Starting phenix.real_space_refine
on Wed Mar  4 03:51:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pml_13538/03_2026/7pml_13538.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pml_13538/03_2026/7pml_13538.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pml_13538/03_2026/7pml_13538.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pml_13538/03_2026/7pml_13538.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pml_13538/03_2026/7pml_13538.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pml_13538/03_2026/7pml_13538.map"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10189
  Number of models: 1
  Model: ""
    Number of chains: 7
    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, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
    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: "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: 2.49, per 1000 atoms: 0.24
  Number of scatterers: 10189
  At special positions: 0
  Unit cell: (106.7, 126.5, 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: 0.76
  Conformation dependent library (CDL) restraints added in 558.5 milliseconds
  

  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
      55.7% alpha, 12.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.40
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.220A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.665A  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 96
      removed outlier: 4.119A  pdb=" N   PHE B  96 " --> pdb=" O   GLY B  92 " (cutoff:3.500A)
    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 helix  chain 'A' and resid 73 through 77
    Processing helix  chain 'A' and resid 81 through 95
    Processing helix  chain 'A' and resid 116 through 119
      removed outlier: 4.207A  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 154
      removed outlier: 3.958A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 185
      removed outlier: 3.630A  pdb=" N   ALA A 176 " --> pdb=" O   SER A 172 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLY A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 207
      removed outlier: 3.730A  pdb=" N   LYS A 195 " --> pdb=" O   ASN A 191 " (cutoff:3.500A)
      removed outlier: 3.792A  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: 4.099A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 278
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 3.577A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 315
      removed outlier: 3.878A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASN A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 338
      removed outlier: 3.509A  pdb=" N   GLY A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ASN A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   VAL A 338 " --> pdb=" O   HIS A 334 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 376
      removed outlier: 3.835A  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
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 504 through 515
      removed outlier: 3.825A  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 569
    Processing helix  chain 'A' and resid 573 through 581
      removed outlier: 3.755A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 3.757A  pdb=" N   GLU A 591 " --> pdb=" O   LYS A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 635 through 653
    Processing helix  chain 'A' and resid 674 through 685
      removed outlier: 3.856A  pdb=" N   GLN A 680 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG A 683 " --> pdb=" O   VAL A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 696
      removed outlier: 3.521A  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
    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: 3.699A  pdb=" N   MET C  82 " --> pdb=" O   ASN C  78 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
      removed outlier: 3.714A  pdb=" N   HIS C 101 " --> pdb=" O   PRO C  98 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 4.163A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   MET C 123 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
    Processing helix  chain 'C' and resid 172 through 175
    Processing helix  chain 'C' and resid 182 through 196
      removed outlier: 3.732A  pdb=" N   THR C 186 " --> pdb=" O   GLY C 182 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ARG C 196 " --> pdb=" O   ILE C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 252 through 260
      Proline residue:  C 258  - end of helix
    Processing helix  chain 'C' and resid 273 through 284
    Processing helix  chain 'C' and resid 289 through 295
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 4.231A  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
    Processing helix  chain 'C' and resid 359 through 366
    Processing helix  chain 'C' and resid 368 through 374
      removed outlier: 4.033A  pdb=" N   ARG C 372 " --> pdb=" O   SER C 368 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28
    Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 16
      removed outlier: 4.160A  pdb=" N   ALA A  11 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103
      removed outlier: 7.754A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   CYS A 661 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.328A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 661 " (cutoff:3.500A)
      removed outlier: 6.311A  pdb=" N   GLN A 157 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   LEU A 436 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ILE A 159 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 7.708A  pdb=" N   ILE A 438 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 6.049A  pdb=" N   VAL A 161 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   GLY A 236 " --> pdb=" O   GLY A 227 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 211
      removed outlier: 5.616A  pdb=" N   ALA A 209 " --> pdb=" O   ASN A 216 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342
    Processing sheet with id=AA6, first strand: chain 'A' and resid 377 through 381
    Processing sheet with id=AA7, first strand: chain 'A' and resid 538 through 539
    Processing sheet with id=AA8, first strand: chain 'A' and resid 700 through 703
    Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.519A  pdb=" N   LYS C  18 " --> pdb=" O   ASP C  11 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AB2, first strand: chain 'C' and resid 71 through 72
    Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170
    Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170
      removed outlier: 5.911A  pdb=" N   ASN C 297 " --> pdb=" O   ILE C 330 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 238 through 241

    531 hydrogen bonds defined for protein.
    1479 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: 1.73

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1699
        1.32 -     1.44: 2746
        1.44 -     1.56: 5847
        1.56 -     1.69: 8
        1.69 -     1.81: 103
  Bond restraints: 10403
  Sorted by residual:
  bond pdb=" O3A ANP A1901 "
       pdb=" PB  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.700  1.555  0.145 2.00e-02 2.50e+03 5.29e+01
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.451  0.121 2.00e-02 2.50e+03 3.64e+01
  bond pdb=" N3B ANP A1901 "
       pdb=" PG  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.795  1.693  0.102 2.00e-02 2.50e+03 2.61e+01
  bond pdb=" O5' ANP A1901 "
       pdb=" PA  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.655  1.582  0.073 2.00e-02 2.50e+03 1.33e+01
  bond pdb=" C   HYP H   6 "
       pdb=" N   ALA H   7 "
    ideal  model  delta    sigma   weight residual
    1.329  1.375 -0.046 1.40e-02 5.10e+03 1.08e+01
  ... (remaining 10398 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.25: 13904
        3.25 -     6.51: 137
        6.51 -     9.76: 8
        9.76 -    13.01: 3
       13.01 -    16.27: 1
  Bond angle restraints: 14053
  Sorted by residual:
  angle pdb=" C   HYP H   6 "
        pdb=" N   ALA H   7 "
        pdb=" CA  ALA H   7 "
      ideal   model   delta    sigma   weight residual
     121.70  111.11   10.59 1.80e+00 3.09e-01 3.46e+01
  angle pdb=" PB  ANP A1901 "
        pdb=" N3B ANP A1901 "
        pdb=" PG  ANP A1901 "
      ideal   model   delta    sigma   weight residual
     126.95  110.68   16.27 3.00e+00 1.11e-01 2.94e+01
  angle pdb=" N   GLY A 563 "
        pdb=" CA  GLY A 563 "
        pdb=" C   GLY A 563 "
      ideal   model   delta    sigma   weight residual
     114.66  120.25   -5.59 1.24e+00 6.50e-01 2.03e+01
  angle pdb=" CA  TRP A 484 "
        pdb=" CB  TRP A 484 "
        pdb=" CG  TRP A 484 "
      ideal   model   delta    sigma   weight residual
     113.60  121.69   -8.09 1.90e+00 2.77e-01 1.81e+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  104.41    7.09 1.70e+00 3.46e-01 1.74e+01
  ... (remaining 14048 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.20: 6120
       32.20 -    64.40: 134
       64.40 -    96.60: 40
       96.60 -   128.80: 3
      128.80 -   161.00: 2
  Dihedral angle restraints: 6299
    sinusoidal: 2605
      harmonic: 3694
  Sorted by residual:
  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
     300.00  168.16  131.84     1      2.00e+01 2.50e-03 4.00e+01
  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   55.19 -115.19     1      2.00e+01 2.50e-03 3.42e+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   54.36 -114.36     1      2.00e+01 2.50e-03 3.39e+01
  ... (remaining 6296 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1192
       0.056 -    0.112: 290
       0.112 -    0.167: 48
       0.167 -    0.223: 2
       0.223 -    0.279: 2
  Chirality restraints: 1534
  Sorted by residual:
  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   -2.64    0.28 2.00e-01 2.50e+01 1.94e+00
  chirality pdb=" CA  MET A 478 "
            pdb=" N   MET A 478 "
            pdb=" C   MET A 478 "
            pdb=" CB  MET A 478 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.24 2.00e-01 2.50e+01 1.38e+00
  chirality pdb=" CA  PHE A 564 "
            pdb=" N   PHE A 564 "
            pdb=" C   PHE A 564 "
            pdb=" CB  PHE A 564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.50e-01
  ... (remaining 1531 not shown)

  Planarity restraints: 1794
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 306 "   -0.002 2.00e-02 2.50e+03   4.17e-02 3.47e+01
        pdb=" CG  TYR C 306 "   -0.000 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 306 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 306 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 306 "    0.058 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 306 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 306 "    0.060 2.00e-02 2.50e+03
        pdb=" OH  TYR C 306 "   -0.061 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 147 "   -0.134 9.50e-02 1.11e+02   7.53e-02 2.81e+01
        pdb=" NE  ARG C 147 "    0.038 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 147 "   -0.087 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 147 "    0.031 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 147 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 773 "   -0.112 9.50e-02 1.11e+02   6.58e-02 2.41e+01
        pdb=" NE  ARG A 773 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 773 "   -0.081 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 773 "    0.029 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 773 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1791 not shown)

  Histogram of nonbonded interaction distances:
        1.64 -     2.29: 11
        2.29 -     2.94: 4427
        2.94 -     3.60: 14701
        3.60 -     4.25: 23064
        4.25 -     4.90: 39502
  Nonbonded interactions: 81705
  Sorted by model distance:
  nonbonded pdb=" O3B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     1.641 2.170
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.731 3.620
  nonbonded pdb=" O1B ANP A1901 "
            pdb="MG    MG A1903 "
     model   vdw
     1.814 2.170
  nonbonded pdb=" O3G ANP A1901 "
            pdb="MG    MG A1902 "
     model   vdw
     2.129 2.170
  nonbonded pdb=" OH  TYR A 456 "
            pdb=" OE1 GLU A 500 "
     model   vdw
     2.155 3.040
  ... (remaining 81700 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:             2.950
  Set stop_for_unknowns flag:              0.010
  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:          0.220
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     10.840
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
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   0.145  10405  Z= 0.250
  Angle     :  0.858  16.267  14059  Z= 0.495
  Chirality :  0.049   0.279   1534
  Planarity :  0.008   0.124   1792
  Dihedral  : 15.933 161.004   3911
  Min Nonbonded Distance : 1.641

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.18 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.35 (0.20), residues: 1235
  helix: -1.72 (0.16), residues: 604
  sheet:  0.40 (0.38), residues: 152
  loop :  0.15 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.088   0.012   ARG C 147 
 TYR   0.061   0.006   TYR C 306 
 PHE   0.060   0.002   PHE A 564 
 TRP   0.074   0.005   TRP A 484 
 HIS   0.015   0.002   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00522 (10403)
  covalent geometry    : angle       0.85532 (14053)
  hydrogen bonds       : bond        0.15857 (  529)
  hydrogen bonds       : angle       6.99780 ( 1479)
  link_TRANS           : bond        0.01144 (    2)
  link_TRANS           : angle       3.47947 (    6)

*********************** 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
  104 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.460 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   93 PHE cc_start: 0.8426 (m-80) cc_final: 0.8212 (m-80)
REVERT: A  503 MET cc_start: 0.8521 (mmm) cc_final: 0.8310 (mmt)
REVERT: C  270 GLU cc_start: 0.7295 (mt-10) cc_final: 0.7088 (mt-10)
  outliers start: 1
  outliers final: 1
  residues processed: 104
  average time/residue: 0.1370
  time to fit residues: 18.9283
Evaluate side-chains
  59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
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 108 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    8.9990
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 147 HIS
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 264 GLN
A 398 ASN
A 463 GLN
A 642 ASN
C 162 ASN
C 280 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.050297 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.036495 restraints weight = 52575.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.2811 rms_B_bonded: 3.98
r_work: 0.2648 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.1884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10405  Z= 0.214
  Angle     :  0.664   7.485  14059  Z= 0.353
  Chirality :  0.044   0.184   1534
  Planarity :  0.004   0.039   1792
  Dihedral  : 11.389 160.252   1429
  Min Nonbonded Distance : 1.875

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  2.86 %
    Favored  : 96.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.81 (0.23), residues: 1235
  helix:  0.57 (0.20), residues: 615
  sheet:  0.86 (0.40), residues: 159
  loop :  0.63 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 692 
 TYR   0.020   0.002   TYR A  79 
 PHE   0.023   0.002   PHE A 564 
 TRP   0.046   0.003   TRP A 484 
 HIS   0.009   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (10403)
  covalent geometry    : angle       0.66433 (14053)
  hydrogen bonds       : bond        0.04619 (  529)
  hydrogen bonds       : angle       5.00144 ( 1479)
  link_TRANS           : bond        0.00263 (    2)
  link_TRANS           : angle       0.73664 (    6)

*********************** 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
  71 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 64
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 GLN cc_start: 0.8865 (mm-40) cc_final: 0.8485 (mm-40)
REVERT: B   36 MET cc_start: 0.9364 (mmt) cc_final: 0.9087 (mmt)
REVERT: B   93 PHE cc_start: 0.8912 (m-80) cc_final: 0.8501 (m-80)
REVERT: A  135 MET cc_start: 0.8539 (mmm) cc_final: 0.8314 (mmm)
REVERT: A  364 MET cc_start: 0.9490 (mmm) cc_final: 0.9241 (mmm)
REVERT: A  503 MET cc_start: 0.9468 (mmm) cc_final: 0.9193 (mmp)
REVERT: C   72 GLU cc_start: 0.8952 (tt0) cc_final: 0.8710 (tp30)
REVERT: C  227 MET cc_start: 0.8349 (mmm) cc_final: 0.8054 (tpp)
  outliers start: 7
  outliers final: 4
  residues processed: 68
  average time/residue: 0.1181
  time to fit residues: 11.3962
Evaluate side-chains
  62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  490 TYR
Chi-restraints excluded: chain A residue  740 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 95 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9990
   chunk 91 optimal weight:    3.9990
   chunk 111 optimal weight:    0.9980
   chunk 94 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A 395 HIS
A 410 ASN
A 492 ASN
A 533 ASN
C 161 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.050838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.037050 restraints weight = 52421.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.2841 rms_B_bonded: 3.97
r_work: 0.2676 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8681
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10405  Z= 0.130
  Angle     :  0.557   7.715  14059  Z= 0.288
  Chirality :  0.041   0.192   1534
  Planarity :  0.004   0.036   1792
  Dihedral  : 10.199 155.190   1428
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  4.42 %
    Favored  : 94.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.53 (0.24), residues: 1235
  helix:  1.39 (0.21), residues: 622
  sheet:  1.12 (0.41), residues: 150
  loop :  0.64 (0.29), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 343 
 TYR   0.014   0.001   TYR A  79 
 PHE   0.011   0.001   PHE C 255 
 TRP   0.027   0.002   TRP A 484 
 HIS   0.006   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 (10403)
  covalent geometry    : angle       0.55686 (14053)
  hydrogen bonds       : bond        0.03780 (  529)
  hydrogen bonds       : angle       4.52777 ( 1479)
  link_TRANS           : bond        0.00158 (    2)
  link_TRANS           : angle       0.62476 (    6)

*********************** 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
  70 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 GLN cc_start: 0.8892 (mm-40) cc_final: 0.8498 (mm-40)
REVERT: B   36 MET cc_start: 0.9351 (mmt) cc_final: 0.9016 (mmt)
REVERT: B   62 SER cc_start: 0.8431 (m) cc_final: 0.8138 (p)
REVERT: B   93 PHE cc_start: 0.8983 (m-80) cc_final: 0.8614 (m-80)
REVERT: B  120 MET cc_start: 0.7923 (mpp) cc_final: 0.7505 (mtt)
REVERT: A   82 GLU cc_start: 0.9096 (mp0) cc_final: 0.8643 (tp30)
REVERT: A  305 MET cc_start: 0.9389 (tpp) cc_final: 0.9061 (tpp)
REVERT: A  478 MET cc_start: 0.8626 (mmt) cc_final: 0.8424 (mmp)
REVERT: C   47 MET cc_start: 0.8923 (tpp) cc_final: 0.8268 (tmm)
REVERT: C  355 MET cc_start: 0.9526 (mmm) cc_final: 0.9299 (mmt)
  outliers start: 7
  outliers final: 3
  residues processed: 65
  average time/residue: 0.1135
  time to fit residues: 10.5178
Evaluate side-chains
  60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 57
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 8 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9990
   chunk 82 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 19 optimal weight:    0.0070
   chunk 17 optimal weight:    5.9990
   chunk 83 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    0.9202

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A  88 ASN
A 406 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.050618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2850 r_free = 0.2850 target = 0.036769 restraints weight = 52512.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.2829 rms_B_bonded: 3.98
r_work: 0.2667 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2667
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.2698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024  10405  Z= 0.134
  Angle     :  0.531   6.707  14059  Z= 0.274
  Chirality :  0.040   0.187   1534
  Planarity :  0.004   0.038   1792
  Dihedral  :  9.655 151.932   1428
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  :  5.90 %
    Favored  : 93.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.24), residues: 1235
  helix:  1.76 (0.22), residues: 616
  sheet:  1.14 (0.41), residues: 150
  loop :  0.68 (0.29), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 343 
 TYR   0.014   0.001   TYR A 456 
 PHE   0.024   0.001   PHE C 223 
 TRP   0.018   0.001   TRP A 484 
 HIS   0.006   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 (10403)
  covalent geometry    : angle       0.53100 (14053)
  hydrogen bonds       : bond        0.03610 (  529)
  hydrogen bonds       : angle       4.39221 ( 1479)
  link_TRANS           : bond        0.00149 (    2)
  link_TRANS           : angle       0.59128 (    6)

*********************** 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
  71 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8486 (mm-40)
REVERT: B   36 MET cc_start: 0.9380 (mmt) cc_final: 0.9024 (mmt)
REVERT: B   62 SER cc_start: 0.8375 (m) cc_final: 0.8079 (p)
REVERT: B   93 PHE cc_start: 0.9072 (m-80) cc_final: 0.8665 (m-80)
REVERT: B  120 MET cc_start: 0.7975 (mpp) cc_final: 0.7744 (pmm)
REVERT: A   82 GLU cc_start: 0.9126 (mp0) cc_final: 0.8807 (tm-30)
REVERT: A  305 MET cc_start: 0.9428 (tpp) cc_final: 0.9107 (tpp)
REVERT: C   47 MET cc_start: 0.8957 (tpp) cc_final: 0.8193 (tmm)
REVERT: C  227 MET cc_start: 0.8905 (tpp) cc_final: 0.8449 (tpp)
REVERT: C  355 MET cc_start: 0.9509 (mmm) cc_final: 0.9287 (mmm)
  outliers start: 9
  outliers final: 5
  residues processed: 68
  average time/residue: 0.0932
  time to fit residues: 9.3422
Evaluate side-chains
  64 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 59
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain A residue   81 HIS
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain C residue  232 SER
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 114 optimal weight:    0.7980
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 80 optimal weight:    7.9990
   chunk 120 optimal weight:    0.5980
   chunk 68 optimal weight:    2.9990
   chunk 79 optimal weight:    0.1980
   chunk 108 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
A  81 HIS
A  88 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.050577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2851 r_free = 0.2851 target = 0.036768 restraints weight = 52637.526|
|-----------------------------------------------------------------------------|
r_work (start): 0.2830 rms_B_bonded: 3.96
r_work: 0.2669 rms_B_bonded: 4.53 restraints_weight: 0.5000
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8690
moved from start:          0.2885

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= 0.133
  Angle     :  0.542  11.337  14059  Z= 0.275
  Chirality :  0.040   0.185   1534
  Planarity :  0.003   0.037   1792
  Dihedral  :  9.391 149.927   1428
  Min Nonbonded Distance : 1.962

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  6.82 %
    Favored  : 92.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.93 (0.24), residues: 1235
  helix:  1.89 (0.22), residues: 619
  sheet:  1.11 (0.41), residues: 150
  loop :  0.64 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 343 
 TYR   0.015   0.001   TYR A  79 
 PHE   0.011   0.001   PHE C 255 
 TRP   0.010   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10403)
  covalent geometry    : angle       0.54239 (14053)
  hydrogen bonds       : bond        0.03495 (  529)
  hydrogen bonds       : angle       4.32129 ( 1479)
  link_TRANS           : bond        0.00135 (    2)
  link_TRANS           : angle       0.58934 (    6)

*********************** 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
  67 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 59
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 GLN cc_start: 0.8882 (mm-40) cc_final: 0.8516 (mm-40)
REVERT: B   36 MET cc_start: 0.9344 (mmt) cc_final: 0.9011 (mmt)
REVERT: B   62 SER cc_start: 0.8392 (m) cc_final: 0.8080 (p)
REVERT: B   93 PHE cc_start: 0.9098 (m-80) cc_final: 0.8695 (m-80)
REVERT: A  150 MET cc_start: 0.9261 (ttt) cc_final: 0.9033 (ttt)
REVERT: A  305 MET cc_start: 0.9411 (tpp) cc_final: 0.9083 (tpp)
REVERT: A  364 MET cc_start: 0.9357 (mmm) cc_final: 0.9125 (mmp)
REVERT: A  515 MET cc_start: 0.9231 (tpp) cc_final: 0.8995 (tpt)
REVERT: C   47 MET cc_start: 0.8967 (tpp) cc_final: 0.8121 (tmm)
REVERT: C  227 MET cc_start: 0.8953 (tpp) cc_final: 0.8446 (tpp)
  outliers start: 8
  outliers final: 4
  residues processed: 63
  average time/residue: 0.1054
  time to fit residues: 9.7050
Evaluate side-chains
  60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain A residue  384 THR
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 61 optimal weight:    0.8980
   chunk 82 optimal weight:    5.9990
   chunk 2 optimal weight:    4.9990
   chunk 119 optimal weight:    0.0570
   chunk 21 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 108 optimal weight:    3.9990
   chunk 8 optimal weight:    6.9990
   chunk 39 optimal weight:    0.6980
   chunk 120 optimal weight:    0.6980
   overall best weight:    0.6700

-------------------------------------------------------------------------------
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 = 0.3334 r_free = 0.3334 target = 0.050853 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.037038 restraints weight = 53341.077|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 4.00
r_work: 0.2677 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8688
moved from start:          0.3061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10405  Z= 0.112
  Angle     :  0.531   9.918  14059  Z= 0.266
  Chirality :  0.040   0.253   1534
  Planarity :  0.003   0.035   1792
  Dihedral  :  9.179 148.794   1428
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.05 %
    Favored  : 98.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.05 (0.24), residues: 1235
  helix:  2.01 (0.22), residues: 619
  sheet:  1.14 (0.42), residues: 150
  loop :  0.67 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 343 
 TYR   0.012   0.001   TYR A 456 
 PHE   0.009   0.001   PHE A 707 
 TRP   0.008   0.001   TRP C 340 
 HIS   0.004   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10403)
  covalent geometry    : angle       0.53047 (14053)
  hydrogen bonds       : bond        0.03287 (  529)
  hydrogen bonds       : angle       4.23335 ( 1479)
  link_TRANS           : bond        0.00128 (    2)
  link_TRANS           : angle       0.61642 (    6)

*********************** 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
  62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 GLN cc_start: 0.8846 (mm-40) cc_final: 0.8471 (mm-40)
REVERT: B   36 MET cc_start: 0.9340 (mmt) cc_final: 0.9052 (mmt)
REVERT: B   62 SER cc_start: 0.8391 (m) cc_final: 0.8090 (p)
REVERT: B   93 PHE cc_start: 0.9087 (m-80) cc_final: 0.8682 (m-80)
REVERT: A   82 GLU cc_start: 0.9169 (mp0) cc_final: 0.8624 (tp30)
REVERT: A  132 MET cc_start: 0.7822 (tpp) cc_final: 0.7604 (tpp)
REVERT: A  305 MET cc_start: 0.9401 (tpp) cc_final: 0.9076 (tpp)
REVERT: C  227 MET cc_start: 0.8964 (tpp) cc_final: 0.8558 (tpp)
REVERT: C  283 MET cc_start: 0.8965 (mmm) cc_final: 0.8665 (mmm)
  outliers start: 6
  outliers final: 4
  residues processed: 59
  average time/residue: 0.0972
  time to fit residues: 8.4362
Evaluate side-chains
  60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 113 optimal weight:    0.4980
   chunk 60 optimal weight:    0.1980
   chunk 96 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 118 optimal weight:    0.6980
   chunk 117 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 77 optimal weight:    0.9980
   chunk 100 optimal weight:    0.9980
   chunk 123 optimal weight:    1.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3338 r_free = 0.3338 target = 0.050948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.037211 restraints weight = 52618.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.2848 rms_B_bonded: 3.96
r_work: 0.2686 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.3205

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= 0.104
  Angle     :  0.533  12.445  14059  Z= 0.262
  Chirality :  0.040   0.220   1534
  Planarity :  0.003   0.035   1792
  Dihedral  :  9.022 148.079   1428
  Min Nonbonded Distance : 1.998

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.89 %
    Favored  : 99.11 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  7.93 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.24), residues: 1235
  helix:  2.09 (0.22), residues: 619
  sheet:  1.17 (0.42), residues: 150
  loop :  0.71 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 343 
 TYR   0.011   0.001   TYR A 456 
 PHE   0.009   0.001   PHE A 707 
 TRP   0.016   0.001   TRP A 781 
 HIS   0.004   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10403)
  covalent geometry    : angle       0.53344 (14053)
  hydrogen bonds       : bond        0.03240 (  529)
  hydrogen bonds       : angle       4.15467 ( 1479)
  link_TRANS           : bond        0.00133 (    2)
  link_TRANS           : angle       0.62404 (    6)

*********************** 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
  62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 GLN cc_start: 0.8834 (mm-40) cc_final: 0.8444 (mm-40)
REVERT: B   62 SER cc_start: 0.8325 (m) cc_final: 0.8106 (p)
REVERT: B   93 PHE cc_start: 0.9075 (m-80) cc_final: 0.8673 (m-80)
REVERT: A   82 GLU cc_start: 0.9163 (mp0) cc_final: 0.8596 (tp30)
REVERT: A  305 MET cc_start: 0.9406 (tpp) cc_final: 0.9065 (tpp)
REVERT: C   47 MET cc_start: 0.8909 (tpp) cc_final: 0.8401 (tmm)
REVERT: C  227 MET cc_start: 0.8958 (tpp) cc_final: 0.8529 (tpp)
REVERT: C  283 MET cc_start: 0.8952 (mmm) cc_final: 0.8697 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 59
  average time/residue: 0.1056
  time to fit residues: 8.9146
Evaluate side-chains
  57 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 54
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 65 optimal weight:    0.2980
   chunk 69 optimal weight:    0.0870
   chunk 60 optimal weight:    0.0870
   chunk 32 optimal weight:    1.9990
   chunk 24 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 111 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.051116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.037347 restraints weight = 52643.266|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 4.00
r_work: 0.2692 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8675
moved from start:          0.3337

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10405  Z= 0.097
  Angle     :  0.534  12.179  14059  Z= 0.263
  Chirality :  0.040   0.208   1534
  Planarity :  0.003   0.055   1792
  Dihedral  :  8.925 147.518   1428
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  8.11 %
    Favored  : 91.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.15 (0.25), residues: 1235
  helix:  2.11 (0.22), residues: 619
  sheet:  1.22 (0.43), residues: 148
  loop :  0.70 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 683 
 TYR   0.011   0.001   TYR A 456 
 PHE   0.009   0.001   PHE C 255 
 TRP   0.018   0.001   TRP A 781 
 HIS   0.009   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (10403)
  covalent geometry    : angle       0.53399 (14053)
  hydrogen bonds       : bond        0.03177 (  529)
  hydrogen bonds       : angle       4.14508 ( 1479)
  link_TRANS           : bond        0.00139 (    2)
  link_TRANS           : angle       0.63617 (    6)

*********************** 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
  62 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.443 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B    8 GLN cc_start: 0.8840 (mm-40) cc_final: 0.8441 (mm-40)
REVERT: B   62 SER cc_start: 0.8340 (m) cc_final: 0.8119 (p)
REVERT: B   93 PHE cc_start: 0.9076 (m-80) cc_final: 0.8672 (m-80)
REVERT: A   82 GLU cc_start: 0.9156 (mp0) cc_final: 0.8825 (tm-30)
REVERT: A  305 MET cc_start: 0.9393 (tpp) cc_final: 0.9045 (tpp)
REVERT: A  783 MET cc_start: 0.9251 (ttt) cc_final: 0.8912 (ppp)
REVERT: A  788 MET cc_start: 0.9186 (mpp) cc_final: 0.8962 (ppp)
REVERT: C   47 MET cc_start: 0.8890 (tpp) cc_final: 0.8310 (tmm)
REVERT: C  227 MET cc_start: 0.8957 (tpp) cc_final: 0.8527 (tpp)
REVERT: C  283 MET cc_start: 0.8958 (mmm) cc_final: 0.8737 (mmm)
  outliers start: 6
  outliers final: 3
  residues processed: 59
  average time/residue: 0.1059
  time to fit residues: 9.2082
Evaluate side-chains
  58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 117 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 95 optimal weight:    2.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 481 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.050261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.036494 restraints weight = 52946.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 3.97
r_work: 0.2664 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8695
moved from start:          0.3392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10405  Z= 0.144
  Angle     :  0.554  12.641  14059  Z= 0.273
  Chirality :  0.040   0.189   1534
  Planarity :  0.003   0.035   1792
  Dihedral  :  8.874 147.986   1428
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 4.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.55 %
    Allowed  :  8.29 %
    Favored  : 91.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.24 (0.25), residues: 1235
  helix:  2.21 (0.22), residues: 617
  sheet:  1.20 (0.44), residues: 148
  loop :  0.73 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 683 
 TYR   0.015   0.001   TYR A 102 
 PHE   0.010   0.001   PHE C 255 
 TRP   0.009   0.001   TRP A 781 
 HIS   0.003   0.001   HIS C  87 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10403)
  covalent geometry    : angle       0.55353 (14053)
  hydrogen bonds       : bond        0.03400 (  529)
  hydrogen bonds       : angle       4.16268 ( 1479)
  link_TRANS           : bond        0.00118 (    2)
  link_TRANS           : angle       0.58935 (    6)

*********************** 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
  63 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 57
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   62 SER cc_start: 0.8398 (m) cc_final: 0.8096 (p)
REVERT: B   93 PHE cc_start: 0.9081 (m-80) cc_final: 0.8692 (m-80)
REVERT: A   82 GLU cc_start: 0.9161 (mp0) cc_final: 0.8871 (tm-30)
REVERT: A  135 MET cc_start: 0.8623 (mmm) cc_final: 0.8418 (mtt)
REVERT: A  783 MET cc_start: 0.9218 (ttt) cc_final: 0.8897 (ppp)
REVERT: A  788 MET cc_start: 0.9087 (mpp) cc_final: 0.8858 (ppp)
REVERT: C   47 MET cc_start: 0.8933 (tpp) cc_final: 0.8293 (tmm)
REVERT: C  227 MET cc_start: 0.8962 (tpp) cc_final: 0.8498 (tpp)
  outliers start: 6
  outliers final: 3
  residues processed: 61
  average time/residue: 0.0971
  time to fit residues: 8.7461
Evaluate side-chains
  58 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 103 optimal weight:    0.8980
   chunk 56 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 1 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 23 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 50 optimal weight:    0.4980
   chunk 97 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3317 r_free = 0.3317 target = 0.050167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.036495 restraints weight = 52267.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 3.94
r_work: 0.2664 rms_B_bonded: 4.52 restraints_weight: 0.5000
r_work (final): 0.2664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8708
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10405  Z= 0.148
  Angle     :  0.570  13.265  14059  Z= 0.278
  Chirality :  0.040   0.183   1534
  Planarity :  0.003   0.035   1792
  Dihedral  :  8.854 147.934   1428
  Min Nonbonded Distance : 1.955

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  8.76 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.20 (0.25), residues: 1235
  helix:  2.18 (0.22), residues: 616
  sheet:  1.19 (0.44), residues: 148
  loop :  0.70 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 683 
 TYR   0.012   0.001   TYR A 456 
 PHE   0.010   0.001   PHE C 255 
 TRP   0.009   0.001   TRP A 781 
 HIS   0.010   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (10403)
  covalent geometry    : angle       0.56993 (14053)
  hydrogen bonds       : bond        0.03391 (  529)
  hydrogen bonds       : angle       4.17214 ( 1479)
  link_TRANS           : bond        0.00132 (    2)
  link_TRANS           : angle       0.58871 (    6)

********************** 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
  60 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.427 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.9471 (mmt) cc_final: 0.8825 (mmm)
REVERT: B   62 SER cc_start: 0.8401 (m) cc_final: 0.8109 (p)
REVERT: B   93 PHE cc_start: 0.9077 (m-80) cc_final: 0.8696 (m-80)
REVERT: A   82 GLU cc_start: 0.9147 (mp0) cc_final: 0.8855 (tm-30)
REVERT: A  132 MET cc_start: 0.7319 (mmm) cc_final: 0.6668 (mmm)
REVERT: A  783 MET cc_start: 0.9254 (ttt) cc_final: 0.8932 (ppp)
REVERT: A  788 MET cc_start: 0.9105 (mpp) cc_final: 0.8858 (ppp)
REVERT: C   47 MET cc_start: 0.8920 (tpp) cc_final: 0.8259 (tmm)
REVERT: C  227 MET cc_start: 0.8965 (tpp) cc_final: 0.8529 (tpp)
REVERT: C  283 MET cc_start: 0.8912 (mmm) cc_final: 0.8643 (mmm)
  outliers start: 5
  outliers final: 5
  residues processed: 58
  average time/residue: 0.1020
  time to fit residues: 8.7716
Evaluate side-chains
  59 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  275 LYS
Chi-restraints excluded: chain A residue  371 MET
Chi-restraints excluded: chain A residue  740 ASP
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 120 optimal weight:    0.8980
   chunk 8 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9980
   chunk 108 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3320 r_free = 0.3320 target = 0.050237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.036581 restraints weight = 53207.035|
|-----------------------------------------------------------------------------|
r_work (start): 0.2827 rms_B_bonded: 3.98
r_work: 0.2668 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.2668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8694
moved from start:          0.3545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10405  Z= 0.132
  Angle     :  0.560  13.320  14059  Z= 0.273
  Chirality :  0.040   0.184   1534
  Planarity :  0.003   0.034   1792
  Dihedral  :  8.785 147.807   1428
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.97 %
    Favored  : 99.03 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  8.57 %
    Favored  : 90.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.19 (0.25), residues: 1235
  helix:  2.19 (0.22), residues: 616
  sheet:  1.18 (0.44), residues: 148
  loop :  0.68 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 683 
 TYR   0.012   0.001   TYR A 456 
 PHE   0.009   0.001   PHE C 255 
 TRP   0.008   0.001   TRP A 781 
 HIS   0.015   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10403)
  covalent geometry    : angle       0.55954 (14053)
  hydrogen bonds       : bond        0.03303 (  529)
  hydrogen bonds       : angle       4.15084 ( 1479)
  link_TRANS           : bond        0.00130 (    2)
  link_TRANS           : angle       0.59971 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2409.89 seconds
wall clock time: 42 minutes 1.05 seconds (2521.05 seconds total)