Starting phenix.real_space_refine
on Mon Jul 28 19:36:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pmg_13532/07_2025/7pmg_13532.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pmg_13532/07_2025/7pmg_13532.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2025/7pmg_13532.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2025/7pmg_13532.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2025/7pmg_13532.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pmg_13532/07_2025/7pmg_13532.cif"
  }
  resolution = 3.3
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      3      5.21       5
     S      63      5.16       5
     C    6482      2.51       5
     N    1730      2.21       5
     O    1906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 10189
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 6105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 747, 6105
          Classifications: {'peptide': 747}
          Link IDs: {'PTRANS': 27, 'TRANS': 719}
          Chain breaks: 5
    Chain: "C"
      Number of atoms: 2909
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 372, 2909
          Classifications: {'peptide': 372}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 352}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HIC:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1059
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ANP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 6.73, per 1000 atoms: 0.66
  Number of scatterers: 10189
  At special positions: 0
  Unit cell: (103.4, 129.8, 155.1, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      63     16.00
     P       5     15.00
     Mg      3     11.99
     O    1906      8.00
     N    1730      7.00
     C    6482      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
  Links applied
    TRANS
      " TRP H   1 " - " ALA H   7 "
      " DTH H   4 " - " ALA H   3 "
  Time building additional restraints: 2.75
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input residue name is d-peptide
        pdb=" CB  DTH H   4 "
  Number of C-beta restraints generated:  2382

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 14 sheets defined
      55.2% alpha, 12.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 73 through 77
      removed outlier: 3.665A  pdb=" N   LEU A  77 " --> pdb=" O   LEU A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 95
      removed outlier: 3.764A  pdb=" N   LYS A  90 " --> pdb=" O   LEU A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 119
      removed outlier: 4.213A  pdb=" N   TYR A 119 " --> pdb=" O   LEU A 116 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 116 through 119'
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 3.705A  pdb=" N   GLU A 145 " --> pdb=" O   ALA A 141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 185
    Processing helix  chain 'A' and resid 191 through 207
      removed outlier: 3.921A  pdb=" N   LYS A 195 " --> pdb=" O   ASN A 191 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ASN A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      Proline residue:  A 201  - end of helix
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 259 through 269
      removed outlier: 4.292A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA A 269 " --> pdb=" O   LEU A 265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 278
      removed outlier: 4.412A  pdb=" N   THR A 276 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 4.057A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 315
      removed outlier: 3.687A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 337
      removed outlier: 3.701A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 376
      removed outlier: 4.092A  pdb=" N   CYS A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 424
    Processing helix  chain 'A' and resid 448 through 480
    Processing helix  chain 'A' and resid 483 through 487
      removed outlier: 4.005A  pdb=" N   LEU A 486 " --> pdb=" O   PRO A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 3.837A  pdb=" N   LYS A 514 " --> pdb=" O   ASP A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 532
    Processing helix  chain 'A' and resid 563 through 568
    Processing helix  chain 'A' and resid 573 through 582
      removed outlier: 3.744A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER A 582 " --> pdb=" O   LYS A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.133A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 653
    Processing helix  chain 'A' and resid 674 through 685
      removed outlier: 3.741A  pdb=" N   GLN A 680 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 696
      removed outlier: 3.725A  pdb=" N   ARG A 692 " --> pdb=" O   LEU A 688 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ALA A 696 " --> pdb=" O   ARG A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 712
    Processing helix  chain 'A' and resid 713 through 715
      No H-bonds generated for 'chain 'A' and resid 713 through 715'
    Processing helix  chain 'A' and resid 723 through 736
      removed outlier: 3.799A  pdb=" N   GLU A 733 " --> pdb=" O   LYS A 729 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 738 through 740
      No H-bonds generated for 'chain 'A' and resid 738 through 740'
    Processing helix  chain 'A' and resid 754 through 792
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 92
      removed outlier: 3.711A  pdb=" N   MET C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 4.051A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
      removed outlier: 3.561A  pdb=" N   SER C 141 " --> pdb=" O   GLN C 137 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 182 through 196
      removed outlier: 3.801A  pdb=" N   THR C 186 " --> pdb=" O   GLY C 182 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   ARG C 196 " --> pdb=" O   ILE C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.702A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   CYS C 217 " --> pdb=" O   LYS C 213 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
      removed outlier: 3.502A  pdb=" N   GLU C 226 " --> pdb=" O   ASP C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 257
    Processing helix  chain 'C' and resid 258 through 262
    Processing helix  chain 'C' and resid 273 through 283
    Processing helix  chain 'C' and resid 289 through 295
      removed outlier: 3.518A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 4.288A  pdb=" N   TYR C 306 " --> pdb=" O   THR C 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 308 through 321
    Processing helix  chain 'C' and resid 334 through 336
      No H-bonds generated for 'chain 'C' and resid 334 through 336'
    Processing helix  chain 'C' and resid 337 through 347
    Processing helix  chain 'C' and resid 348 through 349
      No H-bonds generated for 'chain 'C' and resid 348 through 349'
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 3.794A  pdb=" N   GLN C 354 " --> pdb=" O   THR C 351 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 368 through 374
      removed outlier: 4.296A  pdb=" N   ARG C 372 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.243A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   ASP B  34 " --> pdb=" O   SER B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 53
    Processing helix  chain 'B' and resid 56 through 63
    Processing helix  chain 'B' and resid 67 through 79
      Proline residue:  B  72  - end of helix
    Processing helix  chain 'B' and resid 87 through 95
    Processing helix  chain 'B' and resid 105 through 116
    Processing helix  chain 'B' and resid 121 through 130
    Processing helix  chain 'B' and resid 140 through 150
    Processing sheet with id=AA1, first strand: chain 'A' and resid 11 through 16
      removed outlier: 4.301A  pdb=" N   ALA A  11 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103
      removed outlier: 6.525A  pdb=" N   LEU A 107 " --> pdb=" O   ARG A 660 " (cutoff:3.500A)
      removed outlier: 8.017A  pdb=" N   ILE A 662 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   ALA A 109 " --> pdb=" O   ILE A 662 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   SER A 158 " --> pdb=" O   HIS A 657 " (cutoff:3.500A)
      removed outlier: 7.788A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 5.968A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.559A  pdb=" N   CYS A 661 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.436A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 661 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   GLN A 157 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   LEU A 436 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
      removed outlier: 6.657A  pdb=" N   ILE A 159 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 7.707A  pdb=" N   ILE A 438 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   VAL A 161 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211
      removed outlier: 5.738A  pdb=" N   ALA A 209 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 342
    Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381
    Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703
    Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.903A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   THR C 103 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
      removed outlier: 8.042A  pdb=" N   ALA C 135 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   LEU C 105 " --> pdb=" O   ALA C 135 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72
      removed outlier: 3.657A  pdb=" N   ILE C  75 " --> pdb=" O   GLU C  72 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170
      removed outlier: 6.011A  pdb=" N   ASN C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241
    Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28

    512 hydrogen bonds defined for protein.
    1434 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: 3.63

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1706
        1.31 -     1.44: 2757
        1.44 -     1.56: 5830
        1.56 -     1.69: 8
        1.69 -     1.82: 102
  Bond restraints: 10403
  Sorted by residual:
  bond pdb=" O3A ANP A1901 "
       pdb=" PB  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.700  1.546  0.154 2.00e-02 2.50e+03 5.93e+01
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.432  0.140 2.00e-02 2.50e+03 4.90e+01
  bond pdb=" N3B ANP A1901 "
       pdb=" PG  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.795  1.689  0.106 2.00e-02 2.50e+03 2.83e+01
  bond pdb=" O5' ANP A1901 "
       pdb=" PA  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.655  1.564  0.091 2.00e-02 2.50e+03 2.05e+01
  bond pdb=" C   EEP H   2 "
       pdb=" O   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.263  1.189  0.074 2.00e-02 2.50e+03 1.36e+01
  ... (remaining 10398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.47: 13763
        3.47 -     6.93: 266
        6.93 -    10.40: 18
       10.40 -    13.86: 5
       13.86 -    17.33: 1
  Bond angle restraints: 14053
  Sorted by residual:
  angle pdb=" N   GLY A 563 "
        pdb=" CA  GLY A 563 "
        pdb=" C   GLY A 563 "
      ideal   model   delta    sigma   weight residual
     113.86  123.43   -9.57 1.50e+00 4.44e-01 4.07e+01
  angle pdb=" C   HYP H   6 "
        pdb=" N   ALA H   7 "
        pdb=" CA  ALA H   7 "
      ideal   model   delta    sigma   weight residual
     121.70  111.27   10.43 1.80e+00 3.09e-01 3.35e+01
  angle pdb=" PB  ANP A1901 "
        pdb=" N3B ANP A1901 "
        pdb=" PG  ANP A1901 "
      ideal   model   delta    sigma   weight residual
     126.95  109.62   17.33 3.00e+00 1.11e-01 3.34e+01
  angle pdb=" N   DTH H   4 "
        pdb=" CA  DTH H   4 "
        pdb=" CB  DTH H   4 "
      ideal   model   delta    sigma   weight residual
     111.50  102.04    9.46 1.70e+00 3.46e-01 3.10e+01
  angle pdb=" CD2 TRP H   1 "
        pdb=" CE2 TRP H   1 "
        pdb=" CZ2 TRP H   1 "
      ideal   model   delta    sigma   weight residual
     122.40  117.74    4.66 1.00e+00 1.00e+00 2.17e+01
  ... (remaining 14048 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.62: 5996
       24.62 -    49.24: 224
       49.24 -    73.87: 51
       73.87 -    98.49: 23
       98.49 -   123.11: 5
  Dihedral angle restraints: 6299
    sinusoidal: 2605
      harmonic: 3694
  Sorted by residual:
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   63.07 -123.08     1      2.00e+01 2.50e-03 3.71e+01
  dihedral pdb=" O2A ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" PB  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   61.08 -121.08     1      2.00e+01 2.50e-03 3.64e+01
  dihedral pdb=" C5' ADP C 401 "
           pdb=" O5' ADP C 401 "
           pdb=" PA  ADP C 401 "
           pdb=" O2A ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -178.23  118.24     1      2.00e+01 2.50e-03 3.54e+01
  ... (remaining 6296 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 942
       0.058 -    0.117: 457
       0.117 -    0.175: 113
       0.175 -    0.234: 19
       0.234 -    0.292: 3
  Chirality restraints: 1534
  Sorted by residual:
  chirality pdb=" CA  GLU C 316 "
            pdb=" N   GLU C 316 "
            pdb=" C   GLU C 316 "
            pdb=" CB  GLU C 316 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.13e+00
  chirality pdb=" C3' ANP A1901 "
            pdb=" C2' ANP A1901 "
            pdb=" C4' ANP A1901 "
            pdb=" O3' ANP A1901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.36   -2.65    0.29 2.00e-01 2.50e+01 2.12e+00
  chirality pdb=" C2' ADP C 401 "
            pdb=" C1' ADP C 401 "
            pdb=" C3' ADP C 401 "
            pdb=" O2' ADP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.79    0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 1531 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 564 "   -0.042 2.00e-02 2.50e+03   4.02e-02 2.83e+01
        pdb=" CG  PHE A 564 "    0.093 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 564 "   -0.024 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 564 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 564 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 564 "   -0.012 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 564 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 278 "   -0.134 9.50e-02 1.11e+02   7.49e-02 2.73e+01
        pdb=" NE  ARG A 278 "    0.037 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 278 "   -0.085 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 278 "    0.030 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 278 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 231 "    0.275 9.50e-02 1.11e+02   1.27e-01 2.07e+01
        pdb=" NE  ARG A 231 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 231 "   -0.062 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 231 "    0.016 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 231 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.36: 19
        2.36 -     3.00: 5722
        3.00 -     3.63: 14764
        3.63 -     4.27: 22880
        4.27 -     4.90: 38604
  Nonbonded interactions: 81989
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.727 3.620
  nonbonded pdb=" O1B ANP A1901 "
            pdb="MG    MG A1903 "
     model   vdw
     1.936 2.170
  nonbonded pdb=" O1A ANP A1901 "
            pdb="MG    MG A1903 "
     model   vdw
     1.948 2.170
  nonbonded pdb=" O3G ANP A1901 "
            pdb="MG    MG A1902 "
     model   vdw
     1.963 2.170
  nonbonded pdb=" OH  TYR A 456 "
            pdb=" OE1 GLU A 500 "
     model   vdw
     2.025 3.040
  ... (remaining 81984 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.460
  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:          0.400
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     26.550
  Find NCS groups from input model:        0.110
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
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      :  0.014   0.154  10405  Z= 0.620
  Angle     :  1.187  17.330  14059  Z= 0.662
  Chirality :  0.069   0.292   1534
  Planarity :  0.009   0.127   1792
  Dihedral  : 15.701 123.109   3911
  Min Nonbonded Distance : 1.727

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.37 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.37 (0.21), residues: 1235
  helix: -1.69 (0.17), residues: 581
  sheet:  0.25 (0.35), residues: 180
  loop :  0.00 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.006   TRP C 356 
 HIS   0.018   0.003   HIS C 101 
 PHE   0.093   0.004   PHE A 564 
 TYR   0.032   0.007   TYR A 439 
 ARG   0.087   0.013   ARG A 278 

Details of bonding type rmsd
  link_TRANS           : bond        0.02383 (    2)
  link_TRANS           : angle       4.22962 (    6)
  hydrogen bonds       : bond        0.14129 (  510)
  hydrogen bonds       : angle       6.88607 ( 1434)
  covalent geometry    : bond        0.01445 (10403)
  covalent geometry    : angle       1.18362 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  790 MET cc_start: 0.8908 (tpt) cc_final: 0.8655 (tpp)
REVERT: C   41 GLN cc_start: 0.7833 (tt0) cc_final: 0.7598 (tt0)
REVERT: B   73 MET cc_start: 0.9109 (mtp) cc_final: 0.8410 (ttm)
  outliers start: 1
  outliers final: 1
  residues processed: 93
  average time/residue: 0.3046
  time to fit residues: 38.1942
Evaluate side-chains
  54 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 1.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9980
   chunk 93 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 97 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 72 optimal weight:    0.8980
   chunk 112 optimal weight:    5.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 200 ASN
A 264 GLN
A 398 ASN
A 493 GLN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 ASN
C 137 GLN
C 162 ASN
C 280 ASN
C 296 ASN
B  54 ASN
B  75 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.047186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.033934 restraints weight = 53186.700|
|-----------------------------------------------------------------------------|
r_work (start): 0.2724 rms_B_bonded: 4.01
r_work: 0.2552 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2552
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8766
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10405  Z= 0.156
  Angle     :  0.666   7.832  14059  Z= 0.349
  Chirality :  0.044   0.199   1534
  Planarity :  0.004   0.043   1792
  Dihedral  : 11.240 127.874   1429
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  3.23 %
    Favored  : 96.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.68 (0.23), residues: 1235
  helix:  0.52 (0.20), residues: 602
  sheet:  0.65 (0.37), residues: 182
  loop :  0.55 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C  79 
 HIS   0.008   0.001   HIS C 101 
 PHE   0.022   0.001   PHE A 564 
 TYR   0.017   0.002   TYR A  79 
 ARG   0.006   0.001   ARG C 147 

Details of bonding type rmsd
  link_TRANS           : bond        0.00280 (    2)
  link_TRANS           : angle       1.25348 (    6)
  hydrogen bonds       : bond        0.04193 (  510)
  hydrogen bonds       : angle       5.03606 ( 1434)
  covalent geometry    : bond        0.00346 (10403)
  covalent geometry    : angle       0.66604 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 61
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  488 ASP cc_start: 0.8879 (t0) cc_final: 0.8473 (t0)
REVERT: A  790 MET cc_start: 0.9061 (tpt) cc_final: 0.8842 (tpp)
REVERT: C  106 THR cc_start: 0.9222 (m) cc_final: 0.8558 (p)
REVERT: C  137 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8687 (mm110)
REVERT: C  364 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8837 (pp20)
  outliers start: 7
  outliers final: 3
  residues processed: 67
  average time/residue: 0.2765
  time to fit residues: 25.8458
Evaluate side-chains
  58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue  137 GLN
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   chunk 96 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 108 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 410 ASN
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 137 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.046815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.033356 restraints weight = 55153.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.2708 rms_B_bonded: 4.09
r_work: 0.2538 rms_B_bonded: 4.66 restraints_weight: 0.5000
r_work (final): 0.2538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8788
moved from start:          0.2228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10405  Z= 0.159
  Angle     :  0.594   7.492  14059  Z= 0.307
  Chirality :  0.042   0.165   1534
  Planarity :  0.004   0.039   1792
  Dihedral  : 10.127 129.824   1428
  Min Nonbonded Distance : 1.938

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  3.87 %
    Favored  : 95.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.27 (0.24), residues: 1235
  helix:  1.16 (0.21), residues: 607
  sheet:  0.87 (0.39), residues: 181
  loop :  0.62 (0.30), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP C  79 
 HIS   0.006   0.001   HIS C 101 
 PHE   0.032   0.001   PHE C 223 
 TYR   0.013   0.001   TYR A 102 
 ARG   0.006   0.000   ARG C  95 

Details of bonding type rmsd
  link_TRANS           : bond        0.00272 (    2)
  link_TRANS           : angle       0.78580 (    6)
  hydrogen bonds       : bond        0.03678 (  510)
  hydrogen bonds       : angle       4.74610 ( 1434)
  covalent geometry    : bond        0.00357 (10403)
  covalent geometry    : angle       0.59354 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  478 MET cc_start: 0.9407 (mmp) cc_final: 0.9131 (mmp)
REVERT: A  484 TRP cc_start: 0.8006 (m-90) cc_final: 0.7479 (m-90)
REVERT: A  488 ASP cc_start: 0.8791 (t0) cc_final: 0.8488 (t0)
REVERT: A  790 MET cc_start: 0.9117 (tpt) cc_final: 0.8908 (tpp)
REVERT: C  283 MET cc_start: 0.9201 (mmm) cc_final: 0.8972 (mmm)
REVERT: B   36 MET cc_start: 0.9280 (ttm) cc_final: 0.8846 (tpp)
  outliers start: 5
  outliers final: 2
  residues processed: 58
  average time/residue: 0.2478
  time to fit residues: 20.9530
Evaluate side-chains
  54 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 52
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 1 optimal weight:    0.9980
   chunk 117 optimal weight:    8.9990
   chunk 10 optimal weight:    0.5980
   chunk 56 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 78 optimal weight:    0.6980
   chunk 66 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.047284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.034010 restraints weight = 54129.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.2731 rms_B_bonded: 4.03
r_work: 0.2561 rms_B_bonded: 4.63 restraints_weight: 0.5000
r_work (final): 0.2561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10405  Z= 0.117
  Angle     :  0.551   8.050  14059  Z= 0.282
  Chirality :  0.041   0.167   1534
  Planarity :  0.004   0.036   1792
  Dihedral  :  9.468 131.947   1428
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 4.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  4.52 %
    Favored  : 94.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.51 (0.24), residues: 1235
  helix:  1.46 (0.22), residues: 607
  sheet:  0.89 (0.40), residues: 170
  loop :  0.59 (0.30), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  79 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.018   0.001   PHE C 223 
 TYR   0.014   0.001   TYR C 294 
 ARG   0.003   0.000   ARG C 147 

Details of bonding type rmsd
  link_TRANS           : bond        0.00214 (    2)
  link_TRANS           : angle       0.90687 (    6)
  hydrogen bonds       : bond        0.03270 (  510)
  hydrogen bonds       : angle       4.50718 ( 1434)
  covalent geometry    : bond        0.00260 (10403)
  covalent geometry    : angle       0.55077 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 54
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8833 (p)
REVERT: A  478 MET cc_start: 0.9410 (mmp) cc_final: 0.9053 (mmp)
REVERT: A  484 TRP cc_start: 0.7987 (m-90) cc_final: 0.7361 (m-90)
REVERT: A  488 ASP cc_start: 0.8851 (t0) cc_final: 0.8560 (t70)
REVERT: A  790 MET cc_start: 0.9079 (tpt) cc_final: 0.8868 (tpp)
REVERT: C  283 MET cc_start: 0.9203 (mmm) cc_final: 0.8947 (mmm)
REVERT: B   36 MET cc_start: 0.9278 (ttm) cc_final: 0.8898 (tpp)
  outliers start: 9
  outliers final: 4
  residues processed: 61
  average time/residue: 0.2674
  time to fit residues: 23.3495
Evaluate side-chains
  55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    4.9990
   chunk 112 optimal weight:   20.0000
   chunk 21 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 105 optimal weight:    0.7980
   chunk 68 optimal weight:    5.9990
   chunk 104 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    0.6980
   overall best weight:    1.2982

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.046530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2724 r_free = 0.2724 target = 0.033294 restraints weight = 54398.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.2705 rms_B_bonded: 4.01
r_work: 0.2535 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2535
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8785
moved from start:          0.2686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10405  Z= 0.167
  Angle     :  0.552   7.919  14059  Z= 0.281
  Chirality :  0.041   0.167   1534
  Planarity :  0.004   0.033   1792
  Dihedral  :  9.194 135.812   1428
  Min Nonbonded Distance : 1.920

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.44 %
    Favored  : 93.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.70 (0.25), residues: 1235
  helix:  1.64 (0.22), residues: 606
  sheet:  1.03 (0.40), residues: 183
  loop :  0.62 (0.31), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  79 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.013   0.001   PHE C 223 
 TYR   0.011   0.001   TYR A 456 
 ARG   0.003   0.000   ARG A 278 

Details of bonding type rmsd
  link_TRANS           : bond        0.00235 (    2)
  link_TRANS           : angle       0.81152 (    6)
  hydrogen bonds       : bond        0.03307 (  510)
  hydrogen bonds       : angle       4.46285 ( 1434)
  covalent geometry    : bond        0.00375 (10403)
  covalent geometry    : angle       0.55186 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 THR cc_start: 0.9180 (OUTLIER) cc_final: 0.8858 (p)
REVERT: A  382 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.8912 (p)
REVERT: A  478 MET cc_start: 0.9416 (mmp) cc_final: 0.9028 (mmp)
REVERT: A  488 ASP cc_start: 0.8877 (t0) cc_final: 0.8590 (t70)
REVERT: B   36 MET cc_start: 0.9191 (ttm) cc_final: 0.8787 (tpp)
  outliers start: 7
  outliers final: 3
  residues processed: 61
  average time/residue: 0.2370
  time to fit residues: 21.4476
Evaluate side-chains
  57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 52
  time to evaluate  : 1.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 73 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 80 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 41 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.046262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2700 r_free = 0.2700 target = 0.032768 restraints weight = 55754.862|
|-----------------------------------------------------------------------------|
r_work (start): 0.2687 rms_B_bonded: 4.12
r_work: 0.2517 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8803
moved from start:          0.2828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10405  Z= 0.187
  Angle     :  0.572   8.934  14059  Z= 0.288
  Chirality :  0.041   0.167   1534
  Planarity :  0.004   0.033   1792
  Dihedral  :  9.055 140.788   1428
  Min Nonbonded Distance : 1.921

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  5.81 %
    Favored  : 93.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.82 (0.25), residues: 1235
  helix:  1.80 (0.22), residues: 605
  sheet:  0.98 (0.40), residues: 183
  loop :  0.65 (0.31), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  79 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.012   0.001   PHE A 564 
 TYR   0.011   0.001   TYR A 456 
 ARG   0.003   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00232 (    2)
  link_TRANS           : angle       0.80892 (    6)
  hydrogen bonds       : bond        0.03342 (  510)
  hydrogen bonds       : angle       4.47251 ( 1434)
  covalent geometry    : bond        0.00422 (10403)
  covalent geometry    : angle       0.57150 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 50
  time to evaluate  : 1.133 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 THR cc_start: 0.9215 (OUTLIER) cc_final: 0.8895 (p)
REVERT: A  382 THR cc_start: 0.9221 (OUTLIER) cc_final: 0.8863 (p)
REVERT: A  488 ASP cc_start: 0.8888 (t0) cc_final: 0.8616 (t70)
REVERT: A  788 MET cc_start: 0.8059 (mtt) cc_final: 0.7620 (tpp)
REVERT: B   36 MET cc_start: 0.9154 (ttm) cc_final: 0.8762 (tpp)
  outliers start: 8
  outliers final: 5
  residues processed: 56
  average time/residue: 0.2360
  time to fit residues: 19.7098
Evaluate side-chains
  55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 48
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 76 optimal weight:    1.9990
   chunk 22 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 93 optimal weight:    0.6980
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 73 optimal weight:    0.8980
   chunk 29 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 50 optimal weight:    0.6980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 354 HIS
A 775 GLN
** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.046403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.032928 restraints weight = 55802.088|
|-----------------------------------------------------------------------------|
r_work (start): 0.2689 rms_B_bonded: 4.13
r_work: 0.2518 rms_B_bonded: 4.68 restraints_weight: 0.5000
r_work (final): 0.2518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8799
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  10405  Z= 0.161
  Angle     :  0.566   9.941  14059  Z= 0.283
  Chirality :  0.041   0.167   1534
  Planarity :  0.004   0.035   1792
  Dihedral  :  8.964 145.404   1428
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 5.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  6.91 %
    Favored  : 92.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.87 (0.25), residues: 1235
  helix:  1.89 (0.22), residues: 604
  sheet:  0.94 (0.40), residues: 183
  loop :  0.62 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 781 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.015   0.001   PHE C 223 
 TYR   0.010   0.001   TYR A 456 
 ARG   0.003   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00197 (    2)
  link_TRANS           : angle       0.81034 (    6)
  hydrogen bonds       : bond        0.03258 (  510)
  hydrogen bonds       : angle       4.44174 ( 1434)
  covalent geometry    : bond        0.00364 (10403)
  covalent geometry    : angle       0.56588 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 1.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 THR cc_start: 0.9244 (OUTLIER) cc_final: 0.8915 (p)
REVERT: A  382 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8860 (p)
REVERT: A  488 ASP cc_start: 0.8910 (t0) cc_final: 0.8603 (t70)
REVERT: A  788 MET cc_start: 0.7891 (mtt) cc_final: 0.7508 (tpp)
REVERT: B   36 MET cc_start: 0.9088 (ttm) cc_final: 0.8864 (tpp)
  outliers start: 6
  outliers final: 3
  residues processed: 54
  average time/residue: 0.2126
  time to fit residues: 17.8447
Evaluate side-chains
  55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 50
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 94 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 120 optimal weight:    9.9990
   chunk 18 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 33 optimal weight:    2.9990
   chunk 66 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 111 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.045810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.032504 restraints weight = 54926.021|
|-----------------------------------------------------------------------------|
r_work (start): 0.2676 rms_B_bonded: 4.01
r_work: 0.2505 rms_B_bonded: 4.59 restraints_weight: 0.5000
r_work (final): 0.2505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8821
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.032  10405  Z= 0.212
  Angle     :  0.597  10.523  14059  Z= 0.298
  Chirality :  0.042   0.178   1534
  Planarity :  0.004   0.036   1792
  Dihedral  :  8.977 153.555   1428
  Min Nonbonded Distance : 1.896

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  7.10 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.80 (0.25), residues: 1235
  helix:  1.88 (0.22), residues: 604
  sheet:  0.75 (0.40), residues: 178
  loop :  0.59 (0.31), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP C  79 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.015   0.001   PHE A 564 
 TYR   0.012   0.001   TYR A  10 
 ARG   0.003   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00224 (    2)
  link_TRANS           : angle       0.76938 (    6)
  hydrogen bonds       : bond        0.03424 (  510)
  hydrogen bonds       : angle       4.47478 ( 1434)
  covalent geometry    : bond        0.00476 (10403)
  covalent geometry    : angle       0.59696 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.9520 (ptp) cc_final: 0.9114 (pmm)
REVERT: A  211 THR cc_start: 0.9251 (OUTLIER) cc_final: 0.8922 (p)
REVERT: A  382 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8791 (p)
REVERT: A  417 ASP cc_start: 0.9332 (t0) cc_final: 0.9127 (t0)
REVERT: A  488 ASP cc_start: 0.8848 (t0) cc_final: 0.8551 (t70)
REVERT: A  788 MET cc_start: 0.7976 (mtt) cc_final: 0.7614 (tpp)
REVERT: B   36 MET cc_start: 0.9121 (ttm) cc_final: 0.8765 (tpp)
  outliers start: 9
  outliers final: 4
  residues processed: 57
  average time/residue: 0.2184
  time to fit residues: 19.4829
Evaluate side-chains
  56 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0050
   chunk 121 optimal weight:    0.9990
   chunk 46 optimal weight:    3.9990
   chunk 58 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   chunk 112 optimal weight:   10.0000
   chunk 34 optimal weight:    0.7980
   chunk 43 optimal weight:    0.6980
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.046821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2725 r_free = 0.2725 target = 0.033357 restraints weight = 55219.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.2714 rms_B_bonded: 4.12
r_work: 0.2536 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.2536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8796
moved from start:          0.3244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10405  Z= 0.104
  Angle     :  0.553  10.393  14059  Z= 0.273
  Chirality :  0.040   0.166   1534
  Planarity :  0.003   0.033   1792
  Dihedral  :  8.840 157.535   1428
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 4.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  7.37 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.87 (0.25), residues: 1235
  helix:  1.95 (0.22), residues: 602
  sheet:  0.80 (0.41), residues: 172
  loop :  0.61 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A 781 
 HIS   0.003   0.001   HIS A 418 
 PHE   0.017   0.001   PHE C 223 
 TYR   0.009   0.001   TYR A 456 
 ARG   0.004   0.000   ARG A 692 

Details of bonding type rmsd
  link_TRANS           : bond        0.00193 (    2)
  link_TRANS           : angle       0.86750 (    6)
  hydrogen bonds       : bond        0.02995 (  510)
  hydrogen bonds       : angle       4.33027 ( 1434)
  covalent geometry    : bond        0.00232 (10403)
  covalent geometry    : angle       0.55237 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 1.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  211 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8949 (p)
REVERT: A  382 THR cc_start: 0.9155 (OUTLIER) cc_final: 0.8770 (p)
REVERT: A  488 ASP cc_start: 0.8866 (t0) cc_final: 0.8654 (t70)
REVERT: A  788 MET cc_start: 0.7917 (mtt) cc_final: 0.7597 (tpp)
REVERT: B   36 MET cc_start: 0.9013 (ttm) cc_final: 0.8642 (tpp)
  outliers start: 6
  outliers final: 4
  residues processed: 59
  average time/residue: 0.2122
  time to fit residues: 19.3098
Evaluate side-chains
  59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 1.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 119 optimal weight:    5.9990
   chunk 38 optimal weight:    5.9990
   chunk 115 optimal weight:    9.9990
   chunk 30 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 117 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 76 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.046462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.032971 restraints weight = 55530.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2693 rms_B_bonded: 4.11
r_work: 0.2522 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2522
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8797
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10405  Z= 0.146
  Angle     :  0.579  10.605  14059  Z= 0.286
  Chirality :  0.041   0.216   1534
  Planarity :  0.003   0.034   1792
  Dihedral  :  8.800 160.622   1428
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  7.28 %
    Favored  : 92.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.88 (0.25), residues: 1235
  helix:  1.97 (0.22), residues: 603
  sheet:  0.81 (0.41), residues: 172
  loop :  0.58 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 781 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.016   0.001   PHE A 470 
 TYR   0.010   0.001   TYR A 456 
 ARG   0.003   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00177 (    2)
  link_TRANS           : angle       0.79384 (    6)
  hydrogen bonds       : bond        0.03144 (  510)
  hydrogen bonds       : angle       4.36460 ( 1434)
  covalent geometry    : bond        0.00329 (10403)
  covalent geometry    : angle       0.57920 (14053)

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

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

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2470 Ramachandran restraints generated.
    1235 Oldfield, 0 Emsley, 1235 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 53
  time to evaluate  : 1.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 MET cc_start: 0.9566 (ptp) cc_final: 0.9283 (pmm)
REVERT: A  211 THR cc_start: 0.9245 (OUTLIER) cc_final: 0.8938 (p)
REVERT: A  382 THR cc_start: 0.9150 (OUTLIER) cc_final: 0.8764 (p)
REVERT: A  488 ASP cc_start: 0.8854 (t0) cc_final: 0.8603 (t70)
REVERT: A  788 MET cc_start: 0.7978 (mtt) cc_final: 0.7635 (tpp)
REVERT: C  311 ASP cc_start: 0.9169 (t0) cc_final: 0.8939 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 57
  average time/residue: 0.2134
  time to fit residues: 19.0100
Evaluate side-chains
  55 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 49
  time to evaluate  : 1.171 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  211 THR
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain C residue  160 THR
Chi-restraints excluded: chain C residue  305 MET
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain B residue  111 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0070
   chunk 94 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 34 optimal weight:    0.0270
   chunk 117 optimal weight:    0.5980
   chunk 68 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9980
   overall best weight:    0.5258

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.047131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.034020 restraints weight = 53933.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.2734 rms_B_bonded: 3.98
r_work: 0.2563 rms_B_bonded: 4.60 restraints_weight: 0.5000
r_work (final): 0.2563
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8773
moved from start:          0.3466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  10405  Z= 0.099
  Angle     :  0.548  10.661  14059  Z= 0.270
  Chirality :  0.040   0.191   1534
  Planarity :  0.003   0.035   1792
  Dihedral  :  8.686 162.953   1428
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  7.28 %
    Favored  : 92.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.91 (0.25), residues: 1235
  helix:  1.99 (0.22), residues: 603
  sheet:  0.84 (0.41), residues: 172
  loop :  0.58 (0.31), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 781 
 HIS   0.003   0.001   HIS A 418 
 PHE   0.016   0.001   PHE C 223 
 TYR   0.009   0.001   TYR A 456 
 ARG   0.003   0.000   ARG B  64 

Details of bonding type rmsd
  link_TRANS           : bond        0.00191 (    2)
  link_TRANS           : angle       0.85560 (    6)
  hydrogen bonds       : bond        0.02894 (  510)
  hydrogen bonds       : angle       4.26674 ( 1434)
  covalent geometry    : bond        0.00222 (10403)
  covalent geometry    : angle       0.54819 (14053)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4932.11 seconds
wall clock time: 85 minutes 35.00 seconds (5135.00 seconds total)