Starting phenix.real_space_refine
on Fri Feb 14 11:37:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ran_4781/02_2025/6ran_4781.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ran_4781/02_2025/6ran_4781.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ran_4781/02_2025/6ran_4781.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ran_4781/02_2025/6ran_4781.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ran_4781/02_2025/6ran_4781.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ran_4781/02_2025/6ran_4781.cif"
  }
  resolution = 4.2
  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=   0.002
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      25      5.16       5
     C    6579      2.51       5
     N    1795      2.21       5
     O    1774      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 72 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: 10173
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4741
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4741
          Classifications: {'peptide': 592}
          Link IDs: {'PTRANS': 24, 'TRANS': 567}
    Chain: "B"
      Number of atoms: 4535
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4535
          Classifications: {'peptide': 574}
          Link IDs: {'PTRANS': 18, 'TRANS': 555}
    Chain: "C"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 897
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
  Time building chain proxies: 6.12, per 1000 atoms: 0.60
  Number of scatterers: 10173
  At special positions: 0
  Unit cell: (104.469, 91.545, 159.396, 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      25     16.00
     O    1774      8.00
     N    1795      7.00
     C    6579      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 108 " distance=2.06

  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: 2.46
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2356

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      66.7% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 20
      removed outlier: 3.587A  pdb=" N   ARG A  17 " --> pdb=" O   ALA A  13 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ILE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 24
      Proline residue:  A  24  - end of helix
      No H-bonds generated for 'chain 'A' and resid 21 through 24'
    Processing helix  chain 'A' and resid 25 through 45
      removed outlier: 3.603A  pdb=" N   PHE A  35 " --> pdb=" O   LEU A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 64 through 71
    Processing helix  chain 'A' and resid 72 through 120
    Processing helix  chain 'A' and resid 121 through 128
      removed outlier: 4.313A  pdb=" N   TYR A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 138
      removed outlier: 3.519A  pdb=" N   LEU A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 150
      removed outlier: 3.592A  pdb=" N   ILE A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 173
      removed outlier: 3.848A  pdb=" N   VAL A 155 " --> pdb=" O   GLY A 151 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 4.337A  pdb=" N   VAL A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 222
    Processing helix  chain 'A' and resid 222 through 230
    Processing helix  chain 'A' and resid 231 through 285
      removed outlier: 3.897A  pdb=" N   ARG A 241 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LEU A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   PHE A 260 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   PHE A 261 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.654A  pdb=" N   VAL A 284 " --> pdb=" O   GLY A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 314
      removed outlier: 3.739A  pdb=" N   PHE A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   GLN A 305 " --> pdb=" O   ARG A 301 " (cutoff:3.500A)
      Proline residue:  A 306  - end of helix
      removed outlier: 3.865A  pdb=" N   ASP A 309 " --> pdb=" O   GLN A 305 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   SER A 311 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   ASP A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   PHE A 314 " --> pdb=" O   LEU A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 332
      removed outlier: 4.092A  pdb=" N   GLY A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ARG A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 407
      removed outlier: 3.995A  pdb=" N   VAL A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 433
    Processing helix  chain 'A' and resid 449 through 455
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.797A  pdb=" N   VAL A 466 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLU A 467 " --> pdb=" O   PRO A 463 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   GLU A 468 " --> pdb=" O   GLU A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 482
    Processing helix  chain 'A' and resid 484 through 488
      removed outlier: 3.829A  pdb=" N   THR A 488 " --> pdb=" O   GLY A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 514
    Processing helix  chain 'A' and resid 529 through 544
    Processing helix  chain 'A' and resid 555 through 560
    Processing helix  chain 'A' and resid 578 through 586
      removed outlier: 3.822A  pdb=" N   GLY A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 586 through 602
      removed outlier: 3.685A  pdb=" N   ALA A 590 " --> pdb=" O   GLY A 586 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 5 through 19
      removed outlier: 3.993A  pdb=" N   LEU B   9 " --> pdb=" O   SER B   5 " (cutoff:3.500A)
      Proline residue:  B  15  - end of helix
    Processing helix  chain 'B' and resid 20 through 54
      removed outlier: 3.896A  pdb=" N   TYR B  24 " --> pdb=" O   TYR B  20 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ILE B  35 " --> pdb=" O   GLY B  31 " (cutoff:3.500A)
      Proline residue:  B  42  - end of helix
    Processing helix  chain 'B' and resid 57 through 103
      removed outlier: 4.521A  pdb=" N   TYR B  61 " --> pdb=" O   GLY B  57 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   VAL B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 4.155A  pdb=" N   TYR B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 133
      removed outlier: 3.643A  pdb=" N   ASN B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 158
      removed outlier: 4.050A  pdb=" N   LEU B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 207
      removed outlier: 3.814A  pdb=" N   ALA B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ILE B 168 " --> pdb=" O   TYR B 164 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
      removed outlier: 3.665A  pdb=" N   LEU B 174 " --> pdb=" O   PRO B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 212
    Processing helix  chain 'B' and resid 216 through 243
      removed outlier: 4.091A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 244 through 271
      removed outlier: 3.849A  pdb=" N   PHE B 255 " --> pdb=" O   PHE B 251 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ALA B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 287
    Processing helix  chain 'B' and resid 288 through 318
      removed outlier: 4.204A  pdb=" N   ILE B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
      removed outlier: 4.288A  pdb=" N   LEU B 293 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.540A  pdb=" N   LEU B 335 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 384
      removed outlier: 3.708A  pdb=" N   ALA B 381 " --> pdb=" O   LYS B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 405
      No H-bonds generated for 'chain 'B' and resid 403 through 405'
    Processing helix  chain 'B' and resid 406 through 413
    Processing helix  chain 'B' and resid 427 through 433
    Processing helix  chain 'B' and resid 440 through 451
      removed outlier: 3.751A  pdb=" N   VAL B 444 " --> pdb=" O   ASP B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 460
      removed outlier: 3.802A  pdb=" N   PHE B 460 " --> pdb=" O   GLU B 456 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 466
      removed outlier: 3.719A  pdb=" N   THR B 466 " --> pdb=" O   GLY B 463 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 491
      removed outlier: 3.727A  pdb=" N   LYS B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 521
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 4.212A  pdb=" N   HIS B 538 " --> pdb=" O   ALA B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 563
    Processing helix  chain 'B' and resid 564 through 574
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.924A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 383
      removed outlier: 5.563A  pdb=" N   LYS A 377 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 7.428A  pdb=" N   LEU A 360 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 7.341A  pdb=" N   PHE A 381 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 5.303A  pdb=" N   ARG A 356 " --> pdb=" O   PHE A 381 " (cutoff:3.500A)
      removed outlier: 7.193A  pdb=" N   VAL A 383 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   GLU A 354 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   VAL A 358 " --> pdb=" O   ARG A 414 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 6.483A  pdb=" N   LEU A 519 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 7.808A  pdb=" N   ILE A 552 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   LEU A 521 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.052A  pdb=" N   LYS A 388 " --> pdb=" O   ARG A 564 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   LEU A 566 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 5.785A  pdb=" N   ALA A 390 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   VAL A 392 " --> pdb=" O   PHE A 568 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ILE A 565 " --> pdb=" O   GLU A 576 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   GLU A 576 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 6.843A  pdb=" N   VAL A 567 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 351 through 361
      removed outlier: 6.999A  pdb=" N   LEU B 353 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 7.860A  pdb=" N   LYS B 347 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   ARG B 355 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 5.927A  pdb=" N   GLY B 345 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
      removed outlier: 4.973A  pdb=" N   LEU B 357 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 4.548A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   GLU B 392 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.172A  pdb=" N   GLY B 415 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ASP B 499 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   ALA B 417 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   THR B 366 " --> pdb=" O   TRP B 541 " (cutoff:3.500A)
      removed outlier: 7.813A  pdb=" N   ILE B 543 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 6.129A  pdb=" N   GLY B 368 " --> pdb=" O   ILE B 543 " (cutoff:3.500A)
      removed outlier: 7.214A  pdb=" N   LEU B 545 " --> pdb=" O   GLY B 368 " (cutoff:3.500A)
      removed outlier: 5.978A  pdb=" N   THR B 370 " --> pdb=" O   LEU B 545 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.659A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.529A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    653 hydrogen bonds defined for protein.
    1917 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: 3.44

  Time building geometry restraints manager: 2.89 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1620
        1.31 -     1.44: 3197
        1.44 -     1.57: 5520
        1.57 -     1.70: 2
        1.70 -     1.83: 45
  Bond restraints: 10384
  Sorted by residual:
  bond pdb=" N   PRO A 340 "
       pdb=" CD  PRO A 340 "
    ideal  model  delta    sigma   weight residual
    1.473  1.572 -0.099 1.40e-02 5.10e+03 4.96e+01
  bond pdb=" N   PRO B 291 "
       pdb=" CD  PRO B 291 "
    ideal  model  delta    sigma   weight residual
    1.473  1.539 -0.066 1.40e-02 5.10e+03 2.21e+01
  bond pdb=" CA  GLY B 345 "
       pdb=" C   GLY B 345 "
    ideal  model  delta    sigma   weight residual
    1.516  1.481  0.035 8.20e-03 1.49e+04 1.87e+01
  bond pdb=" CA  GLY B 415 "
       pdb=" C   GLY B 415 "
    ideal  model  delta    sigma   weight residual
    1.520  1.489  0.031 7.30e-03 1.88e+04 1.79e+01
  bond pdb=" N   ILE C  51 "
       pdb=" CA  ILE C  51 "
    ideal  model  delta    sigma   weight residual
    1.456  1.504 -0.048 1.15e-02 7.56e+03 1.76e+01
  ... (remaining 10379 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.41: 11178
        2.41 -     4.83: 2335
        4.83 -     7.24: 466
        7.24 -     9.66: 82
        9.66 -    12.07: 13
  Bond angle restraints: 14074
  Sorted by residual:
  angle pdb=" N   VAL B 210 "
        pdb=" CA  VAL B 210 "
        pdb=" C   VAL B 210 "
      ideal   model   delta    sigma   weight residual
     111.81  103.51    8.30 8.60e-01 1.35e+00 9.31e+01
  angle pdb=" N   GLU B 442 "
        pdb=" CA  GLU B 442 "
        pdb=" C   GLU B 442 "
      ideal   model   delta    sigma   weight residual
     111.07  120.93   -9.86 1.07e+00 8.73e-01 8.49e+01
  angle pdb=" N   VAL A 186 "
        pdb=" CA  VAL A 186 "
        pdb=" C   VAL A 186 "
      ideal   model   delta    sigma   weight residual
     110.42  119.00   -8.58 9.60e-01 1.09e+00 7.98e+01
  angle pdb=" N   VAL B 444 "
        pdb=" CA  VAL B 444 "
        pdb=" CB  VAL B 444 "
      ideal   model   delta    sigma   weight residual
     110.55  120.47   -9.92 1.17e+00 7.31e-01 7.19e+01
  angle pdb=" N   VAL B 576 "
        pdb=" CA  VAL B 576 "
        pdb=" C   VAL B 576 "
      ideal   model   delta    sigma   weight residual
     107.80  119.82  -12.02 1.45e+00 4.76e-01 6.88e+01
  ... (remaining 14069 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.38: 5849
       17.38 -    34.75: 218
       34.75 -    52.13: 52
       52.13 -    69.50: 42
       69.50 -    86.88: 14
  Dihedral angle restraints: 6175
    sinusoidal: 2495
      harmonic: 3680
  Sorted by residual:
  dihedral pdb=" N   THR A 135 "
           pdb=" C   THR A 135 "
           pdb=" CA  THR A 135 "
           pdb=" CB  THR A 135 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.75  -12.35     0      2.50e+00 1.60e-01 2.44e+01
  dihedral pdb=" N   VAL B  90 "
           pdb=" C   VAL B  90 "
           pdb=" CA  VAL B  90 "
           pdb=" CB  VAL B  90 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.67  -12.27     0      2.50e+00 1.60e-01 2.41e+01
  dihedral pdb=" C   VAL B 483 "
           pdb=" N   VAL B 483 "
           pdb=" CA  VAL B 483 "
           pdb=" CB  VAL B 483 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.14   12.14     0      2.50e+00 1.60e-01 2.36e+01
  ... (remaining 6172 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.106: 1010
       0.106 -    0.211: 397
       0.211 -    0.316: 137
       0.316 -    0.421: 39
       0.421 -    0.527: 24
  Chirality restraints: 1607
  Sorted by residual:
  chirality pdb=" CA  LEU A  33 "
            pdb=" N   LEU A  33 "
            pdb=" C   LEU A  33 "
            pdb=" CB  LEU A  33 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.98    0.53 2.00e-01 2.50e+01 6.93e+00
  chirality pdb=" CA  GLU B 442 "
            pdb=" N   GLU B 442 "
            pdb=" C   GLU B 442 "
            pdb=" CB  GLU B 442 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.01    0.50 2.00e-01 2.50e+01 6.35e+00
  chirality pdb=" CA  VAL B  90 "
            pdb=" N   VAL B  90 "
            pdb=" C   VAL B  90 "
            pdb=" CB  VAL B  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    1.94    0.50 2.00e-01 2.50e+01 6.30e+00
  ... (remaining 1604 not shown)

  Planarity restraints: 1790
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 172 "    0.030 2.00e-02 2.50e+03   6.07e-02 3.68e+01
        pdb=" C   LEU A 172 "   -0.105 2.00e-02 2.50e+03
        pdb=" O   LEU A 172 "    0.040 2.00e-02 2.50e+03
        pdb=" N   SER A 173 "    0.035 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  75 "   -0.059 2.00e-02 2.50e+03   2.86e-02 2.04e+01
        pdb=" CG  TRP A  75 "    0.017 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  75 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  75 "    0.021 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  75 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  75 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  75 "    0.041 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  75 "   -0.029 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  75 "    0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  75 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B  22 "   -0.060 2.00e-02 2.50e+03   2.78e-02 1.94e+01
        pdb=" CG  TRP B  22 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP B  22 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP B  22 "    0.024 2.00e-02 2.50e+03
        pdb=" NE1 TRP B  22 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B  22 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B  22 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B  22 "   -0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B  22 "    0.008 2.00e-02 2.50e+03
        pdb=" CH2 TRP B  22 "   -0.026 2.00e-02 2.50e+03
  ... (remaining 1787 not shown)

  Histogram of nonbonded interaction distances:
        2.42 -     2.92: 3616
        2.92 -     3.41: 10205
        3.41 -     3.91: 16524
        3.91 -     4.40: 18254
        4.40 -     4.90: 30613
  Nonbonded interactions: 79212
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG C  19 "
            pdb=" OE1 GLN C  82 "
     model   vdw
     2.421 3.120
  nonbonded pdb=" O   SER C  85 "
            pdb=" OG  SER C  85 "
     model   vdw
     2.450 3.040
  nonbonded pdb=" O   PRO A  47 "
            pdb=" N   PHE A  50 "
     model   vdw
     2.451 3.120
  nonbonded pdb=" N   LEU B 468 "
            pdb=" O   LEU B 468 "
     model   vdw
     2.481 2.496
  nonbonded pdb=" N   LEU B 388 "
            pdb=" O   LEU B 388 "
     model   vdw
     2.485 2.496
  ... (remaining 79207 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  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:          0.370
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.360
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7088
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      :  0.017   0.099  10384  Z= 1.106
  Angle     :  2.079  12.069  14074  Z= 1.489
  Chirality :  0.140   0.527   1607
  Planarity :  0.012   0.092   1790
  Dihedral  : 12.459  86.879   3813
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.03
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.67 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.47 %
    Favored  : 97.44 %
  Cbeta Deviations :  1.61 %
  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:  0.16 (0.22), residues: 1281
  helix:  1.09 (0.18), residues: 784
  sheet:  0.14 (0.44), residues: 131
  loop : -2.07 (0.27), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.060   0.009   TRP B  22 
 HIS   0.007   0.001   HIS A 435 
 PHE   0.049   0.009   PHE A 270 
 TYR   0.058   0.006   TYR B 284 
 ARG   0.004   0.000   ARG B  23 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  334 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 333
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7813 (m-80) cc_final: 0.7140 (m-80)
REVERT: A   40 THR cc_start: 0.8383 (p) cc_final: 0.8134 (t)
REVERT: A  205 MET cc_start: 0.8764 (tmm) cc_final: 0.8363 (tmm)
REVERT: A  359 TRP cc_start: 0.7247 (m100) cc_final: 0.6989 (m100)
REVERT: A  365 LYS cc_start: 0.6656 (mmtm) cc_final: 0.5315 (tptt)
REVERT: B   32 LEU cc_start: 0.9263 (mt) cc_final: 0.8881 (mt)
REVERT: B  102 LEU cc_start: 0.9222 (mt) cc_final: 0.8925 (mt)
REVERT: B  130 ARG cc_start: 0.8858 (ttp80) cc_final: 0.8392 (tmm160)
REVERT: B  132 MET cc_start: 0.8394 (ttp) cc_final: 0.7765 (tmm)
REVERT: B  145 PHE cc_start: 0.8508 (t80) cc_final: 0.8159 (t80)
REVERT: B  161 LEU cc_start: 0.8271 (tp) cc_final: 0.8051 (tp)
REVERT: B  173 PHE cc_start: 0.6584 (t80) cc_final: 0.6322 (t80)
REVERT: B  255 PHE cc_start: 0.6998 (m-10) cc_final: 0.6582 (m-10)
REVERT: B  258 LEU cc_start: 0.8111 (tt) cc_final: 0.7527 (tp)
REVERT: B  289 THR cc_start: 0.6625 (p) cc_final: 0.6383 (p)
REVERT: B  365 MET cc_start: 0.9128 (ppp) cc_final: 0.8798 (ppp)
REVERT: C    6 GLU cc_start: 0.5873 (mp0) cc_final: 0.5667 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 334
  average time/residue: 0.2852
  time to fit residues: 124.9440
Evaluate side-chains
  187 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 187
  time to evaluate  : 1.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    0.7980
   chunk 74 optimal weight:    0.7980
   chunk 116 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
B 111 HIS
C   3 GLN
** C  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.124289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.102907 restraints weight = 27763.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.105526 restraints weight = 15937.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.107330 restraints weight = 10589.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10384  Z= 0.223
  Angle     :  0.663   7.327  14074  Z= 0.360
  Chirality :  0.042   0.197   1607
  Planarity :  0.005   0.058   1790
  Dihedral  :  5.001  27.068   1442
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  2.09 %
    Favored  : 97.72 %
  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:  1.24 (0.23), residues: 1281
  helix:  1.93 (0.18), residues: 788
  sheet:  0.11 (0.40), residues: 137
  loop : -1.47 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 262 
 HIS   0.006   0.001   HIS B 111 
 PHE   0.020   0.002   PHE A 472 
 TYR   0.024   0.002   TYR A 299 
 ARG   0.017   0.001   ARG A 426 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 232
  time to evaluate  : 1.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7563 (m-80) cc_final: 0.6772 (m-10)
REVERT: A  205 MET cc_start: 0.8733 (tmm) cc_final: 0.8413 (tmm)
REVERT: B   32 LEU cc_start: 0.9034 (mt) cc_final: 0.8801 (mt)
REVERT: B  109 PHE cc_start: 0.7926 (t80) cc_final: 0.7700 (t80)
REVERT: B  132 MET cc_start: 0.8700 (ttp) cc_final: 0.7710 (tmm)
REVERT: B  161 LEU cc_start: 0.8402 (tp) cc_final: 0.8160 (tp)
REVERT: B  309 LEU cc_start: 0.7711 (tp) cc_final: 0.7420 (tp)
REVERT: B  365 MET cc_start: 0.9163 (ppp) cc_final: 0.8828 (ppp)
REVERT: B  373 THR cc_start: 0.8676 (m) cc_final: 0.8430 (p)
REVERT: B  434 PHE cc_start: 0.8933 (t80) cc_final: 0.8700 (t80)
REVERT: C    6 GLU cc_start: 0.5893 (mp0) cc_final: 0.5605 (mp0)
REVERT: C   31 TYR cc_start: 0.8002 (p90) cc_final: 0.7758 (p90)
  outliers start: 2
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2256
  time to fit residues: 73.1862
Evaluate side-chains
  161 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.012 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 79 optimal weight:   10.0000
   chunk 93 optimal weight:    0.0010
   chunk 8 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 91 optimal weight:    0.6980
   chunk 108 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 90 optimal weight:    0.7980
   chunk 113 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  71 HIS
A 243 ASN
A 503 GLN
B 280 GLN
B 419 GLN
** C  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.124020 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.102330 restraints weight = 28221.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.104980 restraints weight = 16285.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.106807 restraints weight = 10872.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3749
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7219
moved from start:          0.4330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10384  Z= 0.171
  Angle     :  0.563   6.878  14074  Z= 0.298
  Chirality :  0.040   0.161   1607
  Planarity :  0.005   0.051   1790
  Dihedral  :  4.587  27.974   1442
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  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:  1.51 (0.23), residues: 1281
  helix:  2.04 (0.18), residues: 791
  sheet:  0.32 (0.42), residues: 135
  loop : -1.15 (0.31), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 262 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.015   0.001   PHE B 151 
 TYR   0.019   0.001   TYR B 302 
 ARG   0.007   0.000   ARG B 107 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 224
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 PHE cc_start: 0.8971 (m-80) cc_final: 0.8761 (m-10)
REVERT: A  145 ASN cc_start: 0.7862 (m110) cc_final: 0.6697 (t0)
REVERT: A  205 MET cc_start: 0.8831 (tmm) cc_final: 0.8471 (tmm)
REVERT: A  519 LEU cc_start: 0.8922 (tp) cc_final: 0.8031 (tp)
REVERT: B   32 LEU cc_start: 0.8913 (mt) cc_final: 0.8649 (mt)
REVERT: B   40 LEU cc_start: 0.8873 (tp) cc_final: 0.8187 (tt)
REVERT: B   43 TYR cc_start: 0.7930 (t80) cc_final: 0.7605 (t80)
REVERT: B   91 GLU cc_start: 0.8316 (tt0) cc_final: 0.8096 (tm-30)
REVERT: B  132 MET cc_start: 0.8756 (ttp) cc_final: 0.7656 (tmm)
REVERT: B  434 PHE cc_start: 0.8871 (t80) cc_final: 0.8648 (t80)
REVERT: B  465 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8080 (mp0)
REVERT: B  499 ASP cc_start: 0.7373 (t0) cc_final: 0.6962 (p0)
REVERT: B  546 ASP cc_start: 0.6305 (t0) cc_final: 0.5862 (m-30)
REVERT: C    6 GLU cc_start: 0.5546 (mp0) cc_final: 0.5292 (mp0)
REVERT: C   31 TYR cc_start: 0.8062 (p90) cc_final: 0.7718 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 224
  average time/residue: 0.2319
  time to fit residues: 72.6037
Evaluate side-chains
  162 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 122 optimal weight:    1.9990
   chunk 29 optimal weight:    0.2980
   chunk 75 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 88 optimal weight:    2.9990
   chunk 94 optimal weight:    0.9980
   chunk 62 optimal weight:    0.5980
   chunk 5 optimal weight:    4.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
B 400 HIS
B 419 GLN
C  57 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.122393 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.101490 restraints weight = 28030.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.103891 restraints weight = 16627.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.105552 restraints weight = 11367.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.4714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10384  Z= 0.187
  Angle     :  0.576   9.147  14074  Z= 0.298
  Chirality :  0.041   0.218   1607
  Planarity :  0.004   0.050   1790
  Dihedral  :  4.451  24.210   1442
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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:  1.48 (0.23), residues: 1281
  helix:  1.99 (0.18), residues: 790
  sheet:  0.21 (0.44), residues: 130
  loop : -1.02 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 262 
 HIS   0.005   0.001   HIS B 111 
 PHE   0.024   0.002   PHE A 472 
 TYR   0.023   0.002   TYR C  94 
 ARG   0.005   0.000   ARG B 219 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7434 (m-80) cc_final: 0.7069 (m-80)
REVERT: A   34 LEU cc_start: 0.8322 (mt) cc_final: 0.7857 (tt)
REVERT: A  195 ARG cc_start: 0.8706 (mmm-85) cc_final: 0.8283 (mmt90)
REVERT: A  205 MET cc_start: 0.8824 (tmm) cc_final: 0.8440 (tmm)
REVERT: B   32 LEU cc_start: 0.8871 (mt) cc_final: 0.8618 (mt)
REVERT: B   43 TYR cc_start: 0.7797 (t80) cc_final: 0.7541 (t80)
REVERT: B   91 GLU cc_start: 0.8372 (tt0) cc_final: 0.8166 (tm-30)
REVERT: B  132 MET cc_start: 0.8753 (ttp) cc_final: 0.7710 (tmm)
REVERT: B  434 PHE cc_start: 0.8839 (t80) cc_final: 0.8638 (t80)
REVERT: B  465 GLU cc_start: 0.8311 (mm-30) cc_final: 0.7995 (mp0)
REVERT: B  499 ASP cc_start: 0.7371 (t0) cc_final: 0.6824 (p0)
REVERT: B  546 ASP cc_start: 0.6288 (t0) cc_final: 0.5809 (m-30)
REVERT: C   31 TYR cc_start: 0.8112 (p90) cc_final: 0.7585 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2188
  time to fit residues: 64.1872
Evaluate side-chains
  161 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 79 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 42 optimal weight:    0.9990
   chunk 15 optimal weight:    0.7980
   chunk 103 optimal weight:    1.9990
   chunk 88 optimal weight:    0.3980
   chunk 30 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 113 optimal weight:    5.9990
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
A 308 GLN
B 111 HIS
B 419 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.119596 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.098640 restraints weight = 27202.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.100967 restraints weight = 15884.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.102563 restraints weight = 10703.246|
|-----------------------------------------------------------------------------|
r_work (final): 0.3686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.5008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10384  Z= 0.176
  Angle     :  0.553   8.059  14074  Z= 0.284
  Chirality :  0.040   0.231   1607
  Planarity :  0.004   0.048   1790
  Dihedral  :  4.367  23.360   1442
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.52 (0.23), residues: 1281
  helix:  2.02 (0.18), residues: 790
  sheet:  0.19 (0.44), residues: 130
  loop : -0.95 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 223 
 HIS   0.004   0.001   HIS B 101 
 PHE   0.014   0.001   PHE B  38 
 TYR   0.015   0.001   TYR B  92 
 ARG   0.004   0.000   ARG B 107 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.080 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7478 (m-80) cc_final: 0.7134 (m-80)
REVERT: A   49 PHE cc_start: 0.8879 (m-80) cc_final: 0.8677 (m-10)
REVERT: A  195 ARG cc_start: 0.8718 (mmm-85) cc_final: 0.8212 (mmt90)
REVERT: A  205 MET cc_start: 0.8771 (tmm) cc_final: 0.8378 (tmm)
REVERT: A  544 MET cc_start: 0.8331 (mmp) cc_final: 0.7252 (ppp)
REVERT: B   32 LEU cc_start: 0.8802 (mt) cc_final: 0.8501 (mt)
REVERT: B   43 TYR cc_start: 0.7906 (t80) cc_final: 0.7699 (t80)
REVERT: B   91 GLU cc_start: 0.8367 (tt0) cc_final: 0.8154 (tm-30)
REVERT: B  132 MET cc_start: 0.8752 (ttp) cc_final: 0.7666 (tmm)
REVERT: B  309 LEU cc_start: 0.8050 (tp) cc_final: 0.7636 (tp)
REVERT: B  465 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7938 (mp0)
REVERT: B  546 ASP cc_start: 0.6248 (t0) cc_final: 0.5871 (m-30)
REVERT: C    6 GLU cc_start: 0.5332 (mp0) cc_final: 0.4524 (mt-10)
REVERT: C   18 LEU cc_start: 0.7955 (tt) cc_final: 0.7644 (mt)
REVERT: C   31 TYR cc_start: 0.8140 (p90) cc_final: 0.7601 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.2247
  time to fit residues: 67.6346
Evaluate side-chains
  159 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.951 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 81 optimal weight:    4.9990
   chunk 97 optimal weight:    0.5980
   chunk 27 optimal weight:    6.9990
   chunk 127 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 39 optimal weight:    7.9990
   chunk 111 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
B 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.119558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.098280 restraints weight = 27595.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.100579 restraints weight = 16150.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.102227 restraints weight = 10973.245|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.5235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10384  Z= 0.168
  Angle     :  0.560   9.029  14074  Z= 0.285
  Chirality :  0.040   0.179   1607
  Planarity :  0.004   0.048   1790
  Dihedral  :  4.294  22.175   1442
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  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:  1.56 (0.23), residues: 1281
  helix:  2.05 (0.18), residues: 790
  sheet:  0.10 (0.43), residues: 132
  loop : -0.92 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP B 223 
 HIS   0.004   0.001   HIS B 101 
 PHE   0.022   0.001   PHE A 304 
 TYR   0.014   0.001   TYR B 155 
 ARG   0.005   0.000   ARG A 208 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 1.076 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7411 (m-80) cc_final: 0.7070 (m-80)
REVERT: A  195 ARG cc_start: 0.8619 (mmm-85) cc_final: 0.8033 (mmt180)
REVERT: A  205 MET cc_start: 0.8757 (tmm) cc_final: 0.8357 (tmm)
REVERT: A  544 MET cc_start: 0.8157 (mmp) cc_final: 0.7171 (ppp)
REVERT: A  593 TYR cc_start: 0.6227 (t80) cc_final: 0.5720 (t80)
REVERT: B   32 LEU cc_start: 0.8677 (mt) cc_final: 0.8399 (mt)
REVERT: B   43 TYR cc_start: 0.7883 (t80) cc_final: 0.7676 (t80)
REVERT: B   91 GLU cc_start: 0.8429 (tt0) cc_final: 0.8190 (tm-30)
REVERT: B  132 MET cc_start: 0.8642 (ttp) cc_final: 0.7561 (tmm)
REVERT: B  281 PHE cc_start: 0.8586 (m-80) cc_final: 0.8356 (m-80)
REVERT: B  465 GLU cc_start: 0.8458 (mm-30) cc_final: 0.8069 (mp0)
REVERT: B  546 ASP cc_start: 0.6159 (t0) cc_final: 0.5855 (m-30)
REVERT: C   18 LEU cc_start: 0.7972 (tt) cc_final: 0.7453 (mp)
REVERT: C   31 TYR cc_start: 0.8166 (p90) cc_final: 0.7701 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2192
  time to fit residues: 66.5396
Evaluate side-chains
  162 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 118 optimal weight:    0.0070
   chunk 97 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 113 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 71 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 67 optimal weight:    0.9980
   chunk 78 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0670
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
B 280 GLN
B 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3996 r_free = 0.3996 target = 0.121926 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.099627 restraints weight = 28147.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.102126 restraints weight = 16398.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.103770 restraints weight = 11060.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.3714
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7258
moved from start:          0.5451

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10384  Z= 0.148
  Angle     :  0.543   7.703  14074  Z= 0.274
  Chirality :  0.040   0.177   1607
  Planarity :  0.004   0.047   1790
  Dihedral  :  4.133  20.652   1442
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  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:  1.75 (0.23), residues: 1281
  helix:  2.17 (0.18), residues: 791
  sheet:  0.18 (0.42), residues: 130
  loop : -0.76 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.001   TRP B 223 
 HIS   0.005   0.001   HIS B 111 
 PHE   0.014   0.001   PHE A  49 
 TYR   0.013   0.001   TYR B  92 
 ARG   0.008   0.000   ARG B 142 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 212
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   25 TYR cc_start: 0.7282 (m-80) cc_final: 0.6970 (m-80)
REVERT: A  195 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8166 (mmt180)
REVERT: A  205 MET cc_start: 0.8863 (tmm) cc_final: 0.8472 (tmm)
REVERT: A  544 MET cc_start: 0.8105 (mmp) cc_final: 0.7122 (ptt)
REVERT: A  593 TYR cc_start: 0.6214 (t80) cc_final: 0.5701 (t80)
REVERT: B   32 LEU cc_start: 0.8732 (mt) cc_final: 0.8496 (mt)
REVERT: B   40 LEU cc_start: 0.8874 (tp) cc_final: 0.8189 (tt)
REVERT: B   98 LEU cc_start: 0.8343 (mt) cc_final: 0.8111 (mt)
REVERT: B  132 MET cc_start: 0.8719 (ttp) cc_final: 0.7518 (tmm)
REVERT: B  142 ARG cc_start: 0.7409 (ttp80) cc_final: 0.7200 (tmm-80)
REVERT: B  282 ASN cc_start: 0.8332 (t0) cc_final: 0.7893 (t0)
REVERT: B  434 PHE cc_start: 0.8774 (t80) cc_final: 0.8572 (t80)
REVERT: B  465 GLU cc_start: 0.8384 (mm-30) cc_final: 0.7898 (mp0)
REVERT: B  499 ASP cc_start: 0.7734 (t0) cc_final: 0.6523 (p0)
REVERT: B  546 ASP cc_start: 0.6354 (t0) cc_final: 0.6123 (m-30)
REVERT: C   18 LEU cc_start: 0.8040 (tt) cc_final: 0.7629 (mt)
REVERT: C   31 TYR cc_start: 0.8123 (p90) cc_final: 0.7707 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 212
  average time/residue: 0.2038
  time to fit residues: 62.5749
Evaluate side-chains
  154 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 127 optimal weight:    5.9990
   chunk 70 optimal weight:    4.9990
   chunk 116 optimal weight:    0.5980
   chunk 89 optimal weight:    0.7980
   chunk 76 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   chunk 7 optimal weight:    6.9990
   chunk 118 optimal weight:    0.0040
   chunk 56 optimal weight:   10.0000
   overall best weight:    1.0594

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
B 228 ASN
B 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.119895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.097796 restraints weight = 28244.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.100242 restraints weight = 16400.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.101907 restraints weight = 11027.988|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.5611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10384  Z= 0.189
  Angle     :  0.578   8.236  14074  Z= 0.294
  Chirality :  0.040   0.185   1607
  Planarity :  0.004   0.048   1790
  Dihedral  :  4.244  20.538   1442
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  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:  1.63 (0.23), residues: 1281
  helix:  2.04 (0.18), residues: 792
  sheet:  0.18 (0.42), residues: 135
  loop : -0.73 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP B 223 
 HIS   0.004   0.001   HIS B 101 
 PHE   0.018   0.001   PHE B 151 
 TYR   0.030   0.001   TYR B 155 
 ARG   0.006   0.000   ARG A 426 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 206
  time to evaluate  : 1.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   34 LEU cc_start: 0.8212 (mt) cc_final: 0.7721 (tt)
REVERT: A  165 LEU cc_start: 0.7947 (mt) cc_final: 0.7437 (mt)
REVERT: A  169 MET cc_start: 0.7895 (mtp) cc_final: 0.6947 (mpp)
REVERT: A  195 ARG cc_start: 0.8660 (mmm-85) cc_final: 0.8247 (mmt90)
REVERT: A  205 MET cc_start: 0.8753 (tmm) cc_final: 0.8333 (tmm)
REVERT: A  544 MET cc_start: 0.8131 (mmp) cc_final: 0.7231 (ptt)
REVERT: A  593 TYR cc_start: 0.6225 (t80) cc_final: 0.5696 (t80)
REVERT: B   32 LEU cc_start: 0.8766 (mt) cc_final: 0.8392 (mt)
REVERT: B  132 MET cc_start: 0.8755 (ttp) cc_final: 0.7548 (tmm)
REVERT: B  145 PHE cc_start: 0.8389 (t80) cc_final: 0.8165 (t80)
REVERT: B  299 MET cc_start: 0.6449 (ttt) cc_final: 0.6246 (ttt)
REVERT: B  434 PHE cc_start: 0.8805 (t80) cc_final: 0.8581 (t80)
REVERT: B  465 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8007 (mp0)
REVERT: B  546 ASP cc_start: 0.6366 (t0) cc_final: 0.6081 (m-30)
REVERT: C   31 TYR cc_start: 0.8169 (p90) cc_final: 0.7689 (p90)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1936
  time to fit residues: 58.4649
Evaluate side-chains
  155 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 104 optimal weight:    5.9990
   chunk 113 optimal weight:    0.0070
   chunk 96 optimal weight:    0.0870
   chunk 38 optimal weight:    8.9990
   chunk 13 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 93 optimal weight:    0.0060
   chunk 117 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
B 111 HIS
B 228 ASN
B 419 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.121760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.099645 restraints weight = 28354.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.102085 restraints weight = 16613.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.103769 restraints weight = 11271.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.5774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  10384  Z= 0.161
  Angle     :  0.582  11.987  14074  Z= 0.291
  Chirality :  0.040   0.177   1607
  Planarity :  0.004   0.047   1790
  Dihedral  :  4.190  20.087   1442
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.66 %
    Favored  : 99.24 %
  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:  1.65 (0.23), residues: 1281
  helix:  2.06 (0.18), residues: 792
  sheet:  0.11 (0.42), residues: 135
  loop : -0.71 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.001   TRP B 223 
 HIS   0.004   0.001   HIS A 435 
 PHE   0.024   0.001   PHE B  38 
 TYR   0.014   0.001   TYR A 299 
 ARG   0.006   0.000   ARG A 426 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  195 ARG cc_start: 0.8668 (mmm-85) cc_final: 0.8411 (mmt90)
REVERT: A  205 MET cc_start: 0.8812 (tmm) cc_final: 0.8411 (tmm)
REVERT: A  544 MET cc_start: 0.7901 (mmp) cc_final: 0.7162 (ptt)
REVERT: A  593 TYR cc_start: 0.6200 (t80) cc_final: 0.5687 (t80)
REVERT: B   40 LEU cc_start: 0.8919 (tp) cc_final: 0.8504 (tt)
REVERT: B   63 LEU cc_start: 0.8616 (mm) cc_final: 0.8308 (tp)
REVERT: B  132 MET cc_start: 0.8641 (ttp) cc_final: 0.7561 (tmm)
REVERT: B  281 PHE cc_start: 0.8653 (m-80) cc_final: 0.8377 (m-80)
REVERT: B  282 ASN cc_start: 0.8578 (t0) cc_final: 0.8353 (t0)
REVERT: B  299 MET cc_start: 0.6477 (ttt) cc_final: 0.6270 (ttt)
REVERT: B  465 GLU cc_start: 0.8385 (mm-30) cc_final: 0.7894 (mp0)
REVERT: B  546 ASP cc_start: 0.6286 (t0) cc_final: 0.6030 (m-30)
REVERT: C   18 LEU cc_start: 0.8019 (tt) cc_final: 0.7468 (mp)
REVERT: C   31 TYR cc_start: 0.8127 (p90) cc_final: 0.7701 (p90)
  outliers start: 1
  outliers final: 1
  residues processed: 195
  average time/residue: 0.1846
  time to fit residues: 53.5278
Evaluate side-chains
  156 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 155
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   chunk 7 optimal weight:    2.9990
   chunk 99 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9990
   chunk 120 optimal weight:   20.0000
   chunk 28 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
B 111 HIS
B 419 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.120284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.098589 restraints weight = 28589.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.100794 restraints weight = 16921.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.102412 restraints weight = 11709.757|
|-----------------------------------------------------------------------------|
r_work (final): 0.3693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7309
moved from start:          0.5896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10384  Z= 0.177
  Angle     :  0.581   7.516  14074  Z= 0.292
  Chirality :  0.040   0.178   1607
  Planarity :  0.004   0.047   1790
  Dihedral  :  4.171  19.801   1442
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.65 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  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:  1.63 (0.23), residues: 1281
  helix:  2.03 (0.18), residues: 795
  sheet:  0.12 (0.42), residues: 135
  loop : -0.71 (0.33), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.002   TRP B 223 
 HIS   0.004   0.001   HIS B 101 
 PHE   0.025   0.001   PHE B  38 
 TYR   0.030   0.001   TYR B 155 
 ARG   0.006   0.000   ARG A 426 

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

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

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2562 Ramachandran restraints generated.
    1281 Oldfield, 0 Emsley, 1281 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 MET cc_start: 0.8300 (mmp) cc_final: 0.8076 (mmp)
REVERT: A  169 MET cc_start: 0.8063 (mtp) cc_final: 0.7158 (mtm)
REVERT: A  195 ARG cc_start: 0.8692 (mmm-85) cc_final: 0.8409 (mmt90)
REVERT: A  205 MET cc_start: 0.8867 (tmm) cc_final: 0.8424 (tmm)
REVERT: A  544 MET cc_start: 0.7715 (mmp) cc_final: 0.6899 (ptp)
REVERT: A  593 TYR cc_start: 0.6241 (t80) cc_final: 0.5737 (t80)
REVERT: B   40 LEU cc_start: 0.8900 (tp) cc_final: 0.8494 (tt)
REVERT: B  132 MET cc_start: 0.8541 (ttp) cc_final: 0.7462 (tmm)
REVERT: B  282 ASN cc_start: 0.8525 (t0) cc_final: 0.8260 (t0)
REVERT: B  309 LEU cc_start: 0.8028 (tp) cc_final: 0.7682 (tp)
REVERT: B  465 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7966 (mp0)
REVERT: B  546 ASP cc_start: 0.6358 (t0) cc_final: 0.6110 (m-30)
REVERT: C   18 LEU cc_start: 0.7975 (tt) cc_final: 0.7406 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.1941
  time to fit residues: 56.9109
Evaluate side-chains
  149 residues out of total 1054 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 149
  time to evaluate  : 1.049 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 125 optimal weight:   10.0000
   chunk 100 optimal weight:    0.5980
   chunk 63 optimal weight:    0.9980
   chunk 111 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 104 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 213 ASN
** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 400 HIS
B 419 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.118031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.096840 restraints weight = 28420.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.099122 restraints weight = 16759.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.100699 restraints weight = 11386.343|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7329
moved from start:          0.6065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10384  Z= 0.194
  Angle     :  0.604  10.386  14074  Z= 0.302
  Chirality :  0.041   0.184   1607
  Planarity :  0.004   0.048   1790
  Dihedral  :  4.239  19.808   1442
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.28 %
    Favored  : 99.62 %
  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:  1.50 (0.23), residues: 1281
  helix:  1.90 (0.18), residues: 795
  sheet:  0.13 (0.42), residues: 136
  loop : -0.72 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP B 223 
 HIS   0.006   0.001   HIS B 111 
 PHE   0.024   0.001   PHE B  38 
 TYR   0.017   0.001   TYR B  92 
 ARG   0.007   0.000   ARG A 426 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3191.88 seconds
wall clock time: 57 minutes 47.49 seconds (3467.49 seconds total)