN
K1236 ASN
** K1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1451 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.049441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.033527 restraints weight = 185682.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.034393 restraints weight = 111301.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.034918 restraints weight = 80373.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.035261 restraints weight = 66107.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2930 r_free = 0.2930 target = 0.035343 restraints weight = 58940.877|
|-----------------------------------------------------------------------------|
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.072  17478  Z= 0.397
  Angle     :  0.813  11.249  24869  Z= 0.455
  Chirality :  0.044   0.256   2772
  Planarity :  0.006   0.069   2150
  Dihedral  : 29.904 175.790   4768
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 20.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  4.27 %
    Favored  : 95.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.10 (0.22), residues: 1283
  helix:  1.16 (0.18), residues: 770
  sheet:  0.76 (0.75), residues: 58
  loop :  0.14 (0.28), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.038   0.001   ARG E  52 
 TYR   0.046   0.003   TYR B  88 
 PHE   0.018   0.002   PHE B  61 
 TRP   0.013   0.002   TRP K1509 
 HIS   0.010   0.002   HIS B  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00851 (17478)
  covalent geometry    : angle       0.81294 (24869)
  hydrogen bonds       : bond        0.09512 (  860)
  hydrogen bonds       : angle       4.31766 ( 2278)

*********************** 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
  70 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 69
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8494 (mpp) cc_final: 0.8133 (mpp)
REVERT: B   68 ASP cc_start: 0.9683 (m-30) cc_final: 0.9465 (m-30)
REVERT: E  120 MET cc_start: 0.8897 (mtm) cc_final: 0.8285 (mtp)
REVERT: F   88 TYR cc_start: 0.8019 (m-80) cc_final: 0.7619 (m-80)
REVERT: G   73 ASN cc_start: 0.9060 (t0) cc_final: 0.8776 (t0)
REVERT: H   69 ILE cc_start: 0.9250 (mm) cc_final: 0.8957 (mm)
REVERT: K 1090 PHE cc_start: 0.8766 (m-10) cc_final: 0.8172 (m-80)
REVERT: K 1094 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7936 (mmmt)
REVERT: K 1311 ARG cc_start: 0.5122 (mtm-85) cc_final: 0.4860 (mmp80)
REVERT: K 1339 MET cc_start: -0.1427 (ttm) cc_final: -0.1823 (ttm)
REVERT: K 1349 MET cc_start: 0.2557 (mtt) cc_final: 0.2037 (mmt)
  outliers start: 1
  outliers final: 0
  residues processed: 70
  average time/residue: 0.1325
  time to fit residues: 14.5781
Evaluate side-chains
  52 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 142 optimal weight:    8.9990
   chunk 77 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 112 optimal weight:   10.0000
   chunk 64 optimal weight:    6.9990
   chunk 117 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 83 optimal weight:    7.9990
   chunk 150 optimal weight:    4.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    2.5186

-------------------------------------------------------------------------------
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  39 HIS
E 108 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1415 HIS
K1451 HIS
K1489 GLN
K1659 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.052742 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.037173 restraints weight = 191018.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.038250 restraints weight = 104680.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.038914 restraints weight = 70837.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.039310 restraints weight = 55713.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.039394 restraints weight = 48473.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.4922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  17478  Z= 0.188
  Angle     :  0.613   6.462  24869  Z= 0.353
  Chirality :  0.036   0.153   2772
  Planarity :  0.004   0.045   2150
  Dihedral  : 29.949 178.611   4768
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.23), residues: 1283
  helix:  1.68 (0.18), residues: 778
  sheet:  0.80 (0.76), residues: 58
  loop :  0.13 (0.29), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E  52 
 TYR   0.022   0.002   TYR B  88 
 PHE   0.011   0.001   PHE E  67 
 TRP   0.008   0.001   TRP K1509 
 HIS   0.004   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 (17478)
  covalent geometry    : angle       0.61275 (24869)
  hydrogen bonds       : bond        0.05011 (  860)
  hydrogen bonds       : angle       3.59495 ( 2278)

*********************** 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
  81 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.519 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8865 (tp30) cc_final: 0.8510 (tp30)
REVERT: A  120 MET cc_start: 0.8474 (mpp) cc_final: 0.8096 (mpp)
REVERT: B   68 ASP cc_start: 0.9613 (m-30) cc_final: 0.9303 (m-30)
REVERT: B   88 TYR cc_start: 0.8454 (m-80) cc_final: 0.8232 (m-80)
REVERT: D  100 LEU cc_start: 0.8860 (mt) cc_final: 0.8646 (mt)
REVERT: E  120 MET cc_start: 0.8819 (mtm) cc_final: 0.8149 (mtp)
REVERT: F   88 TYR cc_start: 0.8191 (m-80) cc_final: 0.7960 (m-80)
REVERT: G   73 ASN cc_start: 0.9003 (t0) cc_final: 0.8764 (t0)
REVERT: H   69 ILE cc_start: 0.9347 (mm) cc_final: 0.9121 (mm)
REVERT: K 1090 PHE cc_start: 0.8603 (m-10) cc_final: 0.8013 (m-80)
REVERT: K 1094 LYS cc_start: 0.8104 (mtpt) cc_final: 0.7840 (mmmt)
REVERT: K 1339 MET cc_start: -0.1636 (ttm) cc_final: -0.2200 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1301
  time to fit residues: 16.6082
Evaluate side-chains
  53 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 83 optimal weight:   10.0000
   chunk 104 optimal weight:   10.0000
   chunk 33 optimal weight:    9.9990
   chunk 120 optimal weight:   30.0000
   chunk 76 optimal weight:    1.9990
   chunk 93 optimal weight:    6.9990
   chunk 47 optimal weight:    0.4980
   chunk 28 optimal weight:    0.4980
   chunk 109 optimal weight:    7.9990
   chunk 102 optimal weight:    5.9990
   chunk 130 optimal weight:    7.9990
   overall best weight:    3.1986

-------------------------------------------------------------------------------
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
K1255 HIS
K1449 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.049855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.033981 restraints weight = 184980.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.034914 restraints weight = 108006.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.2940 r_free = 0.2940 target = 0.035491 restraints weight = 76329.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.035845 restraints weight = 61895.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.035927 restraints weight = 54880.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.5403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  17478  Z= 0.226
  Angle     :  0.633   6.466  24869  Z= 0.362
  Chirality :  0.036   0.151   2772
  Planarity :  0.005   0.050   2150
  Dihedral  : 29.926 179.209   4768
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.95 %
    Favored  : 98.05 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.87 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.23), residues: 1283
  helix:  1.75 (0.18), residues: 771
  sheet:  0.68 (0.77), residues: 58
  loop :  0.09 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG F  67 
 TYR   0.018   0.002   TYR B  88 
 PHE   0.012   0.001   PHE E  67 
 TRP   0.006   0.001   TRP K1509 
 HIS   0.006   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (17478)
  covalent geometry    : angle       0.63261 (24869)
  hydrogen bonds       : bond        0.06147 (  860)
  hydrogen bonds       : angle       3.66326 ( 2278)

*********************** 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
  76 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
REVERT: A  105 GLU cc_start: 0.8887 (tp30) cc_final: 0.8529 (tp30)
REVERT: A  120 MET cc_start: 0.8546 (mpp) cc_final: 0.8168 (mpp)
REVERT: B   68 ASP cc_start: 0.9664 (m-30) cc_final: 0.9401 (m-30)
REVERT: D   59 MET cc_start: 0.8823 (tpt) cc_final: 0.8576 (tpp)
REVERT: D  100 LEU cc_start: 0.8880 (mt) cc_final: 0.8669 (mt)
REVERT: E  120 MET cc_start: 0.8922 (mtm) cc_final: 0.8209 (mtp)
REVERT: F   88 TYR cc_start: 0.8254 (m-80) cc_final: 0.7832 (m-80)
REVERT: G   73 ASN cc_start: 0.8977 (t0) cc_final: 0.8751 (t0)
REVERT: H   69 ILE cc_start: 0.9304 (mm) cc_final: 0.9060 (mm)
REVERT: K 1090 PHE cc_start: 0.8668 (m-10) cc_final: 0.8120 (m-80)
REVERT: K 1094 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7928 (mmmt)
REVERT: K 1339 MET cc_start: -0.1800 (ttm) cc_final: -0.2001 (ttm)
  outliers start: 1
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1269
  time to fit residues: 15.4000
Evaluate side-chains
  52 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 131 optimal weight:    6.9990
   chunk 34 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 85 optimal weight:    9.9990
   chunk 101 optimal weight:    4.9990
   chunk 148 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   chunk 124 optimal weight:   20.0000
   overall best weight:    2.1986

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

Flipped N/Q/H residues before XYZ refinement:
A 108 ASN
E  93 GLN
E 108 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.052072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.036641 restraints weight = 192770.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.037716 restraints weight = 105864.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.038385 restraints weight = 71476.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.038783 restraints weight = 56186.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.038866 restraints weight = 49048.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.5574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  17478  Z= 0.175
  Angle     :  0.599   6.862  24869  Z= 0.344
  Chirality :  0.036   0.156   2772
  Planarity :  0.004   0.048   2150
  Dihedral  : 29.870 178.328   4768
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.23), residues: 1283
  helix:  1.86 (0.18), residues: 784
  sheet:  0.73 (0.77), residues: 57
  loop :  0.07 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  52 
 TYR   0.032   0.002   TYR B  88 
 PHE   0.014   0.001   PHE K1075 
 TRP   0.008   0.001   TRP K1129 
 HIS   0.008   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 (17478)
  covalent geometry    : angle       0.59949 (24869)
  hydrogen bonds       : bond        0.04768 (  860)
  hydrogen bonds       : angle       3.48593 ( 2278)

*********************** 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
  82 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8917 (tp30) cc_final: 0.8515 (tp30)
REVERT: A  120 MET cc_start: 0.8571 (mpp) cc_final: 0.8189 (mpp)
REVERT: B   68 ASP cc_start: 0.9649 (m-30) cc_final: 0.9385 (m-30)
REVERT: B   84 MET cc_start: 0.9054 (tpp) cc_final: 0.8655 (tpp)
REVERT: C   90 ASP cc_start: 0.9022 (t0) cc_final: 0.8786 (t0)
REVERT: D   59 MET cc_start: 0.8952 (tpt) cc_final: 0.8677 (tpp)
REVERT: D  100 LEU cc_start: 0.8834 (mt) cc_final: 0.8613 (mt)
REVERT: E   81 ASP cc_start: 0.8479 (t70) cc_final: 0.8223 (t0)
REVERT: E  120 MET cc_start: 0.8819 (mtm) cc_final: 0.8041 (mtp)
REVERT: G   73 ASN cc_start: 0.8926 (t0) cc_final: 0.8678 (t0)
REVERT: H   69 ILE cc_start: 0.9290 (mm) cc_final: 0.9056 (mm)
REVERT: K 1339 MET cc_start: -0.1731 (ttm) cc_final: -0.1958 (ttm)
REVERT: K 1349 MET cc_start: 0.4904 (mmt) cc_final: 0.4383 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.1238
  time to fit residues: 16.2520
Evaluate side-chains
  50 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.531 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 72 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 139 optimal weight:    7.9990
   chunk 140 optimal weight:   10.0000
   chunk 154 optimal weight:   10.0000
   chunk 92 optimal weight:    0.7980
   chunk 152 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0470
   chunk 0 optimal weight:   20.0000
   overall best weight:    1.1282

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.052842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.037343 restraints weight = 196151.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.038408 restraints weight = 109981.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.039045 restraints weight = 75436.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.039436 restraints weight = 60248.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.039578 restraints weight = 52922.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.2983
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.5583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  17478  Z= 0.146
  Angle     :  0.577   7.308  24869  Z= 0.331
  Chirality :  0.035   0.153   2772
  Planarity :  0.004   0.046   2150
  Dihedral  : 29.617 178.853   4768
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.71 %
    Favored  : 99.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.23), residues: 1283
  helix:  1.95 (0.18), residues: 782
  sheet:  0.74 (0.77), residues: 57
  loop :  0.11 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  52 
 TYR   0.021   0.001   TYR B  88 
 PHE   0.033   0.001   PHE A 104 
 TRP   0.005   0.001   TRP K1509 
 HIS   0.008   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (17478)
  covalent geometry    : angle       0.57708 (24869)
  hydrogen bonds       : bond        0.04259 (  860)
  hydrogen bonds       : angle       3.34342 ( 2278)

*********************** 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
  81 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.561 
Fit side-chains
REVERT: A  105 GLU cc_start: 0.8929 (tp30) cc_final: 0.8452 (tp30)
REVERT: A  120 MET cc_start: 0.8528 (mpp) cc_final: 0.8139 (mpp)
REVERT: B   68 ASP cc_start: 0.9603 (m-30) cc_final: 0.9324 (m-30)
REVERT: B   84 MET cc_start: 0.9023 (tpp) cc_final: 0.8671 (tpp)
REVERT: C   90 ASP cc_start: 0.8987 (t0) cc_final: 0.8703 (t0)
REVERT: E   81 ASP cc_start: 0.8539 (t70) cc_final: 0.8229 (t0)
REVERT: E  120 MET cc_start: 0.8839 (mtm) cc_final: 0.8007 (mtp)
REVERT: G   38 ASN cc_start: 0.8395 (m110) cc_final: 0.7594 (m-40)
REVERT: G   41 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: G   73 ASN cc_start: 0.8814 (t0) cc_final: 0.8548 (t0)
REVERT: H   69 ILE cc_start: 0.9276 (mm) cc_final: 0.8987 (mm)
REVERT: H   71 GLU cc_start: 0.9277 (tp30) cc_final: 0.8882 (tp30)
REVERT: K 1075 PHE cc_start: 0.9438 (t80) cc_final: 0.9203 (t80)
REVERT: K 1339 MET cc_start: -0.1991 (ttm) cc_final: -0.2234 (ttm)
REVERT: K 1349 MET cc_start: 0.5159 (mmt) cc_final: 0.4698 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1079
  time to fit residues: 14.4662
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  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 105 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0000
   chunk 141 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 91 optimal weight:   20.0000
   chunk 127 optimal weight:   10.0000
   chunk 122 optimal weight:    0.0980
   chunk 0 optimal weight:   20.0000
   chunk 139 optimal weight:    8.9990
   chunk 92 optimal weight:    0.7980
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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**
G  38 ASN
H  84 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.052806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.037411 restraints weight = 196585.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.038504 restraints weight = 109663.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.039146 restraints weight = 74915.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 55)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.039539 restraints weight = 59788.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.039618 restraints weight = 52491.143|
|-----------------------------------------------------------------------------|
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.5683

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  17478  Z= 0.146
  Angle     :  0.575   7.637  24869  Z= 0.330
  Chirality :  0.035   0.167   2772
  Planarity :  0.004   0.058   2150
  Dihedral  : 29.500 178.678   4768
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.90 (0.23), residues: 1283
  helix:  1.99 (0.18), residues: 782
  sheet:  0.65 (0.76), residues: 57
  loop :  0.09 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.000   ARG C  20 
 TYR   0.016   0.001   TYR B  88 
 PHE   0.020   0.001   PHE E  67 
 TRP   0.006   0.001   TRP K1509 
 HIS   0.008   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (17478)
  covalent geometry    : angle       0.57540 (24869)
  hydrogen bonds       : bond        0.04221 (  860)
  hydrogen bonds       : angle       3.33560 ( 2278)

*********************** 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
  77 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.501 
Fit side-chains
REVERT: A   94 GLU cc_start: 0.8483 (tp30) cc_final: 0.8030 (tp30)
REVERT: A  104 PHE cc_start: 0.9135 (m-10) cc_final: 0.8914 (m-10)
REVERT: A  105 GLU cc_start: 0.8874 (tp30) cc_final: 0.8439 (tp30)
REVERT: A  110 CYS cc_start: 0.9283 (m) cc_final: 0.8907 (t)
REVERT: A  120 MET cc_start: 0.8526 (mpp) cc_final: 0.8130 (mpp)
REVERT: B   68 ASP cc_start: 0.9620 (m-30) cc_final: 0.9333 (m-30)
REVERT: B   84 MET cc_start: 0.9021 (tpp) cc_final: 0.8691 (tpp)
REVERT: C   90 ASP cc_start: 0.8961 (t0) cc_final: 0.8720 (t0)
REVERT: E   81 ASP cc_start: 0.8526 (t70) cc_final: 0.8218 (t0)
REVERT: E  120 MET cc_start: 0.8918 (mtm) cc_final: 0.8123 (mtp)
REVERT: G   41 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7920 (tm-30)
REVERT: G   73 ASN cc_start: 0.8787 (t0) cc_final: 0.8528 (t0)
REVERT: H   69 ILE cc_start: 0.9255 (mm) cc_final: 0.8978 (mm)
REVERT: H   71 GLU cc_start: 0.9305 (tp30) cc_final: 0.8990 (tp30)
REVERT: K 1097 MET cc_start: 0.1247 (ppp) cc_final: 0.0936 (ppp)
REVERT: K 1339 MET cc_start: -0.1999 (ttm) cc_final: -0.2218 (ttm)
REVERT: K 1349 MET cc_start: 0.5101 (mmt) cc_final: 0.4633 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1000
  time to fit residues: 13.4588
Evaluate side-chains
  52 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 7 optimal weight:    5.9990
   chunk 74 optimal weight:    9.9990
   chunk 17 optimal weight:    0.8980
   chunk 84 optimal weight:    0.2980
   chunk 125 optimal weight:   30.0000
   chunk 72 optimal weight:    0.6980
   chunk 138 optimal weight:    7.9990
   chunk 50 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 134 optimal weight:    6.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.053413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.037931 restraints weight = 191297.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.039097 restraints weight = 104730.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.039784 restraints weight = 69653.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.040204 restraints weight = 54254.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 51)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.040446 restraints weight = 47066.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7861
moved from start:          0.5699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17478  Z= 0.134
  Angle     :  0.560   8.630  24869  Z= 0.321
  Chirality :  0.035   0.154   2772
  Planarity :  0.004   0.035   2150
  Dihedral  : 29.317 178.019   4768
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.40 %
    Favored  : 98.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.23), residues: 1283
  helix:  2.11 (0.18), residues: 779
  sheet:  0.79 (0.78), residues: 57
  loop :  0.10 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.000   ARG E  52 
 TYR   0.014   0.001   TYR B  88 
 PHE   0.029   0.001   PHE K1075 
 TRP   0.004   0.001   TRP K1266 
 HIS   0.008   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (17478)
  covalent geometry    : angle       0.55968 (24869)
  hydrogen bonds       : bond        0.03821 (  860)
  hydrogen bonds       : angle       3.23210 ( 2278)

********************** 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
  79 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
REVERT: A  110 CYS cc_start: 0.9251 (m) cc_final: 0.8859 (t)
REVERT: A  120 MET cc_start: 0.8506 (mpp) cc_final: 0.8132 (mpp)
REVERT: B   68 ASP cc_start: 0.9589 (m-30) cc_final: 0.9266 (m-30)
REVERT: B   84 MET cc_start: 0.9016 (tpp) cc_final: 0.8667 (tpp)
REVERT: C   90 ASP cc_start: 0.8912 (t0) cc_final: 0.8646 (t0)
REVERT: E   81 ASP cc_start: 0.8526 (t70) cc_final: 0.8197 (t0)
REVERT: E  120 MET cc_start: 0.8814 (mtm) cc_final: 0.8024 (mtp)
REVERT: G   38 ASN cc_start: 0.8201 (m110) cc_final: 0.7702 (m-40)
REVERT: G   41 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7808 (tm-30)
REVERT: G   62 ILE cc_start: 0.9653 (tt) cc_final: 0.9438 (tt)
REVERT: G   73 ASN cc_start: 0.8751 (t0) cc_final: 0.8457 (t0)
REVERT: H   69 ILE cc_start: 0.9291 (mm) cc_final: 0.9005 (mm)
REVERT: H   71 GLU cc_start: 0.9277 (tp30) cc_final: 0.8874 (tp30)
REVERT: K 1339 MET cc_start: -0.1989 (ttm) cc_final: -0.2234 (ttm)
REVERT: K 1349 MET cc_start: 0.4552 (mmt) cc_final: 0.3923 (mmt)
REVERT: K 1624 MET cc_start: -0.4173 (mpp) cc_final: -0.4404 (mtm)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1103
  time to fit residues: 14.7956
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  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 155
   random chunks:
   chunk 95 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9980
   chunk 145 optimal weight:    7.9990
   chunk 86 optimal weight:    6.9990
   chunk 92 optimal weight:   30.0000
   chunk 33 optimal weight:    5.9990
   chunk 154 optimal weight:   10.0000
   chunk 16 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 104 optimal weight:    0.0670
   chunk 72 optimal weight:    0.1980
   overall best weight:    1.4522

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.052782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.037480 restraints weight = 192613.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.038595 restraints weight = 104437.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.039285 restraints weight = 69904.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.039602 restraints weight = 54686.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.039918 restraints weight = 47912.705|
|-----------------------------------------------------------------------------|
r_work (final): 0.3000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.5856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17478  Z= 0.150
  Angle     :  0.563   7.932  24869  Z= 0.323
  Chirality :  0.034   0.150   2772
  Planarity :  0.004   0.045   2150
  Dihedral  : 29.331 178.822   4768
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.36 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.17 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.08 (0.23), residues: 1283
  helix:  2.17 (0.18), residues: 776
  sheet:  0.72 (0.77), residues: 57
  loop :  0.13 (0.28), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  52 
 TYR   0.013   0.001   TYR B  88 
 PHE   0.026   0.001   PHE A 104 
 TRP   0.006   0.001   TRP K1129 
 HIS   0.008   0.001   HIS K1415 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (17478)
  covalent geometry    : angle       0.56350 (24869)
  hydrogen bonds       : bond        0.04332 (  860)
  hydrogen bonds       : angle       3.28098 ( 2278)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3018.16 seconds
wall clock time: 52 minutes 48.90 seconds (3168.90 seconds total)