Starting phenix.real_space_refine
on Sun Jun 15 06:56:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ham_34596/06_2025/8ham_34596.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ham_34596/06_2025/8ham_34596.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ham_34596/06_2025/8ham_34596.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ham_34596/06_2025/8ham_34596.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ham_34596/06_2025/8ham_34596.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ham_34596/06_2025/8ham_34596.cif"
  }
  resolution = 4.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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     330      5.49       5
     S      46      5.16       5
     C    9835      2.51       5
     N    3130      2.21       5
     O    3836      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 135 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17177
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 815
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 815
          Classifications: {'peptide': 99}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 94}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 720
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 91, 720
          Classifications: {'peptide': 91}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 1, 'TRANS': 89}
          Unresolved non-hydrogen bonds: 14
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'ARG:plan': 1, 'ALY:plan-2': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "C"
      Number of atoms: 819
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 819
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    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: 673
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 84, 673
          Classifications: {'peptide': 84}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 82}
    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: 730
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 730
          Classifications: {'peptide': 94}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "I"
      Number of atoms: 3384
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3384
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
    Chain: "J"
      Number of atoms: 3381
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 165, 3381
          Classifications: {'DNA': 165}
          Link IDs: {'rna3p': 164}
    Chain: "K"
      Number of atoms: 4302
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 517, 4302
          Classifications: {'peptide': 517}
          Link IDs: {'PCIS': 3, 'PTRANS': 29, 'TRANS': 484}
          Chain breaks: 4
  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: 10.00, per 1000 atoms: 0.58
  Number of scatterers: 17177
  At special positions: 0
  Unit cell: (101.43, 161.7, 124.95, 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      46     16.00
     P     330     15.00
     O    3836      8.00
     N    3130      7.00
     C    9835      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 4.39
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2428

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 14 sheets defined
      62.0% alpha, 7.5% beta
      129 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 7.39
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 56
    Processing helix  chain 'A' and resid 63 through 79
    Processing helix  chain 'A' and resid 85 through 114
    Processing helix  chain 'A' and resid 120 through 132
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.775A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 49 through 76
      removed outlier: 3.705A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   GLU B  63 " --> pdb=" O   LYS B  59 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   ASP B  68 " --> pdb=" O   ASN B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
    Processing helix  chain 'C' and resid 16 through 21
    Processing helix  chain 'C' and resid 26 through 37
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.356A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.533A  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
    Processing helix  chain 'D' and resid 103 through 123
      removed outlier: 3.686A  pdb=" N   ALA D 107 " --> pdb=" O   PRO D 103 " (cutoff:3.500A)
    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: 3.559A  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 42
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 3.561A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 94
    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: 4.342A  pdb=" N   VAL G  49 " --> pdb=" O   ALA G  45 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.943A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 97
    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
    Processing helix  chain 'H' and resid 103 through 124
    Processing helix  chain 'K' and resid 1088 through 1104
      Proline residue:  K1096  - end of helix
      removed outlier: 3.514A  pdb=" N   GLN K1104 " --> pdb=" O   ALA K1100 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1108 through 1112
    Processing helix  chain 'K' and resid 1124 through 1129
      removed outlier: 3.510A  pdb=" N   ILE K1128 " --> pdb=" O   ASP K1124 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1134 through 1145
    Processing helix  chain 'K' and resid 1149 through 1168
      removed outlier: 4.061A  pdb=" N   TYR K1153 " --> pdb=" O   GLU K1149 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1172 through 1197
      removed outlier: 4.353A  pdb=" N   ASP K1190 " --> pdb=" O   GLU K1186 " (cutoff:3.500A)
      Proline residue:  K1191  - end of helix
    Processing helix  chain 'K' and resid 1238 through 1244
    Processing helix  chain 'K' and resid 1292 through 1296
    Processing helix  chain 'K' and resid 1308 through 1316
    Processing helix  chain 'K' and resid 1332 through 1350
    Processing helix  chain 'K' and resid 1372 through 1380
    Processing helix  chain 'K' and resid 1443 through 1464
      removed outlier: 4.474A  pdb=" N   THR K1447 " --> pdb=" O   ARG K1443 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   ALA K1448 " --> pdb=" O   CYS K1444 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1495 through 1513
    Processing helix  chain 'K' and resid 1522 through 1530
    Processing helix  chain 'K' and resid 1533 through 1537
    Processing helix  chain 'K' and resid 1543 through 1554
      removed outlier: 4.115A  pdb=" N   ASN K1547 " --> pdb=" O   ASP K1543 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 1617 through 1629
    Processing helix  chain 'K' and resid 1664 through 1675
    Processing helix  chain 'K' and resid 1680 through 1698
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.712A  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
    Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97
      removed outlier: 6.768A  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: 7.294A  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 102
    Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.540A  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: 7.122A  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 1205 through 1206
      removed outlier: 3.526A  pdb=" N   ASP K1276 " --> pdb=" O   PHE K1206 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'K' and resid 1234 through 1237
    Processing sheet with id=AB4, first strand: chain 'K' and resid 1280 through 1282
    Processing sheet with id=AB5, first strand: chain 'K' and resid 1357 through 1370
      removed outlier: 6.529A  pdb=" N   ALA K1395 " --> pdb=" O   VAL K1362 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   SER K1364 " --> pdb=" O   THR K1393 " (cutoff:3.500A)
      removed outlier: 6.605A  pdb=" N   THR K1393 " --> pdb=" O   SER K1364 " (cutoff:3.500A)
      removed outlier: 4.650A  pdb=" N   ASP K1366 " --> pdb=" O   TYR K1391 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TYR K1391 " --> pdb=" O   ASP K1366 " (cutoff:3.500A)
      removed outlier: 4.581A  pdb=" N   THR K1368 " --> pdb=" O   PHE K1389 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   PHE K1389 " --> pdb=" O   THR K1368 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU K1396 " --> pdb=" O   MET K1412 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE K1410 " --> pdb=" O   ALA K1398 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   GLU K1400 " --> pdb=" O   CYS K1408 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   CYS K1408 " --> pdb=" O   GLU K1400 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ILE K1402 " --> pdb=" O   ASP K1406 " (cutoff:3.500A)
      removed outlier: 5.116A  pdb=" N   ASP K1406 " --> pdb=" O   ILE K1402 " (cutoff:3.500A)
      removed outlier: 6.708A  pdb=" N   GLN K1415 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 5.527A  pdb=" N   ILE K1431 " --> pdb=" O   GLN K1415 " (cutoff:3.500A)
      removed outlier: 6.931A  pdb=" N   TYR K1417 " --> pdb=" O   VAL K1429 " (cutoff:3.500A)
      removed outlier: 5.339A  pdb=" N   VAL K1429 " --> pdb=" O   TYR K1417 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   TRP K1472 " --> pdb=" O   ILE K1431 " (cutoff:3.500A)
      removed outlier: 7.734A  pdb=" N   TYR K1433 " --> pdb=" O   TRP K1472 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ASP K1518 " --> pdb=" O   HIS K1636 " (cutoff:3.500A)

    605 hydrogen bonds defined for protein.
    1785 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      310 hydrogen bonds
      620 hydrogen bond angles
      0 basepair planarities
      129 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 10.01

  Time building geometry restraints manager: 5.30 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3318
        1.33 -     1.45: 5725
        1.45 -     1.57: 8432
        1.57 -     1.69: 658
        1.69 -     1.81: 68
  Bond restraints: 18201
  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 4.45e+00
  bond pdb=" NZ  ALY B  12 "
       pdb=" CH  ALY B  12 "
    ideal  model  delta    sigma   weight residual
    1.343  1.384 -0.041 2.00e-02 2.50e+03 4.19e+00
  bond pdb=" C3'  DT I 136 "
       pdb=" O3'  DT I 136 "
    ideal  model  delta    sigma   weight residual
    1.422  1.471 -0.049 3.00e-02 1.11e+03 2.70e+00
  bond pdb=" C   LEU D 101 "
       pdb=" N   LEU D 102 "
    ideal  model  delta    sigma   weight residual
    1.329  1.352 -0.024 1.60e-02 3.91e+03 2.20e+00
  bond pdb=" C3'  DA J  59 "
       pdb=" O3'  DA J  59 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.69e+00
  ... (remaining 18196 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 25591
        2.07 -     4.14: 381
        4.14 -     6.22: 17
        6.22 -     8.29: 4
        8.29 -    10.36: 1
  Bond angle restraints: 25994
  Sorted by residual:
  angle pdb=" CA  LEU K1507 "
        pdb=" CB  LEU K1507 "
        pdb=" CG  LEU K1507 "
      ideal   model   delta    sigma   weight residual
     116.30  105.94   10.36 3.50e+00 8.16e-02 8.76e+00
  angle pdb=" C   ASN B  64 "
        pdb=" N   VAL B  65 "
        pdb=" CA  VAL B  65 "
      ideal   model   delta    sigma   weight residual
     122.97  120.31    2.66 9.80e-01 1.04e+00 7.38e+00
  angle pdb=" C   PHE K1544 "
        pdb=" N   TRP K1545 "
        pdb=" CA  TRP K1545 "
      ideal   model   delta    sigma   weight residual
     120.09  123.41   -3.32 1.25e+00 6.40e-01 7.04e+00
  angle pdb=" CB  MET K1290 "
        pdb=" CG  MET K1290 "
        pdb=" SD  MET K1290 "
      ideal   model   delta    sigma   weight residual
     112.70  120.41   -7.71 3.00e+00 1.11e-01 6.60e+00
  angle pdb=" C   LEU D 101 "
        pdb=" N   LEU D 102 "
        pdb=" CA  LEU D 102 "
      ideal   model   delta    sigma   weight residual
     120.49  116.91    3.58 1.42e+00 4.96e-01 6.35e+00
  ... (remaining 25989 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.73: 8639
       34.73 -    69.46: 1510
       69.46 -   104.19: 30
      104.19 -   138.92: 2
      138.92 -   173.65: 2
  Dihedral angle restraints: 10183
    sinusoidal: 6423
      harmonic: 3760
  Sorted by residual:
  dihedral pdb=" CA  LYS B  20 "
           pdb=" C   LYS B  20 "
           pdb=" N   VAL B  21 "
           pdb=" CA  VAL B  21 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.44  -28.56     0      5.00e+00 4.00e-02 3.26e+01
  dihedral pdb=" CA  MET K1412 "
           pdb=" C   MET K1412 "
           pdb=" N   HIS K1413 "
           pdb=" CA  HIS K1413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.34   20.66     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  ILE F  29 "
           pdb=" C   ILE F  29 "
           pdb=" N   THR F  30 "
           pdb=" CA  THR F  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.83  -20.17     0      5.00e+00 4.00e-02 1.63e+01
  ... (remaining 10180 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 2234
       0.034 -    0.069: 512
       0.069 -    0.103: 98
       0.103 -    0.137: 41
       0.137 -    0.172: 1
  Chirality restraints: 2886
  Sorted by residual:
  chirality pdb=" CA  ILE K1635 "
            pdb=" N   ILE K1635 "
            pdb=" C   ILE K1635 "
            pdb=" CB  ILE K1635 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.36e-01
  chirality pdb=" P    DA J  60 "
            pdb=" OP1  DA J  60 "
            pdb=" OP2  DA J  60 "
            pdb=" O5'  DA J  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.48   -0.14 2.00e-01 2.50e+01 4.61e-01
  chirality pdb=" CB  VAL B  43 "
            pdb=" CA  VAL B  43 "
            pdb=" CG1 VAL B  43 "
            pdb=" CG2 VAL B  43 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 3.99e-01
  ... (remaining 2883 not shown)

  Planarity restraints: 2162
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU D 102 "   -0.031 5.00e-02 4.00e+02   4.70e-02 3.53e+00
        pdb=" N   PRO D 103 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO D 103 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D 103 "   -0.026 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET E 120 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO E 121 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO E 121 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO E 121 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC J  30 "   -0.007 2.00e-02 2.50e+03   1.12e-02 2.84e+00
        pdb=" N1   DC J  30 "    0.007 2.00e-02 2.50e+03
        pdb=" C2   DC J  30 "   -0.026 2.00e-02 2.50e+03
        pdb=" O2   DC J  30 "    0.013 2.00e-02 2.50e+03
        pdb=" N3   DC J  30 "    0.011 2.00e-02 2.50e+03
        pdb=" C4   DC J  30 "   -0.002 2.00e-02 2.50e+03
        pdb=" N4   DC J  30 "   -0.006 2.00e-02 2.50e+03
        pdb=" C5   DC J  30 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DC J  30 "    0.006 2.00e-02 2.50e+03
  ... (remaining 2159 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 3218
        2.79 -     3.32: 16302
        3.32 -     3.84: 34004
        3.84 -     4.37: 38628
        4.37 -     4.90: 55646
  Nonbonded interactions: 147798
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN E 108 "
            pdb=" O   GLY F  42 "
     model   vdw
     2.260 3.120
  nonbonded pdb=" N   GLY C  44 "
            pdb=" O   ILE D  89 "
     model   vdw
     2.268 3.120
  nonbonded pdb=" NE2 HIS A 113 "
            pdb=" OD1 ASP E 123 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OH  TYR E  99 "
            pdb=" OE1 GLU E 133 "
     model   vdw
     2.304 3.040
  nonbonded pdb=" NH2 ARG G  35 "
            pdb=" OP2  DT I 129 "
     model   vdw
     2.309 3.120
  ... (remaining 147793 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 102)
  selection = chain 'F'
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB  \ 
)) or resid 32 through 124))
  selection = chain 'H'
}
ncs_group {
  reference = (chain 'I' and resid 10 through 171)
  selection = (chain 'J' and resid 10 through 171)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.690
  Check model and map are aligned:         0.120
  Set scattering table:                    0.160
  Process input model:                     48.470
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.080
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.300
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   54.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  18201  Z= 0.145
  Angle     :  0.565  10.362  25994  Z= 0.351
  Chirality :  0.033   0.172   2886
  Planarity :  0.004   0.047   2162
  Dihedral  : 25.163 173.648   7755
  Min Nonbonded Distance : 2.260

Molprobity Statistics.
  All-atom Clashscore : 9.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.23), residues: 1258
  helix:  1.94 (0.18), residues: 772
  sheet:  0.25 (0.61), residues: 77
  loop :  0.68 (0.30), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1472 
 HIS   0.009   0.001   HIS K1451 
 PHE   0.024   0.001   PHE K1410 
 TYR   0.016   0.001   TYR K1227 
 ARG   0.006   0.000   ARG E 129 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.12581 (  915)
  hydrogen bonds       : angle       5.04066 ( 2405)
  covalent geometry    : bond        0.00281 (18201)
  covalent geometry    : angle       0.56453 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 1.457 
Fit side-chains
REVERT: A   97 GLU cc_start: 0.8374 (mt-10) cc_final: 0.7867 (mt-10)
REVERT: A  124 ILE cc_start: 0.9712 (mt) cc_final: 0.9507 (tp)
REVERT: B   84 MET cc_start: 0.7405 (tpp) cc_final: 0.7030 (mmm)
REVERT: D   59 MET cc_start: 0.9014 (tpp) cc_final: 0.8581 (tpp)
REVERT: K 1502 TRP cc_start: 0.4260 (t60) cc_final: 0.3669 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 54
  average time/residue: 0.2828
  time to fit residues: 24.9712
Evaluate side-chains
  42 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    8.9990
   chunk 118 optimal weight:    9.9990
   chunk 65 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 63 optimal weight:    0.0270
   chunk 122 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 74 optimal weight:   10.0000
   chunk 91 optimal weight:   10.0000
   chunk 141 optimal weight:    0.7980
   overall best weight:    0.8840

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

Flipped N/Q/H residues before XYZ refinement:
D  84 ASN
E 108 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.064943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.044063 restraints weight = 158523.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.044306 restraints weight = 83970.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.044746 restraints weight = 56197.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.0948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  18201  Z= 0.139
  Angle     :  0.529   8.330  25994  Z= 0.312
  Chirality :  0.034   0.157   2886
  Planarity :  0.004   0.045   2162
  Dihedral  : 28.753 172.997   5132
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.62 (0.23), residues: 1258
  helix:  2.40 (0.18), residues: 784
  sheet:  0.33 (0.59), residues: 79
  loop :  0.81 (0.31), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1545 
 HIS   0.006   0.001   HIS E 113 
 PHE   0.017   0.001   PHE D  65 
 TYR   0.016   0.001   TYR C  50 
 ARG   0.004   0.000   ARG K1441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04148 (  915)
  hydrogen bonds       : angle       3.40353 ( 2405)
  covalent geometry    : bond        0.00294 (18201)
  covalent geometry    : angle       0.52944 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 1.357 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8428 (mt-10) cc_final: 0.8204 (mt-10)
REVERT: A  120 MET cc_start: 0.8611 (mtm) cc_final: 0.8229 (mtp)
REVERT: C   72 ASP cc_start: 0.8895 (m-30) cc_final: 0.8554 (m-30)
REVERT: D   93 GLU cc_start: 0.9271 (mp0) cc_final: 0.9034 (mp0)
REVERT: E   97 GLU cc_start: 0.7718 (mt-10) cc_final: 0.6821 (mt-10)
REVERT: F   63 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8469 (mt-10)
REVERT: H   61 ILE cc_start: 0.9320 (mm) cc_final: 0.9047 (mm)
REVERT: K 1502 TRP cc_start: 0.4595 (t60) cc_final: 0.4201 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.3198
  time to fit residues: 30.3391
Evaluate side-chains
  43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 89 optimal weight:   20.0000
   chunk 64 optimal weight:   10.0000
   chunk 81 optimal weight:    6.9990
   chunk 133 optimal weight:    2.9990
   chunk 129 optimal weight:   20.0000
   chunk 72 optimal weight:    2.9990
   chunk 33 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 111 optimal weight:    6.9990
   chunk 12 optimal weight:    7.9990
   chunk 139 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  64 ASN
C 104 GLN
E  39 HIS
E 108 ASN
F  64 ASN
** G  38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  47 GLN
K1113 GLN
K1266 GLN
** K1291 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1310 ASN
K1415 GLN
** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K1491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.059211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2864 r_free = 0.2864 target = 0.038249 restraints weight = 166703.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2872 r_free = 0.2872 target = 0.038132 restraints weight = 89367.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.038551 restraints weight = 60547.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.2795
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8296
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.050  18201  Z= 0.328
  Angle     :  0.751  10.998  25994  Z= 0.422
  Chirality :  0.042   0.184   2886
  Planarity :  0.006   0.048   2162
  Dihedral  : 29.886 169.534   5132
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.15 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.77 (0.23), residues: 1258
  helix:  1.72 (0.18), residues: 782
  sheet:  0.26 (0.58), residues: 79
  loop :  0.44 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K1545 
 HIS   0.011   0.002   HIS F  75 
 PHE   0.029   0.003   PHE G  25 
 TYR   0.043   0.003   TYR K1298 
 ARG   0.010   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07374 (  915)
  hydrogen bonds       : angle       4.15685 ( 2405)
  covalent geometry    : bond        0.00711 (18201)
  covalent geometry    : angle       0.75075 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 46
  time to evaluate  : 2.721 
Fit side-chains
   revert: symmetry clash
REVERT: A   97 GLU cc_start: 0.8530 (mt-10) cc_final: 0.8302 (mt-10)
REVERT: A  120 MET cc_start: 0.8664 (mtm) cc_final: 0.8026 (mtp)
REVERT: C   56 GLU cc_start: 0.8371 (tt0) cc_final: 0.7531 (tt0)
REVERT: E   97 GLU cc_start: 0.8427 (mt-10) cc_final: 0.7241 (mt-10)
REVERT: F   84 MET cc_start: 0.8452 (tpp) cc_final: 0.8041 (tpp)
REVERT: H   61 ILE cc_start: 0.9553 (mm) cc_final: 0.9267 (mm)
REVERT: H   62 MET cc_start: 0.9444 (tpt) cc_final: 0.9155 (tpp)
REVERT: K 1502 TRP cc_start: 0.4926 (t60) cc_final: 0.4419 (t60)
  outliers start: 2
  outliers final: 1
  residues processed: 48
  average time/residue: 0.4493
  time to fit residues: 34.3741
Evaluate side-chains
  35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 34
  time to evaluate  : 1.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 109 optimal weight:    0.0870
   chunk 48 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 85 optimal weight:    5.9990
   chunk 59 optimal weight:    5.9990
   chunk 115 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 57 optimal weight:    0.3980
   chunk 40 optimal weight:    0.9990
   chunk 33 optimal weight:    7.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.6964

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
K1146 GLN
K1291 HIS
K1413 HIS
K1698 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3539 r_free = 0.3539 target = 0.061058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.040189 restraints weight = 163036.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.2949 r_free = 0.2949 target = 0.040154 restraints weight = 88209.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.040576 restraints weight = 58095.236|
|-----------------------------------------------------------------------------|
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  18201  Z= 0.141
  Angle     :  0.553   8.203  25994  Z= 0.325
  Chirality :  0.034   0.147   2886
  Planarity :  0.004   0.044   2162
  Dihedral  : 29.581 171.907   5132
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.49 (0.24), residues: 1258
  helix:  2.31 (0.18), residues: 784
  sheet:  0.48 (0.58), residues: 77
  loop :  0.68 (0.31), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K1472 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.030   0.001   PHE A 104 
 TYR   0.020   0.001   TYR K1102 
 ARG   0.003   0.000   ARG B  23 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03816 (  915)
  hydrogen bonds       : angle       3.21851 ( 2405)
  covalent geometry    : bond        0.00304 (18201)
  covalent geometry    : angle       0.55319 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 2.086 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8720 (mtm) cc_final: 0.8001 (mtp)
REVERT: E   97 GLU cc_start: 0.7813 (mt-10) cc_final: 0.6475 (mt-10)
REVERT: E  106 ASP cc_start: 0.9137 (m-30) cc_final: 0.8895 (m-30)
REVERT: F   63 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8305 (mt-10)
REVERT: F   84 MET cc_start: 0.8096 (tpp) cc_final: 0.7767 (tpp)
REVERT: H   61 ILE cc_start: 0.9448 (mm) cc_final: 0.9157 (mm)
REVERT: K 1502 TRP cc_start: 0.4779 (t60) cc_final: 0.4428 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 58
  average time/residue: 0.3272
  time to fit residues: 31.5778
Evaluate side-chains
  39 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 2.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 148 optimal weight:    9.9990
   chunk 15 optimal weight:    6.9990
   chunk 79 optimal weight:    7.9990
   chunk 145 optimal weight:    2.9990
   chunk 137 optimal weight:   40.0000
   chunk 150 optimal weight:   20.0000
   chunk 27 optimal weight:    6.9990
   chunk 64 optimal weight:    4.9990
   chunk 140 optimal weight:   40.0000
   chunk 28 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
G  38 ASN
K1698 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.058416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.037460 restraints weight = 168076.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.2838 r_free = 0.2838 target = 0.037307 restraints weight = 90641.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.037696 restraints weight = 60761.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.4541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.111  18201  Z= 0.313
  Angle     :  0.691  11.732  25994  Z= 0.393
  Chirality :  0.040   0.338   2886
  Planarity :  0.005   0.049   2162
  Dihedral  : 29.907 165.658   5132
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.23), residues: 1258
  helix:  1.94 (0.18), residues: 782
  sheet:  0.19 (0.58), residues: 79
  loop :  0.58 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP K1545 
 HIS   0.007   0.002   HIS B  75 
 PHE   0.016   0.002   PHE G  25 
 TYR   0.015   0.002   TYR C  50 
 ARG   0.007   0.001   ARG F  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06425 (  915)
  hydrogen bonds       : angle       3.89690 ( 2405)
  covalent geometry    : bond        0.00686 (18201)
  covalent geometry    : angle       0.69085 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8604 (mtm) cc_final: 0.7866 (mtp)
REVERT: F   84 MET cc_start: 0.8156 (tpp) cc_final: 0.7781 (tpp)
REVERT: H   61 ILE cc_start: 0.9545 (mm) cc_final: 0.9241 (mm)
REVERT: K 1502 TRP cc_start: 0.4740 (t60) cc_final: 0.4330 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.3833
  time to fit residues: 28.5903
Evaluate side-chains
  34 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 1.835 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 31 optimal weight:    0.7980
   chunk 112 optimal weight:   20.0000
   chunk 62 optimal weight:    4.9990
   chunk 152 optimal weight:    4.9990
   chunk 102 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 73 optimal weight:   20.0000
   chunk 33 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 134 optimal weight:    6.9990
   chunk 150 optimal weight:    6.9990
   overall best weight:    2.5186

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

Flipped N/Q/H residues before XYZ refinement:
B  75 HIS
C  24 GLN
K1698 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.058845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.037947 restraints weight = 166073.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 74)----------------|
| r_work = 0.2878 r_free = 0.2878 target = 0.037851 restraints weight = 90254.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.038158 restraints weight = 61874.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.2802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  18201  Z= 0.194
  Angle     :  0.585   8.398  25994  Z= 0.343
  Chirality :  0.035   0.144   2886
  Planarity :  0.004   0.043   2162
  Dihedral  : 30.007 170.654   5132
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.15 %
    Favored  : 97.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.30 (0.24), residues: 1258
  helix:  2.18 (0.18), residues: 784
  sheet:  0.11 (0.58), residues: 79
  loop :  0.63 (0.32), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP K1545 
 HIS   0.006   0.001   HIS B  75 
 PHE   0.013   0.001   PHE H  65 
 TYR   0.009   0.001   TYR K1153 
 ARG   0.002   0.000   ARG C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04353 (  915)
  hydrogen bonds       : angle       3.43299 ( 2405)
  covalent geometry    : bond        0.00422 (18201)
  covalent geometry    : angle       0.58516 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.488 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8640 (mtm) cc_final: 0.7993 (mtp)
REVERT: F   84 MET cc_start: 0.7951 (tpp) cc_final: 0.7301 (tpp)
REVERT: H   61 ILE cc_start: 0.9520 (mm) cc_final: 0.9218 (mm)
REVERT: K 1502 TRP cc_start: 0.4810 (t60) cc_final: 0.4450 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2855
  time to fit residues: 20.7068
Evaluate side-chains
  35 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 1.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 135 optimal weight:   30.0000
   chunk 43 optimal weight:    1.9990
   chunk 90 optimal weight:   10.0000
   chunk 146 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 14 optimal weight:    0.7980
   chunk 80 optimal weight:    6.9990
   chunk 86 optimal weight:    8.9990
   chunk 4 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 149 optimal weight:    8.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
G  38 ASN
K1628 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.058220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2836 r_free = 0.2836 target = 0.037411 restraints weight = 166839.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.037156 restraints weight = 93007.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.037440 restraints weight = 63345.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.2773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.5343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.063  18201  Z= 0.259
  Angle     :  0.648   8.645  25994  Z= 0.372
  Chirality :  0.038   0.156   2886
  Planarity :  0.005   0.051   2162
  Dihedral  : 30.244 167.944   5132
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 14.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.10 (0.24), residues: 1258
  helix:  2.03 (0.18), residues: 784
  sheet:  0.08 (0.59), residues: 77
  loop :  0.51 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP K1158 
 HIS   0.009   0.001   HIS B  75 
 PHE   0.015   0.002   PHE H  65 
 TYR   0.015   0.002   TYR D  40 
 ARG   0.004   0.001   ARG B  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05661 (  915)
  hydrogen bonds       : angle       3.71641 ( 2405)
  covalent geometry    : bond        0.00565 (18201)
  covalent geometry    : angle       0.64831 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  39 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 1.539 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8552 (mtm) cc_final: 0.7851 (mtp)
REVERT: F   84 MET cc_start: 0.8024 (tpp) cc_final: 0.7348 (tpp)
REVERT: H   61 ILE cc_start: 0.9517 (mm) cc_final: 0.9233 (mm)
REVERT: K 1502 TRP cc_start: 0.5183 (t60) cc_final: 0.4872 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 39
  average time/residue: 0.2825
  time to fit residues: 18.9787
Evaluate side-chains
  33 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.537 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 119 optimal weight:   20.0000
   chunk 103 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 124 optimal weight:   20.0000
   chunk 137 optimal weight:   30.0000
   chunk 118 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0570
   chunk 115 optimal weight:   10.0000
   chunk 21 optimal weight:    2.9990
   chunk 129 optimal weight:   10.0000
   overall best weight:    5.6106

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K1525 GLN
K1636 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.056952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.036387 restraints weight = 169901.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.2797 r_free = 0.2797 target = 0.036039 restraints weight = 93578.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.036332 restraints weight = 64710.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.6338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.064  18201  Z= 0.344
  Angle     :  0.739   9.975  25994  Z= 0.420
  Chirality :  0.041   0.184   2886
  Planarity :  0.005   0.044   2162
  Dihedral  : 30.841 171.893   5132
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 18.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.36 (0.23), residues: 1258
  helix:  1.48 (0.18), residues: 786
  sheet:  0.06 (0.63), residues: 67
  loop :  0.06 (0.31), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP K1502 
 HIS   0.011   0.002   HIS F  75 
 PHE   0.020   0.002   PHE K1267 
 TYR   0.013   0.002   TYR D  40 
 ARG   0.008   0.001   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06695 (  915)
  hydrogen bonds       : angle       4.25682 ( 2405)
  covalent geometry    : bond        0.00743 (18201)
  covalent geometry    : angle       0.73915 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.534 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8426 (mtm) cc_final: 0.7864 (mtp)
REVERT: E   97 GLU cc_start: 0.8539 (tt0) cc_final: 0.7675 (mt-10)
REVERT: E  110 CYS cc_start: 0.9144 (m) cc_final: 0.8881 (m)
REVERT: F   84 MET cc_start: 0.7984 (tpp) cc_final: 0.7218 (tpp)
REVERT: H   61 ILE cc_start: 0.9571 (mm) cc_final: 0.9264 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.2491
  time to fit residues: 15.1064
Evaluate side-chains
  30 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 1.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 144 optimal weight:    5.9990
   chunk 27 optimal weight:    5.9990
   chunk 117 optimal weight:   40.0000
   chunk 29 optimal weight:    4.9990
   chunk 80 optimal weight:    5.9990
   chunk 69 optimal weight:    0.6980
   chunk 56 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9980
   chunk 139 optimal weight:   30.0000
   chunk 113 optimal weight:    6.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    1.6582

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K1525 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.058258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2852 r_free = 0.2852 target = 0.037508 restraints weight = 167430.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 70)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.037217 restraints weight = 89652.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.037654 restraints weight = 61229.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.6095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  18201  Z= 0.173
  Angle     :  0.595   9.741  25994  Z= 0.348
  Chirality :  0.036   0.152   2886
  Planarity :  0.004   0.046   2162
  Dihedral  : 30.629 173.889   5132
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.54 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.27 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.96 (0.24), residues: 1258
  helix:  1.97 (0.18), residues: 790
  sheet:  0.24 (0.64), residues: 67
  loop :  0.25 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K1676 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.019   0.002   PHE K1410 
 TYR   0.015   0.001   TYR D  40 
 ARG   0.004   0.000   ARG A 131 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04354 (  915)
  hydrogen bonds       : angle       3.53602 ( 2405)
  covalent geometry    : bond        0.00376 (18201)
  covalent geometry    : angle       0.59471 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8596 (mtm) cc_final: 0.7957 (mtp)
REVERT: E  120 MET cc_start: 0.9034 (mmm) cc_final: 0.8658 (mmm)
REVERT: F   63 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8413 (mt-10)
REVERT: F   84 MET cc_start: 0.7715 (tpp) cc_final: 0.7038 (tpp)
REVERT: H   61 ILE cc_start: 0.9481 (mm) cc_final: 0.9207 (mm)
REVERT: K 1502 TRP cc_start: 0.4823 (t60) cc_final: 0.4578 (t60)
REVERT: K 1691 MET cc_start: 0.5451 (ppp) cc_final: 0.5207 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.2401
  time to fit residues: 18.4159
Evaluate side-chains
  33 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 1.434 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 24 optimal weight:    0.0170
   chunk 105 optimal weight:   20.0000
   chunk 112 optimal weight:    0.9990
   chunk 152 optimal weight:    6.9990
   chunk 37 optimal weight:    0.0670
   chunk 136 optimal weight:    5.9990
   chunk 143 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 86 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   overall best weight:    0.5960

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 108 ASN
F  25 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.059133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2890 r_free = 0.2890 target = 0.038398 restraints weight = 165163.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.038241 restraints weight = 86311.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2914 r_free = 0.2914 target = 0.038633 restraints weight = 56594.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.5949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  18201  Z= 0.143
  Angle     :  0.570   8.665  25994  Z= 0.333
  Chirality :  0.035   0.176   2886
  Planarity :  0.004   0.049   2162
  Dihedral  : 30.243 172.552   5132
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.18 %
    Favored  : 99.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.25 (0.24), residues: 1258
  helix:  2.20 (0.18), residues: 785
  sheet:  0.10 (0.59), residues: 77
  loop :  0.44 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP K1472 
 HIS   0.008   0.001   HIS B  75 
 PHE   0.021   0.001   PHE D  65 
 TYR   0.012   0.001   TYR D  40 
 ARG   0.007   0.000   ARG K1664 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03863 (  915)
  hydrogen bonds       : angle       3.27388 ( 2405)
  covalent geometry    : bond        0.00303 (18201)
  covalent geometry    : angle       0.56961 (25994)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.560 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8797 (mtm) cc_final: 0.8227 (mtp)
REVERT: B   97 LEU cc_start: 0.9342 (tp) cc_final: 0.9086 (tp)
REVERT: E  120 MET cc_start: 0.8807 (mmm) cc_final: 0.8537 (mmm)
REVERT: F   63 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8344 (mt-10)
REVERT: F   84 MET cc_start: 0.7701 (tpp) cc_final: 0.7254 (tpp)
REVERT: G   61 GLU cc_start: 0.8385 (mm-30) cc_final: 0.8138 (mm-30)
REVERT: H   59 MET cc_start: 0.8835 (tpt) cc_final: 0.8604 (tpp)
REVERT: K 1375 MET cc_start: -0.2052 (ttt) cc_final: -0.2961 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.2511
  time to fit residues: 22.2336
Evaluate side-chains
  38 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 1.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 152 optimal weight:    7.9990
   chunk 30 optimal weight:    4.9990
   chunk 121 optimal weight:   30.0000
   chunk 41 optimal weight:    5.9990
   chunk 7 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 79 optimal weight:    7.9990
   chunk 87 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 116 optimal weight:    5.9990
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
G  24 GLN
H  47 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.057968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2847 r_free = 0.2847 target = 0.037451 restraints weight = 167044.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 64)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.037126 restraints weight = 89161.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.037457 restraints weight = 61050.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.2765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.6254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073  18201  Z= 0.223
  Angle     :  0.612   8.866  25994  Z= 0.354
  Chirality :  0.036   0.165   2886
  Planarity :  0.004   0.049   2162
  Dihedral  : 30.344 169.758   5132
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.45 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.24), residues: 1258
  helix:  2.13 (0.18), residues: 790
  sheet:  0.32 (0.64), residues: 67
  loop :  0.32 (0.32), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP K1502 
 HIS   0.007   0.001   HIS B  75 
 PHE   0.018   0.002   PHE D  65 
 TYR   0.013   0.001   TYR E  99 
 ARG   0.005   0.000   ARG F  92 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04979 (  915)
  hydrogen bonds       : angle       3.55541 ( 2405)
  covalent geometry    : bond        0.00488 (18201)
  covalent geometry    : angle       0.61205 (25994)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5810.74 seconds
wall clock time: 105 minutes 54.72 seconds (6354.72 seconds total)