Starting phenix.real_space_refine
on Tue Jun 10 10:13:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zre_14912/06_2025/7zre_14912.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zre_14912/06_2025/7zre_14912.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zre_14912/06_2025/7zre_14912.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zre_14912/06_2025/7zre_14912.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zre_14912/06_2025/7zre_14912.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zre_14912/06_2025/7zre_14912.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 101 atoms to isotropic.
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
     K       9      8.98       5
     P       6      5.49       5
     S      62      5.16       5
     C    7105      2.51       5
     N    1818      2.21       5
     O    1996      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10996
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 4155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4155
          Classifications: {'peptide': 557}
          Link IDs: {'PTRANS': 25, 'TRANS': 531}
    Chain: "C"
      Number of atoms: 1431
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1431
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 13, 'TRANS': 176}
    Chain: "D"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 200
          Classifications: {'peptide': 27}
          Link IDs: {'TRANS': 26}
    Chain: "B"
      Number of atoms: 5001
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 673, 5001
          Classifications: {'peptide': 673}
          Link IDs: {'PTRANS': 26, 'TRANS': 646}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PHD:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 207
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 207
          Unusual residues: {'  K': 7, 'CDL': 2}
          Classifications: {'undetermined': 9}
          Link IDs: {None: 8}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {'  K': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.33, per 1000 atoms: 0.67
  Number of scatterers: 10996
  At special positions: 0
  Unit cell: (89.056, 112.332, 143.704, 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)
     K       9     19.00
     S      62     16.00
     P       6     15.00
     O    1996      8.00
     N    1818      7.00
     C    7105      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
  Time building additional restraints: 2.94
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2632

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 9 sheets defined
      63.5% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 32
      Proline residue:  A  22  - end of helix
    Processing helix  chain 'A' and resid 42 through 51
    Processing helix  chain 'A' and resid 58 through 83
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 119 through 123
    Processing helix  chain 'A' and resid 125 through 131
    Processing helix  chain 'A' and resid 133 through 157
      removed outlier: 3.788A  pdb=" N   ALA A 141 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 177
    Processing helix  chain 'A' and resid 178 through 192
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 4.361A  pdb=" N   GLN A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 274
      removed outlier: 4.558A  pdb=" N   ILE A 262 " --> pdb=" O   ALA A 258 " (cutoff:3.500A)
      Proline residue:  A 263  - end of helix
    Processing helix  chain 'A' and resid 276 through 304
      removed outlier: 4.566A  pdb=" N   GLY A 280 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 312
      removed outlier: 4.401A  pdb=" N   LEU A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 355 through 368
      removed outlier: 3.787A  pdb=" N   VAL A 361 " --> pdb=" O   LEU A 357 " (cutoff:3.500A)
      Proline residue:  A 362  - end of helix
    Processing helix  chain 'A' and resid 377 through 399
    Processing helix  chain 'A' and resid 410 through 437
      removed outlier: 4.365A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 449 through 465
      removed outlier: 4.028A  pdb=" N   PHE A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 508
      Proline residue:  A 499  - end of helix
    Processing helix  chain 'A' and resid 523 through 550
      removed outlier: 4.209A  pdb=" N   PHE A 527 " --> pdb=" O   HIS A 523 " (cutoff:3.500A)
      Proline residue:  A 545  - end of helix
    Processing helix  chain 'A' and resid 550 through 557
    Processing helix  chain 'C' and resid 3 through 34
      Proline residue:  C  23  - end of helix
    Processing helix  chain 'C' and resid 91 through 109
    Processing helix  chain 'C' and resid 133 through 149
      Proline residue:  C 142  - end of helix
    Processing helix  chain 'C' and resid 151 through 162
    Processing helix  chain 'C' and resid 168 through 172
      removed outlier: 3.550A  pdb=" N   ILE C 171 " --> pdb=" O   VAL C 168 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   GLY C 172 " --> pdb=" O   LYS C 169 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 168 through 172'
    Processing helix  chain 'C' and resid 178 through 190
    Processing helix  chain 'D' and resid 2 through 25
    Processing helix  chain 'B' and resid 11 through 23
      removed outlier: 4.272A  pdb=" N   ALA B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 26 through 31
    Processing helix  chain 'B' and resid 33 through 56
    Processing helix  chain 'B' and resid 63 through 103
      removed outlier: 3.751A  pdb=" N   GLN B  93 " --> pdb=" O   ARG B  89 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU B  97 " --> pdb=" O   GLN B  93 " (cutoff:3.500A)
      removed outlier: 5.896A  pdb=" N   VAL B 100 " --> pdb=" O   SER B  96 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   LYS B 101 " --> pdb=" O   LEU B  97 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   THR B 103 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 198 through 208
    Processing helix  chain 'B' and resid 215 through 246
      removed outlier: 4.048A  pdb=" N   TRP B 240 " --> pdb=" O   THR B 236 " (cutoff:3.500A)
      Proline residue:  B 241  - end of helix
      removed outlier: 3.761A  pdb=" N   TRP B 245 " --> pdb=" O   PRO B 241 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   GLY B 246 " --> pdb=" O   PHE B 242 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 251 through 263
    Processing helix  chain 'B' and resid 265 through 284
      removed outlier: 5.522A  pdb=" N   SER B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 4.698A  pdb=" N   ALA B 273 " --> pdb=" O   GLY B 269 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 301
      removed outlier: 3.939A  pdb=" N   VAL B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 342
    Processing helix  chain 'B' and resid 346 through 361
    Processing helix  chain 'B' and resid 366 through 371
    Processing helix  chain 'B' and resid 397 through 407
    Processing helix  chain 'B' and resid 415 through 427
    Processing helix  chain 'B' and resid 452 through 463
    Processing helix  chain 'B' and resid 474 through 486
    Processing helix  chain 'B' and resid 495 through 508
    Processing helix  chain 'B' and resid 522 through 529
    Processing helix  chain 'B' and resid 539 through 546
    Processing helix  chain 'B' and resid 556 through 582
      removed outlier: 3.995A  pdb=" N   GLU B 560 " --> pdb=" O   THR B 556 " (cutoff:3.500A)
      removed outlier: 6.517A  pdb=" N   MET B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   LEU B 569 " --> pdb=" O   GLY B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 595
      Proline residue:  B 592  - end of helix
    Processing helix  chain 'B' and resid 599 through 606
      removed outlier: 3.654A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 631
      removed outlier: 4.458A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   VAL B 629 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 631 through 638
    Processing helix  chain 'B' and resid 645 through 680
      removed outlier: 4.327A  pdb=" N   LEU B 659 " --> pdb=" O   TRP B 655 " (cutoff:3.500A)
      Proline residue:  B 665  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205
    Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404
      removed outlier: 3.572A  pdb=" N   LYS A 407 " --> pdb=" O   TYR A 404 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 44
      removed outlier: 4.409A  pdb=" N   GLY C  51 " --> pdb=" O   ILE C  43 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132
    Processing sheet with id=AA5, first strand: chain 'B' and resid 119 through 120
      removed outlier: 3.720A  pdb=" N   ARG B 107 " --> pdb=" O   LEU B 133 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 144 through 145
    Processing sheet with id=AA7, first strand: chain 'B' and resid 164 through 168
      removed outlier: 3.522A  pdb=" N   ALA B 151 " --> pdb=" O   ARG B 167 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   ARG B 181 " --> pdb=" O   ASP B 154 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 287 through 288
      removed outlier: 6.411A  pdb=" N   ALA B 532 " --> pdb=" O   MET B 548 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   ASP B 550 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   ALA B 534 " --> pdb=" O   ASP B 550 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ASP B 518 " --> pdb=" O   PHD B 307 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASP B 489 " --> pdb=" O   THR B 467 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 317 through 319
      removed outlier: 3.957A  pdb=" N   GLY B 441 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 6.797A  pdb=" N   MET B 383 " --> pdb=" O   PHE B 377 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   PHE B 377 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLY B 385 " --> pdb=" O   VAL B 375 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   THR B 373 " --> pdb=" O   ASN B 387 " (cutoff:3.500A)

    690 hydrogen bonds defined for protein.
    2031 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: 3.60

  Time building geometry restraints manager: 3.45 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1771
        1.31 -     1.44: 2725
        1.44 -     1.57: 6563
        1.57 -     1.69: 13
        1.69 -     1.82: 112
  Bond restraints: 11184
  Sorted by residual:
  bond pdb=" OD1 PHD B 307 "
       pdb=" P   PHD B 307 "
    ideal  model  delta    sigma   weight residual
    1.816  1.592  0.224 2.00e-02 2.50e+03 1.25e+02
  bond pdb=" CB7 CDL A 609 "
       pdb=" OB8 CDL A 609 "
    ideal  model  delta    sigma   weight residual
    1.334  1.424 -0.090 1.10e-02 8.26e+03 6.76e+01
  bond pdb=" CB7 CDL A 608 "
       pdb=" OB8 CDL A 608 "
    ideal  model  delta    sigma   weight residual
    1.334  1.422 -0.088 1.10e-02 8.26e+03 6.43e+01
  bond pdb=" CA7 CDL A 608 "
       pdb=" OA8 CDL A 608 "
    ideal  model  delta    sigma   weight residual
    1.334  1.415 -0.081 1.10e-02 8.26e+03 5.43e+01
  bond pdb=" CA7 CDL A 609 "
       pdb=" OA8 CDL A 609 "
    ideal  model  delta    sigma   weight residual
    1.334  1.414 -0.080 1.10e-02 8.26e+03 5.28e+01
  ... (remaining 11179 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.24: 14672
        2.24 -     4.47: 354
        4.47 -     6.71: 119
        6.71 -     8.95: 25
        8.95 -    11.18: 7
  Bond angle restraints: 15177
  Sorted by residual:
  angle pdb=" C51 CDL A 609 "
        pdb=" CB5 CDL A 609 "
        pdb=" OB6 CDL A 609 "
      ideal   model   delta    sigma   weight residual
     111.33  120.25   -8.92 1.32e+00 5.72e-01 4.55e+01
  angle pdb=" C11 CDL A 608 "
        pdb=" CA5 CDL A 608 "
        pdb=" OA6 CDL A 608 "
      ideal   model   delta    sigma   weight residual
     111.33  120.12   -8.79 1.32e+00 5.72e-01 4.42e+01
  angle pdb=" C11 CDL A 609 "
        pdb=" CA5 CDL A 609 "
        pdb=" OA6 CDL A 609 "
      ideal   model   delta    sigma   weight residual
     111.33  119.83   -8.50 1.32e+00 5.72e-01 4.14e+01
  angle pdb=" C51 CDL A 608 "
        pdb=" CB5 CDL A 608 "
        pdb=" OB6 CDL A 608 "
      ideal   model   delta    sigma   weight residual
     111.33  119.63   -8.30 1.32e+00 5.72e-01 3.94e+01
  angle pdb=" C71 CDL A 609 "
        pdb=" CB7 CDL A 609 "
        pdb=" OB8 CDL A 609 "
      ideal   model   delta    sigma   weight residual
     111.64  120.47   -8.83 1.65e+00 3.69e-01 2.88e+01
  ... (remaining 15172 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.92: 5890
       17.92 -    35.85: 624
       35.85 -    53.77: 152
       53.77 -    71.70: 44
       71.70 -    89.62: 12
  Dihedral angle restraints: 6722
    sinusoidal: 2625
      harmonic: 4097
  Sorted by residual:
  dihedral pdb=" C   PHD B 307 "
           pdb=" N   PHD B 307 "
           pdb=" CA  PHD B 307 "
           pdb=" CB  PHD B 307 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.22   14.62     0      2.50e+00 1.60e-01 3.42e+01
  dihedral pdb=" CA  ALA A 470 "
           pdb=" C   ALA A 470 "
           pdb=" N   PHE A 471 "
           pdb=" CA  PHE A 471 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.10   27.90     0      5.00e+00 4.00e-02 3.11e+01
  dihedral pdb=" N   PHD B 307 "
           pdb=" C   PHD B 307 "
           pdb=" CA  PHD B 307 "
           pdb=" CB  PHD B 307 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  134.98  -12.18     0      2.50e+00 1.60e-01 2.37e+01
  ... (remaining 6719 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.104: 1729
       0.104 -    0.207: 73
       0.207 -    0.311: 4
       0.311 -    0.414: 0
       0.414 -    0.518: 1
  Chirality restraints: 1807
  Sorted by residual:
  chirality pdb=" CA  PHD B 307 "
            pdb=" N   PHD B 307 "
            pdb=" C   PHD B 307 "
            pdb=" CB  PHD B 307 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.71e+00
  chirality pdb=" CA  LEU B 342 "
            pdb=" N   LEU B 342 "
            pdb=" C   LEU B 342 "
            pdb=" CB  LEU B 342 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.78   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" CB  ILE B 393 "
            pdb=" CA  ILE B 393 "
            pdb=" CG1 ILE B 393 "
            pdb=" CG2 ILE B 393 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.91   -0.27 2.00e-01 2.50e+01 1.79e+00
  ... (remaining 1804 not shown)

  Planarity restraints: 1905
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 361 "    0.054 5.00e-02 4.00e+02   8.05e-02 1.04e+01
        pdb=" N   PRO A 362 "   -0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 362 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 362 "    0.045 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 360 "    0.011 2.00e-02 2.50e+03   1.63e-02 4.66e+00
        pdb=" CG  PHE B 360 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 360 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 360 "    0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 360 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 360 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 360 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C  18 "    0.011 2.00e-02 2.50e+03   2.16e-02 4.66e+00
        pdb=" C   THR C  18 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   THR C  18 "    0.014 2.00e-02 2.50e+03
        pdb=" N   GLY C  19 "    0.013 2.00e-02 2.50e+03
  ... (remaining 1902 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.81: 2986
        2.81 -     3.39: 12509
        3.39 -     3.98: 21778
        3.98 -     4.56: 30403
        4.56 -     5.14: 44182
  Nonbonded interactions: 111858
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 107 "
            pdb=" OG1 THR A 111 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR A 339 "
            pdb=" O   CYS A 344 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   TYR C  22 "
            pdb=" OG1 THR C  26 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER B 612 "
            pdb=" OD1 ASP B 614 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG  SER A 241 "
            pdb=" O   ILE A 348 "
     model   vdw
     2.278 3.040
  ... (remaining 111853 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.390
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     28.910
  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:   33.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
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      :  0.006   0.224  11184  Z= 0.354
  Angle     :  0.929  11.183  15177  Z= 0.471
  Chirality :  0.049   0.518   1807
  Planarity :  0.006   0.080   1905
  Dihedral  : 16.337  89.620   4090
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 7.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.62 %
    Favored  : 99.38 %
  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: -0.86 (0.20), residues: 1433
  helix:  0.17 (0.16), residues: 884
  sheet: -1.05 (0.58), residues: 82
  loop : -1.79 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 115 
 HIS   0.003   0.001   HIS B 563 
 PHE   0.037   0.002   PHE B 360 
 TYR   0.030   0.002   TYR B 114 
 ARG   0.007   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11329 (  690)
  hydrogen bonds       : angle       5.99018 ( 2031)
  covalent geometry    : bond        0.00610 (11184)
  covalent geometry    : angle       0.92889 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.217 
Fit side-chains
   revert: symmetry clash
REVERT: A   27 LEU cc_start: 0.8414 (mt) cc_final: 0.8142 (mt)
REVERT: A  365 LEU cc_start: 0.7752 (tp) cc_final: 0.7523 (tp)
REVERT: B  186 TRP cc_start: 0.6306 (p-90) cc_final: 0.5586 (p-90)
REVERT: B  279 MET cc_start: 0.7084 (mmm) cc_final: 0.6817 (mtm)
REVERT: B  393 ILE cc_start: 0.6839 (mm) cc_final: 0.6596 (mm)
REVERT: B  515 MET cc_start: 0.6470 (tmm) cc_final: 0.5536 (tmm)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2187
  time to fit residues: 50.5314
Evaluate side-chains
  134 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 120 optimal weight:    5.9990
   chunk 108 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0670
   chunk 112 optimal weight:    0.0050
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0000
   chunk 83 optimal weight:    0.9980
   chunk 129 optimal weight:    1.9990
   overall best weight:    0.3336

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 252 ASN
** A 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 653 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.149096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.115386 restraints weight = 14176.965|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 1.33
r_work: 0.3141 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3034 rms_B_bonded: 3.30 restraints_weight: 0.2500
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.0842

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11184  Z= 0.105
  Angle     :  0.535   7.332  15177  Z= 0.271
  Chirality :  0.039   0.157   1807
  Planarity :  0.004   0.063   1905
  Dihedral  : 11.258  68.743   1714
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  :  7.51 %
    Favored  : 91.87 %
  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:  0.13 (0.21), residues: 1433
  helix:  1.14 (0.17), residues: 872
  sheet: -1.13 (0.57), residues: 82
  loop : -1.65 (0.25), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 115 
 HIS   0.001   0.000   HIS A 451 
 PHE   0.012   0.001   PHE A 490 
 TYR   0.027   0.001   TYR A 381 
 ARG   0.004   0.000   ARG B 461 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  690)
  hydrogen bonds       : angle       4.94235 ( 2031)
  covalent geometry    : bond        0.00210 (11184)
  covalent geometry    : angle       0.53497 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 146
  time to evaluate  : 1.359 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8390 (mt) cc_final: 0.8119 (mt)
REVERT: A  365 LEU cc_start: 0.7934 (tp) cc_final: 0.7696 (tp)
REVERT: A  445 MET cc_start: 0.5642 (mmt) cc_final: 0.5241 (mmt)
REVERT: B  186 TRP cc_start: 0.6525 (p-90) cc_final: 0.5410 (p-90)
REVERT: B  279 MET cc_start: 0.8009 (mmm) cc_final: 0.7602 (mmt)
REVERT: B  515 MET cc_start: 0.7142 (tmm) cc_final: 0.6636 (tmm)
  outliers start: 7
  outliers final: 3
  residues processed: 148
  average time/residue: 0.1970
  time to fit residues: 44.6621
Evaluate side-chains
  139 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 136
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain B residue  168 GLU
Chi-restraints excluded: chain B residue  283 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 132 optimal weight:    3.9990
   chunk 103 optimal weight:    0.7980
   chunk 78 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 117 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 123 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A   4 GLN
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.143409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.108094 restraints weight = 14592.239|
|-----------------------------------------------------------------------------|
r_work (start): 0.3214 rms_B_bonded: 1.39
r_work: 0.3118 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.43 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7850
moved from start:          0.1271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11184  Z= 0.139
  Angle     :  0.551   7.735  15177  Z= 0.279
  Chirality :  0.041   0.151   1807
  Planarity :  0.004   0.052   1905
  Dihedral  : 10.198  59.485   1714
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 10.25 %
    Favored  : 88.60 %
  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:  0.38 (0.22), residues: 1433
  helix:  1.37 (0.17), residues: 874
  sheet: -1.20 (0.52), residues: 92
  loop : -1.62 (0.25), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 655 
 HIS   0.002   0.001   HIS A 451 
 PHE   0.014   0.001   PHE A 471 
 TYR   0.033   0.002   TYR A 381 
 ARG   0.002   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03995 (  690)
  hydrogen bonds       : angle       4.78117 ( 2031)
  covalent geometry    : bond        0.00313 (11184)
  covalent geometry    : angle       0.55135 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 150
  time to evaluate  : 1.088 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8480 (mt) cc_final: 0.8195 (mt)
REVERT: A  365 LEU cc_start: 0.8253 (tp) cc_final: 0.8013 (tp)
REVERT: B  186 TRP cc_start: 0.6487 (p-90) cc_final: 0.6038 (p-90)
REVERT: B  279 MET cc_start: 0.8064 (mmm) cc_final: 0.7638 (mmt)
REVERT: B  504 ARG cc_start: 0.7378 (mmt90) cc_final: 0.7019 (mmm160)
REVERT: B  515 MET cc_start: 0.7421 (tmm) cc_final: 0.6904 (tmm)
REVERT: B  629 VAL cc_start: 0.8540 (t) cc_final: 0.8306 (t)
  outliers start: 13
  outliers final: 5
  residues processed: 154
  average time/residue: 0.2769
  time to fit residues: 63.5323
Evaluate side-chains
  146 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 141
  time to evaluate  : 1.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   10 THR
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  283 LEU
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 59 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 141 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   chunk 97 optimal weight:    0.7980
   chunk 62 optimal weight:    1.9990
   chunk 98 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   chunk 10 optimal weight:    2.9990
   chunk 90 optimal weight:   20.0000
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.143672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.108610 restraints weight = 14435.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 1.37
r_work: 0.3121 rms_B_bonded: 2.04 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 3.38 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.1383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11184  Z= 0.123
  Angle     :  0.522   7.394  15177  Z= 0.266
  Chirality :  0.040   0.155   1807
  Planarity :  0.004   0.045   1905
  Dihedral  :  9.832  59.983   1714
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 11.48 %
    Favored  : 87.01 %
  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:  0.57 (0.22), residues: 1433
  helix:  1.52 (0.17), residues: 874
  sheet: -1.25 (0.51), residues: 97
  loop : -1.49 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 139 
 HIS   0.001   0.001   HIS A 451 
 PHE   0.010   0.001   PHE B 360 
 TYR   0.028   0.002   TYR A 381 
 ARG   0.002   0.000   ARG A 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03786 (  690)
  hydrogen bonds       : angle       4.70064 ( 2031)
  covalent geometry    : bond        0.00271 (11184)
  covalent geometry    : angle       0.52168 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 144
  time to evaluate  : 1.340 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8491 (mt) cc_final: 0.8198 (mt)
REVERT: A  365 LEU cc_start: 0.8251 (tp) cc_final: 0.8049 (tp)
REVERT: C  141 ILE cc_start: 0.8866 (OUTLIER) cc_final: 0.8577 (mp)
REVERT: B  186 TRP cc_start: 0.6492 (p-90) cc_final: 0.5435 (p-90)
REVERT: B  279 MET cc_start: 0.7998 (mmm) cc_final: 0.7581 (mmt)
REVERT: B  393 ILE cc_start: 0.6771 (mm) cc_final: 0.6554 (mm)
REVERT: B  471 THR cc_start: 0.7275 (m) cc_final: 0.6917 (p)
REVERT: B  504 ARG cc_start: 0.7399 (mmt90) cc_final: 0.6997 (mmm160)
REVERT: B  515 MET cc_start: 0.7468 (tmm) cc_final: 0.6947 (tmm)
REVERT: B  629 VAL cc_start: 0.8485 (t) cc_final: 0.8221 (t)
  outliers start: 17
  outliers final: 7
  residues processed: 153
  average time/residue: 0.2879
  time to fit residues: 66.6038
Evaluate side-chains
  143 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 1.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 72 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   chunk 132 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   chunk 88 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.2786

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.142375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.107378 restraints weight = 14428.552|
|-----------------------------------------------------------------------------|
r_work (start): 0.3148 rms_B_bonded: 1.35
r_work: 0.3055 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.2947 rms_B_bonded: 3.25 restraints_weight: 0.2500
r_work (final): 0.2947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11184  Z= 0.136
  Angle     :  0.538   7.791  15177  Z= 0.273
  Chirality :  0.041   0.187   1807
  Planarity :  0.004   0.043   1905
  Dihedral  :  9.604  58.589   1714
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 12.54 %
    Favored  : 85.87 %
  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:  0.58 (0.22), residues: 1433
  helix:  1.53 (0.17), residues: 872
  sheet: -1.31 (0.50), residues: 99
  loop : -1.46 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  32 
 HIS   0.002   0.001   HIS B 404 
 PHE   0.013   0.001   PHE B 360 
 TYR   0.028   0.002   TYR A 381 
 ARG   0.003   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03915 (  690)
  hydrogen bonds       : angle       4.69308 ( 2031)
  covalent geometry    : bond        0.00306 (11184)
  covalent geometry    : angle       0.53756 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 140
  time to evaluate  : 1.649 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8504 (mt) cc_final: 0.8211 (mt)
REVERT: A  405 LEU cc_start: 0.8251 (mt) cc_final: 0.8009 (mt)
REVERT: C    1 MET cc_start: 0.5108 (mtm) cc_final: 0.4530 (mtt)
REVERT: C  141 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8530 (mp)
REVERT: B  186 TRP cc_start: 0.6478 (p-90) cc_final: 0.5420 (p-90)
REVERT: B  279 MET cc_start: 0.7842 (mmm) cc_final: 0.7481 (mmt)
REVERT: B  471 THR cc_start: 0.7258 (m) cc_final: 0.7030 (p)
REVERT: B  504 ARG cc_start: 0.7382 (mmt90) cc_final: 0.6961 (mmm160)
REVERT: B  515 MET cc_start: 0.7494 (tmm) cc_final: 0.6976 (tmm)
REVERT: B  629 VAL cc_start: 0.8534 (t) cc_final: 0.8243 (t)
  outliers start: 18
  outliers final: 8
  residues processed: 151
  average time/residue: 0.3189
  time to fit residues: 74.0688
Evaluate side-chains
  145 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 2.693 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 110 optimal weight:    6.9990
   chunk 115 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0170
   chunk 15 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 118 optimal weight:    0.3980
   chunk 139 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 109 optimal weight:    1.9990
   overall best weight:    0.8420

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 GLN
B  80 ASN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS
B 653 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.143230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.108564 restraints weight = 14557.785|
|-----------------------------------------------------------------------------|
r_work (start): 0.3196 rms_B_bonded: 1.35
r_work: 0.3101 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2992 rms_B_bonded: 3.33 restraints_weight: 0.2500
r_work (final): 0.2992
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11184  Z= 0.116
  Angle     :  0.520   7.485  15177  Z= 0.264
  Chirality :  0.040   0.159   1807
  Planarity :  0.004   0.041   1905
  Dihedral  :  9.382  57.546   1714
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 13.60 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.22), residues: 1433
  helix:  1.63 (0.17), residues: 874
  sheet: -1.27 (0.54), residues: 84
  loop : -1.41 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B  71 
 HIS   0.001   0.000   HIS A  85 
 PHE   0.013   0.001   PHE B 360 
 TYR   0.025   0.002   TYR A 381 
 ARG   0.002   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03696 (  690)
  hydrogen bonds       : angle       4.61709 ( 2031)
  covalent geometry    : bond        0.00254 (11184)
  covalent geometry    : angle       0.51976 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 1.518 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8493 (mt) cc_final: 0.8192 (mt)
REVERT: A   33 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7648 (m-30)
REVERT: A  363 MET cc_start: 0.8514 (ttm) cc_final: 0.8248 (ttm)
REVERT: C    1 MET cc_start: 0.5071 (mtm) cc_final: 0.4475 (mtt)
REVERT: C  141 ILE cc_start: 0.8856 (OUTLIER) cc_final: 0.8568 (mp)
REVERT: B   51 ILE cc_start: 0.8091 (mm) cc_final: 0.7781 (mm)
REVERT: B  186 TRP cc_start: 0.6445 (p-90) cc_final: 0.5386 (p-90)
REVERT: B  504 ARG cc_start: 0.7401 (mmt90) cc_final: 0.6968 (mmm160)
REVERT: B  515 MET cc_start: 0.7503 (tmm) cc_final: 0.6963 (tmm)
REVERT: B  629 VAL cc_start: 0.8513 (t) cc_final: 0.8191 (t)
  outliers start: 15
  outliers final: 10
  residues processed: 151
  average time/residue: 0.2699
  time to fit residues: 62.2008
Evaluate side-chains
  148 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   33 ASP
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 71 optimal weight:   10.0000
   chunk 66 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 6 optimal weight:    1.9990
   chunk 119 optimal weight:    6.9990
   chunk 26 optimal weight:    0.6980
   chunk 94 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 58 optimal weight:    0.3980
   chunk 97 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.6186

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 ASN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS
B 653 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.137712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.102056 restraints weight = 14890.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 1.40
r_work: 0.3026 rms_B_bonded: 2.09 restraints_weight: 0.5000
r_work: 0.2913 rms_B_bonded: 3.46 restraints_weight: 0.2500
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  11184  Z= 0.155
  Angle     :  0.566   8.405  15177  Z= 0.285
  Chirality :  0.041   0.162   1807
  Planarity :  0.004   0.043   1905
  Dihedral  :  9.472  57.529   1714
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 15.02 %
    Favored  : 83.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.22), residues: 1433
  helix:  1.53 (0.17), residues: 873
  sheet: -1.15 (0.54), residues: 82
  loop : -1.43 (0.26), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 655 
 HIS   0.002   0.001   HIS A  85 
 PHE   0.016   0.001   PHE B 360 
 TYR   0.028   0.002   TYR A 381 
 ARG   0.002   0.000   ARG A 326 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04055 (  690)
  hydrogen bonds       : angle       4.70538 ( 2031)
  covalent geometry    : bond        0.00359 (11184)
  covalent geometry    : angle       0.56550 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 1.311 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8504 (mt) cc_final: 0.8225 (mt)
REVERT: A  363 MET cc_start: 0.8601 (ttm) cc_final: 0.8344 (ttm)
REVERT: C    1 MET cc_start: 0.5095 (mtm) cc_final: 0.4499 (mtt)
REVERT: C  141 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8571 (mp)
REVERT: D   25 ASN cc_start: 0.6400 (m-40) cc_final: 0.6192 (m110)
REVERT: B  186 TRP cc_start: 0.6433 (p-90) cc_final: 0.5359 (p-90)
REVERT: B  279 MET cc_start: 0.7948 (mmm) cc_final: 0.7664 (mmm)
REVERT: B  504 ARG cc_start: 0.7377 (mmt90) cc_final: 0.6948 (mmm160)
REVERT: B  629 VAL cc_start: 0.8547 (t) cc_final: 0.8191 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 146
  average time/residue: 0.2044
  time to fit residues: 44.7844
Evaluate side-chains
  146 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue   60 THR
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain B residue  142 CYS
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  558 LEU
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 18 optimal weight:    0.9990
   chunk 136 optimal weight:    0.7980
   chunk 89 optimal weight:   10.0000
   chunk 68 optimal weight:    0.0370
   chunk 56 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0980
   chunk 7 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0370
   chunk 5 optimal weight:    6.9990
   overall best weight:    0.3536

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

Flipped N/Q/H residues before XYZ refinement:
B  80 ASN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.144654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.110017 restraints weight = 14340.751|
|-----------------------------------------------------------------------------|
r_work (start): 0.3241 rms_B_bonded: 1.34
r_work: 0.3148 rms_B_bonded: 2.00 restraints_weight: 0.5000
r_work: 0.3040 rms_B_bonded: 3.32 restraints_weight: 0.2500
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.1745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  11184  Z= 0.105
  Angle     :  0.523  10.026  15177  Z= 0.262
  Chirality :  0.039   0.150   1807
  Planarity :  0.003   0.040   1905
  Dihedral  :  9.110  59.591   1714
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 15.81 %
    Favored  : 83.04 %
  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 (0.22), residues: 1433
  helix:  1.70 (0.17), residues: 872
  sheet: -1.19 (0.53), residues: 84
  loop : -1.35 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  32 
 HIS   0.001   0.000   HIS B 371 
 PHE   0.017   0.001   PHE B 360 
 TYR   0.024   0.001   TYR A 381 
 ARG   0.003   0.000   ARG C   5 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03498 (  690)
  hydrogen bonds       : angle       4.54441 ( 2031)
  covalent geometry    : bond        0.00220 (11184)
  covalent geometry    : angle       0.52278 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 146
  time to evaluate  : 1.252 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8486 (mt) cc_final: 0.8201 (mt)
REVERT: A  363 MET cc_start: 0.8517 (ttm) cc_final: 0.8251 (ttm)
REVERT: C  141 ILE cc_start: 0.8840 (OUTLIER) cc_final: 0.8521 (mp)
REVERT: B   51 ILE cc_start: 0.8084 (mm) cc_final: 0.7787 (mm)
REVERT: B  186 TRP cc_start: 0.6505 (p-90) cc_final: 0.5404 (p-90)
REVERT: B  279 MET cc_start: 0.7879 (mmm) cc_final: 0.7603 (mmm)
REVERT: B  504 ARG cc_start: 0.7401 (mmt90) cc_final: 0.7054 (mmm160)
REVERT: B  515 MET cc_start: 0.7632 (tmm) cc_final: 0.7206 (tmm)
REVERT: B  629 VAL cc_start: 0.8491 (t) cc_final: 0.8127 (t)
  outliers start: 13
  outliers final: 6
  residues processed: 154
  average time/residue: 0.2046
  time to fit residues: 47.7329
Evaluate side-chains
  144 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 59 optimal weight:   10.0000
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    0.9980
   chunk 90 optimal weight:   20.0000
   chunk 22 optimal weight:    2.9990
   chunk 10 optimal weight:    4.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  80 ASN
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.142269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.107242 restraints weight = 14638.393|
|-----------------------------------------------------------------------------|
r_work (start): 0.3184 rms_B_bonded: 1.35
r_work: 0.3090 rms_B_bonded: 2.01 restraints_weight: 0.5000
r_work: 0.2980 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11184  Z= 0.130
  Angle     :  0.546   9.600  15177  Z= 0.274
  Chirality :  0.040   0.149   1807
  Planarity :  0.004   0.041   1905
  Dihedral  :  9.121  59.872   1714
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 15.81 %
    Favored  : 83.22 %
  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:  0.80 (0.22), residues: 1433
  helix:  1.68 (0.17), residues: 870
  sheet: -1.17 (0.52), residues: 86
  loop : -1.30 (0.26), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  33 
 HIS   0.002   0.001   HIS A  85 
 PHE   0.018   0.001   PHE B 360 
 TYR   0.027   0.002   TYR A 381 
 ARG   0.002   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03797 (  690)
  hydrogen bonds       : angle       4.58356 ( 2031)
  covalent geometry    : bond        0.00293 (11184)
  covalent geometry    : angle       0.54577 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 136
  time to evaluate  : 1.201 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8499 (mt) cc_final: 0.8209 (mt)
REVERT: A  360 MET cc_start: 0.8478 (ttm) cc_final: 0.8268 (ttp)
REVERT: A  363 MET cc_start: 0.8588 (ttm) cc_final: 0.8323 (ttm)
REVERT: C  141 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8610 (mp)
REVERT: D   25 ASN cc_start: 0.6332 (m-40) cc_final: 0.6085 (m110)
REVERT: B   51 ILE cc_start: 0.8133 (mm) cc_final: 0.7808 (mm)
REVERT: B  186 TRP cc_start: 0.6385 (p-90) cc_final: 0.5354 (p-90)
REVERT: B  279 MET cc_start: 0.7910 (mmm) cc_final: 0.7602 (mmm)
REVERT: B  515 MET cc_start: 0.7679 (tmm) cc_final: 0.7290 (tmm)
REVERT: B  629 VAL cc_start: 0.8513 (t) cc_final: 0.8145 (t)
  outliers start: 11
  outliers final: 9
  residues processed: 142
  average time/residue: 0.1995
  time to fit residues: 42.8483
Evaluate side-chains
  142 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 132
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  387 VAL
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain B residue  465 ILE
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 40 optimal weight:    0.0970
   chunk 7 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 9 optimal weight:    4.9990
   chunk 102 optimal weight:    0.2980
   chunk 135 optimal weight:    5.9990
   chunk 134 optimal weight:    0.0670
   chunk 133 optimal weight:    3.9990
   chunk 128 optimal weight:    9.9990
   chunk 56 optimal weight:    1.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    0.4118

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

Flipped N/Q/H residues before XYZ refinement:
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 563 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.144618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.110505 restraints weight = 14392.333|
|-----------------------------------------------------------------------------|
r_work (start): 0.3237 rms_B_bonded: 1.31
r_work: 0.3145 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3037 rms_B_bonded: 3.28 restraints_weight: 0.2500
r_work (final): 0.3037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7827
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  11184  Z= 0.103
  Angle     :  0.536  11.563  15177  Z= 0.266
  Chirality :  0.039   0.157   1807
  Planarity :  0.003   0.040   1905
  Dihedral  :  8.907  59.776   1714
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 15.81 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.95 (0.22), residues: 1433
  helix:  1.83 (0.17), residues: 863
  sheet: -1.29 (0.51), residues: 92
  loop : -1.23 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C  33 
 HIS   0.001   0.000   HIS A  85 
 PHE   0.019   0.001   PHE B 360 
 TYR   0.025   0.001   TYR A 381 
 ARG   0.006   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03462 (  690)
  hydrogen bonds       : angle       4.50509 ( 2031)
  covalent geometry    : bond        0.00213 (11184)
  covalent geometry    : angle       0.53635 (15177)

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

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

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2866 Ramachandran restraints generated.
    1433 Oldfield, 0 Emsley, 1433 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 137
  time to evaluate  : 1.190 
Fit side-chains
REVERT: A   27 LEU cc_start: 0.8493 (mt) cc_final: 0.8208 (mt)
REVERT: A  363 MET cc_start: 0.8519 (ttm) cc_final: 0.8263 (ttm)
REVERT: C    1 MET cc_start: 0.5036 (mtm) cc_final: 0.4588 (mtt)
REVERT: C  141 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8560 (mp)
REVERT: C  170 TYR cc_start: 0.7710 (p90) cc_final: 0.7506 (p90)
REVERT: B   51 ILE cc_start: 0.8071 (mm) cc_final: 0.7774 (mm)
REVERT: B  186 TRP cc_start: 0.6460 (p-90) cc_final: 0.5405 (p-90)
REVERT: B  515 MET cc_start: 0.7580 (tmm) cc_final: 0.7172 (tmm)
REVERT: B  629 VAL cc_start: 0.8489 (t) cc_final: 0.8125 (t)
  outliers start: 12
  outliers final: 8
  residues processed: 145
  average time/residue: 0.2168
  time to fit residues: 48.2269
Evaluate side-chains
  141 residues out of total 1132 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 132
  time to evaluate  : 1.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   66 ILE
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain C residue   12 ILE
Chi-restraints excluded: chain C residue  141 ILE
Chi-restraints excluded: chain D residue   14 LEU
Chi-restraints excluded: chain B residue  168 GLU
Chi-restraints excluded: chain B residue  570 MET
Chi-restraints excluded: chain B residue  618 LEU
Chi-restraints excluded: chain B residue  644 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 7 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 134 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 98 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   chunk 138 optimal weight:    0.0570
   chunk 49 optimal weight:    3.9990
   chunk 75 optimal weight:    2.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
** B 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 563 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.143630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109247 restraints weight = 14398.745|
|-----------------------------------------------------------------------------|
r_work (start): 0.3228 rms_B_bonded: 1.32
r_work: 0.3135 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.3028 rms_B_bonded: 3.29 restraints_weight: 0.2500
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1832

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  11184  Z= 0.112
  Angle     :  0.541  10.201  15177  Z= 0.269
  Chirality :  0.040   0.160   1807
  Planarity :  0.004   0.041   1905
  Dihedral  :  8.864  59.963   1714
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 9.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 16.08 %
    Favored  : 82.95 %
  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:  0.95 (0.22), residues: 1433
  helix:  1.80 (0.17), residues: 863
  sheet: -1.04 (0.53), residues: 86
  loop : -1.24 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C  33 
 HIS   0.002   0.000   HIS B 563 
 PHE   0.010   0.001   PHE B 578 
 TYR   0.025   0.001   TYR A 381 
 ARG   0.006   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03579 (  690)
  hydrogen bonds       : angle       4.51135 ( 2031)
  covalent geometry    : bond        0.00243 (11184)
  covalent geometry    : angle       0.54134 (15177)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6161.04 seconds
wall clock time: 110 minutes 20.22 seconds (6620.22 seconds total)