Starting phenix.real_space_refine
on Wed Mar 12 02:52:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dl7_27498/03_2025/8dl7_27498_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dl7_27498/03_2025/8dl7_27498.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2025/8dl7_27498.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2025/8dl7_27498.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2025/8dl7_27498_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dl7_27498/03_2025/8dl7_27498_neut.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.012 sd=   0.075
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       2      5.49       5
     S      37      5.16       5
     C    4236      2.51       5
     N    1094      2.21       5
     O    1217      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 6586
  Number of models: 1
  Model: ""
    Number of chains: 9
    Chain: "A"
      Number of atoms: 3547
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 467, 3536
          Classifications: {'peptide': 467}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 12, 'TRANS': 454}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 20
      Conformer: "B"
        Number of residues, atoms: 467, 3536
          Classifications: {'peptide': 467}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 12, 'TRANS': 454}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 31
          Unresolved non-hydrogen angles: 37
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 20
          bond proxies already assigned to first conformer: 3596
    Chain: "C"
      Number of atoms: 1373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1373
          Classifications: {'peptide': 213}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203}
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 290
          Unresolved non-hydrogen angles: 372
          Unresolved non-hydrogen dihedrals: 242
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 154
    Chain: "D"
      Number of atoms: 1438
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1438
          Classifications: {'peptide': 219}
          Incomplete info: {'backbone_only': 5, 'truncation_to_alanine': 80}
          Link IDs: {'PTRANS': 14, 'TRANS': 204}
          Unresolved chain link angles: 9
          Unresolved non-hydrogen bonds: 251
          Unresolved non-hydrogen angles: 335
          Unresolved non-hydrogen dihedrals: 207
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 91
    Chain: "F"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Classifications: {'peptide': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'SQ6:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "F"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 70
          Unusual residues: {'EOE': 1}
          Classifications: {'peptide': 6, 'undetermined': 1}
          Link IDs: {'TRANS': 4, None: 2}
            Not linked:
              pdbres="2GX F   4 "
              pdbres="EOE F   5 "
            Not linked:
              pdbres="EOE F   5 "
              pdbres="ARG F   6 "
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Planarities with less than four sites: {'2GX:plan-3': 1, 'EOE:plan-1': 1}
          Unresolved non-hydrogen planarities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 28
          Unusual residues: {'3FB': 1, 'ACA': 1}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'ACA:plan-1': 1, '3FB:plan-2': 1, 'SOW:plan-2': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "F"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'SQI': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 104
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 104
          Unusual residues: {'POV': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A 292 " occ=0.37
      ... (20 atoms not shown)
      pdb=" CZ BPHE A 292 " occ=0.63
  Time building chain proxies: 8.08, per 1000 atoms: 1.23
  Number of scatterers: 6586
  At special positions: 0
  Unit cell: (83.6, 74.8, 145.2, 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      37     16.00
     P       2     15.00
     O    1217      8.00
     N    1094      7.00
     C    4236      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 326 " - pdb=" SG  CYS F   7 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A 367 " - pdb=" SG  CYS A 553 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  43 " - pdb=" SG  CYS C 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  41 " - pdb=" SG  CYS D 115 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of additional links: simple=1, symmetry=0
    Simple link:   pdb=" C   ARG F   8 " - pdb=" N   3FB F   9 "
  Number of custom bonds: simple=6, symmetry=0
  Number of additional bonds: simple=6, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.88
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue is complicated and confusing
        pdb=" CB  3FB F   9 "
  Number of C-beta restraints generated:  1660

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 10 sheets defined
      47.3% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 21
      removed outlier: 3.632A  pdb=" N   LEU A  17 " --> pdb=" O   CYS A  13 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   ALA A  18 " --> pdb=" O   CYS A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 54
      removed outlier: 3.762A  pdb=" N   TYR A  54 " --> pdb=" O   LEU A  50 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 84
      removed outlier: 4.386A  pdb=" N   THR A  61 " --> pdb=" O   SER A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 116
      removed outlier: 3.758A  pdb=" N   VAL A  91 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 126 through 164
      removed outlier: 4.420A  pdb=" N   THR A 130 " --> pdb=" O   GLY A 126 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   SER A 131 " --> pdb=" O   TRP A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 198
      Proline residue:  A 189  - end of helix
    Processing helix  chain 'A' and resid 200 through 230
    Processing helix  chain 'A' and resid 231 through 234
      removed outlier: 3.665A  pdb=" N   ALA A 234 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 231 through 234'
    Processing helix  chain 'A' and resid 285 through 304
      Proline residue:  A 291  - end of helix
    Processing helix  chain 'A' and resid 307 through 317
      removed outlier: 3.545A  pdb=" N   GLY A 311 " --> pdb=" O   VAL A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 336
    Processing helix  chain 'A' and resid 339 through 367
    Processing helix  chain 'A' and resid 369 through 390
      removed outlier: 3.833A  pdb=" N   SER A 390 " --> pdb=" O   LEU A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 483
      removed outlier: 3.511A  pdb=" N   SER A 456 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 485 through 487
      No H-bonds generated for 'chain 'A' and resid 485 through 487'
    Processing helix  chain 'A' and resid 488 through 514
      removed outlier: 3.559A  pdb=" N   HIS A 507 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 547
      removed outlier: 3.686A  pdb=" N   LEU A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   GLY A 547 " --> pdb=" O   GLN A 543 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 99 through 103
      removed outlier: 3.763A  pdb=" N   LEU C 103 " --> pdb=" O   SER C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 147
    Processing helix  chain 'C' and resid 202 through 208
    Processing helix  chain 'D' and resid 47 through 51
    Processing helix  chain 'D' and resid 81 through 84
      removed outlier: 3.533A  pdb=" N   GLN D  84 " --> pdb=" O   PRO D  81 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 81 through 84'
    Processing helix  chain 'D' and resid 106 through 110
      removed outlier: 3.764A  pdb=" N   THR D 110 " --> pdb=" O   SER D 107 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25
      removed outlier: 3.638A  pdb=" N   ASP C  90 " --> pdb=" O   SER C  87 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 32
      removed outlier: 6.312A  pdb=" N   MET C  31 " --> pdb=" O   GLU C 125 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 74
      removed outlier: 6.566A  pdb=" N   TRP C  55 " --> pdb=" O   LEU C  67 " (cutoff:3.500A)
      removed outlier: 4.981A  pdb=" N   TYR C  69 " --> pdb=" O   VAL C  53 " (cutoff:3.500A)
      removed outlier: 6.927A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  69 " (cutoff:3.500A)
      removed outlier: 4.287A  pdb=" N   THR C 117 " --> pdb=" O   GLN C 110 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 137 through 138
      removed outlier: 3.730A  pdb=" N   VAL C 153 " --> pdb=" O   PHE C 138 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ASN C 158 " --> pdb=" O   TYR C 193 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   TYR C 193 " --> pdb=" O   ASN C 158 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 165 through 170
      removed outlier: 6.320A  pdb=" N   HIS C 218 " --> pdb=" O   SER C 223 " (cutoff:3.500A)
      removed outlier: 6.382A  pdb=" N   SER C 223 " --> pdb=" O   HIS C 218 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 22 through 25
    Processing sheet with id=AA7, first strand: chain 'D' and resid 29 through 31
      removed outlier: 6.512A  pdb=" N   MET D  53 " --> pdb=" O   TRP D  69 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   TRP D  69 " --> pdb=" O   MET D  53 " (cutoff:3.500A)
      removed outlier: 6.721A  pdb=" N   TRP D  55 " --> pdb=" O   ILE D  67 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'D' and resid 145 through 146
      removed outlier: 5.556A  pdb=" N   TYR D 200 " --> pdb=" O   GLY D 169 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 145 through 146
      removed outlier: 5.556A  pdb=" N   TYR D 200 " --> pdb=" O   GLY D 169 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'D' and resid 176 through 179
      removed outlier: 4.680A  pdb=" N   ILE D 218 " --> pdb=" O   ILE D 235 " (cutoff:3.500A)

    437 hydrogen bonds defined for protein.
    1239 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.59

  Time building geometry restraints manager: 2.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1172
        1.33 -     1.45: 1704
        1.45 -     1.57: 3763
        1.57 -     1.70: 4
        1.70 -     1.82: 58
  Bond restraints: 6701
  Sorted by residual:
  bond pdb=" N   SOW F  11 "
       pdb=" CB  SOW F  11 "
    ideal  model  delta    sigma   weight residual
    1.435  1.502 -0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" N   VAL A 484 "
       pdb=" CA  VAL A 484 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.039 1.19e-02 7.06e+03 1.05e+01
  bond pdb=" N   ILE A 485 "
       pdb=" CA  ILE A 485 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.19e-02 7.06e+03 9.22e+00
  bond pdb=" N   GLU A 488 "
       pdb=" CA  GLU A 488 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 9.10e-03 1.21e+04 8.85e+00
  bond pdb=" N   VAL A 113 "
       pdb=" CA  VAL A 113 "
    ideal  model  delta    sigma   weight residual
    1.460  1.495 -0.035 1.19e-02 7.06e+03 8.77e+00
  ... (remaining 6696 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     6.96: 9092
        6.96 -    13.92: 5
       13.92 -    20.88: 0
       20.88 -    27.85: 0
       27.85 -    34.81: 1
  Bond angle restraints: 9098
  Sorted by residual:
  angle pdb=" N   SOW F  11 "
        pdb=" CA  SOW F  11 "
        pdb=" C   SOW F  11 "
      ideal   model   delta    sigma   weight residual
     112.87  147.68  -34.81 3.00e+00 1.11e-01 1.35e+02
  angle pdb=" CA  SOW F  11 "
        pdb=" N   SOW F  11 "
        pdb=" CB  SOW F  11 "
      ideal   model   delta    sigma   weight residual
     114.32  100.44   13.88 3.00e+00 1.11e-01 2.14e+01
  angle pdb=" C   CYS F   7 "
        pdb=" CA  CYS F   7 "
        pdb=" CB  CYS F   7 "
      ideal   model   delta    sigma   weight residual
     110.42  101.58    8.84 1.99e+00 2.53e-01 1.97e+01
  angle pdb=" C   ILE A 491 "
        pdb=" N   ILE A 492 "
        pdb=" CA  ILE A 492 "
      ideal   model   delta    sigma   weight residual
     120.56  115.55    5.01 1.26e+00 6.30e-01 1.58e+01
  angle pdb=" N   ALA D 111 "
        pdb=" CA  ALA D 111 "
        pdb=" C   ALA D 111 "
      ideal   model   delta    sigma   weight residual
     107.73  112.51   -4.78 1.34e+00 5.57e-01 1.27e+01
  ... (remaining 9093 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 3500
       17.94 -    35.88: 296
       35.88 -    53.81: 110
       53.81 -    71.75: 21
       71.75 -    89.69: 7
  Dihedral angle restraints: 3934
    sinusoidal: 1340
      harmonic: 2594
  Sorted by residual:
  dihedral pdb=" C   SOW F  11 "
           pdb=" N   SOW F  11 "
           pdb=" CA  SOW F  11 "
           pdb=" CB  SOW F  11 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -149.11   26.51     0      2.50e+00 1.60e-01 1.12e+02
  dihedral pdb=" N   SOW F  11 "
           pdb=" C   SOW F  11 "
           pdb=" CA  SOW F  11 "
           pdb=" CB  SOW F  11 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  100.36   22.44     0      2.50e+00 1.60e-01 8.05e+01
  dihedral pdb=" C   CYS F   7 "
           pdb=" N   CYS F   7 "
           pdb=" CA  CYS F   7 "
           pdb=" CB  CYS F   7 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.34  -13.26     0      2.50e+00 1.60e-01 2.81e+01
  ... (remaining 3931 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.076: 940
       0.076 -    0.152: 114
       0.152 -    0.228: 8
       0.228 -    0.305: 0
       0.305 -    0.381: 1
  Chirality restraints: 1063
  Sorted by residual:
  chirality pdb=" CA  CYS F   7 "
            pdb=" N   CYS F   7 "
            pdb=" C   CYS F   7 "
            pdb=" CB  CYS F   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.89   -0.38 2.00e-01 2.50e+01 3.63e+00
  chirality pdb=" CB  ILE A 152 "
            pdb=" CA  ILE A 152 "
            pdb=" CG1 ILE A 152 "
            pdb=" CG2 ILE A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.28e+00
  chirality pdb=" CA  ILE A 485 "
            pdb=" N   ILE A 485 "
            pdb=" C   ILE A 485 "
            pdb=" CB  ILE A 485 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.05e-01
  ... (remaining 1060 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 155 "   -0.010 2.00e-02 2.50e+03   1.91e-02 3.66e+00
        pdb=" C   GLN A 155 "    0.033 2.00e-02 2.50e+03
        pdb=" O   GLN A 155 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ARG A 156 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG D  59 "   -0.160 9.50e-02 1.11e+02   7.16e-02 3.15e+00
        pdb=" NE  ARG D  59 "    0.009 2.00e-02 2.50e+03
        pdb=" CZ  ARG D  59 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG D  59 "    0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG D  59 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP D  80 "    0.025 5.00e-02 4.00e+02   3.85e-02 2.38e+00
        pdb=" N   PRO D  81 "   -0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO D  81 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D  81 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1200
        2.77 -     3.30: 6177
        3.30 -     3.84: 10308
        3.84 -     4.37: 10967
        4.37 -     4.90: 19837
  Nonbonded interactions: 48489
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 504 "
            pdb=" CAH 2GX F   4 "
     model   vdw
     2.238 3.340
  nonbonded pdb=" OG  SER C  70 "
            pdb=" OD1 ASN C  73 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OE1 GLU A 165 "
            pdb=" OH  TYR D  51 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" O   SER D  26 "
            pdb=" OG1 THR D 133 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" OE1 GLU C 125 "
            pdb=" N   ILE C 126 "
     model   vdw
     2.315 3.120
  ... (remaining 48484 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.37 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  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:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     27.030
  Find NCS groups from input model:        0.100
  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:             0.010
  Load rotamer database and sin/cos tables:20.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   48.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
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      :  0.005   0.067   6701  Z= 0.340
  Angle     :  0.804  34.807   9098  Z= 0.459
  Chirality :  0.050   0.381   1063
  Planarity :  0.004   0.072   1144
  Dihedral  : 16.202  89.691   2259
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.22 %
    Allowed  :  4.49 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 27.13 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.36 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  1.47 (0.29), residues: 893
  helix:  2.03 (0.27), residues: 401
  sheet:  1.39 (0.38), residues: 214
  loop : -0.97 (0.35), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 299 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 308 
 TYR   0.008   0.001   TYR C 160 
 ARG   0.003   0.000   ARG D  32 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 46
  time to evaluate  : 0.736 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7950 (OUTLIER) cc_final: 0.7711 (tmm)
REVERT: A  194 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8258 (tm-30)
REVERT: A  198 PHE cc_start: 0.8182 (OUTLIER) cc_final: 0.7862 (t80)
REVERT: C  125 GLU cc_start: 0.6373 (tp30) cc_final: 0.6036 (tp30)
REVERT: D  108 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8466 (tm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 62
  average time/residue: 1.3273
  time to fit residues: 86.5669
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  112 MET
Chi-restraints excluded: chain A residue  186 ILE
Chi-restraints excluded: chain A residue  194 GLN
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  455 VAL
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain C residue   51 THR
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:   10.0000
   chunk 66 optimal weight:   50.0000
   chunk 37 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 35 optimal weight:    6.9990
   chunk 68 optimal weight:    7.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 79 optimal weight:   20.0000
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 194 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.073577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2958 r_free = 0.2958 target = 0.050066 restraints weight = 50426.232|
|-----------------------------------------------------------------------------|
r_work (start): 0.2887 rms_B_bonded: 4.98
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2886
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2886 r_free = 0.2886    target_work(ls_wunit_k1) = 0.048         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2886
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.0779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6701  Z= 0.234
  Angle     :  0.717  41.562   9098  Z= 0.327
  Chirality :  0.041   0.178   1063
  Planarity :  0.003   0.045   1144
  Dihedral  :  9.080  80.923   1104
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.60 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 24.74 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.18 (0.29), residues: 893
  helix:  2.90 (0.26), residues: 403
  sheet:  1.56 (0.38), residues: 208
  loop : -0.93 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  69 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.009   0.001   TYR C  69 
 ARG   0.007   0.001   ARG F   8 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 45
  time to evaluate  : 0.816 
Fit side-chains
REVERT: A  112 MET cc_start: 0.8000 (ttm) cc_final: 0.7773 (tmm)
REVERT: A  312 MET cc_start: 0.9279 (mmm) cc_final: 0.9066 (mmm)
REVERT: D   22 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8658 (tt0)
REVERT: D  108 GLU cc_start: 0.8788 (tm-30) cc_final: 0.8446 (tm-30)
REVERT: D  118 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8371 (tptp)
  outliers start: 23
  outliers final: 9
  residues processed: 63
  average time/residue: 1.2522
  time to fit residues: 83.5161
Evaluate side-chains
  54 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue   61 GLU
Chi-restraints excluded: chain D residue  118 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 43 optimal weight:    0.6980
   chunk 54 optimal weight:    8.9990
   chunk 35 optimal weight:   20.0000
   chunk 52 optimal weight:   10.0000
   chunk 14 optimal weight:    1.9990
   chunk 56 optimal weight:    3.9990
   chunk 74 optimal weight:    0.4980
   chunk 68 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9980
   chunk 64 optimal weight:   30.0000
   overall best weight:    1.6384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.074462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.051102 restraints weight = 49906.962|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 4.98
r_work (final): 0.2909
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2908
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2908 r_free = 0.2908    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2908
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.0957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6701  Z= 0.193
  Angle     :  0.704  41.854   9098  Z= 0.317
  Chirality :  0.041   0.184   1063
  Planarity :  0.003   0.047   1144
  Dihedral  :  8.354  82.537   1088
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 3.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.26 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 25.60 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.37 (0.29), residues: 893
  helix:  3.18 (0.26), residues: 402
  sheet:  1.54 (0.38), residues: 208
  loop : -0.93 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.008   0.001   TYR C  69 
 ARG   0.006   0.001   ARG F   8 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 46
  time to evaluate  : 0.772 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7953 (ttm) cc_final: 0.7747 (tmm)
REVERT: D   22 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8651 (tt0)
REVERT: D  108 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: D  118 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8400 (tptp)
  outliers start: 18
  outliers final: 9
  residues processed: 60
  average time/residue: 1.4014
  time to fit residues: 88.3729
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   24 MET
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  118 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 17 optimal weight:    0.6980
   chunk 60 optimal weight:   10.0000
   chunk 53 optimal weight:    3.9990
   chunk 36 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 87 optimal weight:   40.0000
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.072956 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.048776 restraints weight = 54231.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 5.10
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2845
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2845 r_free = 0.2845    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2845
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.1183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6701  Z= 0.293
  Angle     :  0.742  41.833   9098  Z= 0.342
  Chirality :  0.042   0.178   1063
  Planarity :  0.003   0.047   1144
  Dihedral  :  8.472  84.260   1088
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.71 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 24.40 %
    Favored  : 71.33 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.31 (0.29), residues: 893
  helix:  3.06 (0.26), residues: 403
  sheet:  1.49 (0.38), residues: 214
  loop : -0.89 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  69 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.009   0.001   TYR C  69 
 ARG   0.004   0.000   ARG F   8 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 48
  time to evaluate  : 0.720 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7866 (ttm) cc_final: 0.7536 (tmm)
REVERT: A  198 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.8024 (t80)
REVERT: D   22 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.8645 (tt0)
REVERT: D  108 GLU cc_start: 0.8866 (tm-30) cc_final: 0.8514 (tm-30)
REVERT: D  118 LYS cc_start: 0.8818 (OUTLIER) cc_final: 0.8455 (tptp)
REVERT: F    6 ARG cc_start: 0.7355 (OUTLIER) cc_final: 0.7122 (mmm160)
  outliers start: 25
  outliers final: 10
  residues processed: 68
  average time/residue: 1.4555
  time to fit residues: 103.6985
Evaluate side-chains
  58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 44
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  136 THR
Chi-restraints excluded: chain F residue    6 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 23 optimal weight:    7.9990
   chunk 27 optimal weight:    8.9990
   chunk 57 optimal weight:   50.0000
   chunk 61 optimal weight:   50.0000
   chunk 14 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 58 optimal weight:   20.0000
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN
C  26 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.075752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.052368 restraints weight = 49901.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 5.02
r_work (final): 0.2943
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2941
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2941 r_free = 0.2941    target_work(ls_wunit_k1) = 0.051         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2941
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.1346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6701  Z= 0.150
  Angle     :  0.709  41.855   9098  Z= 0.315
  Chirality :  0.040   0.215   1063
  Planarity :  0.003   0.048   1144
  Dihedral  :  8.175  85.067   1088
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.37 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.07 %
    Allowed  : 26.11 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.45 (0.30), residues: 893
  helix:  3.26 (0.26), residues: 403
  sheet:  1.52 (0.38), residues: 208
  loop : -0.88 (0.36), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.007   0.001   TYR A  64 
 ARG   0.004   0.000   ARG F   8 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 50
  time to evaluate  : 0.679 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8009 (ttt) cc_final: 0.7663 (ttt)
REVERT: A  112 MET cc_start: 0.7670 (ttm) cc_final: 0.7414 (tmm)
REVERT: D   22 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.8644 (tt0)
REVERT: D  108 GLU cc_start: 0.8878 (tm-30) cc_final: 0.8527 (tm-30)
REVERT: D  118 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8434 (tptp)
  outliers start: 18
  outliers final: 9
  residues processed: 65
  average time/residue: 1.3005
  time to fit residues: 88.9690
Evaluate side-chains
  58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue   78 ILE
Chi-restraints excluded: chain D residue  118 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 10 optimal weight:   10.0000
   chunk 37 optimal weight:    3.9990
   chunk 61 optimal weight:   50.0000
   chunk 82 optimal weight:   40.0000
   chunk 74 optimal weight:    9.9990
   chunk 19 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 59 optimal weight:   20.0000
   chunk 3 optimal weight:    0.9980
   chunk 73 optimal weight:    3.9990
   overall best weight:    3.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.072287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.048301 restraints weight = 47833.200|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.79
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.046         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8308
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   6701  Z= 0.353
  Angle     :  0.785  41.813   9098  Z= 0.363
  Chirality :  0.043   0.184   1063
  Planarity :  0.004   0.049   1144
  Dihedral  :  8.549  82.164   1088
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 3.88
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.60 %
    Favored  : 96.29 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.43 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.27 (0.29), residues: 893
  helix:  2.99 (0.26), residues: 403
  sheet:  1.43 (0.37), residues: 214
  loop : -0.81 (0.36), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP D  69 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.013   0.001   PHE A 308 
 TYR   0.011   0.001   TYR C 160 
 ARG   0.004   0.000   ARG F   6 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 48
  time to evaluate  : 0.750 
Fit side-chains
REVERT: A  111 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7945 (ttt)
REVERT: A  112 MET cc_start: 0.7758 (ttm) cc_final: 0.7425 (tmm)
REVERT: D   22 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8629 (tt0)
REVERT: D  108 GLU cc_start: 0.8911 (tm-30) cc_final: 0.8527 (tm-30)
REVERT: D  118 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8479 (tptp)
  outliers start: 22
  outliers final: 11
  residues processed: 65
  average time/residue: 1.3946
  time to fit residues: 95.2172
Evaluate side-chains
  59 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.738 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  111 MET
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 80 optimal weight:   50.0000
   chunk 73 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 68 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 2 optimal weight:    0.8980
   chunk 52 optimal weight:    9.9990
   chunk 11 optimal weight:    2.9990
   chunk 14 optimal weight:    8.9990
   chunk 48 optimal weight:    7.9990
   chunk 64 optimal weight:   30.0000
   overall best weight:    2.9788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.072786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2920 r_free = 0.2920 target = 0.048649 restraints weight = 51875.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.2834 rms_B_bonded: 4.99
r_work (final): 0.2834
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2829
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2829 r_free = 0.2829    target_work(ls_wunit_k1) = 0.047         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2829
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   6701  Z= 0.302
  Angle     :  0.773  41.850   9098  Z= 0.356
  Chirality :  0.042   0.195   1063
  Planarity :  0.003   0.049   1144
  Dihedral  :  8.449  79.788   1088
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.96
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.82 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 25.60 %
    Favored  : 70.65 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.21 (0.29), residues: 893
  helix:  3.02 (0.26), residues: 402
  sheet:  1.37 (0.38), residues: 208
  loop : -0.88 (0.36), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  69 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 308 
 TYR   0.010   0.001   TYR C 160 
 ARG   0.002   0.000   ARG F   8 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 45
  time to evaluate  : 0.746 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7754 (ttm) cc_final: 0.7393 (tmm)
REVERT: D   22 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.8622 (tt0)
REVERT: D  108 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8537 (tm-30)
REVERT: D  118 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8473 (tptp)
  outliers start: 22
  outliers final: 13
  residues processed: 63
  average time/residue: 1.3327
  time to fit residues: 88.8789
Evaluate side-chains
  58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 43
  time to evaluate  : 0.715 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue   50 LEU
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain D residue   22 GLN
Chi-restraints excluded: chain D residue  118 LYS
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 69 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 18 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 74 optimal weight:    5.9990
   chunk 47 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 65 optimal weight:   30.0000
   chunk 64 optimal weight:    9.9990
   chunk 39 optimal weight:    3.9990
   overall best weight:    4.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.071254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.047089 restraints weight = 50687.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.2800 rms_B_bonded: 4.86
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2800
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2800 r_free = 0.2800    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2800 r_free = 0.2800    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2800
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8358
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.062   6701  Z= 0.423
  Angle     :  0.823  41.857   9098  Z= 0.387
  Chirality :  0.044   0.190   1063
  Planarity :  0.004   0.049   1144
  Dihedral  :  8.679  78.968   1088
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.93 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 25.94 %
    Favored  : 70.48 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.07 (0.29), residues: 893
  helix:  2.79 (0.26), residues: 403
  sheet:  1.34 (0.37), residues: 214
  loop : -0.84 (0.37), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP D  69 
 HIS   0.005   0.001   HIS A 535 
 PHE   0.015   0.002   PHE A 459 
 TYR   0.013   0.001   TYR C 160 
 ARG   0.003   0.000   ARG A 179 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 43
  time to evaluate  : 0.718 
Fit side-chains
REVERT: A  112 MET cc_start: 0.7819 (ttm) cc_final: 0.7388 (tmm)
REVERT: A  198 PHE cc_start: 0.8377 (OUTLIER) cc_final: 0.8149 (t80)
REVERT: D  108 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8533 (tm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 62
  average time/residue: 1.3654
  time to fit residues: 89.1528
Evaluate side-chains
  56 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.711 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  198 PHE
Chi-restraints excluded: chain A residue  202 VAL
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  352 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  389 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   25 THR
Chi-restraints excluded: chain C residue   33 THR
Chi-restraints excluded: chain D residue  136 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 75 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 39 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0010
   chunk 83 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.7988

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.075753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.052304 restraints weight = 43899.210|
|-----------------------------------------------------------------------------|
r_work (start): 0.2927 rms_B_bonded: 4.68
r_work: 0.2762 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2759 r_free = 0.2759    target_work(ls_wunit_k1) = 0.045         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8285
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6701  Z= 0.167
  Angle     :  0.762  41.875   9098  Z= 0.342
  Chirality :  0.041   0.239   1063
  Planarity :  0.003   0.050   1144
  Dihedral  :  8.217  78.553   1088
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  4.16 %
    Favored  : 95.73 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 28.33 %
    Favored  : 69.97 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.40 (0.30), residues: 893
  helix:  3.16 (0.26), residues: 403
  sheet:  1.47 (0.38), residues: 208
  loop : -0.79 (0.37), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 308 
 TYR   0.009   0.001   TYR A  64 
 ARG   0.003   0.000   ARG A 156 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.779 
Fit side-chains
REVERT: D  108 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8797 (tm-30)
  outliers start: 10
  outliers final: 8
  residues processed: 56
  average time/residue: 1.4406
  time to fit residues: 84.8922
Evaluate side-chains
  55 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.924 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   33 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 16 optimal weight:    2.9990
   chunk 83 optimal weight:    0.2980
   chunk 62 optimal weight:   30.0000
   chunk 74 optimal weight:   10.0000
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0770
   chunk 23 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.2744

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.075233 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2998 r_free = 0.2998 target = 0.051534 restraints weight = 53104.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.2913 rms_B_bonded: 5.08
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2907
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2907 r_free = 0.2907    target_work(ls_wunit_k1) = 0.050         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2907
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6701  Z= 0.192
  Angle     :  0.783  41.858   9098  Z= 0.349
  Chirality :  0.041   0.213   1063
  Planarity :  0.003   0.050   1144
  Dihedral  :  8.142  78.916   1087
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.15 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 29.35 %
    Favored  : 69.45 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.40 (0.30), residues: 893
  helix:  3.19 (0.26), residues: 403
  sheet:  1.28 (0.38), residues: 216
  loop : -0.71 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 
 PHE   0.009   0.001   PHE A 308 
 TYR   0.007   0.001   TYR C  69 
 ARG   0.002   0.000   ARG F   6 

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

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

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1786 Ramachandran restraints generated.
    893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.763 
Fit side-chains
REVERT: D  108 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8546 (tm-30)
  outliers start: 7
  outliers final: 8
  residues processed: 56
  average time/residue: 1.5205
  time to fit residues: 89.1723
Evaluate side-chains
  53 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   41 MET
Chi-restraints excluded: chain A residue   46 VAL
Chi-restraints excluded: chain A residue  109 ILE
Chi-restraints excluded: chain A residue  320 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  507 HIS
Chi-restraints excluded: chain C residue   33 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:   50.0000
   chunk 4 optimal weight:    6.9990
   chunk 83 optimal weight:   40.0000
   chunk 47 optimal weight:    8.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 81 optimal weight:   30.0000
   chunk 1 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A 100 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.074857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.050704 restraints weight = 61599.086|
|-----------------------------------------------------------------------------|
r_work (start): 0.2886 rms_B_bonded: 5.44
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2887
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2887 r_free = 0.2887    target_work(ls_wunit_k1) = 0.049         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2887
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.1573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6701  Z= 0.207
  Angle     :  0.782  41.860   9098  Z= 0.349
  Chirality :  0.041   0.210   1063
  Planarity :  0.003   0.050   1144
  Dihedral  :  8.143  78.927   1087
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  3.71 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 28.84 %
    Favored  : 69.80 %
  Cbeta Deviations :  0.24 %
  Peptide Plane:
    Cis-proline     : 2.86 %
    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:  2.40 (0.30), residues: 893
  helix:  3.19 (0.26), residues: 403
  sheet:  1.27 (0.37), residues: 216
  loop : -0.71 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP D  69 
 HIS   0.004   0.001   HIS A 535 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.008   0.001   TYR C  69 
 ARG   0.002   0.000   ARG F   8 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4341.74 seconds
wall clock time: 74 minutes 43.12 seconds (4483.12 seconds total)