Starting phenix.real_space_refine
on Wed Mar  4 03:16:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pm9_13525/03_2026/7pm9_13525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pm9_13525/03_2026/7pm9_13525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pm9_13525/03_2026/7pm9_13525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pm9_13525/03_2026/7pm9_13525.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pm9_13525/03_2026/7pm9_13525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pm9_13525/03_2026/7pm9_13525.map"
  }
  resolution = 3.7
  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       4      5.49       5
     Mg      2      5.21       5
     S      62      5.16       5
     C    6422      2.51       5
     N    1713      2.21       5
     O    1883      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 47 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: 10086
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "H"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 29
          Classifications: {'peptide': 3}
          Link IDs: {'TRANS': 2}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 2
          Planarities with less than four sites: {'EEP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "H"
      Number of atoms: 26
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 26
          Classifications: {'peptide': 4}
          Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1}
          Link IDs: {'TRANS': 3}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'HYP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 1059
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1059
          Classifications: {'peptide': 139}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 3, 'TRANS': 135}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 37
          Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "A"
      Number of atoms: 6007
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 735, 6007
          Classifications: {'peptide': 735}
          Link IDs: {'PTRANS': 27, 'TRANS': 707}
          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: "A"
      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}
    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: 2.26, per 1000 atoms: 0.22
  Number of scatterers: 10086
  At special positions: 0
  Unit cell: (109.18, 137.8, 149.46, 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      62     16.00
     P       4     15.00
     Mg      2     11.99
     O    1883      8.00
     N    1713      7.00
     C    6422      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: 0.75
  Conformation dependent library (CDL) restraints added in 442.0 milliseconds
  

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 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:  2358

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 14 sheets defined
      55.5% alpha, 12.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'B' and resid 5 through 19
    Processing helix  chain 'B' and resid 29 through 39
      removed outlier: 4.174A  pdb=" N   GLY B  33 " --> pdb=" O   TYR B  29 " (cutoff:3.500A)
      removed outlier: 4.580A  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 65 through 70
      removed outlier: 3.742A  pdb=" N   GLY A  70 " --> pdb=" O   ASP A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 94
    Processing helix  chain 'A' and resid 120 through 128
    Processing helix  chain 'A' and resid 138 through 153
      removed outlier: 4.139A  pdb=" N   VAL A 142 " --> pdb=" O   HIS A 138 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ALA A 143 " --> pdb=" O   ILE A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 185
      removed outlier: 3.621A  pdb=" N   PHE A 180 " --> pdb=" O   ALA A 176 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   GLY A 185 " --> pdb=" O   ALA A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 207
      removed outlier: 3.571A  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 249
      removed outlier: 3.684A  pdb=" N   ARG A 248 " --> pdb=" O   GLU A 245 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 269
      removed outlier: 4.386A  pdb=" N   TYR A 263 " --> pdb=" O   TYR A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 273 through 278
      removed outlier: 4.166A  pdb=" N   THR A 276 " --> pdb=" O   GLU A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 285 through 290
    Processing helix  chain 'A' and resid 300 through 315
      removed outlier: 3.679A  pdb=" N   GLU A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   ASN A 307 " --> pdb=" O   LYS A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 336
      removed outlier: 3.530A  pdb=" N   GLY A 324 " --> pdb=" O   SER A 320 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLY A 336 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 354 through 365
      removed outlier: 3.527A  pdb=" N   THR A 358 " --> pdb=" O   HIS A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 377
      removed outlier: 3.526A  pdb=" N   CYS A 376 " --> pdb=" O   ALA A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 424
      removed outlier: 3.769A  pdb=" N   ASP A 417 " --> pdb=" O   ASN A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 480
      removed outlier: 3.968A  pdb=" N   GLN A 464 " --> pdb=" O   LYS A 460 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   GLU A 480 " --> pdb=" O   GLU A 476 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 501
    Processing helix  chain 'A' and resid 504 through 515
    Processing helix  chain 'A' and resid 519 through 532
    Processing helix  chain 'A' and resid 563 through 569
      removed outlier: 3.938A  pdb=" N   LYS A 567 " --> pdb=" O   GLY A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 582
      removed outlier: 3.587A  pdb=" N   LEU A 580 " --> pdb=" O   GLN A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 594
      removed outlier: 4.350A  pdb=" N   PHE A 593 " --> pdb=" O   LEU A 589 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   GLN A 594 " --> pdb=" O   PRO A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 653
    Processing helix  chain 'A' and resid 674 through 684
      removed outlier: 3.521A  pdb=" N   ALA A 678 " --> pdb=" O   ASP A 674 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   VAL A 679 " --> pdb=" O   GLU A 675 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLN A 680 " --> pdb=" O   LYS A 676 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 697
      removed outlier: 3.976A  pdb=" N   GLY A 697 " --> pdb=" O   ILE A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 711
    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
      removed outlier: 3.793A  pdb=" N   ARG A 784 " --> pdb=" O   GLY A 780 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 55 through 61
    Processing helix  chain 'C' and resid 78 through 93
    Processing helix  chain 'C' and resid 97 through 101
    Processing helix  chain 'C' and resid 113 through 126
      removed outlier: 3.856A  pdb=" N   GLU C 117 " --> pdb=" O   LYS C 113 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   MET C 123 " --> pdb=" O   MET C 119 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 137 through 146
      removed outlier: 3.568A  pdb=" N   LEU C 142 " --> pdb=" O   ALA C 138 " (cutoff:3.500A)
      removed outlier: 3.576A  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 181 through 196
      removed outlier: 3.926A  pdb=" N   GLU C 195 " --> pdb=" O   LYS C 191 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ARG C 196 " --> pdb=" O   ILE C 192 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 202 through 217
      removed outlier: 3.859A  pdb=" N   GLU C 207 " --> pdb=" O   THR C 203 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ILE C 208 " --> pdb=" O   ALA C 204 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 222 through 233
    Processing helix  chain 'C' and resid 234 through 237
    Processing helix  chain 'C' and resid 252 through 263
      removed outlier: 3.770A  pdb=" N   ARG C 256 " --> pdb=" O   ASN C 252 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   CYS C 257 " --> pdb=" O   GLU C 253 " (cutoff:3.500A)
      Proline residue:  C 258  - end of helix
      removed outlier: 4.196A  pdb=" N   LEU C 261 " --> pdb=" O   CYS C 257 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   PHE C 262 " --> pdb=" O   PRO C 258 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 285
      removed outlier: 3.658A  pdb=" N   CYS C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 286 through 296
      removed outlier: 3.773A  pdb=" N   ARG C 290 " --> pdb=" O   ASP C 286 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LYS C 291 " --> pdb=" O   ILE C 287 " (cutoff:3.500A)
      removed outlier: 5.404A  pdb=" N   ASP C 292 " --> pdb=" O   ASP C 288 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   LEU C 293 " --> pdb=" O   ILE C 289 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA C 295 " --> pdb=" O   LYS C 291 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 301 through 306
      removed outlier: 3.828A  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
    Processing helix  chain 'C' and resid 350 through 356
      removed outlier: 3.755A  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: 3.671A  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 13 through 16
      removed outlier: 3.580A  pdb=" N   LEU A  40 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 100 through 103
      removed outlier: 7.783A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 158 " (cutoff:3.500A)
      removed outlier: 5.759A  pdb=" N   ILE A 160 " --> pdb=" O   VAL A 659 " (cutoff:3.500A)
      removed outlier: 7.160A  pdb=" N   CYS A 661 " --> pdb=" O   ILE A 160 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   SER A 162 " --> pdb=" O   CYS A 661 " (cutoff:3.500A)
      removed outlier: 6.106A  pdb=" N   GLN A 157 " --> pdb=" O   GLY A 434 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   LEU A 436 " --> pdb=" O   GLN A 157 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ILE A 159 " --> pdb=" O   LEU A 436 " (cutoff:3.500A)
      removed outlier: 3.599A  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 344
      removed outlier: 3.603A  pdb=" N   ARG A 343 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   SER A 347 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 378 through 382
    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: 3.637A  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: 3.852A  pdb=" N   THR C 106 " --> pdb=" O   CYS C  10 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   ASN C  12 " --> pdb=" O   THR C 106 " (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: 3.526A  pdb=" N   VAL C 152 " --> pdb=" O   VAL C 163 " (cutoff:3.500A)
      removed outlier: 6.486A  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

    514 hydrogen bonds defined for protein.
    1443 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: 1.40

  Time building geometry restraints manager: 0.91 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: 1676
        1.32 -     1.44: 2734
        1.44 -     1.56: 5784
        1.56 -     1.69: 6
        1.69 -     1.81: 100
  Bond restraints: 10300
  Sorted by residual:
  bond pdb=" CA  EEP H   2 "
       pdb=" C   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.572  1.450  0.122 2.00e-02 2.50e+03 3.71e+01
  bond pdb=" C   EEP H   2 "
       pdb=" O   EEP H   2 "
    ideal  model  delta    sigma   weight residual
    1.263  1.201  0.062 2.00e-02 2.50e+03 9.49e+00
  bond pdb=" CA  TRP H   1 "
       pdb=" C   TRP H   1 "
    ideal  model  delta    sigma   weight residual
    1.525  1.463  0.062 2.10e-02 2.27e+03 8.71e+00
  bond pdb=" C   HYP H   6 "
       pdb=" N   ALA H   7 "
    ideal  model  delta    sigma   weight residual
    1.329  1.370 -0.041 1.40e-02 5.10e+03 8.43e+00
  bond pdb=" CE1 HIC C  73 "
       pdb=" NE2 HIC C  73 "
    ideal  model  delta    sigma   weight residual
    1.347  1.403 -0.056 2.00e-02 2.50e+03 7.75e+00
  ... (remaining 10295 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 13503
        2.38 -     4.75: 349
        4.75 -     7.13: 50
        7.13 -     9.51: 8
        9.51 -    11.88: 4
  Bond angle restraints: 13914
  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  109.82   11.88 1.80e+00 3.09e-01 4.36e+01
  angle pdb=" N   LEU A 782 "
        pdb=" CA  LEU A 782 "
        pdb=" C   LEU A 782 "
      ideal   model   delta    sigma   weight residual
     111.14  117.11   -5.97 1.08e+00 8.57e-01 3.05e+01
  angle pdb=" N   HYP H   6 "
        pdb=" CA  HYP H   6 "
        pdb=" CB  HYP H   6 "
      ideal   model   delta    sigma   weight residual
     103.00  107.77   -4.77 1.10e+00 8.26e-01 1.88e+01
  angle pdb=" CA  TYR A 787 "
        pdb=" CB  TYR A 787 "
        pdb=" CG  TYR A 787 "
      ideal   model   delta    sigma   weight residual
     113.90  121.55   -7.65 1.80e+00 3.09e-01 1.81e+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  102.08    8.02 1.90e+00 2.77e-01 1.78e+01
  ... (remaining 13909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.88: 6066
       34.88 -    69.76: 108
       69.76 -   104.64: 31
      104.64 -   139.53: 4
      139.53 -   174.41: 1
  Dihedral angle restraints: 6210
    sinusoidal: 2553
      harmonic: 3657
  Sorted by residual:
  dihedral pdb=" O1B ADP C 401 "
           pdb=" O3A ADP C 401 "
           pdb=" PB  ADP C 401 "
           pdb=" PA  ADP C 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00  114.40 -174.41     1      2.00e+01 2.50e-03 4.79e+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   72.24 -132.24     1      2.00e+01 2.50e-03 4.01e+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  172.66  127.34     1      2.00e+01 2.50e-03 3.86e+01
  ... (remaining 6207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1102
       0.050 -    0.101: 312
       0.101 -    0.151: 92
       0.151 -    0.202: 9
       0.202 -    0.252: 5
  Chirality restraints: 1520
  Sorted by residual:
  chirality pdb=" CA  MET A 648 "
            pdb=" N   MET A 648 "
            pdb=" C   MET A 648 "
            pdb=" CB  MET A 648 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  TYR A 787 "
            pdb=" N   TYR A 787 "
            pdb=" C   TYR A 787 "
            pdb=" CB  TYR A 787 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  HIS A 418 "
            pdb=" N   HIS A 418 "
            pdb=" C   HIS A 418 "
            pdb=" CB  HIS A 418 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.30    0.21 2.00e-01 2.50e+01 1.12e+00
  ... (remaining 1517 not shown)

  Planarity restraints: 1776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG C 116 "    0.138 9.50e-02 1.11e+02   7.90e-02 3.26e+01
        pdb=" NE  ARG C 116 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  ARG C 116 "    0.094 2.00e-02 2.50e+03
        pdb=" NH1 ARG C 116 "   -0.033 2.00e-02 2.50e+03
        pdb=" NH2 ARG C 116 "   -0.026 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR C 306 "   -0.003 2.00e-02 2.50e+03   3.90e-02 3.04e+01
        pdb=" CG  TYR C 306 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR C 306 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD2 TYR C 306 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR C 306 "    0.053 2.00e-02 2.50e+03
        pdb=" CE2 TYR C 306 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR C 306 "    0.058 2.00e-02 2.50e+03
        pdb=" OH  TYR C 306 "   -0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 231 "    0.121 9.50e-02 1.11e+02   7.00e-02 2.64e+01
        pdb=" NE  ARG A 231 "   -0.036 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 231 "    0.085 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 231 "   -0.030 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 231 "   -0.024 2.00e-02 2.50e+03
  ... (remaining 1773 not shown)

  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 26
        2.37 -     3.00: 5491
        3.00 -     3.63: 15183
        3.63 -     4.27: 22416
        4.27 -     4.90: 37848
  Nonbonded interactions: 80964
  Sorted by model distance:
  nonbonded pdb=" CD1 TRP H   1 "
            pdb=" SG  CYS H   5 "
     model   vdw
     1.731 3.620
  nonbonded pdb=" OG1 THR A 170 "
            pdb="MG    MG A1901 "
     model   vdw
     2.157 2.170
  nonbonded pdb=" OH  TYR A 100 "
            pdb=" OH  TYR A 119 "
     model   vdw
     2.170 3.040
  nonbonded pdb=" OG  SER A 165 "
            pdb=" O   ASN A 216 "
     model   vdw
     2.175 3.040
  nonbonded pdb=" NZ  LYS A 633 "
            pdb=" O   GLY C  23 "
     model   vdw
     2.182 3.120
  ... (remaining 80959 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 group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.430
  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:             0.000
  Extract box with map and model:          0.120
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.370
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
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   0.122  10302  Z= 0.225
  Angle     :  0.931  11.883  13920  Z= 0.543
  Chirality :  0.052   0.252   1520
  Planarity :  0.008   0.085   1774
  Dihedral  : 16.175 174.408   3846
  Min Nonbonded Distance : 1.731

Molprobity Statistics.
  All-atom Clashscore : 7.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.09 %
    Favored  : 99.81 %
  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: -1.87 (0.20), residues: 1221
  helix: -1.55 (0.16), residues: 614
  sheet:  0.01 (0.41), residues: 141
  loop : -0.92 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.095   0.012   ARG C 116 
 TYR   0.059   0.007   TYR C 306 
 PHE   0.028   0.003   PHE C 266 
 TRP   0.029   0.003   TRP C 356 
 HIS   0.007   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (10300)
  covalent geometry    : angle       0.92723 (13914)
  hydrogen bonds       : bond        0.15774 (  512)
  hydrogen bonds       : angle       6.99107 ( 1443)
  link_TRANS           : bond        0.00930 (    2)
  link_TRANS           : angle       4.22393 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 177
  time to evaluate  : 0.384 
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   66 ASP cc_start: 0.8173 (p0) cc_final: 0.7937 (t70)
REVERT: A  759 LEU cc_start: 0.9142 (mt) cc_final: 0.8778 (tt)
REVERT: C   80 ASP cc_start: 0.7890 (p0) cc_final: 0.7686 (p0)
  outliers start: 1
  outliers final: 1
  residues processed: 178
  average time/residue: 0.0998
  time to fit residues: 24.5991
Evaluate side-chains
  101 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    0.0170
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    7.9990
   chunk 33 optimal weight:    5.9990
   chunk 123 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.8820

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

Flipped N/Q/H residues before XYZ refinement:
B  42 ASN
B  75 GLN
A  72 ASN
A 156 ASN
A 264 GLN
A 395 HIS
A 418 HIS
** A 755 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  12 ASN
C  41 GLN
** C  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 121 GLN
C 280 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.066124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.048064 restraints weight = 49140.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.049834 restraints weight = 24479.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.050988 restraints weight = 15262.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.051772 restraints weight = 10883.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.052263 restraints weight = 8558.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  10302  Z= 0.159
  Angle     :  0.691  10.257  13920  Z= 0.360
  Chirality :  0.045   0.265   1520
  Planarity :  0.004   0.055   1774
  Dihedral  : 10.420 165.443   1395
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  6.52 %
    Favored  : 91.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.35 (0.23), residues: 1221
  helix:  0.49 (0.20), residues: 613
  sheet:  0.51 (0.38), residues: 167
  loop : -0.02 (0.28), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 155 
 TYR   0.030   0.002   TYR A 787 
 PHE   0.016   0.002   PHE A 564 
 TRP   0.017   0.002   TRP A 484 
 HIS   0.005   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (10300)
  covalent geometry    : angle       0.68997 (13914)
  hydrogen bonds       : bond        0.04158 (  512)
  hydrogen bonds       : angle       5.11799 ( 1443)
  link_TRANS           : bond        0.00326 (    2)
  link_TRANS           : angle       1.54505 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.381 
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: A  135 MET cc_start: 0.9125 (tpp) cc_final: 0.8896 (tpt)
REVERT: A  305 MET cc_start: 0.9104 (OUTLIER) cc_final: 0.8782 (tmm)
REVERT: A  363 LEU cc_start: 0.9307 (mt) cc_final: 0.8982 (tp)
REVERT: A  507 ASP cc_start: 0.8268 (t0) cc_final: 0.8018 (t0)
REVERT: A  744 PHE cc_start: 0.8579 (m-80) cc_final: 0.8061 (m-80)
REVERT: A  759 LEU cc_start: 0.9177 (mt) cc_final: 0.8862 (pp)
REVERT: C   57 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8838 (tp30)
REVERT: C  355 MET cc_start: 0.8915 (mmm) cc_final: 0.8587 (mmm)
  outliers start: 18
  outliers final: 8
  residues processed: 128
  average time/residue: 0.0857
  time to fit residues: 16.6701
Evaluate side-chains
  104 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ASN
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  679 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 95 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 49 optimal weight:    0.6980
   chunk 59 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 14 optimal weight:    7.9990
   chunk 67 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
A 252 GLN
A 410 ASN
A 430 HIS
A 525 GLN
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 162 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.063739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2978 r_free = 0.2978 target = 0.046186 restraints weight = 49204.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.047804 restraints weight = 25119.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.048891 restraints weight = 15872.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.049615 restraints weight = 11413.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.050067 restraints weight = 9032.373|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.3372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  10302  Z= 0.190
  Angle     :  0.653  12.764  13920  Z= 0.335
  Chirality :  0.043   0.179   1520
  Planarity :  0.004   0.042   1774
  Dihedral  :  9.141 127.974   1394
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  8.85 %
    Favored  : 89.48 %
  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:  0.70 (0.23), residues: 1221
  helix:  1.00 (0.21), residues: 618
  sheet:  0.51 (0.38), residues: 161
  loop : -0.16 (0.27), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 752 
 TYR   0.027   0.001   TYR A 787 
 PHE   0.015   0.002   PHE C 255 
 TRP   0.016   0.001   TRP A 484 
 HIS   0.006   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (10300)
  covalent geometry    : angle       0.65302 (13914)
  hydrogen bonds       : bond        0.04045 (  512)
  hydrogen bonds       : angle       4.89715 ( 1443)
  link_TRANS           : bond        0.00251 (    2)
  link_TRANS           : angle       0.96451 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 97
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  305 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8727 (tmm)
REVERT: A  478 MET cc_start: 0.8547 (mmm) cc_final: 0.8283 (mmm)
REVERT: A  512 GLU cc_start: 0.8061 (tp30) cc_final: 0.7850 (tp30)
REVERT: A  744 PHE cc_start: 0.8463 (m-80) cc_final: 0.8001 (m-80)
REVERT: A  759 LEU cc_start: 0.9202 (mt) cc_final: 0.8918 (pp)
REVERT: A  767 LEU cc_start: 0.8735 (pp) cc_final: 0.8404 (tt)
REVERT: C   47 MET cc_start: 0.7992 (ppp) cc_final: 0.7743 (ppp)
  outliers start: 18
  outliers final: 11
  residues processed: 107
  average time/residue: 0.0815
  time to fit residues: 13.5576
Evaluate side-chains
  99 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   42 ASN
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  139 ILE
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  328 ILE
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  737 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 77 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 60 optimal weight:    0.0980
   chunk 26 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 67 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 4 optimal weight:    1.9990
   chunk 91 optimal weight:    0.0970
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 463 GLN
** C  41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.064942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.047292 restraints weight = 49376.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.048935 restraints weight = 25109.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.050043 restraints weight = 15866.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.050760 restraints weight = 11455.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.051203 restraints weight = 9069.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3710

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10302  Z= 0.118
  Angle     :  0.605  11.885  13920  Z= 0.303
  Chirality :  0.041   0.173   1520
  Planarity :  0.004   0.043   1774
  Dihedral  :  7.830 103.809   1394
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  9.96 %
    Favored  : 88.55 %
  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:  0.98 (0.24), residues: 1221
  helix:  1.29 (0.21), residues: 617
  sheet:  0.53 (0.38), residues: 162
  loop : -0.09 (0.28), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 752 
 TYR   0.023   0.001   TYR A 787 
 PHE   0.012   0.001   PHE C 255 
 TRP   0.010   0.001   TRP A 484 
 HIS   0.009   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10300)
  covalent geometry    : angle       0.60469 (13914)
  hydrogen bonds       : bond        0.03498 (  512)
  hydrogen bonds       : angle       4.66861 ( 1443)
  link_TRANS           : bond        0.00197 (    2)
  link_TRANS           : angle       0.88920 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 101
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  150 MET cc_start: 0.8608 (ttp) cc_final: 0.8365 (ttp)
REVERT: A  239 MET cc_start: 0.8154 (tpp) cc_final: 0.7872 (tmm)
REVERT: A  305 MET cc_start: 0.9024 (OUTLIER) cc_final: 0.8691 (tmm)
REVERT: A  512 GLU cc_start: 0.8082 (tp30) cc_final: 0.7878 (tp30)
REVERT: A  671 PHE cc_start: 0.7847 (OUTLIER) cc_final: 0.7610 (t80)
REVERT: A  744 PHE cc_start: 0.8417 (m-80) cc_final: 0.7956 (m-80)
REVERT: A  759 LEU cc_start: 0.9181 (mt) cc_final: 0.8905 (pp)
REVERT: C   47 MET cc_start: 0.8052 (ppp) cc_final: 0.7849 (ppp)
  outliers start: 16
  outliers final: 6
  residues processed: 112
  average time/residue: 0.0797
  time to fit residues: 13.7131
Evaluate side-chains
  90 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 82
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain A residue  679 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9990
   chunk 32 optimal weight:    0.2980
   chunk 18 optimal weight:    4.9990
   chunk 91 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 123 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 111 HIS
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.064588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.046963 restraints weight = 49074.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.048605 restraints weight = 25074.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.049692 restraints weight = 15870.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.050361 restraints weight = 11433.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.050864 restraints weight = 9104.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10302  Z= 0.130
  Angle     :  0.602  11.152  13920  Z= 0.298
  Chirality :  0.041   0.170   1520
  Planarity :  0.004   0.040   1774
  Dihedral  :  7.094  85.810   1394
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.10 %
    Favored  : 86.31 %
  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:  1.05 (0.24), residues: 1221
  helix:  1.38 (0.21), residues: 619
  sheet:  0.51 (0.38), residues: 161
  loop : -0.07 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 752 
 TYR   0.022   0.001   TYR A 787 
 PHE   0.011   0.001   PHE C 255 
 TRP   0.011   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10300)
  covalent geometry    : angle       0.60145 (13914)
  hydrogen bonds       : bond        0.03375 (  512)
  hydrogen bonds       : angle       4.57482 ( 1443)
  link_TRANS           : bond        0.00212 (    2)
  link_TRANS           : angle       0.86852 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 92
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.7451 (tpt) cc_final: 0.7022 (tpt)
REVERT: A  305 MET cc_start: 0.9042 (OUTLIER) cc_final: 0.8707 (tmm)
REVERT: A  478 MET cc_start: 0.8884 (mmm) cc_final: 0.8634 (tpt)
REVERT: A  744 PHE cc_start: 0.8404 (m-80) cc_final: 0.7952 (m-80)
REVERT: A  759 LEU cc_start: 0.9181 (mt) cc_final: 0.8900 (pp)
REVERT: C   47 MET cc_start: 0.8070 (ppp) cc_final: 0.7836 (ppp)
REVERT: C  117 GLU cc_start: 0.8377 (mp0) cc_final: 0.8014 (mm-30)
  outliers start: 17
  outliers final: 10
  residues processed: 104
  average time/residue: 0.0773
  time to fit residues: 12.4336
Evaluate side-chains
  94 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain B residue   95 VAL
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 100 optimal weight:    0.8980
   chunk 99 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 79 optimal weight:    4.9990
   chunk 101 optimal weight:    2.9990
   chunk 6 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 78 optimal weight:    0.3980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.064917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.047357 restraints weight = 49026.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.048993 restraints weight = 24965.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.050080 restraints weight = 15791.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.050811 restraints weight = 11360.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.051289 restraints weight = 8961.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3108
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10302  Z= 0.116
  Angle     :  0.578   9.837  13920  Z= 0.287
  Chirality :  0.041   0.182   1520
  Planarity :  0.004   0.039   1774
  Dihedral  :  6.975  81.103   1394
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.73 %
    Favored  : 86.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.13 (0.24), residues: 1221
  helix:  1.45 (0.21), residues: 620
  sheet:  0.42 (0.39), residues: 159
  loop :  0.01 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 752 
 TYR   0.021   0.001   TYR A 787 
 PHE   0.010   0.001   PHE C 255 
 TRP   0.010   0.001   TRP A 374 
 HIS   0.008   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (10300)
  covalent geometry    : angle       0.57800 (13914)
  hydrogen bonds       : bond        0.03211 (  512)
  hydrogen bonds       : angle       4.57255 ( 1443)
  link_TRANS           : bond        0.00210 (    2)
  link_TRANS           : angle       0.85593 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.7204 (tpt) cc_final: 0.6831 (tpt)
REVERT: A  305 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8672 (tmm)
REVERT: A  478 MET cc_start: 0.8841 (mmm) cc_final: 0.8590 (tpt)
REVERT: A  671 PHE cc_start: 0.7719 (OUTLIER) cc_final: 0.7496 (t80)
REVERT: A  744 PHE cc_start: 0.8357 (m-80) cc_final: 0.7932 (m-80)
REVERT: A  759 LEU cc_start: 0.9174 (mt) cc_final: 0.8908 (pp)
REVERT: C   47 MET cc_start: 0.8078 (ppp) cc_final: 0.7853 (ppp)
REVERT: C  117 GLU cc_start: 0.8404 (mp0) cc_final: 0.8012 (mm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 101
  average time/residue: 0.0752
  time to fit residues: 11.9091
Evaluate side-chains
  95 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 81
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain B residue   75 GLN
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  132 MET
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  671 PHE
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain C residue   30 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 114 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 78 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 117 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 77 optimal weight:    0.9990
   chunk 68 optimal weight:    0.0570
   overall best weight:    0.7902

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
B 111 HIS
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.064804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.047098 restraints weight = 49367.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.048718 restraints weight = 25268.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.049803 restraints weight = 16071.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.050491 restraints weight = 11601.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.050930 restraints weight = 9236.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.4383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10302  Z= 0.127
  Angle     :  0.594   9.894  13920  Z= 0.295
  Chirality :  0.041   0.193   1520
  Planarity :  0.004   0.041   1774
  Dihedral  :  6.840  79.447   1394
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.47 %
    Favored  : 98.53 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.85 %
    Favored  : 85.57 %
  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:  1.12 (0.24), residues: 1221
  helix:  1.44 (0.22), residues: 619
  sheet:  0.42 (0.39), residues: 159
  loop :  0.01 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B  64 
 TYR   0.020   0.001   TYR A 787 
 PHE   0.013   0.001   PHE A 470 
 TRP   0.008   0.001   TRP C  79 
 HIS   0.004   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10300)
  covalent geometry    : angle       0.59408 (13914)
  hydrogen bonds       : bond        0.03271 (  512)
  hydrogen bonds       : angle       4.59454 ( 1443)
  link_TRANS           : bond        0.00217 (    2)
  link_TRANS           : angle       0.85792 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 85
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.7023 (tpt) cc_final: 0.6576 (tpt)
REVERT: A  305 MET cc_start: 0.9022 (OUTLIER) cc_final: 0.8693 (tmm)
REVERT: A  478 MET cc_start: 0.8865 (mmm) cc_final: 0.8624 (tpt)
REVERT: A  744 PHE cc_start: 0.8370 (m-80) cc_final: 0.7923 (m-80)
REVERT: A  759 LEU cc_start: 0.9179 (mt) cc_final: 0.8906 (pp)
REVERT: C   47 MET cc_start: 0.8056 (ppp) cc_final: 0.7812 (ppp)
REVERT: C  117 GLU cc_start: 0.8412 (mp0) cc_final: 0.8017 (mm-30)
  outliers start: 17
  outliers final: 11
  residues processed: 96
  average time/residue: 0.0813
  time to fit residues: 12.0383
Evaluate side-chains
  91 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain C residue   30 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0670
   chunk 123 optimal weight:    0.6980
   chunk 74 optimal weight:    4.9990
   chunk 37 optimal weight:    0.2980
   chunk 69 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 28 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.065120 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.047593 restraints weight = 48487.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.049165 restraints weight = 24882.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.050273 restraints weight = 15921.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.050984 restraints weight = 11474.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.051494 restraints weight = 9074.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.4520

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10302  Z= 0.113
  Angle     :  0.597  12.352  13920  Z= 0.293
  Chirality :  0.041   0.209   1520
  Planarity :  0.004   0.041   1774
  Dihedral  :  6.689  79.180   1394
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 12.48 %
    Favored  : 85.57 %
  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:  1.10 (0.24), residues: 1221
  helix:  1.40 (0.22), residues: 620
  sheet:  0.45 (0.39), residues: 159
  loop :  0.01 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  64 
 TYR   0.019   0.001   TYR A 787 
 PHE   0.026   0.001   PHE B  12 
 TRP   0.012   0.001   TRP A 374 
 HIS   0.006   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10300)
  covalent geometry    : angle       0.59727 (13914)
  hydrogen bonds       : bond        0.03143 (  512)
  hydrogen bonds       : angle       4.56363 ( 1443)
  link_TRANS           : bond        0.00214 (    2)
  link_TRANS           : angle       0.84981 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 ASN cc_start: 0.7143 (p0) cc_final: 0.6459 (t0)
REVERT: B  120 MET cc_start: 0.6807 (tpt) cc_final: 0.6203 (tpt)
REVERT: A  305 MET cc_start: 0.8998 (OUTLIER) cc_final: 0.8659 (tmm)
REVERT: A  478 MET cc_start: 0.8843 (mmm) cc_final: 0.8599 (tpt)
REVERT: A  744 PHE cc_start: 0.8360 (OUTLIER) cc_final: 0.7990 (m-80)
REVERT: A  759 LEU cc_start: 0.9174 (mt) cc_final: 0.8900 (pp)
REVERT: C  117 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.7938 (mm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 96
  average time/residue: 0.0790
  time to fit residues: 11.8812
Evaluate side-chains
  94 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 79
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  119 LYS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  737 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  117 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 6 optimal weight:    7.9990
   chunk 121 optimal weight:    0.0070
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 103 optimal weight:    0.8980
   chunk 100 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 53 optimal weight:    0.7980
   chunk 24 optimal weight:    0.0870
   chunk 118 optimal weight:    0.8980
   chunk 61 optimal weight:    1.9990
   overall best weight:    0.5176

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.065219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.047774 restraints weight = 48816.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.049409 restraints weight = 24995.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.050493 restraints weight = 15830.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.051197 restraints weight = 11405.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.051683 restraints weight = 9019.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.4618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10302  Z= 0.112
  Angle     :  0.605  11.585  13920  Z= 0.297
  Chirality :  0.042   0.202   1520
  Planarity :  0.004   0.041   1774
  Dihedral  :  6.572  78.874   1394
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.80 %
    Favored  : 98.20 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 13.13 %
    Favored  : 85.20 %
  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:  1.13 (0.24), residues: 1221
  helix:  1.44 (0.22), residues: 620
  sheet:  0.43 (0.40), residues: 159
  loop :  0.01 (0.29), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  64 
 TYR   0.018   0.001   TYR A 787 
 PHE   0.023   0.001   PHE B  12 
 TRP   0.009   0.001   TRP C 356 
 HIS   0.008   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10300)
  covalent geometry    : angle       0.60438 (13914)
  hydrogen bonds       : bond        0.03143 (  512)
  hydrogen bonds       : angle       4.54216 ( 1443)
  link_TRANS           : bond        0.00214 (    2)
  link_TRANS           : angle       0.84563 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   42 ASN cc_start: 0.7139 (p0) cc_final: 0.6456 (t0)
REVERT: B  120 MET cc_start: 0.6866 (tpt) cc_final: 0.6153 (tpt)
REVERT: A  305 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8658 (tmm)
REVERT: A  346 ASP cc_start: 0.8682 (p0) cc_final: 0.8357 (m-30)
REVERT: A  478 MET cc_start: 0.8835 (mmm) cc_final: 0.8590 (tpt)
REVERT: A  744 PHE cc_start: 0.8342 (OUTLIER) cc_final: 0.7981 (m-80)
REVERT: A  759 LEU cc_start: 0.9165 (mt) cc_final: 0.8890 (pp)
  outliers start: 18
  outliers final: 13
  residues processed: 90
  average time/residue: 0.0812
  time to fit residues: 11.4695
Evaluate side-chains
  96 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain B residue  111 HIS
Chi-restraints excluded: chain B residue  119 LYS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  282 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 119 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9990
   chunk 77 optimal weight:    0.6980
   chunk 88 optimal weight:    7.9990
   chunk 30 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9980
   chunk 73 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 117 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.064830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3021 r_free = 0.3021 target = 0.047253 restraints weight = 48283.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.048850 restraints weight = 24896.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.049923 restraints weight = 15845.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.050596 restraints weight = 11525.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.051117 restraints weight = 9183.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8342
moved from start:          0.4661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10302  Z= 0.132
  Angle     :  0.619  11.863  13920  Z= 0.302
  Chirality :  0.042   0.197   1520
  Planarity :  0.004   0.041   1774
  Dihedral  :  6.582  78.786   1394
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.31 %
    Favored  : 85.20 %
  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:  1.15 (0.24), residues: 1221
  helix:  1.45 (0.22), residues: 626
  sheet:  0.42 (0.40), residues: 159
  loop :  0.02 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  64 
 TYR   0.018   0.001   TYR A 787 
 PHE   0.021   0.001   PHE B  12 
 TRP   0.009   0.001   TRP C 356 
 HIS   0.004   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (10300)
  covalent geometry    : angle       0.61923 (13914)
  hydrogen bonds       : bond        0.03198 (  512)
  hydrogen bonds       : angle       4.54514 ( 1443)
  link_TRANS           : bond        0.00227 (    2)
  link_TRANS           : angle       0.85189 (    6)

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

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

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2442 Ramachandran restraints generated.
    1221 Oldfield, 0 Emsley, 1221 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 81
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.7022 (tpt) cc_final: 0.6283 (tpt)
REVERT: A  305 MET cc_start: 0.9019 (OUTLIER) cc_final: 0.8675 (tmm)
REVERT: A  346 ASP cc_start: 0.8701 (p0) cc_final: 0.8391 (m-30)
REVERT: A  478 MET cc_start: 0.8837 (mmm) cc_final: 0.8590 (tpt)
REVERT: A  689 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8577 (tm-30)
REVERT: A  744 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.8003 (m-80)
REVERT: A  759 LEU cc_start: 0.9164 (mt) cc_final: 0.8892 (pp)
  outliers start: 16
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0805
  time to fit residues: 11.7251
Evaluate side-chains
  95 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 80
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Chi-restraints excluded: chain B residue  119 LYS
Chi-restraints excluded: chain A residue  101 THR
Chi-restraints excluded: chain A residue  105 ILE
Chi-restraints excluded: chain A residue  142 VAL
Chi-restraints excluded: chain A residue  261 ILE
Chi-restraints excluded: chain A residue  305 MET
Chi-restraints excluded: chain A residue  307 ASN
Chi-restraints excluded: chain A residue  418 HIS
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain A residue  689 GLU
Chi-restraints excluded: chain A residue  735 LEU
Chi-restraints excluded: chain A residue  744 PHE
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  282 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 82 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0570
   chunk 117 optimal weight:    3.9990
   chunk 12 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0070
   chunk 24 optimal weight:    0.1980
   chunk 5 optimal weight:   20.0000
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.4318

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
** A  88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  12 ASN
** C  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.065651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.048058 restraints weight = 48589.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.049688 restraints weight = 24955.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.050792 restraints weight = 15854.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.051525 restraints weight = 11409.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.051997 restraints weight = 8998.924|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8313
moved from start:          0.4811

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10302  Z= 0.108
  Angle     :  0.612  12.831  13920  Z= 0.297
  Chirality :  0.041   0.210   1520
  Planarity :  0.004   0.041   1774
  Dihedral  :  6.428  77.635   1394
  Min Nonbonded Distance : 1.999

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 13.41 %
    Favored  : 85.10 %
  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:  1.21 (0.24), residues: 1221
  helix:  1.52 (0.22), residues: 626
  sheet:  0.54 (0.41), residues: 154
  loop : -0.03 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  64 
 TYR   0.016   0.001   TYR A 787 
 PHE   0.019   0.001   PHE B  12 
 TRP   0.011   0.001   TRP C  86 
 HIS   0.005   0.001   HIS C 275 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10300)
  covalent geometry    : angle       0.61187 (13914)
  hydrogen bonds       : bond        0.03066 (  512)
  hydrogen bonds       : angle       4.51477 ( 1443)
  link_TRANS           : bond        0.00218 (    2)
  link_TRANS           : angle       0.84513 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1839.90 seconds
wall clock time: 32 minutes 29.91 seconds (1949.91 seconds total)