Starting phenix.real_space_refine
on Thu Feb 13 04:44:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zds_14668/02_2025/7zds_14668_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zds_14668/02_2025/7zds_14668.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zds_14668/02_2025/7zds_14668.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zds_14668/02_2025/7zds_14668.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zds_14668/02_2025/7zds_14668_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zds_14668/02_2025/7zds_14668_neut.cif"
  }
  resolution = 3.26
  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=   0.006
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      29      5.16       5
     C    5600      2.51       5
     N    1538      2.21       5
     O    1569      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 79 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 8736
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "C"
      Number of atoms: 4319
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 564, 4319
          Classifications: {'peptide': 564}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 18, 'TRANS': 545}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "D"
      Number of atoms: 4417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4417
          Classifications: {'peptide': 565}
          Link IDs: {'PTRANS': 26, 'TRANS': 538}
  Time building chain proxies: 5.32, per 1000 atoms: 0.61
  Number of scatterers: 8736
  At special positions: 0
  Unit cell: (122.202, 86.211, 105.462, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      29     16.00
     O    1569      8.00
     N    1538      7.00
     C    5600      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: 2.25
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2090

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 4 sheets defined
      64.0% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.84
  Creating SS restraints...
    Processing helix  chain 'C' and resid 4 through 12
      removed outlier: 3.629A  pdb=" N   ALA C   9 " --> pdb=" O   LEU C   5 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   LEU C  10 " --> pdb=" O   PRO C   6 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 15 through 50
      removed outlier: 3.630A  pdb=" N   ALA C  25 " --> pdb=" O   GLY C  21 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 104
      removed outlier: 3.506A  pdb=" N   ARG C  67 " --> pdb=" O   ALA C  63 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   HIS C  94 " --> pdb=" O   ARG C  90 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 109 through 113
      removed outlier: 3.746A  pdb=" N   ARG C 113 " --> pdb=" O   GLY C 110 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 115 through 131
      removed outlier: 3.767A  pdb=" N   ASN C 121 " --> pdb=" O   GLY C 117 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL C 124 " --> pdb=" O   LEU C 120 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR C 129 " --> pdb=" O   ALA C 125 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 132 through 137
    Processing helix  chain 'C' and resid 137 through 156
    Processing helix  chain 'C' and resid 159 through 175
      removed outlier: 3.845A  pdb=" N   THR C 165 " --> pdb=" O   THR C 161 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 185
    Processing helix  chain 'C' and resid 185 through 208
      removed outlier: 3.538A  pdb=" N   GLY C 189 " --> pdb=" O   GLY C 185 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 209 through 215
      removed outlier: 3.868A  pdb=" N   ILE C 215 " --> pdb=" O   ALA C 211 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 220 through 269
      removed outlier: 3.707A  pdb=" N   GLN C 225 " --> pdb=" O   ARG C 221 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   LEU C 226 " --> pdb=" O   TYR C 222 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN C 240 " --> pdb=" O   ALA C 236 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU C 243 " --> pdb=" O   ARG C 239 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   THR C 244 " --> pdb=" O   GLN C 240 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL C 259 " --> pdb=" O   GLY C 255 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   SER C 267 " --> pdb=" O   LEU C 263 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLY C 269 " --> pdb=" O   MET C 265 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 290
      removed outlier: 3.658A  pdb=" N   LEU C 282 " --> pdb=" O   ALA C 278 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE C 283 " --> pdb=" O   LEU C 279 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 296 through 316
      removed outlier: 3.900A  pdb=" N   GLN C 302 " --> pdb=" O   THR C 298 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   HIS C 303 " --> pdb=" O   GLY C 299 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLY C 305 " --> pdb=" O   PHE C 301 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ILE C 314 " --> pdb=" O   SER C 310 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 378 through 387
      removed outlier: 3.786A  pdb=" N   LEU C 382 " --> pdb=" O   GLY C 378 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   LEU C 383 " --> pdb=" O   LYS C 379 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 408 through 415
      removed outlier: 4.020A  pdb=" N   GLN C 414 " --> pdb=" O   ALA C 410 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 429 through 435
    Processing helix  chain 'C' and resid 442 through 454
      removed outlier: 3.525A  pdb=" N   SER C 447 " --> pdb=" O   ASP C 443 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLY C 454 " --> pdb=" O   LEU C 450 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 492
    Processing helix  chain 'C' and resid 506 through 521
      removed outlier: 3.590A  pdb=" N   MET C 520 " --> pdb=" O   LEU C 516 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 534 through 539
      removed outlier: 4.556A  pdb=" N   SER C 537 " --> pdb=" O   ARG C 534 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG C 538 " --> pdb=" O   GLY C 535 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 5 through 17
    Processing helix  chain 'D' and resid 22 through 54
      removed outlier: 3.509A  pdb=" N   SER D  27 " --> pdb=" O   TRP D  23 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG D  28 " --> pdb=" O   LEU D  24 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ILE D  39 " --> pdb=" O   GLY D  35 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 59 through 61
      No H-bonds generated for 'chain 'D' and resid 59 through 61'
    Processing helix  chain 'D' and resid 62 through 115
      removed outlier: 3.612A  pdb=" N   LEU D  71 " --> pdb=" O   THR D  67 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU D  84 " --> pdb=" O   VAL D  80 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ARG D  85 " --> pdb=" O   TRP D  81 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ILE D  94 " --> pdb=" O   ALA D  90 " (cutoff:3.500A)
      Proline residue:  D 111  - end of helix
    Processing helix  chain 'D' and resid 118 through 127
      removed outlier: 3.849A  pdb=" N   LEU D 125 " --> pdb=" O   SER D 121 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 127 through 132
    Processing helix  chain 'D' and resid 133 through 138
      removed outlier: 3.728A  pdb=" N   TYR D 137 " --> pdb=" O   MET D 133 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 139 through 159
      removed outlier: 4.159A  pdb=" N   VAL D 148 " --> pdb=" O   MET D 144 " (cutoff:3.500A)
      Proline residue:  D 151  - end of helix
    Processing helix  chain 'D' and resid 164 through 194
      removed outlier: 3.784A  pdb=" N   LEU D 169 " --> pdb=" O   ALA D 165 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR D 172 " --> pdb=" O   ILE D 168 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ALA D 173 " --> pdb=" O   LEU D 169 " (cutoff:3.500A)
      Proline residue:  D 174  - end of helix
      Proline residue:  D 177  - end of helix
      removed outlier: 3.971A  pdb=" N   GLY D 186 " --> pdb=" O   LEU D 182 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG D 192 " --> pdb=" O   ALA D 188 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 194 through 203
      removed outlier: 4.098A  pdb=" N   GLY D 203 " --> pdb=" O   ALA D 199 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 203 through 210
    Processing helix  chain 'D' and resid 211 through 218
      removed outlier: 3.607A  pdb=" N   LEU D 215 " --> pdb=" O   GLY D 211 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   ILE D 217 " --> pdb=" O   GLU D 213 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   PHE D 218 " --> pdb=" O   THR D 214 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 223 through 274
      removed outlier: 3.786A  pdb=" N   SER D 227 " --> pdb=" O   ALA D 223 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ARG D 244 " --> pdb=" O   MET D 240 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   LEU D 245 " --> pdb=" O   GLU D 241 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   LEU D 248 " --> pdb=" O   ARG D 244 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   SER D 250 " --> pdb=" O   ALA D 246 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   LEU D 253 " --> pdb=" O   SER D 249 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLU D 254 " --> pdb=" O   SER D 250 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   SER D 258 " --> pdb=" O   GLU D 254 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ILE D 261 " --> pdb=" O   THR D 257 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   LEU D 273 " --> pdb=" O   GLY D 269 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 286 through 311
      removed outlier: 3.816A  pdb=" N   ALA D 293 " --> pdb=" O   ALA D 289 " (cutoff:3.500A)
      Proline residue:  D 298  - end of helix
      removed outlier: 3.880A  pdb=" N   PHE D 301 " --> pdb=" O   ALA D 297 " (cutoff:3.500A)
      Proline residue:  D 303  - end of helix
    Processing helix  chain 'D' and resid 311 through 330
      removed outlier: 3.728A  pdb=" N   ALA D 315 " --> pdb=" O   TYR D 311 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   SER D 323 " --> pdb=" O   GLY D 319 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 390 through 398
    Processing helix  chain 'D' and resid 417 through 422
    Processing helix  chain 'D' and resid 438 through 444
      removed outlier: 3.697A  pdb=" N   VAL D 443 " --> pdb=" O   LEU D 439 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LEU D 444 " --> pdb=" O   ARG D 440 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 451 through 462
      removed outlier: 3.617A  pdb=" N   ASN D 461 " --> pdb=" O   ALA D 457 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ALA D 462 " --> pdb=" O   ALA D 458 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 473 through 477
      removed outlier: 4.071A  pdb=" N   ASP D 476 " --> pdb=" O   GLN D 473 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 487 through 501
      removed outlier: 3.702A  pdb=" N   ARG D 493 " --> pdb=" O   GLY D 489 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA D 495 " --> pdb=" O   ALA D 491 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 517 through 529
      removed outlier: 3.748A  pdb=" N   ARG D 523 " --> pdb=" O   HIS D 519 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 359 through 362
      removed outlier: 6.219A  pdb=" N   ILE C 359 " --> pdb=" O   ASP C 343 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   ASP C 343 " --> pdb=" O   ILE C 359 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   GLU C 396 " --> pdb=" O   ARG C 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 416 through 419
      removed outlier: 6.741A  pdb=" N   VAL C 496 " --> pdb=" O   LEU C 527 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   VAL C 529 " --> pdb=" O   VAL C 496 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU C 498 " --> pdb=" O   VAL C 529 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   ILE C 369 " --> pdb=" O   MET C 528 " (cutoff:3.500A)
      removed outlier: 7.936A  pdb=" N   THR C 530 " --> pdb=" O   ILE C 369 " (cutoff:3.500A)
      removed outlier: 6.096A  pdb=" N   ILE C 371 " --> pdb=" O   THR C 530 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   GLN C 541 " --> pdb=" O   HIS C 368 " (cutoff:3.500A)
      removed outlier: 6.744A  pdb=" N   ASP C 546 " --> pdb=" O   ILE C 550 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ILE C 550 " --> pdb=" O   ASP C 546 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'D' and resid 364 through 373
      removed outlier: 6.523A  pdb=" N   LEU D 365 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
      removed outlier: 8.051A  pdb=" N   THR D 358 " --> pdb=" O   LEU D 365 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   GLY D 367 " --> pdb=" O   PHE D 356 " (cutoff:3.500A)
      removed outlier: 4.712A  pdb=" N   PHE D 356 " --> pdb=" O   GLY D 367 " (cutoff:3.500A)
      removed outlier: 5.623A  pdb=" N   LEU D 369 " --> pdb=" O   GLU D 354 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLU D 354 " --> pdb=" O   LEU D 369 " (cutoff:3.500A)
      removed outlier: 5.664A  pdb=" N   ALA D 352 " --> pdb=" O   ARG D 407 " (cutoff:3.500A)
      removed outlier: 7.628A  pdb=" N   ARG D 407 " --> pdb=" O   ALA D 352 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   GLU D 354 " --> pdb=" O   SER D 405 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   SER D 405 " --> pdb=" O   GLU D 354 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER D 401 " --> pdb=" O   THR D 358 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'D' and resid 425 through 428
      removed outlier: 6.329A  pdb=" N   SER D 426 " --> pdb=" O   LEU D 508 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   ASP D 510 " --> pdb=" O   SER D 426 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   VAL D 428 " --> pdb=" O   ASP D 510 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU D 507 " --> pdb=" O   LEU D 538 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   VAL D 540 " --> pdb=" O   LEU D 507 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU D 509 " --> pdb=" O   VAL D 540 " (cutoff:3.500A)
      removed outlier: 7.043A  pdb=" N   VAL D 380 " --> pdb=" O   TRP D 554 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   MET D 556 " --> pdb=" O   VAL D 380 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   VAL D 382 " --> pdb=" O   MET D 556 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   GLU D 563 " --> pdb=" O   VAL D 555 " (cutoff:3.500A)

    491 hydrogen bonds defined for protein.
    1455 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: 2.34

  Time building geometry restraints manager: 2.57 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1836
        1.33 -     1.45: 1933
        1.45 -     1.57: 5083
        1.57 -     1.69: 1
        1.69 -     1.81: 55
  Bond restraints: 8908
  Sorted by residual:
  bond pdb=" N   VAL C 344 "
       pdb=" CA  VAL C 344 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.99e+00
  bond pdb=" N   GLU C 460 "
       pdb=" CA  GLU C 460 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.033 1.19e-02 7.06e+03 7.88e+00
  bond pdb=" N   SER C 466 "
       pdb=" CA  SER C 466 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.25e-02 6.40e+03 7.21e+00
  bond pdb=" C   PRO C 178 "
       pdb=" O   PRO C 178 "
    ideal  model  delta    sigma   weight residual
    1.240  1.210  0.030 1.12e-02 7.97e+03 7.20e+00
  bond pdb=" N   ARG C 332 "
       pdb=" CA  ARG C 332 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.21e-02 6.83e+03 6.86e+00
  ... (remaining 8903 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 11507
        1.54 -     3.09: 496
        3.09 -     4.63: 83
        4.63 -     6.18: 17
        6.18 -     7.72: 4
  Bond angle restraints: 12107
  Sorted by residual:
  angle pdb=" CA  PRO D 432 "
        pdb=" N   PRO D 432 "
        pdb=" CD  PRO D 432 "
      ideal   model   delta    sigma   weight residual
     112.00  104.84    7.16 1.40e+00 5.10e-01 2.62e+01
  angle pdb=" N   VAL C 312 "
        pdb=" CA  VAL C 312 "
        pdb=" C   VAL C 312 "
      ideal   model   delta    sigma   weight residual
     112.96  109.00    3.96 1.00e+00 1.00e+00 1.57e+01
  angle pdb=" C   GLU C 460 "
        pdb=" CA  GLU C 460 "
        pdb=" CB  GLU C 460 "
      ideal   model   delta    sigma   weight residual
     110.88  116.68   -5.80 1.57e+00 4.06e-01 1.36e+01
  angle pdb=" CA  GLN C 354 "
        pdb=" C   GLN C 354 "
        pdb=" O   GLN C 354 "
      ideal   model   delta    sigma   weight residual
     122.14  117.63    4.51 1.24e+00 6.50e-01 1.32e+01
  angle pdb=" CA  ALA C 355 "
        pdb=" C   ALA C 355 "
        pdb=" O   ALA C 355 "
      ideal   model   delta    sigma   weight residual
     120.63  116.77    3.86 1.08e+00 8.57e-01 1.27e+01
  ... (remaining 12102 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 4790
       17.54 -    35.08: 432
       35.08 -    52.62: 69
       52.62 -    70.16: 17
       70.16 -    87.69: 11
  Dihedral angle restraints: 5319
    sinusoidal: 2080
      harmonic: 3239
  Sorted by residual:
  dihedral pdb=" CA  GLU D  84 "
           pdb=" C   GLU D  84 "
           pdb=" N   ARG D  85 "
           pdb=" CA  ARG D  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.24   23.76     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" C   GLU C 460 "
           pdb=" N   GLU C 460 "
           pdb=" CA  GLU C 460 "
           pdb=" CB  GLU C 460 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.30    9.70     0      2.50e+00 1.60e-01 1.51e+01
  dihedral pdb=" CA  PHE C 291 "
           pdb=" C   PHE C 291 "
           pdb=" N   GLU C 292 "
           pdb=" CA  GLU C 292 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.24   18.76     0      5.00e+00 4.00e-02 1.41e+01
  ... (remaining 5316 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1135
       0.051 -    0.103: 239
       0.103 -    0.154: 37
       0.154 -    0.206: 2
       0.206 -    0.257: 2
  Chirality restraints: 1415
  Sorted by residual:
  chirality pdb=" CA  LEU C 425 "
            pdb=" N   LEU C 425 "
            pdb=" C   LEU C 425 "
            pdb=" CB  LEU C 425 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CA  GLU C 460 "
            pdb=" N   GLU C 460 "
            pdb=" C   GLU C 460 "
            pdb=" CB  GLU C 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CA  PHE C 426 "
            pdb=" N   PHE C 426 "
            pdb=" C   PHE C 426 "
            pdb=" CB  PHE C 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.05e+00
  ... (remaining 1412 not shown)

  Planarity restraints: 1550
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN D 431 "   -0.073 5.00e-02 4.00e+02   1.06e-01 1.79e+01
        pdb=" N   PRO D 432 "    0.183 5.00e-02 4.00e+02
        pdb=" CA  PRO D 432 "   -0.053 5.00e-02 4.00e+02
        pdb=" CD  PRO D 432 "   -0.057 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 295 "    0.038 5.00e-02 4.00e+02   5.76e-02 5.30e+00
        pdb=" N   PRO C 296 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO C 296 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO C 296 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C 341 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.10e+00
        pdb=" C   LEU C 341 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   LEU C 341 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG C 342 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1547 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 56
        2.59 -     3.17: 7352
        3.17 -     3.75: 13456
        3.75 -     4.32: 18944
        4.32 -     4.90: 31727
  Nonbonded interactions: 71535
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 427 "
            pdb=" OD2 ASP D 207 "
     model   vdw
     2.017 3.040
  nonbonded pdb=" OG  SER C 438 "
            pdb=" OG  SER C 441 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OG  SER D 417 "
            pdb=" OG  SER D 420 "
     model   vdw
     2.178 3.040
  nonbonded pdb=" O   SER C 427 "
            pdb=" OG  SER C 427 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   PHE C 426 "
            pdb=" OD2 ASP D 207 "
     model   vdw
     2.230 3.040
  ... (remaining 71530 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:             1.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     21.750
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.030
  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:2.730
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8433
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.126   8908  Z= 0.338
  Angle     :  0.737   7.720  12107  Z= 0.458
  Chirality :  0.044   0.257   1415
  Planarity :  0.005   0.106   1550
  Dihedral  : 14.062  87.694   3229
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.87 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.62 (0.23), residues: 1125
  helix: -1.95 (0.18), residues: 654
  sheet: -1.10 (0.69), residues: 57
  loop : -1.11 (0.28), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP D 463 
 HIS   0.004   0.001   HIS C 491 
 PHE   0.011   0.001   PHE C 426 
 TYR   0.012   0.001   TYR C   7 
 ARG   0.013   0.001   ARG D 560 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.908 
Fit side-chains
REVERT: C  517 LEU cc_start: 0.8199 (tt) cc_final: 0.7661 (mp)
REVERT: C  521 MET cc_start: 0.8904 (mtm) cc_final: 0.8495 (mtt)
REVERT: D   54 MET cc_start: 0.8788 (mmm) cc_final: 0.8582 (mmp)
REVERT: D  377 GLN cc_start: 0.7846 (mt0) cc_final: 0.7527 (tt0)
REVERT: D  558 ASP cc_start: 0.6614 (t70) cc_final: 0.6349 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 110
  average time/residue: 0.2673
  time to fit residues: 38.8141
Evaluate side-chains
  91 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.1980
   chunk 84 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 87 optimal weight:    0.9990
   chunk 33 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    6.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
C  93 GLN
C 121 ASN
C 512 GLN
D  16 GLN
D  89 HIS
D 191 ASN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.137616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.101302 restraints weight = 10109.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 1.40
r_work: 0.2896 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 3.83 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8608
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8908  Z= 0.205
  Angle     :  0.616   8.429  12107  Z= 0.314
  Chirality :  0.042   0.161   1415
  Planarity :  0.005   0.043   1550
  Dihedral  :  4.482  21.770   1228
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  7.15 %
    Favored  : 91.86 %
  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: -0.76 (0.24), residues: 1125
  helix: -0.07 (0.20), residues: 654
  sheet: -0.74 (0.66), residues: 65
  loop : -0.98 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  41 
 HIS   0.006   0.001   HIS C 556 
 PHE   0.016   0.001   PHE C 164 
 TYR   0.014   0.002   TYR D  88 
 ARG   0.004   0.000   ARG D 139 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.880 
Fit side-chains
REVERT: C  517 LEU cc_start: 0.8140 (tt) cc_final: 0.7765 (mp)
REVERT: C  521 MET cc_start: 0.9054 (mtm) cc_final: 0.8601 (mtt)
REVERT: D   94 ILE cc_start: 0.9256 (OUTLIER) cc_final: 0.8984 (mp)
REVERT: D  234 ASP cc_start: 0.8453 (t0) cc_final: 0.7891 (m-30)
REVERT: D  377 GLN cc_start: 0.8025 (mt0) cc_final: 0.7590 (tt0)
REVERT: D  566 ARG cc_start: 0.5840 (ttp80) cc_final: 0.5369 (mtp180)
  outliers start: 9
  outliers final: 4
  residues processed: 113
  average time/residue: 0.2344
  time to fit residues: 36.2586
Evaluate side-chains
  101 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 96
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  399 LEU
Chi-restraints excluded: chain C residue  427 SER
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 82 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    0.8980
   chunk 95 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 55 optimal weight:    9.9990
   chunk 1 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
C 121 ASN
C 210 GLN
C 424 HIS
D  89 HIS
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.134417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.099240 restraints weight = 10227.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.2999 rms_B_bonded: 1.29
r_work: 0.2859 rms_B_bonded: 1.88 restraints_weight: 0.5000
r_work: 0.2730 rms_B_bonded: 3.07 restraints_weight: 0.2500
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1585

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   8908  Z= 0.348
  Angle     :  0.632   9.113  12107  Z= 0.311
  Chirality :  0.044   0.198   1415
  Planarity :  0.004   0.036   1550
  Dihedral  :  4.424  18.872   1228
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 10.12 %
    Favored  : 88.23 %
  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: -0.29 (0.25), residues: 1125
  helix:  0.44 (0.20), residues: 656
  sheet: -0.74 (0.65), residues: 63
  loop : -1.02 (0.29), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 463 
 HIS   0.005   0.001   HIS C 491 
 PHE   0.013   0.001   PHE C 426 
 TYR   0.018   0.002   TYR D  88 
 ARG   0.004   0.000   ARG C  73 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 0.963 
Fit side-chains
REVERT: C  323 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7245 (mm-30)
REVERT: C  399 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7963 (mp)
REVERT: C  490 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8420 (mm)
REVERT: C  517 LEU cc_start: 0.8083 (tt) cc_final: 0.7741 (mp)
REVERT: D   94 ILE cc_start: 0.9244 (OUTLIER) cc_final: 0.8992 (mp)
REVERT: D  234 ASP cc_start: 0.8344 (t0) cc_final: 0.7769 (m-30)
REVERT: D  377 GLN cc_start: 0.8034 (mt0) cc_final: 0.7597 (tt0)
REVERT: D  566 ARG cc_start: 0.5869 (ttp80) cc_final: 0.5595 (mtp-110)
  outliers start: 15
  outliers final: 9
  residues processed: 110
  average time/residue: 0.2535
  time to fit residues: 37.4019
Evaluate side-chains
  107 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  399 LEU
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    0.6980
   chunk 54 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 55 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 77 optimal weight:    0.2980
   chunk 48 optimal weight:    0.7980
   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 121 ASN
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.137484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.101399 restraints weight = 10039.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.30
r_work: 0.2885 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.2755 rms_B_bonded: 3.37 restraints_weight: 0.2500
r_work (final): 0.2755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8571
moved from start:          0.1849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8908  Z= 0.205
  Angle     :  0.559   9.214  12107  Z= 0.274
  Chirality :  0.040   0.154   1415
  Planarity :  0.004   0.037   1550
  Dihedral  :  4.219  16.816   1228
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 6.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 11.88 %
    Favored  : 85.81 %
  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:  0.23 (0.25), residues: 1125
  helix:  0.97 (0.21), residues: 657
  sheet: -0.70 (0.65), residues: 65
  loop : -0.98 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  41 
 HIS   0.004   0.001   HIS D 134 
 PHE   0.011   0.001   PHE C 426 
 TYR   0.016   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 139 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 106
  time to evaluate  : 0.944 
Fit side-chains
REVERT: C  490 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8398 (mm)
REVERT: C  517 LEU cc_start: 0.8055 (tt) cc_final: 0.7797 (mp)
REVERT: D   94 ILE cc_start: 0.9232 (OUTLIER) cc_final: 0.8979 (mp)
REVERT: D  234 ASP cc_start: 0.8343 (t0) cc_final: 0.7821 (m-30)
REVERT: D  377 GLN cc_start: 0.7906 (mt0) cc_final: 0.7473 (tt0)
REVERT: D  463 TRP cc_start: 0.7802 (m-10) cc_final: 0.7436 (m-10)
REVERT: D  566 ARG cc_start: 0.5777 (ttp80) cc_final: 0.5459 (mtp180)
  outliers start: 21
  outliers final: 11
  residues processed: 121
  average time/residue: 0.2132
  time to fit residues: 35.8206
Evaluate side-chains
  109 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0770
   chunk 85 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   chunk 64 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 27 optimal weight:    0.0060
   chunk 59 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.5154

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.138920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.104926 restraints weight = 9986.970|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.38
r_work: 0.2919 rms_B_bonded: 1.98 restraints_weight: 0.5000
r_work: 0.2791 rms_B_bonded: 3.22 restraints_weight: 0.2500
r_work (final): 0.2791
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8908  Z= 0.177
  Angle     :  0.547   8.900  12107  Z= 0.266
  Chirality :  0.040   0.135   1415
  Planarity :  0.004   0.038   1550
  Dihedral  :  4.068  15.742   1228
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 13.97 %
    Favored  : 84.38 %
  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 (0.25), residues: 1125
  helix:  1.22 (0.21), residues: 659
  sheet: -0.56 (0.66), residues: 66
  loop : -0.95 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  41 
 HIS   0.004   0.001   HIS D 134 
 PHE   0.009   0.001   PHE C 181 
 TYR   0.015   0.001   TYR D  88 
 ARG   0.003   0.000   ARG D 139 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 105
  time to evaluate  : 0.816 
Fit side-chains
REVERT: C  451 ARG cc_start: 0.8556 (ttm-80) cc_final: 0.8348 (mtm180)
REVERT: C  490 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8412 (mm)
REVERT: C  517 LEU cc_start: 0.8147 (tt) cc_final: 0.7852 (mp)
REVERT: D   94 ILE cc_start: 0.9195 (OUTLIER) cc_final: 0.8977 (mp)
REVERT: D  234 ASP cc_start: 0.8299 (t0) cc_final: 0.7802 (m-30)
REVERT: D  377 GLN cc_start: 0.7813 (mt0) cc_final: 0.7435 (tt0)
REVERT: D  463 TRP cc_start: 0.7798 (m-10) cc_final: 0.7438 (m-10)
  outliers start: 15
  outliers final: 12
  residues processed: 116
  average time/residue: 0.2616
  time to fit residues: 41.5913
Evaluate side-chains
  107 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 93
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  339 LEU
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 89 optimal weight:    4.9990
   chunk 53 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 70 optimal weight:    0.8980
   chunk 94 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 56 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 81 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
D  51 HIS
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.137900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.104445 restraints weight = 9982.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.35
r_work: 0.2899 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.34 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8566
moved from start:          0.2148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8908  Z= 0.218
  Angle     :  0.560   8.949  12107  Z= 0.271
  Chirality :  0.041   0.160   1415
  Planarity :  0.004   0.038   1550
  Dihedral  :  4.022  15.788   1228
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 14.63 %
    Favored  : 83.06 %
  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 (0.25), residues: 1125
  helix:  1.35 (0.21), residues: 652
  sheet: -0.49 (0.67), residues: 66
  loop : -0.94 (0.30), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  41 
 HIS   0.004   0.001   HIS D  93 
 PHE   0.010   0.001   PHE C 181 
 TYR   0.015   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 452 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.916 
Fit side-chains
REVERT: C  490 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8433 (mm)
REVERT: C  517 LEU cc_start: 0.8172 (tt) cc_final: 0.7873 (mp)
REVERT: D   94 ILE cc_start: 0.9216 (OUTLIER) cc_final: 0.8990 (mp)
REVERT: D  234 ASP cc_start: 0.8338 (t0) cc_final: 0.7842 (m-30)
REVERT: D  370 ASN cc_start: 0.8307 (OUTLIER) cc_final: 0.7852 (t0)
REVERT: D  463 TRP cc_start: 0.7905 (m-10) cc_final: 0.7504 (m-10)
  outliers start: 21
  outliers final: 15
  residues processed: 110
  average time/residue: 0.2239
  time to fit residues: 34.1447
Evaluate side-chains
  109 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.935 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  486 LEU
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 89 optimal weight:    0.0010
   chunk 33 optimal weight:    5.9990
   chunk 39 optimal weight:    6.9990
   chunk 93 optimal weight:    7.9990
   chunk 80 optimal weight:    0.9990
   chunk 74 optimal weight:    0.7980
   chunk 100 optimal weight:    1.9990
   chunk 32 optimal weight:    0.0970
   chunk 43 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   overall best weight:    0.5788

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.164461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.130326 restraints weight = 9687.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3470 rms_B_bonded: 1.34
r_work: 0.3290 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3154 rms_B_bonded: 4.11 restraints_weight: 0.2500
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8587
moved from start:          0.2261

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8908  Z= 0.179
  Angle     :  0.554   9.371  12107  Z= 0.266
  Chirality :  0.041   0.259   1415
  Planarity :  0.003   0.039   1550
  Dihedral  :  3.942  15.466   1228
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 15.29 %
    Favored  : 82.62 %
  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 (0.25), residues: 1125
  helix:  1.49 (0.21), residues: 655
  sheet: -0.43 (0.66), residues: 66
  loop : -0.88 (0.30), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 463 
 HIS   0.004   0.001   HIS C 556 
 PHE   0.009   0.001   PHE C 181 
 TYR   0.015   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 451 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 1.042 
Fit side-chains
REVERT: C  490 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8445 (mm)
REVERT: C  517 LEU cc_start: 0.8214 (tt) cc_final: 0.7894 (mp)
REVERT: D   94 ILE cc_start: 0.9215 (OUTLIER) cc_final: 0.8994 (mp)
REVERT: D  234 ASP cc_start: 0.8396 (t0) cc_final: 0.7881 (m-30)
REVERT: D  370 ASN cc_start: 0.8402 (OUTLIER) cc_final: 0.7900 (t0)
  outliers start: 19
  outliers final: 13
  residues processed: 113
  average time/residue: 0.2302
  time to fit residues: 35.8253
Evaluate side-chains
  110 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 94
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 90 optimal weight:    0.0980
   chunk 109 optimal weight:    0.0970
   chunk 38 optimal weight:    0.6980
   chunk 5 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 68 optimal weight:    0.4980
   chunk 82 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.163408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 96)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.129164 restraints weight = 9698.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 1.35
r_work: 0.3300 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3162 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8575
moved from start:          0.2379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8908  Z= 0.163
  Angle     :  0.547   9.156  12107  Z= 0.261
  Chirality :  0.040   0.244   1415
  Planarity :  0.003   0.039   1550
  Dihedral  :  3.859  14.131   1228
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.73 %
    Favored  : 82.07 %
  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:  0.99 (0.25), residues: 1125
  helix:  1.66 (0.20), residues: 655
  sheet: -0.22 (0.68), residues: 65
  loop : -0.83 (0.30), residues: 405

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP D 463 
 HIS   0.003   0.001   HIS D 134 
 PHE   0.009   0.001   PHE C 181 
 TYR   0.014   0.001   TYR D  88 
 ARG   0.004   0.000   ARG C 452 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 98
  time to evaluate  : 0.970 
Fit side-chains
REVERT: C  490 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8438 (mm)
REVERT: C  517 LEU cc_start: 0.8192 (tt) cc_final: 0.7885 (mp)
REVERT: D   63 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8693 (mp)
REVERT: D   94 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8979 (mp)
REVERT: D  234 ASP cc_start: 0.8382 (t0) cc_final: 0.7875 (m-30)
REVERT: D  244 ARG cc_start: 0.8109 (mtt90) cc_final: 0.7803 (mtt90)
REVERT: D  370 ASN cc_start: 0.8384 (OUTLIER) cc_final: 0.7918 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 113
  average time/residue: 0.2371
  time to fit residues: 36.6122
Evaluate side-chains
  112 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 1.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   63 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 92 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 89 optimal weight:    0.0970
   chunk 101 optimal weight:    0.9990
   chunk 70 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0470
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.165488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.131525 restraints weight = 9626.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.36
r_work: 0.3207 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3070 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8573
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8908  Z= 0.169
  Angle     :  0.548  10.480  12107  Z= 0.261
  Chirality :  0.040   0.328   1415
  Planarity :  0.003   0.039   1550
  Dihedral  :  3.821  12.781   1228
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 15.40 %
    Favored  : 82.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.11 (0.25), residues: 1125
  helix:  1.75 (0.20), residues: 660
  sheet: -0.19 (0.67), residues: 65
  loop : -0.81 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 463 
 HIS   0.004   0.001   HIS C 556 
 PHE   0.008   0.001   PHE C 181 
 TYR   0.014   0.001   TYR D  88 
 ARG   0.006   0.000   ARG C 452 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 97
  time to evaluate  : 0.909 
Fit side-chains
REVERT: C  262 MET cc_start: 0.8823 (mmp) cc_final: 0.8604 (mmp)
REVERT: C  490 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8436 (mm)
REVERT: C  517 LEU cc_start: 0.8178 (tt) cc_final: 0.7887 (mp)
REVERT: D   94 ILE cc_start: 0.9187 (OUTLIER) cc_final: 0.8985 (mp)
REVERT: D  234 ASP cc_start: 0.8333 (t0) cc_final: 0.7825 (m-30)
REVERT: D  244 ARG cc_start: 0.8074 (mtt90) cc_final: 0.7793 (mtt90)
REVERT: D  370 ASN cc_start: 0.8358 (OUTLIER) cc_final: 0.7929 (t0)
REVERT: D  377 GLN cc_start: 0.7709 (mt0) cc_final: 0.7400 (tt0)
  outliers start: 20
  outliers final: 15
  residues processed: 111
  average time/residue: 0.2273
  time to fit residues: 34.3339
Evaluate side-chains
  112 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue   84 GLU
Chi-restraints excluded: chain D residue   94 ILE
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0770
   chunk 4 optimal weight:    1.9990
   chunk 34 optimal weight:    5.9990
   chunk 85 optimal weight:    0.2980
   chunk 15 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 22 optimal weight:    0.7980
   chunk 97 optimal weight:    4.9990
   chunk 93 optimal weight:    0.0770
   overall best weight:    0.4296

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.167739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.133394 restraints weight = 9887.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 1.28
r_work: 0.3289 rms_B_bonded: 2.48 restraints_weight: 0.5000
r_work: 0.3153 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   8908  Z= 0.161
  Angle     :  0.548  10.312  12107  Z= 0.259
  Chirality :  0.040   0.339   1415
  Planarity :  0.003   0.037   1550
  Dihedral  :  3.788  12.497   1228
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.73 %
    Favored  : 82.29 %
  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:  1.20 (0.25), residues: 1125
  helix:  1.82 (0.20), residues: 660
  sheet: -0.08 (0.68), residues: 65
  loop : -0.78 (0.30), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 463 
 HIS   0.003   0.001   HIS D 134 
 PHE   0.008   0.001   PHE C 181 
 TYR   0.014   0.001   TYR D  88 
 ARG   0.009   0.000   ARG C 452 

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

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

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2250 Ramachandran restraints generated.
    1125 Oldfield, 0 Emsley, 1125 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.987 
Fit side-chains
REVERT: C  315 SER cc_start: 0.8103 (OUTLIER) cc_final: 0.7519 (p)
REVERT: C  490 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8443 (mm)
REVERT: C  517 LEU cc_start: 0.8196 (tt) cc_final: 0.7917 (mp)
REVERT: D  234 ASP cc_start: 0.8294 (t0) cc_final: 0.7801 (m-30)
REVERT: D  244 ARG cc_start: 0.8065 (mtt90) cc_final: 0.7783 (mtt90)
REVERT: D  370 ASN cc_start: 0.8415 (OUTLIER) cc_final: 0.7967 (t0)
REVERT: D  377 GLN cc_start: 0.7720 (mt0) cc_final: 0.7418 (tt0)
REVERT: D  452 GLU cc_start: 0.7213 (tp30) cc_final: 0.6987 (tp30)
  outliers start: 18
  outliers final: 13
  residues processed: 107
  average time/residue: 0.2381
  time to fit residues: 35.0130
Evaluate side-chains
  107 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   88 THR
Chi-restraints excluded: chain C residue  161 THR
Chi-restraints excluded: chain C residue  225 GLN
Chi-restraints excluded: chain C residue  315 SER
Chi-restraints excluded: chain C residue  340 THR
Chi-restraints excluded: chain C residue  341 LEU
Chi-restraints excluded: chain C residue  418 VAL
Chi-restraints excluded: chain C residue  423 VAL
Chi-restraints excluded: chain C residue  436 LEU
Chi-restraints excluded: chain C residue  490 LEU
Chi-restraints excluded: chain C residue  533 LEU
Chi-restraints excluded: chain D residue  149 SER
Chi-restraints excluded: chain D residue  369 LEU
Chi-restraints excluded: chain D residue  370 ASN
Chi-restraints excluded: chain D residue  380 VAL
Chi-restraints excluded: chain D residue  540 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9990
   chunk 103 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 92 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
** D 442 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.165403 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 94)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.130460 restraints weight = 9923.220|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 1.34
r_work: 0.3245 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3110 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3110
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8599
moved from start:          0.2451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.079   8908  Z= 0.242
  Angle     :  0.580   9.576  12107  Z= 0.277
  Chirality :  0.042   0.335   1415
  Planarity :  0.004   0.036   1550
  Dihedral  :  3.871  13.282   1228
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 6.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.13 %
    Favored  : 97.87 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 15.95 %
    Favored  : 82.07 %
  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:  1.00 (0.25), residues: 1125
  helix:  1.66 (0.20), residues: 657
  sheet: -0.15 (0.67), residues: 65
  loop : -0.84 (0.30), residues: 403

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP D 463 
 HIS   0.004   0.001   HIS D 134 
 PHE   0.010   0.001   PHE C 181 
 TYR   0.015   0.001   TYR D  88 
 ARG   0.008   0.000   ARG C 452 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4546.61 seconds
wall clock time: 81 minutes 15.66 seconds (4875.66 seconds total)