Starting phenix.real_space_refine
on Wed Jul 30 05:33:18 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ram_24369/07_2025/7ram_24369.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ram_24369/07_2025/7ram_24369.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.43
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ram_24369/07_2025/7ram_24369.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ram_24369/07_2025/7ram_24369.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ram_24369/07_2025/7ram_24369.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ram_24369/07_2025/7ram_24369.cif"
  }
  resolution = 3.43
  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=   0.001 sd=   0.035
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      61      5.16       5
     C    7659      2.51       5
     N    2031      2.21       5
     O    2255      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.08s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12006
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5403
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 674, 5403
          Classifications: {'peptide': 674}
          Link IDs: {'PTRANS': 33, 'TRANS': 640}
    Chain: "B"
      Number of atoms: 1873
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1873
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 19, 'TRANS': 217}
    Chain: "C"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 297, 2471
          Classifications: {'peptide': 297}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 281}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 2259
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 289, 2259
          Classifications: {'peptide': 289}
          Link IDs: {'PTRANS': 15, 'TRANS': 273}
  Time building chain proxies: 7.89, per 1000 atoms: 0.66
  Number of scatterers: 12006
  At special positions: 0
  Unit cell: (98.58, 100.7, 182.32, 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      61     16.00
     O    2255      8.00
     N    2031      7.00
     C    7659      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=14, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  60 " - pdb=" SG  CYS B  54 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  96 " - pdb=" SG  CYS B  47 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 196 " - pdb=" SG  CYS A 212 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 331 " - pdb=" SG  CYS A 384 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 496 " - pdb=" SG  CYS A 523 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 572 " - pdb=" SG  CYS A 625 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 648 " - pdb=" SG  CYS A 651 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 144 " - pdb=" SG  CYS C 345 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 154 " - pdb=" SG  CYS B 159 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 143 " - pdb=" SG  CYS C 151 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 169 " - pdb=" SG  CYS C 220 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  49 " - pdb=" SG  CYS D 100 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 150 " - pdb=" SG  CYS D 189 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 235 " - pdb=" SG  CYS D 290 " distance=2.03

  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: 2.85
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2882

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 20 sheets defined
      32.9% alpha, 16.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 99
      removed outlier: 3.744A  pdb=" N   PHE A  98 " --> pdb=" O   ARG A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 109
      removed outlier: 3.612A  pdb=" N   GLN A 109 " --> pdb=" O   GLN A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 124
    Processing helix  chain 'A' and resid 128 through 133
      removed outlier: 4.093A  pdb=" N   ASP A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 264 through 267
    Processing helix  chain 'A' and resid 283 through 287
      removed outlier: 3.683A  pdb=" N   LEU A 287 " --> pdb=" O   LYS A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 294
    Processing helix  chain 'A' and resid 299 through 304
    Processing helix  chain 'A' and resid 309 through 317
      removed outlier: 3.904A  pdb=" N   ARG A 315 " --> pdb=" O   SER A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 329
      removed outlier: 3.715A  pdb=" N   TYR A 321 " --> pdb=" O   SER A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 336 through 354
      removed outlier: 4.287A  pdb=" N   ALA A 342 " --> pdb=" O   THR A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 355 through 359
    Processing helix  chain 'A' and resid 363 through 385
      removed outlier: 3.747A  pdb=" N   LEU A 385 " --> pdb=" O   MET A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 397 through 410
    Processing helix  chain 'A' and resid 411 through 414
      removed outlier: 3.669A  pdb=" N   ILE A 414 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 411 through 414'
    Processing helix  chain 'A' and resid 416 through 431
      removed outlier: 3.674A  pdb=" N   LEU A 420 " --> pdb=" O   ASP A 416 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   ARG A 422 " --> pdb=" O   THR A 418 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LEU A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   GLN A 430 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 435
    Processing helix  chain 'A' and resid 437 through 440
      removed outlier: 3.670A  pdb=" N   ALA A 440 " --> pdb=" O   PRO A 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 437 through 440'
    Processing helix  chain 'A' and resid 441 through 455
    Processing helix  chain 'A' and resid 463 through 473
      removed outlier: 3.528A  pdb=" N   GLU A 467 " --> pdb=" O   PHE A 463 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   LEU A 470 " --> pdb=" O   GLN A 466 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 495
      removed outlier: 3.603A  pdb=" N   GLU A 487 " --> pdb=" O   THR A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 508
    Processing helix  chain 'A' and resid 515 through 520
      removed outlier: 3.751A  pdb=" N   LEU A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 538
      removed outlier: 4.000A  pdb=" N   ARG A 538 " --> pdb=" O   GLU A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 560
      removed outlier: 3.803A  pdb=" N   GLN A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 567
      removed outlier: 3.593A  pdb=" N   THR A 566 " --> pdb=" O   THR A 563 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   PHE A 567 " --> pdb=" O   LEU A 564 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 563 through 567'
    Processing helix  chain 'A' and resid 608 through 612
    Processing helix  chain 'A' and resid 672 through 679
    Processing helix  chain 'B' and resid 46 through 56
      removed outlier: 3.773A  pdb=" N   LEU B  56 " --> pdb=" O   ARG B  52 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 87
    Processing helix  chain 'B' and resid 102 through 113
    Processing helix  chain 'B' and resid 117 through 127
    Processing helix  chain 'B' and resid 132 through 137
      removed outlier: 3.619A  pdb=" N   VAL B 137 " --> pdb=" O   ARG B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 176
      removed outlier: 3.500A  pdb=" N   THR B 175 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   GLU B 176 " --> pdb=" O   ILE B 173 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 172 through 176'
    Processing helix  chain 'B' and resid 215 through 217
      No H-bonds generated for 'chain 'B' and resid 215 through 217'
    Processing helix  chain 'B' and resid 218 through 236
      removed outlier: 3.939A  pdb=" N   PHE B 222 " --> pdb=" O   GLY B 218 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 252
      removed outlier: 3.598A  pdb=" N   HIS B 245 " --> pdb=" O   PRO B 241 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 117
    Processing helix  chain 'C' and resid 148 through 162
      removed outlier: 3.937A  pdb=" N   GLU C 154 " --> pdb=" O   THR C 150 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 216
      removed outlier: 3.506A  pdb=" N   LEU C 211 " --> pdb=" O   GLY C 207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 231
    Processing helix  chain 'C' and resid 242 through 252
    Processing helix  chain 'C' and resid 323 through 338
      removed outlier: 3.905A  pdb=" N   ARG C 338 " --> pdb=" O   TYR C 334 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 339 through 346
      removed outlier: 6.697A  pdb=" N   ASN C 342 " --> pdb=" O   TYR C 339 " (cutoff:3.500A)
      Proline residue:  C 343  - end of helix
      removed outlier: 3.904A  pdb=" N   GLU C 346 " --> pdb=" O   PRO C 343 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 339 through 346'
    Processing helix  chain 'C' and resid 355 through 360
      removed outlier: 3.853A  pdb=" N   ASN C 360 " --> pdb=" O   GLU C 356 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 361 through 366
      removed outlier: 4.064A  pdb=" N   LEU C 364 " --> pdb=" O   THR C 361 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG C 366 " --> pdb=" O   VAL C 363 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 412 through 435
      removed outlier: 3.702A  pdb=" N   TYR C 418 " --> pdb=" O   PRO C 414 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER C 421 " --> pdb=" O   ASP C 417 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   PHE C 424 " --> pdb=" O   ASP C 420 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 436 through 438
      No H-bonds generated for 'chain 'C' and resid 436 through 438'
    Processing helix  chain 'C' and resid 451 through 456
      removed outlier: 3.775A  pdb=" N   LEU C 455 " --> pdb=" O   ASN C 451 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 457 through 458
      No H-bonds generated for 'chain 'C' and resid 457 through 458'
    Processing helix  chain 'C' and resid 459 through 463
      removed outlier: 3.942A  pdb=" N   LEU C 462 " --> pdb=" O   TRP C 459 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 91 through 95
    Processing helix  chain 'D' and resid 251 through 255
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 53
    Processing sheet with id=AA2, first strand: chain 'A' and resid 57 through 58
      removed outlier: 3.520A  pdb=" N   PHE B  60 " --> pdb=" O   THR A  58 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88
    Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 88
      removed outlier: 6.053A  pdb=" N   VAL B 178 " --> pdb=" O   ALA B 194 " (cutoff:3.500A)
      removed outlier: 6.672A  pdb=" N   ALA B 194 " --> pdb=" O   VAL B 178 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   PHE B 189 " --> pdb=" O   VAL B 210 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG B 204 " --> pdb=" O   ILE B 195 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 137 through 138
      removed outlier: 3.610A  pdb=" N   GLN A 272 " --> pdb=" O   ARG A 137 " (cutoff:3.500A)
      removed outlier: 5.991A  pdb=" N   ILE A 269 " --> pdb=" O   VAL A 280 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   VAL A 280 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLU A 277 " --> pdb=" O   GLY A 252 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   PHE A 234 " --> pdb=" O   THR A 231 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   TYR A 225 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 583 through 584
    Processing sheet with id=AA7, first strand: chain 'A' and resid 592 through 593
      removed outlier: 3.575A  pdb=" N   ILE A 616 " --> pdb=" O   TYR A 603 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 668 through 670
      removed outlier: 3.519A  pdb=" N   ALA A 654 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 99 through 100
      removed outlier: 6.584A  pdb=" N   VAL B  99 " --> pdb=" O   ARG C 236 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 151 through 155
    Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 87
      removed outlier: 3.510A  pdb=" N   MET C  86 " --> pdb=" O   ILE C 136 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   PHE C 126 " --> pdb=" O   ARG C 139 " (cutoff:3.500A)
      removed outlier: 8.545A  pdb=" N   TYR C 124 " --> pdb=" O   PRO C 141 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 173 through 174
    Processing sheet with id=AB4, first strand: chain 'C' and resid 186 through 191
      removed outlier: 3.713A  pdb=" N   VAL C 191 " --> pdb=" O   LYS C 194 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'D' and resid 29 through 30
      removed outlier: 3.763A  pdb=" N   PHE D  45 " --> pdb=" O   VAL D  87 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR D  83 " --> pdb=" O   CYS D  49 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   GLY D  51 " --> pdb=" O   PHE D  81 " (cutoff:3.500A)
      removed outlier: 3.850A  pdb=" N   VAL D  82 " --> pdb=" O   GLU D  74 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   VAL D  84 " --> pdb=" O   ARG D  72 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ARG D  72 " --> pdb=" O   VAL D  84 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'D' and resid 36 through 38
      removed outlier: 6.766A  pdb=" N   LYS D  37 " --> pdb=" O   TYR D 120 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   GLY D  96 " --> pdb=" O   ILE D 119 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 138 through 140
      removed outlier: 6.079A  pdb=" N   VAL D 138 " --> pdb=" O   TYR D 206 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL D 205 " --> pdb=" O   GLY D 185 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   GLY D 185 " --> pdb=" O   VAL D 205 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 159 through 160
    Processing sheet with id=AB9, first strand: chain 'D' and resid 171 through 173
    Processing sheet with id=AC1, first strand: chain 'D' and resid 216 through 219
    Processing sheet with id=AC2, first strand: chain 'D' and resid 224 through 226
      removed outlier: 7.008A  pdb=" N   TYR D 225 " --> pdb=" O   HIS D 310 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LYS D 303 " --> pdb=" O   CYS D 290 " (cutoff:3.500A)

    411 hydrogen bonds defined for protein.
    1074 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: 3.99

  Time building geometry restraints manager: 3.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 3895
        1.35 -     1.47: 3010
        1.47 -     1.60: 5295
        1.60 -     1.72: 0
        1.72 -     1.84: 93
  Bond restraints: 12293
  Sorted by residual:
  bond pdb=" C   PRO C 140 "
       pdb=" N   PRO C 141 "
    ideal  model  delta    sigma   weight residual
    1.332  1.362 -0.030 1.12e-02 7.97e+03 7.24e+00
  bond pdb=" C   VAL D 168 "
       pdb=" N   PRO D 169 "
    ideal  model  delta    sigma   weight residual
    1.334  1.384 -0.051 2.34e-02 1.83e+03 4.67e+00
  bond pdb=" CA  ILE A 364 "
       pdb=" CB  ILE A 364 "
    ideal  model  delta    sigma   weight residual
    1.534  1.544 -0.009 6.80e-03 2.16e+04 1.80e+00
  bond pdb=" CA  ILE A 364 "
       pdb=" C   ILE A 364 "
    ideal  model  delta    sigma   weight residual
    1.520  1.531 -0.012 8.80e-03 1.29e+04 1.78e+00
  bond pdb=" C   VAL D 266 "
       pdb=" N   PRO D 267 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.59e+00
  ... (remaining 12288 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.55: 16336
        1.55 -     3.10: 346
        3.10 -     4.65: 40
        4.65 -     6.19: 15
        6.19 -     7.74: 8
  Bond angle restraints: 16745
  Sorted by residual:
  angle pdb=" N   LEU A 441 "
        pdb=" CA  LEU A 441 "
        pdb=" C   LEU A 441 "
      ideal   model   delta    sigma   weight residual
     114.04  108.41    5.63 1.24e+00 6.50e-01 2.06e+01
  angle pdb=" N   GLN A 332 "
        pdb=" CA  GLN A 332 "
        pdb=" C   GLN A 332 "
      ideal   model   delta    sigma   weight residual
     113.72  108.15    5.57 1.52e+00 4.33e-01 1.34e+01
  angle pdb=" N   THR B  92 "
        pdb=" CA  THR B  92 "
        pdb=" C   THR B  92 "
      ideal   model   delta    sigma   weight residual
     109.81  117.55   -7.74 2.21e+00 2.05e-01 1.23e+01
  angle pdb=" N   GLY D  96 "
        pdb=" CA  GLY D  96 "
        pdb=" C   GLY D  96 "
      ideal   model   delta    sigma   weight residual
     110.58  114.92   -4.34 1.35e+00 5.49e-01 1.03e+01
  angle pdb=" CA  GLN B 237 "
        pdb=" CB  GLN B 237 "
        pdb=" CG  GLN B 237 "
      ideal   model   delta    sigma   weight residual
     114.10  120.30   -6.20 2.00e+00 2.50e-01 9.60e+00
  ... (remaining 16740 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 6681
       17.86 -    35.71: 603
       35.71 -    53.57: 109
       53.57 -    71.43: 27
       71.43 -    89.29: 17
  Dihedral angle restraints: 7437
    sinusoidal: 2992
      harmonic: 4445
  Sorted by residual:
  dihedral pdb=" CB  CYS A  60 "
           pdb=" SG  CYS A  60 "
           pdb=" SG  CYS B  54 "
           pdb=" CB  CYS B  54 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -150.25   64.25     1      1.00e+01 1.00e-02 5.43e+01
  dihedral pdb=" CA  CYS A 331 "
           pdb=" C   CYS A 331 "
           pdb=" N   GLN A 332 "
           pdb=" CA  GLN A 332 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.99  -27.01     0      5.00e+00 4.00e-02 2.92e+01
  dihedral pdb=" CB  CYS A 331 "
           pdb=" SG  CYS A 331 "
           pdb=" SG  CYS A 384 "
           pdb=" CB  CYS A 384 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.20   42.20     1      1.00e+01 1.00e-02 2.49e+01
  ... (remaining 7434 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 1416
       0.039 -    0.078: 347
       0.078 -    0.118: 147
       0.118 -    0.157: 7
       0.157 -    0.196: 4
  Chirality restraints: 1921
  Sorted by residual:
  chirality pdb=" CA  THR B  92 "
            pdb=" N   THR B  92 "
            pdb=" C   THR B  92 "
            pdb=" CB  THR B  92 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.33    0.20 2.00e-01 2.50e+01 9.60e-01
  chirality pdb=" CB  ILE A 364 "
            pdb=" CA  ILE A 364 "
            pdb=" CG1 ILE A 364 "
            pdb=" CG2 ILE A 364 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.75e-01
  chirality pdb=" CA  VAL C 146 "
            pdb=" N   VAL C 146 "
            pdb=" C   VAL C 146 "
            pdb=" CB  VAL C 146 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.28    0.16 2.00e-01 2.50e+01 6.75e-01
  ... (remaining 1918 not shown)

  Planarity restraints: 2142
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 120 "    0.033 5.00e-02 4.00e+02   5.09e-02 4.15e+00
        pdb=" N   PRO C 121 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO C 121 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO C 121 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL D 168 "   -0.026 5.00e-02 4.00e+02   3.98e-02 2.53e+00
        pdb=" N   PRO D 169 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO D 169 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO D 169 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 436 "    0.025 5.00e-02 4.00e+02   3.77e-02 2.28e+00
        pdb=" N   PRO A 437 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 437 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 437 "    0.021 5.00e-02 4.00e+02
  ... (remaining 2139 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 271
        2.70 -     3.25: 11859
        3.25 -     3.80: 17715
        3.80 -     4.35: 23153
        4.35 -     4.90: 38970
  Nonbonded interactions: 91968
  Sorted by model distance:
  nonbonded pdb=" O   PRO C 183 "
            pdb=" OG  SER C 200 "
     model   vdw
     2.154 3.040
  nonbonded pdb=" O   VAL C 146 "
            pdb=" ND2 ASN C 233 "
     model   vdw
     2.253 3.120
  nonbonded pdb=" O   VAL A 688 "
            pdb=" OH  TYR A 695 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG  SER A 653 "
            pdb=" O   LEU A 698 "
     model   vdw
     2.257 3.040
  nonbonded pdb=" O   THR A 245 "
            pdb=" NE2 GLN A 286 "
     model   vdw
     2.259 3.120
  ... (remaining 91963 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:             3.540
  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:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.100
  Process input model:                     30.050
  Find NCS groups from input model:        0.160
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
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      :  0.002   0.051  12307  Z= 0.116
  Angle     :  0.572   7.744  16773  Z= 0.311
  Chirality :  0.041   0.196   1921
  Planarity :  0.004   0.051   2142
  Dihedral  : 14.509  89.286   4513
  Min Nonbonded Distance : 2.154

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  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: -0.56 (0.23), residues: 1485
  helix:  0.18 (0.27), residues: 370
  sheet: -0.12 (0.33), residues: 297
  loop : -0.66 (0.23), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 459 
 HIS   0.005   0.001   HIS B 236 
 PHE   0.020   0.001   PHE C 172 
 TYR   0.009   0.001   TYR C 339 
 ARG   0.004   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.26319 (  409)
  hydrogen bonds       : angle       8.47069 ( 1074)
  SS BOND              : bond        0.00207 (   14)
  SS BOND              : angle       1.58663 (   28)
  covalent geometry    : bond        0.00232 (12293)
  covalent geometry    : angle       0.56875 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.253 
Fit side-chains
   revert: symmetry clash
REVERT: A  387 GLN cc_start: 0.7351 (tp40) cc_final: 0.7059 (tm-30)
REVERT: A  402 ASP cc_start: 0.7604 (m-30) cc_final: 0.7141 (t0)
REVERT: A  478 MET cc_start: 0.6152 (tpp) cc_final: 0.5914 (tpt)
REVERT: A  676 VAL cc_start: 0.8005 (t) cc_final: 0.7690 (t)
REVERT: C  445 GLU cc_start: 0.7666 (pp20) cc_final: 0.7396 (pp20)
REVERT: D   40 GLN cc_start: 0.8438 (mm110) cc_final: 0.8196 (mm110)
REVERT: D  197 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7419 (mttt)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2135
  time to fit residues: 47.4823
Evaluate side-chains
  104 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 124 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 75 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   chunk 115 optimal weight:    0.1980
   chunk 44 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 133 optimal weight:    0.7980
   overall best weight:    0.7182

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

Flipped N/Q/H residues before XYZ refinement:
A 512 HIS
B  84 GLN
B 203 ASN
B 236 HIS
** C 233 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 = 0.3971 r_free = 0.3971 target = 0.149425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.111210 restraints weight = 17430.648|
|-----------------------------------------------------------------------------|
r_work (start): 0.3498 rms_B_bonded: 3.02
r_work: 0.3357 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.1108

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12307  Z= 0.156
  Angle     :  0.612  10.037  16773  Z= 0.316
  Chirality :  0.044   0.193   1921
  Planarity :  0.004   0.054   2142
  Dihedral  :  4.567  27.487   1649
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  :  7.10 %
    Favored  : 92.02 %
  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: -0.41 (0.23), residues: 1485
  helix:  0.61 (0.27), residues: 382
  sheet: -0.14 (0.32), residues: 297
  loop : -0.71 (0.23), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP C 459 
 HIS   0.009   0.001   HIS C 446 
 PHE   0.014   0.002   PHE A 235 
 TYR   0.012   0.001   TYR C 114 
 ARG   0.003   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04606 (  409)
  hydrogen bonds       : angle       5.75241 ( 1074)
  SS BOND              : bond        0.00338 (   14)
  SS BOND              : angle       1.66987 (   28)
  covalent geometry    : bond        0.00363 (12293)
  covalent geometry    : angle       0.60893 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 120
  time to evaluate  : 1.283 
Fit side-chains
REVERT: A  387 GLN cc_start: 0.7442 (tp40) cc_final: 0.6912 (tm-30)
REVERT: A  402 ASP cc_start: 0.7699 (m-30) cc_final: 0.7318 (t0)
REVERT: B  127 SER cc_start: 0.9150 (t) cc_final: 0.8841 (t)
REVERT: C  462 LEU cc_start: 0.8748 (tt) cc_final: 0.8531 (tt)
REVERT: D   40 GLN cc_start: 0.8599 (mm110) cc_final: 0.8360 (mm110)
  outliers start: 12
  outliers final: 10
  residues processed: 126
  average time/residue: 0.2169
  time to fit residues: 41.5217
Evaluate side-chains
  113 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  512 HIS
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  244 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 136 optimal weight:    5.9990
   chunk 129 optimal weight:    0.0570
   chunk 28 optimal weight:    0.7980
   chunk 45 optimal weight:    0.8980
   chunk 90 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 127 optimal weight:    3.9990
   chunk 84 optimal weight:    0.4980
   chunk 27 optimal weight:    0.0970
   chunk 2 optimal weight:    0.0770
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.3054

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

Flipped N/Q/H residues before XYZ refinement:
** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 203 ASN
C 117 GLN
C 233 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.151658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.113573 restraints weight = 17428.854|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 3.06
r_work: 0.3381 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3381
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7398
moved from start:          0.1349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.077  12307  Z= 0.112
  Angle     :  0.552  10.091  16773  Z= 0.285
  Chirality :  0.042   0.189   1921
  Planarity :  0.004   0.054   2142
  Dihedral  :  4.430  25.045   1649
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  9.90 %
    Favored  : 89.14 %
  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 (0.23), residues: 1485
  helix:  0.95 (0.28), residues: 381
  sheet:  0.16 (0.33), residues: 276
  loop : -0.77 (0.22), residues: 828

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C 459 
 HIS   0.009   0.001   HIS A 512 
 PHE   0.015   0.001   PHE A 678 
 TYR   0.014   0.001   TYR A 603 
 ARG   0.005   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03734 (  409)
  hydrogen bonds       : angle       5.31023 ( 1074)
  SS BOND              : bond        0.00262 (   14)
  SS BOND              : angle       1.37839 (   28)
  covalent geometry    : bond        0.00259 (12293)
  covalent geometry    : angle       0.55002 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 1.414 
Fit side-chains
REVERT: A  402 ASP cc_start: 0.7615 (m-30) cc_final: 0.7168 (t0)
REVERT: C  462 LEU cc_start: 0.8688 (tt) cc_final: 0.8295 (tt)
REVERT: D   40 GLN cc_start: 0.8580 (mm110) cc_final: 0.8363 (mm110)
  outliers start: 13
  outliers final: 6
  residues processed: 131
  average time/residue: 0.2327
  time to fit residues: 45.6652
Evaluate side-chains
  114 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 108
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain C residue  237 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 130 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 89 optimal weight:    3.9990
   chunk 127 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 131 optimal weight:    0.9980
   chunk 62 optimal weight:    8.9990
   chunk 134 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 652 GLN
C 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.148762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.110256 restraints weight = 17395.302|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 3.06
r_work: 0.3333 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12307  Z= 0.152
  Angle     :  0.575   9.571  16773  Z= 0.292
  Chirality :  0.043   0.184   1921
  Planarity :  0.004   0.056   2142
  Dihedral  :  4.508  24.242   1649
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.90 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.22 (0.23), residues: 1485
  helix:  1.03 (0.28), residues: 382
  sheet:  0.03 (0.32), residues: 279
  loop : -0.76 (0.22), residues: 824

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 459 
 HIS   0.009   0.001   HIS C 446 
 PHE   0.013   0.001   PHE A 235 
 TYR   0.015   0.001   TYR D 273 
 ARG   0.005   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03528 (  409)
  hydrogen bonds       : angle       5.10997 ( 1074)
  SS BOND              : bond        0.00303 (   14)
  SS BOND              : angle       1.31804 (   28)
  covalent geometry    : bond        0.00369 (12293)
  covalent geometry    : angle       0.57247 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 1.306 
Fit side-chains
REVERT: A  384 CYS cc_start: 0.7877 (OUTLIER) cc_final: 0.7637 (t)
REVERT: C  462 LEU cc_start: 0.8668 (tt) cc_final: 0.8323 (tt)
REVERT: D   40 GLN cc_start: 0.8615 (mm110) cc_final: 0.8341 (mm110)
  outliers start: 21
  outliers final: 10
  residues processed: 126
  average time/residue: 0.2161
  time to fit residues: 41.7608
Evaluate side-chains
  116 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 1.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  384 CYS
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain D residue  140 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 129 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 48 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9990
   chunk 125 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 70 optimal weight:    0.3980
   chunk 117 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0870
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 117 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.149289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.111069 restraints weight = 17409.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3501 rms_B_bonded: 3.03
r_work: 0.3362 rms_B_bonded: 3.61 restraints_weight: 0.5000
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.1667

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  12307  Z= 0.128
  Angle     :  0.554   9.852  16773  Z= 0.283
  Chirality :  0.042   0.186   1921
  Planarity :  0.004   0.055   2142
  Dihedral  :  4.466  23.459   1649
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 12.49 %
    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: -0.17 (0.23), residues: 1485
  helix:  1.10 (0.28), residues: 383
  sheet:  0.03 (0.32), residues: 280
  loop : -0.73 (0.22), residues: 822

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 459 
 HIS   0.006   0.001   HIS C 446 
 PHE   0.012   0.001   PHE A 235 
 TYR   0.010   0.001   TYR C 114 
 ARG   0.006   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03256 (  409)
  hydrogen bonds       : angle       4.96706 ( 1074)
  SS BOND              : bond        0.00275 (   14)
  SS BOND              : angle       1.28880 (   28)
  covalent geometry    : bond        0.00306 (12293)
  covalent geometry    : angle       0.55145 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 109
  time to evaluate  : 1.342 
Fit side-chains
REVERT: A  381 MET cc_start: 0.7702 (tpt) cc_final: 0.7492 (tpt)
REVERT: C  462 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8223 (tt)
REVERT: D   40 GLN cc_start: 0.8578 (mm110) cc_final: 0.8301 (mm110)
  outliers start: 23
  outliers final: 9
  residues processed: 126
  average time/residue: 0.2174
  time to fit residues: 41.6761
Evaluate side-chains
  116 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue  140 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 11 optimal weight:    0.2980
   chunk 66 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 142 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 140 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 124 optimal weight:    5.9990
   chunk 16 optimal weight:    0.7980
   chunk 118 optimal weight:    1.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN
** A 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.148940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.110569 restraints weight = 17641.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3482 rms_B_bonded: 3.07
r_work: 0.3339 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3339
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12307  Z= 0.131
  Angle     :  0.558  10.225  16773  Z= 0.284
  Chirality :  0.042   0.185   1921
  Planarity :  0.004   0.056   2142
  Dihedral  :  4.508  32.756   1649
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.05 %
    Favored  : 94.95 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 13.45 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.17 (0.23), residues: 1485
  helix:  1.13 (0.28), residues: 382
  sheet:  0.01 (0.32), residues: 280
  loop : -0.74 (0.22), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP C 459 
 HIS   0.006   0.001   HIS C 446 
 PHE   0.013   0.001   PHE A 235 
 TYR   0.010   0.001   TYR C 114 
 ARG   0.007   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03206 (  409)
  hydrogen bonds       : angle       4.90601 ( 1074)
  SS BOND              : bond        0.00331 (   14)
  SS BOND              : angle       1.47571 (   28)
  covalent geometry    : bond        0.00317 (12293)
  covalent geometry    : angle       0.55535 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 1.411 
Fit side-chains
REVERT: A  381 MET cc_start: 0.7569 (tpt) cc_final: 0.7369 (tpt)
REVERT: A  575 LEU cc_start: 0.8253 (mm) cc_final: 0.8042 (mm)
REVERT: C   88 MET cc_start: 0.8044 (mtp) cc_final: 0.7784 (mtp)
REVERT: C  462 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8202 (tt)
REVERT: D   40 GLN cc_start: 0.8567 (mm110) cc_final: 0.8286 (mm110)
REVERT: D  116 HIS cc_start: 0.7956 (p90) cc_final: 0.7677 (p90)
  outliers start: 17
  outliers final: 10
  residues processed: 125
  average time/residue: 0.2141
  time to fit residues: 40.8057
Evaluate side-chains
  119 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 108
  time to evaluate  : 1.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  333 MET
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue  140 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 70 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 44 optimal weight:    0.9980
   chunk 135 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 138 optimal weight:    3.9990
   chunk 140 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 136 optimal weight:    0.8980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN
A 560 GLN
C 117 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.147610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.109238 restraints weight = 17643.096|
|-----------------------------------------------------------------------------|
r_work (start): 0.3477 rms_B_bonded: 3.01
r_work: 0.3338 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  12307  Z= 0.160
  Angle     :  0.587  10.248  16773  Z= 0.297
  Chirality :  0.043   0.180   1921
  Planarity :  0.004   0.056   2142
  Dihedral  :  4.592  31.937   1649
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.12 %
    Favored  : 84.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.25 (0.22), residues: 1485
  helix:  1.07 (0.28), residues: 381
  sheet: -0.07 (0.31), residues: 286
  loop : -0.77 (0.22), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP C 459 
 HIS   0.008   0.001   HIS C 446 
 PHE   0.023   0.002   PHE D 178 
 TYR   0.018   0.001   TYR D 273 
 ARG   0.008   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03308 (  409)
  hydrogen bonds       : angle       4.93745 ( 1074)
  SS BOND              : bond        0.00275 (   14)
  SS BOND              : angle       1.70515 (   28)
  covalent geometry    : bond        0.00391 (12293)
  covalent geometry    : angle       0.58340 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 1.597 
Fit side-chains
REVERT: A  559 MET cc_start: 0.7754 (mmt) cc_final: 0.7463 (mmm)
REVERT: C   88 MET cc_start: 0.8125 (mtp) cc_final: 0.7836 (mtp)
REVERT: C  462 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8283 (tt)
REVERT: D   40 GLN cc_start: 0.8635 (mm110) cc_final: 0.8352 (mm110)
REVERT: D  116 HIS cc_start: 0.7959 (p90) cc_final: 0.7641 (p90)
  outliers start: 19
  outliers final: 13
  residues processed: 123
  average time/residue: 0.2272
  time to fit residues: 42.5384
Evaluate side-chains
  122 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 VAL
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  628 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  321 ILE
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue  140 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 30 optimal weight:    0.9990
   chunk 18 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 136 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 117 optimal weight:    0.6980
   chunk 55 optimal weight:    7.9990
   chunk 107 optimal weight:    0.0770
   chunk 1 optimal weight:    1.9990
   chunk 51 optimal weight:    0.5980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN
C 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.149079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.110483 restraints weight = 17691.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3493 rms_B_bonded: 3.09
r_work: 0.3352 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.1905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12307  Z= 0.127
  Angle     :  0.564  10.399  16773  Z= 0.286
  Chirality :  0.042   0.193   1921
  Planarity :  0.004   0.056   2142
  Dihedral  :  4.552  32.138   1649
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 13.75 %
    Favored  : 84.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.15 (0.22), residues: 1485
  helix:  1.13 (0.28), residues: 382
  sheet:  0.03 (0.32), residues: 280
  loop : -0.71 (0.22), residues: 823

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP C 459 
 HIS   0.006   0.001   HIS C 446 
 PHE   0.013   0.001   PHE A 235 
 TYR   0.016   0.001   TYR D 273 
 ARG   0.009   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03107 (  409)
  hydrogen bonds       : angle       4.88036 ( 1074)
  SS BOND              : bond        0.00247 (   14)
  SS BOND              : angle       1.55449 (   28)
  covalent geometry    : bond        0.00309 (12293)
  covalent geometry    : angle       0.56109 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 1.806 
Fit side-chains
REVERT: A  381 MET cc_start: 0.7505 (tpt) cc_final: 0.7173 (tpt)
REVERT: A  478 MET cc_start: 0.6063 (tpt) cc_final: 0.5445 (tpt)
REVERT: A  559 MET cc_start: 0.7811 (mmt) cc_final: 0.7510 (mmm)
REVERT: C   88 MET cc_start: 0.8100 (mtp) cc_final: 0.7808 (mtp)
REVERT: C  115 SER cc_start: 0.7365 (OUTLIER) cc_final: 0.7160 (p)
REVERT: C  462 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8283 (tt)
REVERT: D   40 GLN cc_start: 0.8631 (mm110) cc_final: 0.8347 (mm110)
REVERT: D  116 HIS cc_start: 0.7887 (p90) cc_final: 0.7487 (p90)
  outliers start: 25
  outliers final: 15
  residues processed: 131
  average time/residue: 0.2456
  time to fit residues: 49.2745
Evaluate side-chains
  125 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  628 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  321 ILE
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue  140 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 79 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 60 optimal weight:    0.0770
   chunk 97 optimal weight:    0.7980
   chunk 66 optimal weight:    1.9990
   chunk 133 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 144 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 112 optimal weight:    0.7980
   overall best weight:    0.7342

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

Flipped N/Q/H residues before XYZ refinement:
A 152 GLN
A 378 GLN
C 117 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.147556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.108708 restraints weight = 17554.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 3.05
r_work: 0.3324 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7466
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  12307  Z= 0.145
  Angle     :  0.582  10.377  16773  Z= 0.294
  Chirality :  0.043   0.187   1921
  Planarity :  0.004   0.056   2142
  Dihedral  :  4.577  32.533   1649
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 14.56 %
    Favored  : 84.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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 (0.22), residues: 1485
  helix:  1.09 (0.28), residues: 382
  sheet: -0.05 (0.31), residues: 286
  loop : -0.78 (0.22), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 459 
 HIS   0.007   0.001   HIS C 446 
 PHE   0.020   0.001   PHE A 678 
 TYR   0.017   0.001   TYR D 273 
 ARG   0.009   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03145 (  409)
  hydrogen bonds       : angle       4.91383 ( 1074)
  SS BOND              : bond        0.00274 (   14)
  SS BOND              : angle       1.67299 (   28)
  covalent geometry    : bond        0.00355 (12293)
  covalent geometry    : angle       0.57868 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 1.288 
Fit side-chains
REVERT: A  381 MET cc_start: 0.7530 (tpt) cc_final: 0.7198 (tpt)
REVERT: A  478 MET cc_start: 0.6114 (tpt) cc_final: 0.5431 (tpt)
REVERT: A  559 MET cc_start: 0.7809 (mmt) cc_final: 0.7520 (mmm)
REVERT: B  208 LEU cc_start: 0.8547 (mt) cc_final: 0.8322 (mt)
REVERT: C   88 MET cc_start: 0.8128 (mtp) cc_final: 0.7833 (mtp)
REVERT: C  462 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8312 (tt)
REVERT: D   40 GLN cc_start: 0.8638 (mm110) cc_final: 0.8352 (mm110)
REVERT: D  116 HIS cc_start: 0.7864 (p90) cc_final: 0.7453 (p90)
  outliers start: 17
  outliers final: 15
  residues processed: 121
  average time/residue: 0.2406
  time to fit residues: 44.0670
Evaluate side-chains
  122 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 106
  time to evaluate  : 1.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  628 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  321 ILE
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue  140 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 115 optimal weight:    0.5980
   chunk 11 optimal weight:    0.9980
   chunk 137 optimal weight:    1.9990
   chunk 52 optimal weight:    0.7980
   chunk 145 optimal weight:    5.9990
   chunk 122 optimal weight:    0.0980
   chunk 49 optimal weight:    6.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN
C 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.148424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.110120 restraints weight = 17409.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.3471 rms_B_bonded: 3.04
r_work: 0.3328 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.2015

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  12307  Z= 0.140
  Angle     :  0.583  10.425  16773  Z= 0.293
  Chirality :  0.043   0.190   1921
  Planarity :  0.004   0.056   2142
  Dihedral  :  4.575  32.583   1649
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 14.63 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.22 (0.22), residues: 1485
  helix:  1.09 (0.28), residues: 382
  sheet: -0.03 (0.32), residues: 286
  loop : -0.77 (0.22), residues: 817

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP C 459 
 HIS   0.007   0.001   HIS C 446 
 PHE   0.014   0.001   PHE A 235 
 TYR   0.016   0.001   TYR D 273 
 ARG   0.009   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03082 (  409)
  hydrogen bonds       : angle       4.88860 ( 1074)
  SS BOND              : bond        0.00270 (   14)
  SS BOND              : angle       1.63062 (   28)
  covalent geometry    : bond        0.00342 (12293)
  covalent geometry    : angle       0.57932 (16745)

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

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

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2970 Ramachandran restraints generated.
    1485 Oldfield, 0 Emsley, 1485 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 110
  time to evaluate  : 1.299 
Fit side-chains
REVERT: A  381 MET cc_start: 0.7548 (tpt) cc_final: 0.7219 (tpt)
REVERT: A  478 MET cc_start: 0.6036 (tpt) cc_final: 0.5463 (tpt)
REVERT: A  559 MET cc_start: 0.7786 (mmt) cc_final: 0.7498 (mmm)
REVERT: B  208 LEU cc_start: 0.8504 (mt) cc_final: 0.8270 (mt)
REVERT: C  115 SER cc_start: 0.7530 (OUTLIER) cc_final: 0.7320 (p)
REVERT: C  462 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8301 (tt)
REVERT: D   40 GLN cc_start: 0.8631 (mm110) cc_final: 0.8338 (mm110)
REVERT: D  116 HIS cc_start: 0.7792 (p90) cc_final: 0.7336 (p90)
  outliers start: 19
  outliers final: 15
  residues processed: 125
  average time/residue: 0.2778
  time to fit residues: 51.8294
Evaluate side-chains
  125 residues out of total 1353 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 2.543 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 THR
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  408 LEU
Chi-restraints excluded: chain A residue  531 HIS
Chi-restraints excluded: chain A residue  553 LEU
Chi-restraints excluded: chain A residue  588 VAL
Chi-restraints excluded: chain A residue  628 THR
Chi-restraints excluded: chain B residue   83 SER
Chi-restraints excluded: chain B residue  126 LEU
Chi-restraints excluded: chain B residue  138 MET
Chi-restraints excluded: chain B residue  143 GLU
Chi-restraints excluded: chain B residue  203 ASN
Chi-restraints excluded: chain C residue  115 SER
Chi-restraints excluded: chain C residue  237 VAL
Chi-restraints excluded: chain C residue  321 ILE
Chi-restraints excluded: chain C residue  462 LEU
Chi-restraints excluded: chain D residue  140 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 115 optimal weight:    0.9980
   chunk 31 optimal weight:    0.1980
   chunk 48 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 88 optimal weight:    0.0870
   chunk 83 optimal weight:    0.7980
   chunk 47 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   chunk 139 optimal weight:    0.4980
   chunk 53 optimal weight:    0.9990
   chunk 140 optimal weight:    1.9990
   overall best weight:    0.4158

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

Flipped N/Q/H residues before XYZ refinement:
A 378 GLN
C 117 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.150592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.112302 restraints weight = 17435.300|
|-----------------------------------------------------------------------------|
r_work (start): 0.3502 rms_B_bonded: 3.05
r_work: 0.3361 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7439
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12307  Z= 0.112
  Angle     :  0.558  11.422  16773  Z= 0.282
  Chirality :  0.042   0.199   1921
  Planarity :  0.004   0.056   2142
  Dihedral  :  4.456  31.710   1649
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.32 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 14.93 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.22), residues: 1485
  helix:  1.20 (0.28), residues: 381
  sheet: -0.04 (0.32), residues: 289
  loop : -0.70 (0.22), residues: 815

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP C 459 
 HIS   0.004   0.001   HIS C 446 
 PHE   0.021   0.001   PHE A 678 
 TYR   0.015   0.001   TYR D 273 
 ARG   0.010   0.000   ARG D  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02898 (  409)
  hydrogen bonds       : angle       4.84385 ( 1074)
  SS BOND              : bond        0.00247 (   14)
  SS BOND              : angle       1.58207 (   28)
  covalent geometry    : bond        0.00270 (12293)
  covalent geometry    : angle       0.55506 (16745)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5687.13 seconds
wall clock time: 101 minutes 53.52 seconds (6113.52 seconds total)