Starting phenix.real_space_refine
on Fri Feb 14 19:41:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pmf_13531/02_2025/7pmf_13531.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pmf_13531/02_2025/7pmf_13531.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pmf_13531/02_2025/7pmf_13531.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pmf_13531/02_2025/7pmf_13531.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pmf_13531/02_2025/7pmf_13531.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pmf_13531/02_2025/7pmf_13531.cif"
  }
  resolution = 3.4
  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    6443      2.51       5
     N    1719      2.21       5
     O    1892      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-5592/modules/chem_data/mon_lib"
  Total number of atoms: 10125
  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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 6041
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 739, 6041
          Classifications: {'peptide': 739}
          Link IDs: {'PTRANS': 27, 'TRANS': 711}
          Chain breaks: 6
    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: 6.41, per 1000 atoms: 0.63
  Number of scatterers: 10125
  At special positions: 0
  Unit cell: (105.6, 129.8, 150.7, 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    1892      8.00
     N    1719      7.00
     C    6443      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: 2.55
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 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:  2366

  Finding SS restraints...
    Secondary structure from input PDB file:
      63 helices and 14 sheets defined
      55.5% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.394A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.587A  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 helix  chain 'A' and resid 81 through 95
    Processing helix  chain 'A' and resid 116 through 119
      removed outlier: 4.458A  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: 3.651A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 185
    Processing helix  chain 'A' and resid 191 through 198
      removed outlier: 3.669A  pdb=" N   LYS A 195 " --> pdb=" O   ASN A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 207
    Processing helix  chain 'A' and resid 245 through 250
    Processing helix  chain 'A' and resid 259 through 268
      removed outlier: 4.230A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 271
      No H-bonds generated for 'chain 'A' and resid 269 through 271'
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 4.101A  pdb=" N   THR A 276 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 284
    Processing helix  chain 'A' and resid 285 through 290
      removed outlier: 3.882A  pdb=" N   GLN A 290 " --> pdb=" O   HIS A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 314
      removed outlier: 3.564A  pdb=" N   MET A 305 " --> pdb=" O   ASP A 301 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   VAL A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASN A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 338
      removed outlier: 3.521A  pdb=" N   MET A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
    Processing helix  chain 'A' and resid 367 through 375
      removed outlier: 3.767A  pdb=" N   HIS A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 424
      removed outlier: 4.047A  pdb=" N   ALA A 422 " --> pdb=" O   HIS A 418 " (cutoff:3.500A)
    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: 3.604A  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: 3.537A  pdb=" N   ILE A 577 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.227A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   GLN A 594 " --> pdb=" O   PRO A 590 " (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: 3.848A  pdb=" N   GLN A 680 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 696
    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 725 through 736
      removed outlier: 3.972A  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: 3.544A  pdb=" N   LYS C  84 " --> pdb=" O   ASP C  80 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'C' and resid 112 through 126
      removed outlier: 3.943A  pdb=" N   ARG C 116 " --> pdb=" O   PRO C 112 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   MET C 123 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
      removed outlier: 3.544A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 3.608A  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 195
      removed outlier: 3.804A  pdb=" N   THR C 186 " --> pdb=" O   GLY C 182 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   LYS C 191 " --> pdb=" O   ASP C 187 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.591A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
      removed outlier: 3.593A  pdb=" N   GLU C 226 " --> pdb=" O   ASP C 222 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 252 through 260
      Proline residue:  C 258  - end of helix
    Processing helix  chain 'C' and resid 273 through 283
    Processing helix  chain 'C' and resid 289 through 295
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 3.743A  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 349
      removed outlier: 3.610A  pdb=" N   SER C 348 " --> pdb=" O   SER C 344 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 350 through 355
      removed outlier: 3.543A  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: 4.364A  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: 4.085A  pdb=" N   ALA A  11 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU A  48 " --> pdb=" O   LEU A  40 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103
      removed outlier: 3.534A  pdb=" N   ILE A 662 " --> pdb=" O   ALA A 109 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 5.884A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   CYS A 661 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 661 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   GLN A 157 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   LEU A 436 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   ILE A 159 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 7.677A  pdb=" N   ILE A 438 " --> pdb=" O   ILE A 159 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   VAL A 161 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
      removed outlier: 3.760A  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 209
    Processing sheet with id=AA5, first strand: chain 'A' and resid 341 through 342
      removed outlier: 3.510A  pdb=" N   ALA A 341 " --> pdb=" O   ALA A 349 " (cutoff:3.500A)
    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
      removed outlier: 3.811A  pdb=" N   SER A 700 " --> pdb=" O   PHE A 751 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 29 through 32
      removed outlier: 3.906A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   THR C 103 " --> pdb=" O   TYR C 133 " (cutoff:3.500A)
      removed outlier: 8.124A  pdb=" N   ALA C 135 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU C 105 " --> pdb=" O   ALA C 135 " (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: 5.988A  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

    513 hydrogen bonds defined for protein.
    1440 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: 3.54

  Time building geometry restraints manager: 2.95 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1684
        1.31 -     1.44: 2737
        1.44 -     1.56: 5806
        1.56 -     1.69: 8
        1.69 -     1.81: 103
  Bond restraints: 10338
  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 5.96e+01
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.446  0.126 2.00e-02 2.50e+03 3.97e+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 2.80e+01
  bond pdb=" O5' ANP A1901 "
       pdb=" PA  ANP A1901 "
    ideal  model  delta    sigma   weight residual
    1.655  1.577  0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" CA  TRP H   1 "
       pdb=" C   TRP H   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.454  0.071 2.10e-02 2.27e+03 1.13e+01
  ... (remaining 10333 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.66: 13830
        3.66 -     7.33: 122
        7.33 -    10.99: 11
       10.99 -    14.66: 1
       14.66 -    18.32: 1
  Bond angle restraints: 13965
  Sorted by residual:
  angle pdb=" PB  ANP A1901 "
        pdb=" N3B ANP A1901 "
        pdb=" PG  ANP A1901 "
      ideal   model   delta    sigma   weight residual
     126.95  108.63   18.32 3.00e+00 1.11e-01 3.73e+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  110.98   10.72 1.80e+00 3.09e-01 3.55e+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  101.72    9.78 1.70e+00 3.46e-01 3.31e+01
  angle pdb=" N   GLY A 563 "
        pdb=" CA  GLY A 563 "
        pdb=" C   GLY A 563 "
      ideal   model   delta    sigma   weight residual
     113.86  122.10   -8.24 1.50e+00 4.44e-01 3.02e+01
  angle pdb=" C   TRP H   1 "
        pdb=" CA  TRP H   1 "
        pdb=" CB  TRP H   1 "
      ideal   model   delta    sigma   weight residual
     110.10  100.45    9.65 1.90e+00 2.77e-01 2.58e+01
  ... (remaining 13960 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    28.14: 6049
       28.14 -    56.29: 155
       56.29 -    84.43: 42
       84.43 -   112.57: 6
      112.57 -   140.72: 3
  Dihedral angle restraints: 6255
    sinusoidal: 2586
      harmonic: 3669
  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
     300.00  159.28  140.72     1      2.00e+01 2.50e-03 4.26e+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
     300.00  170.09  129.91     1      2.00e+01 2.50e-03 3.94e+01
  dihedral pdb=" CA  PHE A 593 "
           pdb=" C   PHE A 593 "
           pdb=" N   GLN A 594 "
           pdb=" CA  GLN A 594 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.03  -28.97     0      5.00e+00 4.00e-02 3.36e+01
  ... (remaining 6252 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1097
       0.060 -    0.120: 356
       0.120 -    0.180: 63
       0.180 -    0.241: 7
       0.241 -    0.301: 1
  Chirality restraints: 1524
  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   -2.66    0.30 2.00e-01 2.50e+01 2.26e+00
  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    2.27    0.24 2.00e-01 2.50e+01 1.39e+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    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  ... (remaining 1521 not shown)

  Planarity restraints: 1782
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 306 "   -0.005 2.00e-02 2.50e+03   5.00e-02 5.01e+01
        pdb=" CG  TYR C 306 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 306 "   -0.066 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 306 "    0.007 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 306 "    0.070 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 306 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 306 "    0.072 2.00e-02 2.50e+03
        pdb=" OH  TYR C 306 "   -0.074 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 206 "    0.163 9.50e-02 1.11e+02   9.40e-02 4.69e+01
        pdb=" NE  ARG C 206 "   -0.048 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 206 "    0.113 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 206 "   -0.040 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 206 "   -0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 183 "    0.141 9.50e-02 1.11e+02   8.12e-02 3.51e+01
        pdb=" NE  ARG C 183 "   -0.042 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 183 "    0.097 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 183 "   -0.035 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 183 "   -0.028 2.00e-02 2.50e+03
  ... (remaining 1779 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.36: 18
        2.36 -     3.00: 5608
        3.00 -     3.63: 14770
        3.63 -     4.27: 22588
        4.27 -     4.90: 38355
  Nonbonded interactions: 81339
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.731 3.620
  nonbonded pdb=" O3B ADP C 401 "
            pdb="MG    MG C 402 "
     model   vdw
     1.916 2.170
  nonbonded pdb=" O1A ANP A1901 "
            pdb="MG    MG A1903 "
     model   vdw
     1.980 2.170
  nonbonded pdb=" OH  TYR A 456 "
            pdb=" OE1 GLU A 500 "
     model   vdw
     2.039 3.040
  nonbonded pdb=" O1B ANP A1901 "
            pdb="MG    MG A1903 "
     model   vdw
     2.079 2.170
  ... (remaining 81334 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:             2.740
  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:          0.420
  Check model and map are aligned:         0.090
  Set scattering table:                    0.090
  Process input model:                     26.190
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
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      :  0.010   0.154  10338  Z= 0.619
  Angle     :  0.996  18.321  13965  Z= 0.569
  Chirality :  0.059   0.301   1524
  Planarity :  0.008   0.094   1780
  Dihedral  : 15.340 140.715   3883
  Min Nonbonded Distance : 1.731

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.08 %
  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: -1.44 (0.21), residues: 1225
  helix: -1.75 (0.16), residues: 602
  sheet:  0.15 (0.38), residues: 159
  loop :  0.14 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.048   0.005   TRP C  79 
 HIS   0.014   0.003   HIS A 418 
 PHE   0.075   0.003   PHE A 564 
 TYR   0.074   0.007   TYR C 306 
 ARG   0.114   0.012   ARG C 206 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 92
  time to evaluate  : 1.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 1
  residues processed: 93
  average time/residue: 0.3068
  time to fit residues: 38.0753
Evaluate side-chains
  59 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 58
  time to evaluate  : 1.300 
-------------------------------------------------------------------------------
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: 123
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 93 optimal weight:    0.6980
   chunk 51 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 49 optimal weight:    0.8980
   chunk 96 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 111 optimal weight:    0.7980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** A  81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 GLN
A 264 GLN
A 430 HIS
A 464 GLN
A 468 HIS
A 474 GLN
C  59 GLN
C 162 ASN
C 280 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.047446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.034123 restraints weight = 56929.410|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 4.04
r_work: 0.2601 rms_B_bonded: 4.69 restraints_weight: 0.5000
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8643
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10338  Z= 0.215
  Angle     :  0.635   7.259  13965  Z= 0.335
  Chirality :  0.044   0.215   1524
  Planarity :  0.004   0.042   1780
  Dihedral  :  9.975 120.859   1420
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  3.06 %
    Favored  : 96.66 %
  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:  0.64 (0.23), residues: 1225
  helix:  0.44 (0.20), residues: 620
  sheet:  0.66 (0.40), residues: 155
  loop :  0.61 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 484 
 HIS   0.007   0.001   HIS A 418 
 PHE   0.026   0.001   PHE B  12 
 TYR   0.012   0.001   TYR A 102 
 ARG   0.007   0.000   ARG A 343 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 69
  time to evaluate  : 1.188 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.3788 (mtt) cc_final: 0.3125 (mmt)
REVERT: A  135 MET cc_start: 0.9132 (mmm) cc_final: 0.8916 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 70
  average time/residue: 0.2477
  time to fit residues: 25.0043
Evaluate side-chains
  60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 58
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   73 MET
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 116 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 4 optimal weight:   10.0000
   chunk 67 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 34 optimal weight:    4.9990
   chunk 37 optimal weight:    0.8980
   chunk 68 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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  59 GLN
C 161 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.047393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.034024 restraints weight = 58307.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.2765 rms_B_bonded: 4.08
r_work: 0.2603 rms_B_bonded: 4.72 restraints_weight: 0.5000
r_work (final): 0.2603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.2351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10338  Z= 0.193
  Angle     :  0.569   7.992  13965  Z= 0.294
  Chirality :  0.042   0.174   1524
  Planarity :  0.004   0.031   1780
  Dihedral  :  8.676 121.217   1419
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.73 %
    Favored  : 99.27 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  3.71 %
    Favored  : 95.91 %
  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:  1.43 (0.24), residues: 1225
  helix:  1.27 (0.21), residues: 618
  sheet:  0.76 (0.40), residues: 162
  loop :  0.80 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 523 
 HIS   0.006   0.001   HIS A 418 
 PHE   0.019   0.001   PHE C 223 
 TYR   0.011   0.001   TYR A  79 
 ARG   0.004   0.000   ARG A 343 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 63
  time to evaluate  : 1.145 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.9204 (tpp) cc_final: 0.8781 (mmt)
REVERT: A  305 MET cc_start: 0.9132 (tpp) cc_final: 0.8635 (tmm)
REVERT: A  478 MET cc_start: 0.8829 (mmp) cc_final: 0.8374 (mmp)
REVERT: C   57 GLU cc_start: 0.8933 (mp0) cc_final: 0.8692 (mp0)
REVERT: C  176 MET cc_start: 0.9373 (mmm) cc_final: 0.9029 (mmt)
  outliers start: 4
  outliers final: 2
  residues processed: 66
  average time/residue: 0.2582
  time to fit residues: 24.9314
Evaluate side-chains
  59 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 1 optimal weight:    6.9990
   chunk 46 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 20 optimal weight:    0.9980
   chunk 101 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 68 optimal weight:    3.9990
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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  59 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.047286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.034066 restraints weight = 58007.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.2771 rms_B_bonded: 4.04
r_work: 0.2609 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8659
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10338  Z= 0.183
  Angle     :  0.539   7.731  13965  Z= 0.274
  Chirality :  0.041   0.170   1524
  Planarity :  0.003   0.035   1780
  Dihedral  :  8.146 122.434   1419
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 4.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  3.90 %
    Favored  : 95.73 %
  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:  1.75 (0.24), residues: 1225
  helix:  1.67 (0.22), residues: 621
  sheet:  0.87 (0.40), residues: 159
  loop :  0.73 (0.30), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 340 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.018   0.001   PHE C 223 
 TYR   0.010   0.001   TYR A  79 
 ARG   0.003   0.000   ARG A 343 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 58
  time to evaluate  : 1.233 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.9192 (tpp) cc_final: 0.8675 (mmp)
REVERT: B  120 MET cc_start: 0.4289 (mtt) cc_final: 0.3881 (mmt)
REVERT: A  132 MET cc_start: 0.8222 (ttp) cc_final: 0.7947 (tmm)
REVERT: A  305 MET cc_start: 0.9184 (tpp) cc_final: 0.8806 (tpp)
REVERT: A  478 MET cc_start: 0.8948 (mmp) cc_final: 0.8483 (mmp)
REVERT: C   57 GLU cc_start: 0.9052 (mp0) cc_final: 0.8832 (mp0)
REVERT: C  100 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: C  176 MET cc_start: 0.9392 (mmm) cc_final: 0.9075 (mmt)
  outliers start: 4
  outliers final: 1
  residues processed: 60
  average time/residue: 0.2418
  time to fit residues: 21.3167
Evaluate side-chains
  60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 59
  time to evaluate  : 1.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 83 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9980
   chunk 8 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 115 optimal weight:    3.9990
   chunk 110 optimal weight:    0.2980
   chunk 27 optimal weight:    0.2980
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.8982

-------------------------------------------------------------------------------
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 = 0.3283 r_free = 0.3283 target = 0.047262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.034076 restraints weight = 57582.597|
|-----------------------------------------------------------------------------|
r_work (start): 0.2773 rms_B_bonded: 4.01
r_work: 0.2609 rms_B_bonded: 4.71 restraints_weight: 0.5000
r_work (final): 0.2609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.2839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10338  Z= 0.180
  Angle     :  0.523   7.641  13965  Z= 0.264
  Chirality :  0.040   0.168   1524
  Planarity :  0.003   0.029   1780
  Dihedral  :  7.754 125.524   1419
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.90 %
    Favored  : 99.10 %
  Rotamer:
    Outliers :  0.37 %
    Allowed  :  4.55 %
    Favored  : 95.08 %
  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:  1.90 (0.25), residues: 1225
  helix:  1.87 (0.22), residues: 619
  sheet:  0.75 (0.41), residues: 154
  loop :  0.74 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 340 
 HIS   0.005   0.001   HIS A 418 
 PHE   0.011   0.001   PHE C 255 
 TYR   0.009   0.001   TYR A  79 
 ARG   0.004   0.000   ARG B  37 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 61
  time to evaluate  : 1.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.9247 (tpp) cc_final: 0.8690 (mmp)
REVERT: B  120 MET cc_start: 0.4516 (mtt) cc_final: 0.4102 (mmt)
REVERT: B  140 ASN cc_start: 0.9562 (p0) cc_final: 0.9270 (t0)
REVERT: A  305 MET cc_start: 0.9212 (tpp) cc_final: 0.8937 (tpp)
REVERT: A  478 MET cc_start: 0.9056 (mmp) cc_final: 0.8496 (mmm)
REVERT: C   57 GLU cc_start: 0.9079 (mp0) cc_final: 0.8862 (mp0)
REVERT: C  100 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8646 (tm-30)
REVERT: C  176 MET cc_start: 0.9425 (mmm) cc_final: 0.8842 (mpp)
REVERT: C  360 GLN cc_start: 0.9244 (mp10) cc_final: 0.9024 (pm20)
  outliers start: 4
  outliers final: 3
  residues processed: 64
  average time/residue: 0.2428
  time to fit residues: 23.0301
Evaluate side-chains
  62 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 59
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 97 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 101 optimal weight:    5.9990
   chunk 17 optimal weight:    0.0980
   chunk 41 optimal weight:    0.2980
   chunk 14 optimal weight:    0.0980
   chunk 13 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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 149 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.047904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2816 r_free = 0.2816 target = 0.034644 restraints weight = 57791.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.2793 rms_B_bonded: 4.09
r_work: 0.2631 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2631
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8639
moved from start:          0.3098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10338  Z= 0.128
  Angle     :  0.503   6.997  13965  Z= 0.252
  Chirality :  0.040   0.166   1524
  Planarity :  0.003   0.032   1780
  Dihedral  :  7.214 125.924   1419
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.98 %
    Favored  : 99.02 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  5.20 %
    Favored  : 94.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.25), residues: 1225
  helix:  2.08 (0.22), residues: 607
  sheet:  0.72 (0.41), residues: 154
  loop :  0.74 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 340 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.009   0.001   PHE B  12 
 TYR   0.009   0.001   TYR A  79 
 ARG   0.004   0.000   ARG A 233 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 58
  time to evaluate  : 1.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.9257 (tpp) cc_final: 0.8685 (mmp)
REVERT: B  120 MET cc_start: 0.5129 (mtt) cc_final: 0.4822 (mmt)
REVERT: A  132 MET cc_start: 0.8400 (ttp) cc_final: 0.7953 (tmm)
REVERT: A  305 MET cc_start: 0.9229 (tpp) cc_final: 0.8967 (tpp)
REVERT: A  478 MET cc_start: 0.9132 (mmp) cc_final: 0.8568 (mmm)
REVERT: C   57 GLU cc_start: 0.9095 (mp0) cc_final: 0.8862 (mp0)
REVERT: C  100 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8629 (tm-30)
REVERT: C  132 MET cc_start: 0.9237 (ptm) cc_final: 0.8931 (ptm)
REVERT: C  176 MET cc_start: 0.9411 (mmm) cc_final: 0.8824 (mpp)
REVERT: C  205 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8310 (mt-10)
REVERT: C  360 GLN cc_start: 0.9273 (mp10) cc_final: 0.9009 (pm20)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.2296
  time to fit residues: 21.3937
Evaluate side-chains
  60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 1.129 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 120 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9990
   chunk 113 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 642 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.047521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2800 r_free = 0.2800 target = 0.034264 restraints weight = 58122.258|
|-----------------------------------------------------------------------------|
r_work (start): 0.2779 rms_B_bonded: 4.07
r_work: 0.2615 rms_B_bonded: 4.74 restraints_weight: 0.5000
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.3188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10338  Z= 0.165
  Angle     :  0.513   7.601  13965  Z= 0.256
  Chirality :  0.040   0.185   1524
  Planarity :  0.003   0.059   1780
  Dihedral  :  6.992 127.727   1419
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 4.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.06 %
    Favored  : 98.94 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.57 %
    Favored  : 93.87 %
  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:  2.18 (0.25), residues: 1225
  helix:  2.22 (0.22), residues: 606
  sheet:  0.79 (0.42), residues: 154
  loop :  0.77 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 340 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.010   0.001   PHE C 255 
 TYR   0.008   0.001   TYR A  79 
 ARG   0.016   0.000   ARG A  41 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 58
  time to evaluate  : 1.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  105 MET cc_start: 0.9250 (tpp) cc_final: 0.8651 (mmp)
REVERT: B  120 MET cc_start: 0.5453 (mtt) cc_final: 0.5139 (mmt)
REVERT: B  140 ASN cc_start: 0.9535 (p0) cc_final: 0.9325 (t0)
REVERT: A  305 MET cc_start: 0.9264 (tpp) cc_final: 0.9023 (tpp)
REVERT: A  478 MET cc_start: 0.9188 (mmp) cc_final: 0.8688 (mmm)
REVERT: C   57 GLU cc_start: 0.9143 (mp0) cc_final: 0.8884 (mp0)
REVERT: C  100 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8617 (tm-30)
REVERT: C  132 MET cc_start: 0.9262 (ptm) cc_final: 0.8953 (ptm)
REVERT: C  176 MET cc_start: 0.9428 (mmm) cc_final: 0.8833 (mpp)
REVERT: C  205 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8374 (mt-10)
REVERT: C  360 GLN cc_start: 0.9303 (mp10) cc_final: 0.9025 (pm20)
  outliers start: 6
  outliers final: 5
  residues processed: 64
  average time/residue: 0.2102
  time to fit residues: 20.5948
Evaluate side-chains
  60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 1 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    0.6980
   chunk 119 optimal weight:    0.6980
   chunk 95 optimal weight:    0.9980
   chunk 108 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.047460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.034181 restraints weight = 58389.109|
|-----------------------------------------------------------------------------|
r_work (start): 0.2775 rms_B_bonded: 4.09
r_work: 0.2613 rms_B_bonded: 4.76 restraints_weight: 0.5000
r_work (final): 0.2613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.3263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10338  Z= 0.167
  Angle     :  0.527  11.872  13965  Z= 0.258
  Chirality :  0.040   0.168   1524
  Planarity :  0.003   0.030   1780
  Dihedral  :  6.935 128.268   1419
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.57 %
    Favored  : 93.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.25), residues: 1225
  helix:  2.26 (0.22), residues: 606
  sheet:  0.79 (0.42), residues: 154
  loop :  0.78 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 340 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.011   0.001   PHE C 223 
 TYR   0.009   0.001   TYR A  79 
 ARG   0.009   0.000   ARG A  41 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 59
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.9255 (mmm) cc_final: 0.8821 (mmm)
REVERT: B  105 MET cc_start: 0.9255 (tpp) cc_final: 0.8648 (mmp)
REVERT: B  120 MET cc_start: 0.5488 (mtt) cc_final: 0.5173 (mmt)
REVERT: B  140 ASN cc_start: 0.9506 (p0) cc_final: 0.9279 (t0)
REVERT: A  305 MET cc_start: 0.9288 (tpp) cc_final: 0.9046 (tpp)
REVERT: A  382 THR cc_start: 0.8874 (OUTLIER) cc_final: 0.8515 (p)
REVERT: A  478 MET cc_start: 0.9191 (mmp) cc_final: 0.8810 (mmm)
REVERT: C   57 GLU cc_start: 0.9157 (mp0) cc_final: 0.8895 (mp0)
REVERT: C  100 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8610 (tm-30)
REVERT: C  132 MET cc_start: 0.9248 (ptm) cc_final: 0.8956 (ptm)
REVERT: C  176 MET cc_start: 0.9424 (mmm) cc_final: 0.8835 (mpp)
REVERT: C  205 GLU cc_start: 0.8818 (mt-10) cc_final: 0.8358 (mt-10)
REVERT: C  283 MET cc_start: 0.8804 (mmm) cc_final: 0.8445 (mmm)
REVERT: C  360 GLN cc_start: 0.9322 (mp10) cc_final: 0.9048 (pm20)
  outliers start: 7
  outliers final: 5
  residues processed: 65
  average time/residue: 0.2147
  time to fit residues: 21.3396
Evaluate side-chains
  61 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 13 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 18 optimal weight:    0.2980
   chunk 93 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0070
   overall best weight:    0.5800

-------------------------------------------------------------------------------
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 = 0.3294 r_free = 0.3294 target = 0.047664 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.034476 restraints weight = 57887.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.2788 rms_B_bonded: 4.08
r_work: 0.2625 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10338  Z= 0.145
  Angle     :  0.525  10.929  13965  Z= 0.256
  Chirality :  0.040   0.245   1524
  Planarity :  0.003   0.032   1780
  Dihedral  :  6.859 128.285   1419
  Min Nonbonded Distance : 1.994

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.22 %
    Favored  : 98.78 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  :  5.85 %
    Favored  : 93.69 %
  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:  2.25 (0.25), residues: 1225
  helix:  2.29 (0.22), residues: 606
  sheet:  0.79 (0.41), residues: 154
  loop :  0.79 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 340 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.015   0.001   PHE C 223 
 TYR   0.009   0.001   TYR A 102 
 ARG   0.008   0.000   ARG A  41 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.9335 (mmm) cc_final: 0.8893 (mmm)
REVERT: B  105 MET cc_start: 0.9262 (tpp) cc_final: 0.8637 (mmp)
REVERT: B  120 MET cc_start: 0.5526 (mtt) cc_final: 0.5256 (mmt)
REVERT: B  140 ASN cc_start: 0.9542 (p0) cc_final: 0.9276 (t0)
REVERT: A  305 MET cc_start: 0.9291 (tpp) cc_final: 0.8839 (tpp)
REVERT: A  382 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8560 (p)
REVERT: A  478 MET cc_start: 0.9193 (mmp) cc_final: 0.8801 (mmm)
REVERT: C   57 GLU cc_start: 0.9162 (mp0) cc_final: 0.8888 (mp0)
REVERT: C  100 GLU cc_start: 0.8965 (tm-30) cc_final: 0.8616 (tm-30)
REVERT: C  132 MET cc_start: 0.9229 (ptm) cc_final: 0.8951 (ptm)
REVERT: C  176 MET cc_start: 0.9430 (mmm) cc_final: 0.8827 (mpp)
REVERT: C  205 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8329 (mt-10)
REVERT: C  227 MET cc_start: 0.8850 (tpp) cc_final: 0.8647 (tpp)
REVERT: C  283 MET cc_start: 0.8844 (mmm) cc_final: 0.8512 (mmm)
REVERT: C  360 GLN cc_start: 0.9330 (mp10) cc_final: 0.9048 (pm20)
  outliers start: 5
  outliers final: 4
  residues processed: 62
  average time/residue: 0.2128
  time to fit residues: 21.0949
Evaluate side-chains
  60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 9 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 112 optimal weight:    0.8980
   chunk 117 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 111 optimal weight:    0.8980
   chunk 20 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3287 r_free = 0.3287 target = 0.047435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2801 r_free = 0.2801 target = 0.034230 restraints weight = 58169.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.2778 rms_B_bonded: 4.08
r_work: 0.2615 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.2615
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8662
moved from start:          0.3418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10338  Z= 0.167
  Angle     :  0.515  10.745  13965  Z= 0.252
  Chirality :  0.040   0.253   1524
  Planarity :  0.003   0.030   1780
  Dihedral  :  6.831 128.467   1419
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.66 %
    Favored  : 93.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.31 (0.25), residues: 1225
  helix:  2.34 (0.22), residues: 606
  sheet:  0.84 (0.42), residues: 154
  loop :  0.82 (0.30), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 340 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.012   0.001   PHE C 223 
 TYR   0.008   0.001   TYR A  79 
 ARG   0.008   0.000   ARG A  41 

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

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

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2450 Ramachandran restraints generated.
    1225 Oldfield, 0 Emsley, 1225 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 1.042 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   36 MET cc_start: 0.9321 (mmm) cc_final: 0.8882 (mmm)
REVERT: B  105 MET cc_start: 0.9259 (tpp) cc_final: 0.8634 (mmp)
REVERT: B  120 MET cc_start: 0.5578 (mtt) cc_final: 0.5240 (mmt)
REVERT: B  140 ASN cc_start: 0.9548 (p0) cc_final: 0.9281 (t0)
REVERT: A  305 MET cc_start: 0.9294 (tpp) cc_final: 0.8780 (tpp)
REVERT: A  382 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8537 (p)
REVERT: A  478 MET cc_start: 0.9212 (mmp) cc_final: 0.8840 (mmm)
REVERT: C   57 GLU cc_start: 0.9178 (mp0) cc_final: 0.8894 (mp0)
REVERT: C  100 GLU cc_start: 0.8974 (tm-30) cc_final: 0.8623 (tm-30)
REVERT: C  132 MET cc_start: 0.9235 (ptm) cc_final: 0.8961 (ptm)
REVERT: C  176 MET cc_start: 0.9434 (mmm) cc_final: 0.8836 (mpp)
REVERT: C  205 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8330 (mt-10)
REVERT: C  227 MET cc_start: 0.8894 (tpp) cc_final: 0.8651 (tpp)
REVERT: C  283 MET cc_start: 0.8829 (mmm) cc_final: 0.8504 (mmm)
REVERT: C  360 GLN cc_start: 0.9339 (mp10) cc_final: 0.9047 (pm20)
  outliers start: 6
  outliers final: 5
  residues processed: 61
  average time/residue: 0.2042
  time to fit residues: 19.2687
Evaluate side-chains
  60 residues out of total 1088 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 1.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   67 ILE
Chi-restraints excluded: chain A residue  332 ILE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  587 LYS
Chi-restraints excluded: chain C residue   17 VAL
Chi-restraints excluded: chain C residue  257 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 123
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   chunk 100 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 112 optimal weight:    0.5980
   chunk 69 optimal weight:    0.5980
   chunk 85 optimal weight:    8.9990
   chunk 99 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 64 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0370
   overall best weight:    0.5458

-------------------------------------------------------------------------------
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 = 0.3296 r_free = 0.3296 target = 0.047748 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2814 r_free = 0.2814 target = 0.034585 restraints weight = 57874.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.2792 rms_B_bonded: 4.08
r_work: 0.2628 rms_B_bonded: 4.77 restraints_weight: 0.5000
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.3511

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10338  Z= 0.139
  Angle     :  0.514  12.145  13965  Z= 0.250
  Chirality :  0.040   0.239   1524
  Planarity :  0.003   0.032   1780
  Dihedral  :  6.781 127.536   1419
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 4.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  0.56 %
    Allowed  :  5.85 %
    Favored  : 93.59 %
  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:  2.30 (0.25), residues: 1225
  helix:  2.35 (0.22), residues: 606
  sheet:  0.84 (0.41), residues: 154
  loop :  0.78 (0.29), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 340 
 HIS   0.004   0.001   HIS A 418 
 PHE   0.013   0.001   PHE C 223 
 TYR   0.009   0.001   TYR A 102 
 ARG   0.008   0.000   ARG A  41 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4890.76 seconds
wall clock time: 87 minutes 39.22 seconds (5259.22 seconds total)