Starting phenix.real_space_refine
on Wed Jul 30 12:05:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zri_14915/07_2025/7zri_14915.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zri_14915/07_2025/7zri_14915.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2025/7zri_14915.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2025/7zri_14915.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2025/7zri_14915.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zri_14915/07_2025/7zri_14915.cif"
  }
  resolution = 3.5
  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=   0.007
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 1040 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       7      8.98       5
     P       5      5.49       5
     S      62      5.16       5
     C    7123      2.51       5
     N    1822      2.21       5
     O    1995      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 11014
  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: 5021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 676, 5021
          Classifications: {'peptide': 676}
          Link IDs: {'PTRANS': 26, 'TRANS': 649}
    Chain: "A"
      Number of atoms: 105
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 105
          Unusual residues: {'  K': 5, 'CDL': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
    Chain: "B"
      Number of atoms: 102
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 102
          Unusual residues: {'  K': 2, 'CDL': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 6.85, per 1000 atoms: 0.62
  Number of scatterers: 11014
  At special positions: 0
  Unit cell: (104.236, 110.308, 155.848, 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       7     19.00
     S      62     16.00
     P       5     15.00
     O    1995      8.00
     N    1822      7.00
     C    7123      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: 2.60
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2638

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      62.4% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.06
  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 39 through 51
      removed outlier: 3.586A  pdb=" N   VAL A  45 " --> pdb=" O   GLY A  41 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 58 through 83
    Processing helix  chain 'A' and resid 98 through 111
    Processing helix  chain 'A' and resid 125 through 132
      removed outlier: 3.584A  pdb=" N   GLN A 129 " --> pdb=" O   SER A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 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 193
      removed outlier: 4.149A  pdb=" N   LEU A 184 " --> pdb=" O   PRO A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 4.027A  pdb=" N   GLN A 222 " --> pdb=" O   PRO A 218 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ILE A 225 " --> pdb=" O   SER A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 274
      removed outlier: 4.527A  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 277 through 305
      removed outlier: 4.078A  pdb=" N   LEU A 283 " --> pdb=" O   GLN A 279 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ILE A 290 " --> pdb=" O   ALA A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 313
      removed outlier: 4.432A  pdb=" N   ALA A 311 " --> pdb=" O   PRO A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 342
    Processing helix  chain 'A' and resid 350 through 354
    Processing helix  chain 'A' and resid 355 through 368
      removed outlier: 3.737A  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 379 through 399
      removed outlier: 3.718A  pdb=" N   PHE A 386 " --> pdb=" O   GLY A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 435
      removed outlier: 3.754A  pdb=" N   LEU A 416 " --> pdb=" O   ARG A 412 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   THR A 424 " --> pdb=" O   ALA A 420 " (cutoff:3.500A)
      Proline residue:  A 425  - end of helix
      removed outlier: 3.726A  pdb=" N   ALA A 433 " --> pdb=" O   LEU A 429 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'A' and resid 449 through 465
      removed outlier: 4.286A  pdb=" N   PHE A 453 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 495
    Processing helix  chain 'A' and resid 496 through 508
    Processing helix  chain 'A' and resid 524 through 540
    Processing helix  chain 'A' and resid 543 through 549
      removed outlier: 3.954A  pdb=" N   LEU A 549 " --> pdb=" O   PRO A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 557
    Processing helix  chain 'C' and resid 3 through 20
    Processing helix  chain 'C' and resid 21 through 34
    Processing helix  chain 'C' and resid 34 through 39
    Processing helix  chain 'C' and resid 91 through 109
    Processing helix  chain 'C' and resid 133 through 138
    Processing helix  chain 'C' and resid 140 through 149
    Processing helix  chain 'C' and resid 151 through 162
    Processing helix  chain 'C' and resid 177 through 190
    Processing helix  chain 'D' and resid 5 through 25
      removed outlier: 3.903A  pdb=" N   LEU D  10 " --> pdb=" O   ILE D   6 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 23
      removed outlier: 3.906A  pdb=" N   GLN B  16 " --> pdb=" O   THR B  12 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   ALA B  17 " --> pdb=" O   LEU B  13 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ALA B  21 " --> pdb=" O   ALA B  17 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LYS B  23 " --> pdb=" O   LYS B  19 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 26
      No H-bonds generated for 'chain 'B' and resid 24 through 26'
    Processing helix  chain 'B' and resid 33 through 55
    Processing helix  chain 'B' and resid 61 through 98
      removed outlier: 3.563A  pdb=" N   SER B  65 " --> pdb=" O   ASN B  61 " (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 237
    Processing helix  chain 'B' and resid 239 through 247
      removed outlier: 3.972A  pdb=" N   TRP B 245 " --> pdb=" O   PRO B 241 " (cutoff:3.500A)
      removed outlier: 3.838A  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 264 through 269
    Processing helix  chain 'B' and resid 270 through 284
    Processing helix  chain 'B' and resid 291 through 299
      removed outlier: 3.887A  pdb=" N   VAL B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 341
    Processing helix  chain 'B' and resid 346 through 361
    Processing helix  chain 'B' and resid 367 through 371
      removed outlier: 4.221A  pdb=" N   HIS B 371 " --> pdb=" O   GLN B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 397 through 409
    Processing helix  chain 'B' and resid 413 through 427
    Processing helix  chain 'B' and resid 453 through 464
    Processing helix  chain 'B' and resid 474 through 486
      removed outlier: 3.673A  pdb=" N   GLU B 484 " --> pdb=" O   ALA B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 495 through 510
      removed outlier: 3.725A  pdb=" N   GLY B 510 " --> pdb=" O   TYR B 506 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 522 through 528
    Processing helix  chain 'B' and resid 539 through 546
    Processing helix  chain 'B' and resid 556 through 582
      removed outlier: 4.205A  pdb=" N   GLU B 560 " --> pdb=" O   THR B 556 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   LEU B 569 " --> pdb=" O   GLY B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 582 through 595
      removed outlier: 4.098A  pdb=" N   LYS B 586 " --> pdb=" O   ASN B 582 " (cutoff:3.500A)
      Proline residue:  B 592  - end of helix
      removed outlier: 3.685A  pdb=" N   PHE B 595 " --> pdb=" O   ILE B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 599 through 606
      removed outlier: 4.013A  pdb=" N   ALA B 604 " --> pdb=" O   GLN B 601 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ASN B 606 " --> pdb=" O   ASN B 603 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 612 through 638
      removed outlier: 4.008A  pdb=" N   ILE B 628 " --> pdb=" O   ASN B 624 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   VAL B 629 " --> pdb=" O   ALA B 625 " (cutoff:3.500A)
      Proline residue:  B 633  - end of helix
    Processing helix  chain 'B' and resid 648 through 679
      removed outlier: 4.370A  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
    Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45
      removed outlier: 6.086A  pdb=" N   ILE C  43 " --> pdb=" O   ARG C  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 163 through 164
      removed outlier: 3.789A  pdb=" N   VAL C 175 " --> pdb=" O   GLN C 164 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 134
    Processing sheet with id=AA6, first strand: chain 'B' and resid 138 through 140
      removed outlier: 3.522A  pdb=" N   ASP B 138 " --> pdb=" O   ILE B 182 " (cutoff:3.500A)
      removed outlier: 4.338A  pdb=" N   THR B 180 " --> pdb=" O   ILE B 140 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B 165 " --> pdb=" O   VAL B 153 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289
      removed outlier: 6.006A  pdb=" N   ALA B 532 " --> pdb=" O   MET B 548 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   ASP B 550 " --> pdb=" O   ALA B 532 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ALA B 534 " --> pdb=" O   ASP B 550 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 513 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 306 " --> pdb=" O   VAL B 468 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ASP B 489 " --> pdb=" O   THR B 467 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 317 through 323
      removed outlier: 7.735A  pdb=" N   ALA B 444 " --> pdb=" O   SER B 320 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   PHE B 322 " --> pdb=" O   VAL B 442 " (cutoff:3.500A)
      removed outlier: 8.171A  pdb=" N   VAL B 442 " --> pdb=" O   PHE B 322 " (cutoff:3.500A)
      removed outlier: 5.023A  pdb=" N   VAL B 439 " --> pdb=" O   GLU B 435 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   GLU B 435 " --> pdb=" O   VAL B 439 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY B 441 " --> pdb=" O   VAL B 433 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   VAL B 432 " --> pdb=" O   GLY B 396 " (cutoff:3.500A)
      removed outlier: 4.330A  pdb=" N   GLY B 396 " --> pdb=" O   VAL B 432 " (cutoff:3.500A)
      removed outlier: 3.839A  pdb=" N   VAL B 434 " --> pdb=" O   ARG B 394 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ARG B 394 " --> pdb=" O   VAL B 434 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   ILE B 393 " --> pdb=" O   ILE B 386 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   THR B 378 " --> pdb=" O   MET B 383 " (cutoff:3.500A)
      removed outlier: 5.147A  pdb=" N   GLY B 385 " --> pdb=" O   PRO B 376 " (cutoff:3.500A)

    654 hydrogen bonds defined for protein.
    1923 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: 3.38

  Time building geometry restraints manager: 3.08 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: 1774
        1.31 -     1.43: 2711
        1.43 -     1.56: 6596
        1.56 -     1.69: 12
        1.69 -     1.81: 112
  Bond restraints: 11205
  Sorted by residual:
  bond pdb=" CB7 CDL B 702 "
       pdb=" OB8 CDL B 702 "
    ideal  model  delta    sigma   weight residual
    1.334  1.423 -0.089 1.10e-02 8.26e+03 6.49e+01
  bond pdb=" CB7 CDL A 606 "
       pdb=" OB8 CDL A 606 "
    ideal  model  delta    sigma   weight residual
    1.334  1.421 -0.087 1.10e-02 8.26e+03 6.32e+01
  bond pdb=" CA7 CDL A 606 "
       pdb=" OA8 CDL A 606 "
    ideal  model  delta    sigma   weight residual
    1.334  1.421 -0.087 1.10e-02 8.26e+03 6.21e+01
  bond pdb=" CA7 CDL B 702 "
       pdb=" OA8 CDL B 702 "
    ideal  model  delta    sigma   weight residual
    1.334  1.417 -0.083 1.10e-02 8.26e+03 5.66e+01
  bond pdb=" OB2 CDL A 606 "
       pdb=" PB2 CDL A 606 "
    ideal  model  delta    sigma   weight residual
    1.579  1.668 -0.089 1.50e-02 4.44e+03 3.49e+01
  ... (remaining 11200 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.96: 14582
        1.96 -     3.92: 408
        3.92 -     5.88: 168
        5.88 -     7.84: 32
        7.84 -     9.80: 14
  Bond angle restraints: 15204
  Sorted by residual:
  angle pdb=" C11 CDL B 702 "
        pdb=" CA5 CDL B 702 "
        pdb=" OA6 CDL B 702 "
      ideal   model   delta    sigma   weight residual
     111.33  121.01   -9.68 1.32e+00 5.72e-01 5.36e+01
  angle pdb=" C51 CDL B 702 "
        pdb=" CB5 CDL B 702 "
        pdb=" OB6 CDL B 702 "
      ideal   model   delta    sigma   weight residual
     111.33  120.39   -9.06 1.32e+00 5.72e-01 4.69e+01
  angle pdb=" C11 CDL A 606 "
        pdb=" CA5 CDL A 606 "
        pdb=" OA6 CDL A 606 "
      ideal   model   delta    sigma   weight residual
     111.33  120.17   -8.84 1.32e+00 5.72e-01 4.47e+01
  angle pdb=" C51 CDL A 606 "
        pdb=" CB5 CDL A 606 "
        pdb=" OB6 CDL A 606 "
      ideal   model   delta    sigma   weight residual
     111.33  119.99   -8.66 1.32e+00 5.72e-01 4.29e+01
  angle pdb=" C31 CDL A 606 "
        pdb=" CA7 CDL A 606 "
        pdb=" OA8 CDL A 606 "
      ideal   model   delta    sigma   weight residual
     111.64  121.44   -9.80 1.65e+00 3.69e-01 3.54e+01
  ... (remaining 15199 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.81: 5834
       16.81 -    33.63: 661
       33.63 -    50.44: 170
       50.44 -    67.25: 58
       67.25 -    84.06: 12
  Dihedral angle restraints: 6735
    sinusoidal: 2629
      harmonic: 4106
  Sorted by residual:
  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  153.10   26.90     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  THR B 236 "
           pdb=" C   THR B 236 "
           pdb=" N   ALA B 237 "
           pdb=" CA  ALA B 237 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.96   23.04     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  ALA B 106 "
           pdb=" C   ALA B 106 "
           pdb=" N   ARG B 107 "
           pdb=" CA  ARG B 107 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.34  -19.66     0      5.00e+00 4.00e-02 1.55e+01
  ... (remaining 6732 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.042: 1231
       0.042 -    0.084: 418
       0.084 -    0.127: 143
       0.127 -    0.169: 14
       0.169 -    0.211: 5
  Chirality restraints: 1811
  Sorted by residual:
  chirality pdb=" CB  THR B 516 "
            pdb=" CA  THR B 516 "
            pdb=" OG1 THR B 516 "
            pdb=" CG2 THR B 516 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CA  THR A 424 "
            pdb=" N   THR A 424 "
            pdb=" C   THR A 424 "
            pdb=" CB  THR A 424 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.32    0.21 2.00e-01 2.50e+01 1.09e+00
  chirality pdb=" CB  ILE A  34 "
            pdb=" CA  ILE A  34 "
            pdb=" CG1 ILE A  34 "
            pdb=" CG2 ILE A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.74e-01
  ... (remaining 1808 not shown)

  Planarity restraints: 1909
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 215 "   -0.042 5.00e-02 4.00e+02   6.43e-02 6.61e+00
        pdb=" N   PRO B 216 "    0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B 216 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 216 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS B 586 "   -0.012 2.00e-02 2.50e+03   2.50e-02 6.27e+00
        pdb=" C   LYS B 586 "    0.043 2.00e-02 2.50e+03
        pdb=" O   LYS B 586 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR B 587 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 126 "    0.009 2.00e-02 2.50e+03   1.59e-02 5.07e+00
        pdb=" CG  TYR A 126 "   -0.033 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 126 "    0.024 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 126 "    0.001 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 126 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 126 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 126 "    0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR A 126 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 1906 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.78: 2429
        2.78 -     3.37: 12346
        3.37 -     3.96: 21390
        3.96 -     4.55: 29872
        4.55 -     5.14: 44616
  Nonbonded interactions: 110653
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 107 "
            pdb=" OG1 THR A 111 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OG1 THR C  72 "
            pdb=" O   MET C  75 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   SER A 119 "
            pdb=" OG1 THR A 123 "
     model   vdw
     2.274 3.040
  nonbonded pdb=" O   THR A 248 "
            pdb=" OG1 THR A 251 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   LEU C  14 "
            pdb=" OG1 THR C  18 "
     model   vdw
     2.302 3.040
  ... (remaining 110648 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:             3.970
  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:             0.020
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     27.060
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.850
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8010
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   0.089  11205  Z= 0.338
  Angle     :  0.919   9.799  15204  Z= 0.465
  Chirality :  0.047   0.211   1811
  Planarity :  0.006   0.064   1909
  Dihedral  : 16.165  84.064   4097
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  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: -1.22 (0.21), residues: 1439
  helix: -0.00 (0.17), residues: 857
  sheet: -1.69 (0.59), residues: 77
  loop : -1.98 (0.25), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C  32 
 HIS   0.002   0.000   HIS A 242 
 PHE   0.029   0.002   PHE A 260 
 TYR   0.033   0.002   TYR A 126 
 ARG   0.005   0.000   ARG A 172 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10685 (  654)
  hydrogen bonds       : angle       5.29085 ( 1923)
  covalent geometry    : bond        0.00588 (11205)
  covalent geometry    : angle       0.91908 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 1.162 
Fit side-chains
REVERT: A  363 MET cc_start: 0.9147 (ttm) cc_final: 0.8814 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.2021
  time to fit residues: 43.7361
Evaluate side-chains
  116 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.157 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 108 optimal weight:   20.0000
   chunk 60 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 57 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 129 optimal weight:   20.0000
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
A  61 GLN
C 165 GLN
** B 338 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 = 0.3801 r_free = 0.3801 target = 0.146460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.106079 restraints weight = 15576.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.106357 restraints weight = 16811.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.107597 restraints weight = 11415.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.1134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  11205  Z= 0.224
  Angle     :  0.620   6.362  15204  Z= 0.317
  Chirality :  0.042   0.226   1811
  Planarity :  0.004   0.055   1909
  Dihedral  : 11.492  74.721   1715
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.24 %
    Favored  : 95.76 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  9.52 %
    Favored  : 89.60 %
  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: -0.55 (0.22), residues: 1439
  helix:  0.64 (0.18), residues: 869
  sheet: -1.68 (0.54), residues: 87
  loop : -1.92 (0.26), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C  32 
 HIS   0.005   0.001   HIS A 242 
 PHE   0.016   0.002   PHE A 354 
 TYR   0.025   0.002   TYR A 381 
 ARG   0.003   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04054 (  654)
  hydrogen bonds       : angle       4.65624 ( 1923)
  covalent geometry    : bond        0.00532 (11205)
  covalent geometry    : angle       0.61990 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 1.169 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7269 (m-10) cc_final: 0.6971 (m-10)
REVERT: B  469 MET cc_start: 0.7689 (tmm) cc_final: 0.7245 (ttt)
  outliers start: 10
  outliers final: 7
  residues processed: 131
  average time/residue: 0.2101
  time to fit residues: 41.5657
Evaluate side-chains
  123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 1.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain C residue    8 LEU
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  614 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 15 optimal weight:    0.7980
   chunk 23 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   chunk 74 optimal weight:    0.1980
   chunk 61 optimal weight:    3.9990
   chunk 107 optimal weight:    8.9990
   chunk 101 optimal weight:    0.7980
   chunk 20 optimal weight:    4.9990
   chunk 42 optimal weight:    3.9990
   chunk 103 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
C 154 GLN
** B 338 GLN ** 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 = 0.3813 r_free = 0.3813 target = 0.147564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.107434 restraints weight = 15769.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.107405 restraints weight = 16079.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.108726 restraints weight = 11044.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8152
moved from start:          0.1251

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  11205  Z= 0.143
  Angle     :  0.550   7.933  15204  Z= 0.277
  Chirality :  0.040   0.233   1811
  Planarity :  0.004   0.056   1909
  Dihedral  : 10.676  74.085   1715
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.78 %
    Favored  : 86.17 %
  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: -0.12 (0.22), residues: 1439
  helix:  0.99 (0.18), residues: 869
  sheet: -1.75 (0.53), residues: 84
  loop : -1.71 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  32 
 HIS   0.003   0.001   HIS A 242 
 PHE   0.010   0.001   PHE A 527 
 TYR   0.021   0.001   TYR A 381 
 ARG   0.002   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  654)
  hydrogen bonds       : angle       4.47128 ( 1923)
  covalent geometry    : bond        0.00334 (11205)
  covalent geometry    : angle       0.54984 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 1.194 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7274 (m-10) cc_final: 0.6772 (m-10)
REVERT: C  130 ASN cc_start: 0.8381 (t0) cc_final: 0.8077 (t0)
REVERT: B  469 MET cc_start: 0.7618 (tmm) cc_final: 0.7298 (ttt)
  outliers start: 12
  outliers final: 11
  residues processed: 134
  average time/residue: 0.1980
  time to fit residues: 40.7332
Evaluate side-chains
  126 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 115
  time to evaluate  : 1.805 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  154 GLN
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  516 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    0.6980
   chunk 110 optimal weight:    4.9990
   chunk 86 optimal weight:    0.2980
   chunk 97 optimal weight:    2.9990
   chunk 99 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 78 optimal weight:    9.9990
   chunk 70 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 104 optimal weight:    5.9990
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
C 154 GLN
** B 338 GLN ** 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 = 0.3812 r_free = 0.3812 target = 0.147526 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.107551 restraints weight = 15650.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.107543 restraints weight = 16749.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.109099 restraints weight = 10869.447|
|-----------------------------------------------------------------------------|
r_work (final): 0.3294
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8148
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11205  Z= 0.142
  Angle     :  0.544   8.670  15204  Z= 0.273
  Chirality :  0.040   0.137   1811
  Planarity :  0.004   0.055   1909
  Dihedral  : 10.183  74.346   1715
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.10 %
    Favored  : 84.58 %
  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:  0.06 (0.22), residues: 1439
  helix:  1.14 (0.18), residues: 870
  sheet: -1.78 (0.53), residues: 87
  loop : -1.64 (0.27), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  32 
 HIS   0.002   0.000   HIS A 242 
 PHE   0.010   0.001   PHE A 527 
 TYR   0.020   0.001   TYR A 381 
 ARG   0.002   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03563 (  654)
  hydrogen bonds       : angle       4.37990 ( 1923)
  covalent geometry    : bond        0.00332 (11205)
  covalent geometry    : angle       0.54369 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 1.192 
Fit side-chains
REVERT: A  176 TRP cc_start: 0.7343 (m-10) cc_final: 0.6842 (m-10)
REVERT: A  397 MET cc_start: 0.8740 (mmt) cc_final: 0.8365 (mmt)
REVERT: C  130 ASN cc_start: 0.8369 (t0) cc_final: 0.8069 (t0)
REVERT: C  154 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7392 (tp40)
REVERT: B  469 MET cc_start: 0.7440 (tmm) cc_final: 0.7215 (ttt)
  outliers start: 15
  outliers final: 11
  residues processed: 135
  average time/residue: 0.2056
  time to fit residues: 42.2544
Evaluate side-chains
  130 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 118
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  154 GLN
Chi-restraints excluded: chain D residue    7 THR
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue  236 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  516 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    0.0970
   chunk 79 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 39 optimal weight:    0.5980
   chunk 59 optimal weight:    0.9990
   chunk 96 optimal weight:    3.9990
   chunk 125 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 138 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0070
   overall best weight:    0.4798

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

Flipped N/Q/H residues before XYZ refinement:
C 154 GLN
** B 338 GLN ** 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 = 0.3840 r_free = 0.3840 target = 0.149970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.110365 restraints weight = 15676.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.110896 restraints weight = 16116.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.112381 restraints weight = 9961.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1433

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11205  Z= 0.101
  Angle     :  0.513   8.934  15204  Z= 0.257
  Chirality :  0.038   0.142   1811
  Planarity :  0.003   0.055   1909
  Dihedral  :  9.602  73.437   1715
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 15.42 %
    Favored  : 83.61 %
  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:  0.37 (0.23), residues: 1439
  helix:  1.40 (0.18), residues: 862
  sheet: -1.69 (0.54), residues: 84
  loop : -1.48 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  71 
 HIS   0.001   0.000   HIS A 451 
 PHE   0.009   0.001   PHE A 109 
 TYR   0.017   0.001   TYR A 381 
 ARG   0.001   0.000   ARG C  68 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03263 (  654)
  hydrogen bonds       : angle       4.22608 ( 1923)
  covalent geometry    : bond        0.00219 (11205)
  covalent geometry    : angle       0.51262 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 126
  time to evaluate  : 1.097 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7323 (m-10) cc_final: 0.6798 (m-10)
REVERT: A  352 ASP cc_start: 0.9035 (t0) cc_final: 0.8793 (t0)
REVERT: A  397 MET cc_start: 0.8728 (mmt) cc_final: 0.8359 (mmt)
REVERT: C  154 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7386 (tp40)
  outliers start: 11
  outliers final: 8
  residues processed: 136
  average time/residue: 0.2083
  time to fit residues: 42.3456
Evaluate side-chains
  123 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 114
  time to evaluate  : 1.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain C residue   34 PHE
Chi-restraints excluded: chain C residue  154 GLN
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  516 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 124 optimal weight:    9.9990
   chunk 123 optimal weight:    5.9990
   chunk 108 optimal weight:    7.9990
   chunk 130 optimal weight:    9.9990
   chunk 99 optimal weight:    0.5980
   chunk 55 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
C 154 GLN
** B 338 GLN ** 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 = 0.3843 r_free = 0.3843 target = 0.150199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.110001 restraints weight = 15724.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.110294 restraints weight = 16354.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.112139 restraints weight = 10024.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8105
moved from start:          0.1493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11205  Z= 0.112
  Angle     :  0.517   9.057  15204  Z= 0.258
  Chirality :  0.039   0.135   1811
  Planarity :  0.003   0.055   1909
  Dihedral  :  9.367  73.758   1715
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 15.95 %
    Favored  : 82.56 %
  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:  0.42 (0.23), residues: 1439
  helix:  1.43 (0.18), residues: 866
  sheet: -1.71 (0.54), residues: 84
  loop : -1.47 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 300 
 HIS   0.001   0.000   HIS A 451 
 PHE   0.010   0.001   PHE A 109 
 TYR   0.018   0.001   TYR A 381 
 ARG   0.001   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03265 (  654)
  hydrogen bonds       : angle       4.20048 ( 1923)
  covalent geometry    : bond        0.00253 (11205)
  covalent geometry    : angle       0.51726 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 117
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
REVERT: A  176 TRP cc_start: 0.7340 (m-10) cc_final: 0.6813 (m-10)
REVERT: A  352 ASP cc_start: 0.9075 (t0) cc_final: 0.8794 (t70)
REVERT: A  397 MET cc_start: 0.8734 (mmt) cc_final: 0.8384 (mmt)
REVERT: C   75 MET cc_start: 0.7035 (OUTLIER) cc_final: 0.6635 (ptt)
  outliers start: 17
  outliers final: 13
  residues processed: 131
  average time/residue: 0.2028
  time to fit residues: 40.1731
Evaluate side-chains
  128 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 1.181 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue  154 GLN
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  516 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 51 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 125 optimal weight:    5.9990
   chunk 57 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 85 optimal weight:   20.0000
   chunk 142 optimal weight:    0.6980
   chunk 66 optimal weight:    0.8980
   chunk 138 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 74 optimal weight:    0.3980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
C 135 GLN
C 154 GLN
** B 338 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 = 0.3841 r_free = 0.3841 target = 0.150141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.110036 restraints weight = 15840.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.110072 restraints weight = 16646.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.111306 restraints weight = 10772.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8114
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  11205  Z= 0.112
  Angle     :  0.519   9.225  15204  Z= 0.259
  Chirality :  0.039   0.135   1811
  Planarity :  0.003   0.054   1909
  Dihedral  :  9.145  74.021   1715
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 16.12 %
    Favored  : 82.03 %
  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:  0.49 (0.23), residues: 1439
  helix:  1.47 (0.18), residues: 866
  sheet: -1.58 (0.59), residues: 74
  loop : -1.43 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 300 
 HIS   0.001   0.000   HIS A 451 
 PHE   0.010   0.001   PHE A 109 
 TYR   0.021   0.001   TYR A 126 
 ARG   0.001   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03237 (  654)
  hydrogen bonds       : angle       4.17945 ( 1923)
  covalent geometry    : bond        0.00253 (11205)
  covalent geometry    : angle       0.51936 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 1.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  352 ASP cc_start: 0.9093 (t0) cc_final: 0.8795 (t70)
REVERT: A  397 MET cc_start: 0.8739 (mmt) cc_final: 0.8386 (mmt)
REVERT: A  446 LEU cc_start: 0.8248 (OUTLIER) cc_final: 0.7756 (tt)
REVERT: C   75 MET cc_start: 0.7063 (OUTLIER) cc_final: 0.6659 (ptt)
  outliers start: 21
  outliers final: 15
  residues processed: 138
  average time/residue: 0.2085
  time to fit residues: 43.6755
Evaluate side-chains
  133 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain C residue  154 GLN
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  516 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 17 optimal weight:    0.3980
   chunk 102 optimal weight:    0.6980
   chunk 97 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 87 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 111 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 8 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 154 GLN
** B 338 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.150423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.110376 restraints weight = 15662.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.110966 restraints weight = 14968.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.112077 restraints weight = 10140.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.1601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  11205  Z= 0.111
  Angle     :  0.525   9.387  15204  Z= 0.261
  Chirality :  0.039   0.135   1811
  Planarity :  0.003   0.054   1909
  Dihedral  :  8.934  74.303   1715
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 16.74 %
    Favored  : 81.59 %
  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:  0.49 (0.23), residues: 1439
  helix:  1.47 (0.18), residues: 869
  sheet: -1.53 (0.60), residues: 74
  loop : -1.47 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 300 
 HIS   0.001   0.000   HIS A 451 
 PHE   0.010   0.001   PHE A 109 
 TYR   0.023   0.002   TYR A 126 
 ARG   0.001   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03221 (  654)
  hydrogen bonds       : angle       4.16196 ( 1923)
  covalent geometry    : bond        0.00250 (11205)
  covalent geometry    : angle       0.52499 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 125
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  352 ASP cc_start: 0.9084 (t0) cc_final: 0.8765 (t70)
REVERT: A  397 MET cc_start: 0.8790 (mmt) cc_final: 0.8448 (mmt)
REVERT: A  446 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7701 (tt)
REVERT: C  130 ASN cc_start: 0.8279 (t0) cc_final: 0.8063 (t0)
  outliers start: 19
  outliers final: 15
  residues processed: 140
  average time/residue: 0.2113
  time to fit residues: 44.7074
Evaluate side-chains
  135 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 119
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  516 THR
Chi-restraints excluded: chain B residue  645 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 69 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 118 optimal weight:    0.3980
   chunk 20 optimal weight:    0.7980
   chunk 52 optimal weight:    0.9980
   chunk 106 optimal weight:    0.4980
   chunk 115 optimal weight:    7.9990
   chunk 132 optimal weight:    0.6980
   chunk 55 optimal weight:    0.0570
   chunk 67 optimal weight:    5.9990
   overall best weight:    0.4298

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

Flipped N/Q/H residues before XYZ refinement:
** B 338 GLN ** 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 = 0.3863 r_free = 0.3863 target = 0.151984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.112389 restraints weight = 15772.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.112087 restraints weight = 16960.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.113866 restraints weight = 10584.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11205  Z= 0.099
  Angle     :  0.522   9.707  15204  Z= 0.257
  Chirality :  0.039   0.137   1811
  Planarity :  0.003   0.054   1909
  Dihedral  :  8.629  74.346   1715
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.96 %
    Favored  : 96.04 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 17.18 %
    Favored  : 81.32 %
  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:  0.65 (0.23), residues: 1439
  helix:  1.62 (0.18), residues: 860
  sheet: -1.47 (0.61), residues: 75
  loop : -1.37 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 300 
 HIS   0.001   0.000   HIS A 351 
 PHE   0.011   0.001   PHE A 109 
 TYR   0.019   0.002   TYR A 126 
 ARG   0.001   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03106 (  654)
  hydrogen bonds       : angle       4.11110 ( 1923)
  covalent geometry    : bond        0.00219 (11205)
  covalent geometry    : angle       0.52183 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 130
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  352 ASP cc_start: 0.9058 (t0) cc_final: 0.8734 (t70)
REVERT: A  397 MET cc_start: 0.8756 (mmt) cc_final: 0.8392 (mmt)
REVERT: A  446 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7621 (tt)
REVERT: C   64 TYR cc_start: 0.8645 (m-10) cc_final: 0.8440 (m-10)
REVERT: C   75 MET cc_start: 0.7096 (OUTLIER) cc_final: 0.6680 (ptt)
  outliers start: 17
  outliers final: 15
  residues processed: 143
  average time/residue: 0.1939
  time to fit residues: 42.0427
Evaluate side-chains
  138 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 1.078 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue   74 ILE
Chi-restraints excluded: chain B residue  127 ARG
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  516 THR
Chi-restraints excluded: chain B residue  645 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 95 optimal weight:    3.9990
   chunk 43 optimal weight:    1.9990
   chunk 107 optimal weight:    8.9990
   chunk 0 optimal weight:    6.9990
   chunk 18 optimal weight:    2.9990
   chunk 71 optimal weight:    2.9990
   chunk 85 optimal weight:    9.9990
   chunk 80 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   chunk 123 optimal weight:    8.9990
   chunk 78 optimal weight:    1.9990
   overall best weight:    1.6986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.147870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.108919 restraints weight = 15759.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.108416 restraints weight = 18081.801|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.109971 restraints weight = 13245.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.3306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11205  Z= 0.172
  Angle     :  0.576   9.364  15204  Z= 0.287
  Chirality :  0.041   0.183   1811
  Planarity :  0.004   0.054   1909
  Dihedral  :  8.759  77.428   1715
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 17.09 %
    Favored  : 81.23 %
  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 (0.23), residues: 1439
  helix:  1.36 (0.18), residues: 871
  sheet: -1.68 (0.57), residues: 85
  loop : -1.42 (0.28), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 176 
 HIS   0.003   0.001   HIS A 351 
 PHE   0.012   0.001   PHE A 453 
 TYR   0.030   0.002   TYR A 126 
 ARG   0.002   0.000   ARG B  89 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03574 (  654)
  hydrogen bonds       : angle       4.27437 ( 1923)
  covalent geometry    : bond        0.00414 (11205)
  covalent geometry    : angle       0.57571 (15204)

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

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

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2878 Ramachandran restraints generated.
    1439 Oldfield, 0 Emsley, 1439 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 117
  time to evaluate  : 1.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  397 MET cc_start: 0.8830 (mmt) cc_final: 0.8544 (mmt)
REVERT: A  446 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7839 (tt)
REVERT: C   75 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6679 (ptt)
REVERT: C  130 ASN cc_start: 0.8343 (t0) cc_final: 0.8101 (t0)
  outliers start: 19
  outliers final: 14
  residues processed: 131
  average time/residue: 0.2101
  time to fit residues: 42.0795
Evaluate side-chains
  129 residues out of total 1135 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   34 ILE
Chi-restraints excluded: chain A residue  108 SER
Chi-restraints excluded: chain A residue  130 MET
Chi-restraints excluded: chain A residue  183 LEU
Chi-restraints excluded: chain A residue  293 ILE
Chi-restraints excluded: chain A residue  357 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain C residue   75 MET
Chi-restraints excluded: chain C residue   85 SER
Chi-restraints excluded: chain B residue   12 THR
Chi-restraints excluded: chain B residue  433 VAL
Chi-restraints excluded: chain B residue  516 THR
Chi-restraints excluded: chain B residue  645 THR
Chi-restraints excluded: chain B residue  662 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 52 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 108 optimal weight:   20.0000
   chunk 135 optimal weight:    0.8980
   chunk 124 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 84 optimal weight:    4.9990
   chunk 35 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 165 ASN
** B 338 GLN ** 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 = 0.3833 r_free = 0.3833 target = 0.149510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.110537 restraints weight = 15674.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.110142 restraints weight = 17901.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.111384 restraints weight = 12377.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11205  Z= 0.121
  Angle     :  0.557   9.889  15204  Z= 0.276
  Chirality :  0.039   0.162   1811
  Planarity :  0.003   0.055   1909
  Dihedral  :  8.601  77.552   1715
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 17.71 %
    Favored  : 80.88 %
  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:  0.50 (0.23), residues: 1439
  helix:  1.42 (0.18), residues: 871
  sheet: -1.55 (0.62), residues: 75
  loop : -1.34 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B  71 
 HIS   0.001   0.000   HIS A 451 
 PHE   0.010   0.001   PHE A 543 
 TYR   0.025   0.002   TYR A 126 
 ARG   0.001   0.000   ARG B 504 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03328 (  654)
  hydrogen bonds       : angle       4.21876 ( 1923)
  covalent geometry    : bond        0.00281 (11205)
  covalent geometry    : angle       0.55669 (15204)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3499.52 seconds
wall clock time: 61 minutes 42.10 seconds (3702.10 seconds total)