Starting phenix.real_space_refine
on Fri Feb 14 16:31:37 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7pm9_13525/02_2025/7pm9_13525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7pm9_13525/02_2025/7pm9_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7pm9_13525/02_2025/7pm9_13525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7pm9_13525/02_2025/7pm9_13525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7pm9_13525/02_2025/7pm9_13525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7pm9_13525/02_2025/7pm9_13525.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2}
          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: 6.39, per 1000 atoms: 0.63
  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: 2.74
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  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: 1.16
  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: 3.63

  Time building geometry restraints manager: 3.01 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:             4.430
  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:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     25.020
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.660
-------------------------------------------------------------------------------
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  10300  Z= 0.285
  Angle     :  0.927  11.883  13914  Z= 0.541
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.87 (0.20), 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
 TRP   0.029   0.003   TRP C 356 
 HIS   0.007   0.001   HIS A 418 
 PHE   0.028   0.003   PHE C 266 
 TYR   0.059   0.007   TYR C 306 
 ARG   0.095   0.012   ARG C 116 

*********************** 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  : 1.167 
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: 0.8774 (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: 0.2548
  time to fit residues: 62.0324
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  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    5 CYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 97 optimal weight:    7.9990
   chunk 37 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 72 optimal weight:    1.9990
   chunk 112 optimal weight:    0.6980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 252 GLN
A 264 GLN
A 395 HIS
A 525 GLN
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 = 0.3505 r_free = 0.3505 target = 0.066503 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.048493 restraints weight = 48369.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.050265 restraints weight = 24203.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.051435 restraints weight = 15098.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8311
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10300  Z= 0.219
  Angle     :  0.688  10.158  13914  Z= 0.359
  Chirality :  0.045   0.273   1520
  Planarity :  0.004   0.044   1774
  Dihedral  : 10.546 167.646   1395
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.57 %
    Favored  : 99.43 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  6.15 %
    Favored  : 92.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.31 (0.23), residues: 1221
  helix:  0.47 (0.20), residues: 619
  sheet:  0.52 (0.38), residues: 168
  loop : -0.09 (0.27), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 484 
 HIS   0.005   0.001   HIS A 354 
 PHE   0.016   0.002   PHE A 564 
 TYR   0.031   0.002   TYR A 787 
 ARG   0.009   0.001   ARG A 155 

*********************** 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
  135 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 1.235 
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: B   66 ASP cc_start: 0.8074 (p0) cc_final: 0.7872 (t70)
REVERT: A  305 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8828 (tmm)
REVERT: A  363 LEU cc_start: 0.9332 (mt) cc_final: 0.9115 (tp)
REVERT: A  507 ASP cc_start: 0.8252 (t0) cc_final: 0.7992 (t0)
REVERT: A  744 PHE cc_start: 0.8637 (m-80) cc_final: 0.8015 (m-80)
REVERT: A  759 LEU cc_start: 0.9189 (mt) cc_final: 0.8890 (pp)
REVERT: C   57 GLU cc_start: 0.9065 (mm-30) cc_final: 0.8831 (tp30)
REVERT: C  355 MET cc_start: 0.8930 (mmm) cc_final: 0.8617 (mmm)
  outliers start: 17
  outliers final: 7
  residues processed: 126
  average time/residue: 0.2086
  time to fit residues: 39.5029
Evaluate side-chains
  103 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
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  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 12 optimal weight:    0.0370
   chunk 28 optimal weight:    4.9990
   chunk 119 optimal weight:    0.5980
   chunk 18 optimal weight:    8.9990
   chunk 95 optimal weight:    1.9990
   chunk 29 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 111 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.9262

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
C 162 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.065240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.047549 restraints weight = 48941.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.049214 restraints weight = 24895.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.050318 restraints weight = 15643.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
moved from start:          0.3291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10300  Z= 0.214
  Angle     :  0.623  13.272  13914  Z= 0.318
  Chirality :  0.042   0.183   1520
  Planarity :  0.004   0.042   1774
  Dihedral  :  9.079 129.707   1394
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  7.82 %
    Favored  : 90.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.23), residues: 1221
  helix:  1.09 (0.21), residues: 618
  sheet:  0.54 (0.37), residues: 165
  loop : -0.09 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A 354 
 PHE   0.012   0.001   PHE C 255 
 TYR   0.026   0.001   TYR A 787 
 ARG   0.004   0.000   ARG A 155 

*********************** 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
  116 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 102
  time to evaluate  : 1.356 
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  305 MET cc_start: 0.9091 (OUTLIER) cc_final: 0.8758 (tmm)
REVERT: A  478 MET cc_start: 0.8571 (mmm) cc_final: 0.8302 (mmm)
REVERT: A  744 PHE cc_start: 0.8468 (m-80) cc_final: 0.7977 (m-80)
REVERT: A  759 LEU cc_start: 0.9182 (mt) cc_final: 0.8908 (pp)
REVERT: A  767 LEU cc_start: 0.8729 (pp) cc_final: 0.8376 (tt)
REVERT: C   47 MET cc_start: 0.8015 (ppp) cc_final: 0.7789 (ppp)
REVERT: C   57 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8780 (tp30)
  outliers start: 14
  outliers final: 9
  residues processed: 111
  average time/residue: 0.2008
  time to fit residues: 33.7988
Evaluate side-chains
  94 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 1.460 
-------------------------------------------------------------------------------
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
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 66 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9990
   chunk 122 optimal weight:    0.6980
   chunk 16 optimal weight:    1.9990
   chunk 79 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0980
   chunk 70 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 74 optimal weight:    5.9990
   chunk 49 optimal weight:    0.7980
   chunk 24 optimal weight:    3.9990
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 410 ASN
** 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 = 0.3491 r_free = 0.3491 target = 0.065427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.047750 restraints weight = 48902.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.049412 restraints weight = 25043.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.050468 restraints weight = 15880.284|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8344
moved from start:          0.3681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10300  Z= 0.185
  Angle     :  0.600  12.375  13914  Z= 0.299
  Chirality :  0.041   0.173   1520
  Planarity :  0.004   0.041   1774
  Dihedral  :  7.674 100.823   1394
  Min Nonbonded Distance : 1.947

Molprobity Statistics.
  All-atom Clashscore : 7.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  :  9.22 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.02 (0.24), residues: 1221
  helix:  1.32 (0.21), residues: 617
  sheet:  0.47 (0.38), residues: 167
  loop : -0.03 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 484 
 HIS   0.005   0.001   HIS A 354 
 PHE   0.012   0.001   PHE A 671 
 TYR   0.023   0.001   TYR A 787 
 ARG   0.004   0.000   ARG A 327 

*********************** 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: 18
    poor density    : 99
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  239 MET cc_start: 0.8165 (tpp) cc_final: 0.7909 (tmm)
REVERT: A  305 MET cc_start: 0.9110 (OUTLIER) cc_final: 0.8781 (tmm)
REVERT: A  744 PHE cc_start: 0.8472 (m-80) cc_final: 0.7988 (m-80)
REVERT: A  759 LEU cc_start: 0.9182 (mt) cc_final: 0.8917 (pp)
REVERT: C   57 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8812 (tp30)
  outliers start: 18
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1968
  time to fit residues: 33.2866
Evaluate side-chains
  89 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 91 optimal weight:    0.1980
   chunk 93 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 100 optimal weight:    4.9990
   chunk 89 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   chunk 80 optimal weight:    0.8980
   chunk 109 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 71 optimal weight:    0.3980
   chunk 7 optimal weight:    5.9990
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3492 r_free = 0.3492 target = 0.065432 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.047950 restraints weight = 48127.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.049604 restraints weight = 24692.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.050683 restraints weight = 15617.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.3940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10300  Z= 0.169
  Angle     :  0.598  11.568  13914  Z= 0.294
  Chirality :  0.041   0.171   1520
  Planarity :  0.004   0.040   1774
  Dihedral  :  7.082  86.092   1394
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.31 %
    Favored  : 98.69 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 10.80 %
    Favored  : 87.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.24), residues: 1221
  helix:  1.35 (0.21), residues: 618
  sheet:  0.58 (0.39), residues: 159
  loop :  0.02 (0.28), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 484 
 HIS   0.008   0.001   HIS B 111 
 PHE   0.011   0.001   PHE C 255 
 TYR   0.022   0.001   TYR A 787 
 ARG   0.003   0.000   ARG A 779 

*********************** 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
  111 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 1.066 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.7148 (tpt) cc_final: 0.6777 (tpt)
REVERT: A  305 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8721 (tmm)
REVERT: A  478 MET cc_start: 0.8873 (mmm) cc_final: 0.8658 (tpt)
REVERT: A  671 PHE cc_start: 0.7720 (OUTLIER) cc_final: 0.7504 (t80)
REVERT: A  744 PHE cc_start: 0.8408 (m-80) cc_final: 0.7951 (m-80)
REVERT: A  759 LEU cc_start: 0.9176 (mt) cc_final: 0.8912 (pp)
REVERT: C   57 GLU cc_start: 0.8977 (mm-30) cc_final: 0.8726 (tp30)
  outliers start: 19
  outliers final: 11
  residues processed: 106
  average time/residue: 0.1789
  time to fit residues: 28.9695
Evaluate side-chains
  97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 1.416 
-------------------------------------------------------------------------------
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   95 VAL
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  671 PHE
Chi-restraints excluded: chain A residue  679 VAL
Chi-restraints excluded: chain C residue  288 ASP
Chi-restraints excluded: chain C residue  300 SER
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 19 optimal weight:    2.9990
   chunk 66 optimal weight:    0.4980
   chunk 68 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 116 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 46 optimal weight:    0.2980
   chunk 81 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   overall best weight:    0.9586

-------------------------------------------------------------------------------
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**
A 430 HIS
A 463 GLN
** C  78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.064735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.047218 restraints weight = 48756.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.048833 restraints weight = 25117.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.049877 restraints weight = 15948.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8368
moved from start:          0.4116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10300  Z= 0.204
  Angle     :  0.596   9.280  13914  Z= 0.294
  Chirality :  0.041   0.178   1520
  Planarity :  0.004   0.038   1774
  Dihedral  :  6.886  79.216   1394
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 11.27 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.24), residues: 1221
  helix:  1.39 (0.22), residues: 617
  sheet:  0.40 (0.39), residues: 159
  loop :  0.08 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  79 
 HIS   0.005   0.001   HIS A 354 
 PHE   0.012   0.001   PHE C 127 
 TYR   0.021   0.001   TYR A 787 
 ARG   0.004   0.000   ARG A 155 

*********************** 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
  106 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 1.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.6900 (tpt) cc_final: 0.6527 (tpt)
REVERT: A  305 MET cc_start: 0.9118 (OUTLIER) cc_final: 0.8779 (tmm)
REVERT: A  478 MET cc_start: 0.8961 (mmm) cc_final: 0.8742 (tpt)
REVERT: A  671 PHE cc_start: 0.7762 (OUTLIER) cc_final: 0.7561 (t80)
REVERT: A  744 PHE cc_start: 0.8436 (m-80) cc_final: 0.8021 (m-80)
REVERT: A  759 LEU cc_start: 0.9176 (mt) cc_final: 0.8922 (pp)
REVERT: C   57 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8787 (tp30)
  outliers start: 20
  outliers final: 12
  residues processed: 101
  average time/residue: 0.1932
  time to fit residues: 29.9802
Evaluate side-chains
  94 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
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  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
Chi-restraints excluded: chain C residue   30 VAL
Chi-restraints excluded: chain C residue  288 ASP
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 117 optimal weight:    0.1980
   chunk 63 optimal weight:    1.9990
   chunk 114 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 6 optimal weight:    7.9990
   chunk 72 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 83 optimal weight:   10.0000
   chunk 66 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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  78 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 = 0.3462 r_free = 0.3462 target = 0.064103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.046216 restraints weight = 49416.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.047818 restraints weight = 25465.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.048894 restraints weight = 16244.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8390
moved from start:          0.4260

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  10300  Z= 0.231
  Angle     :  0.605  10.177  13914  Z= 0.301
  Chirality :  0.041   0.178   1520
  Planarity :  0.004   0.042   1774
  Dihedral  :  6.806  78.743   1394
  Min Nonbonded Distance : 1.893

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 11.45 %
    Favored  : 86.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.08 (0.24), residues: 1221
  helix:  1.38 (0.22), residues: 616
  sheet:  0.36 (0.39), residues: 159
  loop :  0.06 (0.28), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  79 
 HIS   0.009   0.001   HIS B 111 
 PHE   0.014   0.001   PHE A 470 
 TYR   0.021   0.001   TYR A 787 
 ARG   0.006   0.000   ARG B  64 

*********************** 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
  97 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 1.195 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.6671 (tpt) cc_final: 0.6317 (tpt)
REVERT: A  305 MET cc_start: 0.9085 (OUTLIER) cc_final: 0.8745 (tmm)
REVERT: A  744 PHE cc_start: 0.8429 (m-80) cc_final: 0.8028 (m-80)
REVERT: A  759 LEU cc_start: 0.9186 (mt) cc_final: 0.8934 (pp)
REVERT: C   57 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8773 (tp30)
  outliers start: 18
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1886
  time to fit residues: 26.9008
Evaluate side-chains
  90 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
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  300 SER
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 30 optimal weight:    0.5980
   chunk 62 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 25 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 86 optimal weight:    0.9990
   chunk 17 optimal weight:    3.9990
   chunk 116 optimal weight:    4.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
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 418 HIS
** 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 = 0.3468 r_free = 0.3468 target = 0.064291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.046755 restraints weight = 48723.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.048357 restraints weight = 25137.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.049439 restraints weight = 15950.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10300  Z= 0.212
  Angle     :  0.606  10.675  13914  Z= 0.298
  Chirality :  0.041   0.168   1520
  Planarity :  0.004   0.043   1774
  Dihedral  :  6.700  78.737   1394
  Min Nonbonded Distance : 1.924

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 11.64 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.24), residues: 1221
  helix:  1.41 (0.22), residues: 617
  sheet:  0.34 (0.39), residues: 159
  loop :  0.03 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 484 
 HIS   0.011   0.001   HIS A 418 
 PHE   0.014   0.001   PHE A 470 
 TYR   0.021   0.001   TYR A 787 
 ARG   0.005   0.000   ARG B  64 

*********************** 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
  100 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.6913 (tpt) cc_final: 0.6383 (tpt)
REVERT: A  305 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8741 (tmm)
REVERT: A  512 GLU cc_start: 0.8218 (tp30) cc_final: 0.7746 (tp30)
REVERT: A  744 PHE cc_start: 0.8417 (m-80) cc_final: 0.8029 (m-80)
REVERT: A  759 LEU cc_start: 0.9181 (mt) cc_final: 0.8928 (pp)
REVERT: C   57 GLU cc_start: 0.8987 (mm-30) cc_final: 0.8755 (tp30)
  outliers start: 17
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1928
  time to fit residues: 29.0510
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  : 1.327 
-------------------------------------------------------------------------------
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  300 SER
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 81 optimal weight:    1.9990
   chunk 8 optimal weight:   10.0000
   chunk 97 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0870
   chunk 75 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    0.0980
   chunk 114 optimal weight:    0.5980
   chunk 85 optimal weight:    2.9990
   overall best weight:    0.7560

-------------------------------------------------------------------------------
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  78 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 = 0.3479 r_free = 0.3479 target = 0.064736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.047121 restraints weight = 48583.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.048724 restraints weight = 25081.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.049819 restraints weight = 15949.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8373
moved from start:          0.4475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10300  Z= 0.187
  Angle     :  0.612  12.514  13914  Z= 0.298
  Chirality :  0.041   0.181   1520
  Planarity :  0.004   0.042   1774
  Dihedral  :  6.570  78.557   1394
  Min Nonbonded Distance : 1.965

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 12.10 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.24), residues: 1221
  helix:  1.44 (0.22), residues: 617
  sheet:  0.34 (0.40), residues: 159
  loop :  0.04 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 484 
 HIS   0.004   0.001   HIS A 354 
 PHE   0.027   0.001   PHE B  12 
 TYR   0.018   0.001   TYR A 787 
 ARG   0.004   0.000   ARG B  64 

*********************** 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
  100 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 1.190 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.6860 (tpt) cc_final: 0.6333 (tpt)
REVERT: A  305 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8734 (tmm)
REVERT: A  346 ASP cc_start: 0.8824 (p0) cc_final: 0.8462 (m-30)
REVERT: A  478 MET cc_start: 0.8296 (mmm) cc_final: 0.7992 (mmm)
REVERT: A  744 PHE cc_start: 0.8407 (m-80) cc_final: 0.8014 (m-80)
REVERT: A  759 LEU cc_start: 0.9173 (mt) cc_final: 0.8924 (pp)
REVERT: C   57 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8728 (tp30)
REVERT: C  117 GLU cc_start: 0.8422 (mp0) cc_final: 0.7902 (mm-30)
REVERT: C  305 MET cc_start: 0.9276 (mmm) cc_final: 0.8979 (tpp)
  outliers start: 14
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1853
  time to fit residues: 27.8382
Evaluate side-chains
  94 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
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  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  157 ASP
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 31 optimal weight:    0.0870
   chunk 38 optimal weight:    0.5980
   chunk 114 optimal weight:    0.6980
   chunk 25 optimal weight:    4.9990
   chunk 113 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 116 optimal weight:    3.9990
   chunk 85 optimal weight:    7.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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  78 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 = 0.065090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.047560 restraints weight = 48450.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.049117 restraints weight = 24979.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.050242 restraints weight = 16031.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10300  Z= 0.180
  Angle     :  0.622  11.757  13914  Z= 0.302
  Chirality :  0.041   0.196   1520
  Planarity :  0.004   0.042   1774
  Dihedral  :  6.434  78.331   1394
  Min Nonbonded Distance : 1.981

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.20 %
    Favored  : 86.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.24), residues: 1221
  helix:  1.45 (0.22), residues: 617
  sheet:  0.39 (0.40), residues: 159
  loop :  0.05 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 484 
 HIS   0.007   0.001   HIS B 111 
 PHE   0.025   0.001   PHE B  12 
 TYR   0.018   0.001   TYR A 787 
 ARG   0.004   0.000   ARG B  64 

********************** 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: 13
    poor density    : 84
  time to evaluate  : 1.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  120 MET cc_start: 0.6873 (tpt) cc_final: 0.6307 (tpt)
REVERT: A  305 MET cc_start: 0.9056 (OUTLIER) cc_final: 0.8711 (tmm)
REVERT: A  346 ASP cc_start: 0.8778 (p0) cc_final: 0.8455 (m-30)
REVERT: A  478 MET cc_start: 0.8354 (mmm) cc_final: 0.8151 (mmm)
REVERT: A  744 PHE cc_start: 0.8395 (m-80) cc_final: 0.8007 (m-80)
REVERT: A  759 LEU cc_start: 0.9168 (mt) cc_final: 0.8922 (pp)
REVERT: C   57 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8709 (tp30)
REVERT: C  117 GLU cc_start: 0.8443 (mp0) cc_final: 0.7891 (mm-30)
  outliers start: 13
  outliers final: 11
  residues processed: 93
  average time/residue: 0.1891
  time to fit residues: 27.3716
Evaluate side-chains
  93 residues out of total 1085 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 1.120 
-------------------------------------------------------------------------------
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  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  157 ASP
Chi-restraints excluded: chain C residue  300 SER
Chi-restraints excluded: chain C residue  374 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    0.2980
   chunk 120 optimal weight:    0.7980
   chunk 97 optimal weight:    2.9990
   chunk 90 optimal weight:    0.9980
   chunk 71 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 118 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 60 optimal weight:    0.5980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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  78 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 = 0.064833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.047288 restraints weight = 48273.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.048908 restraints weight = 24875.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.049991 restraints weight = 15798.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  10300  Z= 0.192
  Angle     :  0.627  11.293  13914  Z= 0.306
  Chirality :  0.042   0.197   1520
  Planarity :  0.004   0.041   1774
  Dihedral  :  6.401  78.313   1394
  Min Nonbonded Distance : 1.940

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 12.29 %
    Favored  : 86.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.24), residues: 1221
  helix:  1.49 (0.22), residues: 617
  sheet:  0.38 (0.40), residues: 159
  loop :  0.06 (0.29), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 484 
 HIS   0.005   0.001   HIS B 111 
 PHE   0.023   0.001   PHE B  12 
 TYR   0.019   0.001   TYR A 787 
 ARG   0.004   0.000   ARG B  64 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3371.98 seconds
wall clock time: 61 minutes 36.46 seconds (3696.46 seconds total)