Starting phenix.real_space_refine
on Sun Aug 24 06:54:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bxg_16318/08_2025/8bxg_16318_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bxg_16318/08_2025/8bxg_16318.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2025/8bxg_16318.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2025/8bxg_16318.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2025/8bxg_16318_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bxg_16318/08_2025/8bxg_16318_trim.cif"
  }
  resolution = 3.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   1.000
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: 7
    Type Number    sf(0)   Gaussians
     K       2      8.98       5
     P       4      5.49       5
     S      54      5.16       5
     C    5547      2.51       5
     N    1426      2.21       5
     O    1472      1.98       5
     H    8796      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 17301
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 547, 8584
          Classifications: {'peptide': 547}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 528}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 8567
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 546, 8567
          Classifications: {'peptide': 546}
          Modifications used: {'NH3': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 527}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 75
          Unusual residues: {'  K': 1, 'AMP%rna2p': 1, 'PGW': 1}
          Classifications: {'RNA_mixed': 1, 'undetermined': 2}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 75
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 75
          Unusual residues: {'  K': 1, 'AMP%rna2p': 1, 'PGW': 1}
          Classifications: {'RNA_mixed': 1, 'undetermined': 2}
          Modifications used: {'rna2p': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 3.92, per 1000 atoms: 0.23
  Number of scatterers: 17301
  At special positions: 0
  Unit cell: (92.6978, 73.7595, 111.636, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     K       2     19.00
     S      54     16.00
     P       4     15.00
     O    1472      8.00
     N    1426      7.00
     C    5547      6.00
     H    8796      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.69
  Conformation dependent library (CDL) restraints added in 897.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 2 sheets defined
      78.8% alpha, 2.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.49
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 26
      removed outlier: 5.714A  pdb=" N   VAL A  20 " --> pdb=" O   ALA A  16 " (cutoff:3.500A)
      Proline residue:  A  21  - end of helix
    Processing helix  chain 'A' and resid 29 through 42
    Processing helix  chain 'A' and resid 52 through 72
    Processing helix  chain 'A' and resid 75 through 82
    Processing helix  chain 'A' and resid 82 through 97
      removed outlier: 4.647A  pdb=" N   ALA A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LEU A  92 " --> pdb=" O   GLY A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 109
    Processing helix  chain 'A' and resid 112 through 123
      removed outlier: 3.843A  pdb=" N   GLU A 116 " --> pdb=" O   TRP A 112 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   LEU A 117 " --> pdb=" O   GLN A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 136
      removed outlier: 3.534A  pdb=" N   GLU A 136 " --> pdb=" O   GLN A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 171
      Proline residue:  A 161  - end of helix
      removed outlier: 3.765A  pdb=" N   ILE A 166 " --> pdb=" O   LEU A 162 " (cutoff:3.500A)
      Proline residue:  A 167  - end of helix
      removed outlier: 3.824A  pdb=" N   ALA A 170 " --> pdb=" O   ILE A 166 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   THR A 171 " --> pdb=" O   PRO A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 183
    Processing helix  chain 'A' and resid 185 through 200
      removed outlier: 4.043A  pdb=" N   LEU A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLY A 199 " --> pdb=" O   VAL A 195 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   ARG A 200 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 212
    Processing helix  chain 'A' and resid 217 through 238
    Processing helix  chain 'A' and resid 240 through 255
      removed outlier: 4.046A  pdb=" N   GLY A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA A 245 " --> pdb=" O   MET A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 284
      Proline residue:  A 267  - end of helix
      removed outlier: 4.637A  pdb=" N   GLY A 270 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   LEU A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   PHE A 276 " --> pdb=" O   LEU A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 292
      removed outlier: 3.767A  pdb=" N   LEU A 290 " --> pdb=" O   PHE A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 316
      removed outlier: 3.741A  pdb=" N   LEU A 299 " --> pdb=" O   ARG A 295 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   GLY A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   ILE A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.293A  pdb=" N   ARG A 316 " --> pdb=" O   TRP A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 333
    Processing helix  chain 'A' and resid 337 through 350
      removed outlier: 3.861A  pdb=" N   VAL A 341 " --> pdb=" O   GLU A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 370
      removed outlier: 3.781A  pdb=" N   LYS A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   SER A 359 " --> pdb=" O   GLU A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 385
      removed outlier: 3.642A  pdb=" N   LEU A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   GLN A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   SER A 384 " --> pdb=" O   ARG A 380 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER A 385 " --> pdb=" O   LEU A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 421
      removed outlier: 3.630A  pdb=" N   SER A 421 " --> pdb=" O   LEU A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 440
      removed outlier: 3.672A  pdb=" N   ARG A 439 " --> pdb=" O   GLU A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 453 through 460
    Processing helix  chain 'A' and resid 473 through 488
    Processing helix  chain 'A' and resid 499 through 510
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 536 through 560
      removed outlier: 3.775A  pdb=" N   GLU A 542 " --> pdb=" O   TYR A 538 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   MET A 560 " --> pdb=" O   GLU A 556 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 27
      removed outlier: 3.789A  pdb=" N   VAL B  20 " --> pdb=" O   ALA B  16 " (cutoff:3.500A)
      Proline residue:  B  21  - end of helix
    Processing helix  chain 'B' and resid 31 through 42
      removed outlier: 3.845A  pdb=" N   LEU B  35 " --> pdb=" O   VAL B  31 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 51 through 74
      removed outlier: 3.574A  pdb=" N   LEU B  74 " --> pdb=" O   ILE B  70 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 77 through 82
      removed outlier: 4.297A  pdb=" N   LYS B  81 " --> pdb=" O   GLN B  77 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   LEU B  82 " --> pdb=" O   ARG B  78 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 77 through 82'
    Processing helix  chain 'B' and resid 89 through 108
      removed outlier: 3.846A  pdb=" N   GLN B  93 " --> pdb=" O   GLY B  89 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY B  99 " --> pdb=" O   VAL B  95 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU B 100 " --> pdb=" O   ILE B  96 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   LEU B 103 " --> pdb=" O   GLY B  99 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU B 108 " --> pdb=" O   PHE B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 113 through 123
      removed outlier: 3.977A  pdb=" N   LEU B 117 " --> pdb=" O   GLN B 113 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   GLY B 119 " --> pdb=" O   ALA B 115 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   MET B 120 " --> pdb=" O   GLU B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 138
    Processing helix  chain 'B' and resid 142 through 158
    Processing helix  chain 'B' and resid 159 through 165
    Processing helix  chain 'B' and resid 165 through 172
    Processing helix  chain 'B' and resid 176 through 202
    Processing helix  chain 'B' and resid 203 through 213
      removed outlier: 3.807A  pdb=" N   SER B 213 " --> pdb=" O   PHE B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 237
      removed outlier: 3.643A  pdb=" N   VAL B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 255
      removed outlier: 3.835A  pdb=" N   LEU B 247 " --> pdb=" O   MET B 243 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 266
    Processing helix  chain 'B' and resid 268 through 284
      removed outlier: 3.984A  pdb=" N   PHE B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   PHE B 277 " --> pdb=" O   LEU B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 292
    Processing helix  chain 'B' and resid 293 through 314
      removed outlier: 3.876A  pdb=" N   VAL B 297 " --> pdb=" O   PRO B 293 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   PHE B 303 " --> pdb=" O   LEU B 299 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 315 through 319
    Processing helix  chain 'B' and resid 321 through 331
      removed outlier: 4.411A  pdb=" N   ARG B 326 " --> pdb=" O   ASN B 322 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   TRP B 327 " --> pdb=" O   LYS B 323 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 349
      removed outlier: 3.925A  pdb=" N   VAL B 341 " --> pdb=" O   GLU B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 353 through 370
    Processing helix  chain 'B' and resid 370 through 384
      removed outlier: 3.930A  pdb=" N   LEU B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 422
      removed outlier: 3.592A  pdb=" N   ILE B 413 " --> pdb=" O   ARG B 409 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU B 417 " --> pdb=" O   ILE B 413 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   LEU B 418 " --> pdb=" O   THR B 414 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 440
      removed outlier: 3.552A  pdb=" N   ARG B 439 " --> pdb=" O   GLU B 436 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LYS B 440 " --> pdb=" O   THR B 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 436 through 440'
    Processing helix  chain 'B' and resid 452 through 456
      removed outlier: 3.611A  pdb=" N   LEU B 456 " --> pdb=" O   MET B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 460 through 464
    Processing helix  chain 'B' and resid 473 through 488
      removed outlier: 3.742A  pdb=" N   MET B 483 " --> pdb=" O   GLN B 479 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 510
      removed outlier: 3.911A  pdb=" N   ARG B 505 " --> pdb=" O   ASP B 501 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 534
    Processing helix  chain 'B' and resid 536 through 560
      removed outlier: 3.519A  pdb=" N   ALA B 544 " --> pdb=" O   ALA B 540 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ASP B 545 " --> pdb=" O   ARG B 541 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B 546 " --> pdb=" O   GLU B 542 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   PHE B 547 " --> pdb=" O   ARG B 543 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   MET B 560 " --> pdb=" O   GLU B 556 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 445 through 447
      removed outlier: 6.659A  pdb=" N   ILE A 403 " --> pdb=" O   ILE A 468 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   LEU A 467 " --> pdb=" O   ILE A 494 " (cutoff:3.500A)
      removed outlier: 7.659A  pdb=" N   ARG A 496 " --> pdb=" O   LEU A 467 " (cutoff:3.500A)
      removed outlier: 7.409A  pdb=" N   ASN A 469 " --> pdb=" O   ARG A 496 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   ALA A 495 " --> pdb=" O   GLU A 515 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 424 through 428
      removed outlier: 6.518A  pdb=" N   VAL B 402 " --> pdb=" O   VAL B 426 " (cutoff:3.500A)
      removed outlier: 8.288A  pdb=" N   LEU B 428 " --> pdb=" O   VAL B 402 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE B 404 " --> pdb=" O   LEU B 428 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL B 466 " --> pdb=" O   ARG B 401 " (cutoff:3.500A)

    558 hydrogen bonds defined for protein.
    1644 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: 4.27

  Time building geometry restraints manager: 2.46 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8790
        1.03 -     1.23: 31
        1.23 -     1.42: 3393
        1.42 -     1.62: 5127
        1.62 -     1.81: 106
  Bond restraints: 17447
  Sorted by residual:
  bond pdb=" CG  PRO B 205 "
       pdb=" CD  PRO B 205 "
    ideal  model  delta    sigma   weight residual
    1.503  1.444  0.059 3.40e-02 8.65e+02 2.97e+00
  bond pdb=" CB  PRO B 317 "
       pdb=" CG  PRO B 317 "
    ideal  model  delta    sigma   weight residual
    1.492  1.557 -0.065 5.00e-02 4.00e+02 1.70e+00
  bond pdb=" C4' AMP A 602 "
       pdb=" O4' AMP A 602 "
    ideal  model  delta    sigma   weight residual
    1.426  1.452 -0.026 2.00e-02 2.50e+03 1.66e+00
  bond pdb=" CB  PRO B 205 "
       pdb=" CG  PRO B 205 "
    ideal  model  delta    sigma   weight residual
    1.492  1.556 -0.064 5.00e-02 4.00e+02 1.64e+00
  bond pdb=" C4' AMP B 602 "
       pdb=" O4' AMP B 602 "
    ideal  model  delta    sigma   weight residual
    1.426  1.451 -0.025 2.00e-02 2.50e+03 1.61e+00
  ... (remaining 17442 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.88: 31394
        1.88 -     3.76: 199
        3.76 -     5.64: 34
        5.64 -     7.52: 5
        7.52 -     9.39: 2
  Bond angle restraints: 31634
  Sorted by residual:
  angle pdb=" CA  PRO B 205 "
        pdb=" N   PRO B 205 "
        pdb=" CD  PRO B 205 "
      ideal   model   delta    sigma   weight residual
     112.00  105.41    6.59 1.40e+00 5.10e-01 2.22e+01
  angle pdb=" CA  PRO B 317 "
        pdb=" N   PRO B 317 "
        pdb=" CD  PRO B 317 "
      ideal   model   delta    sigma   weight residual
     112.00  106.38    5.62 1.40e+00 5.10e-01 1.61e+01
  angle pdb=" N   PRO B 205 "
        pdb=" CD  PRO B 205 "
        pdb=" CG  PRO B 205 "
      ideal   model   delta    sigma   weight residual
     103.20   97.94    5.26 1.50e+00 4.44e-01 1.23e+01
  angle pdb=" C1' AMP A 602 "
        pdb=" C2' AMP A 602 "
        pdb=" C3' AMP A 602 "
      ideal   model   delta    sigma   weight residual
     111.00  101.61    9.39 3.00e+00 1.11e-01 9.81e+00
  angle pdb=" C1' AMP B 602 "
        pdb=" C2' AMP B 602 "
        pdb=" C3' AMP B 602 "
      ideal   model   delta    sigma   weight residual
     111.00  101.79    9.21 3.00e+00 1.11e-01 9.43e+00
  ... (remaining 31629 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.50: 7648
       34.50 -    69.01: 409
       69.01 -   103.51: 24
      103.51 -   138.01: 1
      138.01 -   172.52: 6
  Dihedral angle restraints: 8088
    sinusoidal: 4519
      harmonic: 3569
  Sorted by residual:
  dihedral pdb=" C5' AMP B 602 "
           pdb=" O5' AMP B 602 "
           pdb=" P   AMP B 602 "
           pdb=" O3P AMP B 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   65.59 -125.59     1      2.00e+01 2.50e-03 3.80e+01
  dihedral pdb=" C03 PGW B 603 "
           pdb=" C01 PGW B 603 "
           pdb=" C02 PGW B 603 "
           pdb=" O03 PGW B 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
     295.35  122.83  172.52     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" O01 PGW B 603 "
           pdb=" C01 PGW B 603 "
           pdb=" C02 PGW B 603 "
           pdb=" O03 PGW B 603 "
      ideal   model   delta sinusoidal    sigma   weight residual
      59.30 -112.75  172.05     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 8085 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 1125
       0.040 -    0.080: 197
       0.080 -    0.119: 63
       0.119 -    0.159: 4
       0.159 -    0.199: 2
  Chirality restraints: 1391
  Sorted by residual:
  chirality pdb=" C3' AMP A 602 "
            pdb=" C2' AMP A 602 "
            pdb=" C4' AMP A 602 "
            pdb=" O3' AMP A 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.71    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" C3' AMP B 602 "
            pdb=" C2' AMP B 602 "
            pdb=" C4' AMP B 602 "
            pdb=" O3' AMP B 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.70    0.19 2.00e-01 2.50e+01 9.29e-01
  chirality pdb=" CA  ILE A 494 "
            pdb=" N   ILE A 494 "
            pdb=" C   ILE A 494 "
            pdb=" CB  ILE A 494 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 1388 not shown)

  Planarity restraints: 2501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 316 "    0.068 5.00e-02 4.00e+02   1.00e-01 1.61e+01
        pdb=" N   PRO B 317 "   -0.173 5.00e-02 4.00e+02
        pdb=" CA  PRO B 317 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 317 "    0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 204 "    0.057 5.00e-02 4.00e+02   8.25e-02 1.09e+01
        pdb=" N   PRO B 205 "   -0.142 5.00e-02 4.00e+02
        pdb=" CA  PRO B 205 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO B 205 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 160 "    0.046 5.00e-02 4.00e+02   6.87e-02 7.56e+00
        pdb=" N   PRO A 161 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A 161 "    0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 161 "    0.038 5.00e-02 4.00e+02
  ... (remaining 2498 not shown)

  Histogram of nonbonded interaction distances:
        1.60 -     2.31: 3705
        2.31 -     3.01: 47171
        3.01 -     3.72: 60982
        3.72 -     4.43: 91969
        4.43 -     5.14: 144625
  Nonbonded interactions: 348452
  Sorted by model distance:
  nonbonded pdb=" HB2 GLN A 492 "
            pdb="HE21 GLN A 492 "
     model   vdw
     1.598 2.270
  nonbonded pdb="HH22 ARG B 295 "
            pdb=" OE2 GLU B 355 "
     model   vdw
     1.679 2.450
  nonbonded pdb=" OD1 ASP A 285 "
            pdb=" H   GLY A 287 "
     model   vdw
     1.695 2.450
  nonbonded pdb=" O   VAL A 202 "
            pdb=" HG1 THR A 203 "
     model   vdw
     1.703 2.450
  nonbonded pdb=" OE1 GLU A 436 "
            pdb=" H   GLU A 436 "
     model   vdw
     1.745 2.450
  ... (remaining 348447 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 385 or resid 400 through 603))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  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:             0.080
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.060
  Set scattering table:                    0.060
  Process input model:                     19.970
  Find NCS groups from input model:        0.240
  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:             0.000
  Load rotamer database and sin/cos tables:1.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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      :  0.003   0.065   8651  Z= 0.142
  Angle     :  0.575   9.395  11691  Z= 0.283
  Chirality :  0.035   0.199   1391
  Planarity :  0.005   0.100   1447
  Dihedral  : 19.908 172.517   3200
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  : 26.93 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.42 (0.28), residues: 1085
  helix:  2.00 (0.19), residues: 811
  sheet: -1.24 (0.69), residues: 60
  loop : -2.71 (0.42), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 541 
 TYR   0.007   0.001   TYR B 503 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.006   0.001   TRP A  80 
 HIS   0.003   0.001   HIS B 434 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 ( 8651)
  covalent geometry    : angle       0.57468 (11691)
  hydrogen bonds       : bond        0.06499 (  558)
  hydrogen bonds       : angle       3.75213 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  131 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.452 
Fit side-chains
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1562
  time to fit residues: 31.4822
Evaluate side-chains
  128 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    1.9990
   chunk 106 optimal weight:    5.9990
   chunk 38 optimal weight:    0.9980
   overall best weight:    1.6786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.126708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.108850 restraints weight = 37258.865|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 2.00
r_work: 0.3225 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.0270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8651  Z= 0.148
  Angle     :  0.545   7.596  11691  Z= 0.268
  Chirality :  0.035   0.152   1391
  Planarity :  0.004   0.072   1447
  Dihedral  : 14.354 171.488   1281
  Min Nonbonded Distance : 2.374

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 26.81 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.28), residues: 1085
  helix:  2.00 (0.19), residues: 804
  sheet: -1.34 (0.69), residues: 60
  loop : -2.55 (0.42), residues: 221

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  25 
 TYR   0.008   0.001   TYR A 503 
 PHE   0.008   0.001   PHE A 154 
 TRP   0.007   0.001   TRP A  44 
 HIS   0.002   0.000   HIS A 502 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 8651)
  covalent geometry    : angle       0.54511 (11691)
  hydrogen bonds       : bond        0.04285 (  558)
  hydrogen bonds       : angle       3.78014 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  138 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 128
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5796 (OUTLIER) cc_final: 0.5286 (m-70)
  outliers start: 10
  outliers final: 5
  residues processed: 133
  average time/residue: 0.1578
  time to fit residues: 32.6090
Evaluate side-chains
  134 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 128
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain B residue   86 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 76 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 69 optimal weight:    3.9990
   chunk 98 optimal weight:    5.9990
   chunk 23 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0980
   chunk 24 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.1186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.125398 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.107490 restraints weight = 37648.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3332 rms_B_bonded: 2.00
r_work: 0.3208 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3069 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.0440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   8651  Z= 0.177
  Angle     :  0.556   7.304  11691  Z= 0.275
  Chirality :  0.035   0.149   1391
  Planarity :  0.004   0.064   1447
  Dihedral  : 13.860 174.073   1281
  Min Nonbonded Distance : 2.406

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 26.24 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.27), residues: 1085
  helix:  1.80 (0.19), residues: 809
  sheet: -1.46 (0.68), residues: 60
  loop : -2.65 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  25 
 TYR   0.007   0.001   TYR A 503 
 PHE   0.009   0.001   PHE B 303 
 TRP   0.008   0.001   TRP A  44 
 HIS   0.005   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 8651)
  covalent geometry    : angle       0.55607 (11691)
  hydrogen bonds       : bond        0.04656 (  558)
  hydrogen bonds       : angle       3.88867 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 128
  time to evaluate  : 0.439 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5820 (OUTLIER) cc_final: 0.5329 (m-70)
REVERT: A  507 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8446 (mmm160)
  outliers start: 15
  outliers final: 11
  residues processed: 137
  average time/residue: 0.1616
  time to fit residues: 33.9662
Evaluate side-chains
  140 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 127
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 0 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   chunk 76 optimal weight:    4.9990
   chunk 86 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   chunk 104 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   overall best weight:    2.5988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.106528 restraints weight = 37646.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 2.00
r_work: 0.3187 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3047 rms_B_bonded: 4.25 restraints_weight: 0.2500
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.0651

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8651  Z= 0.213
  Angle     :  0.581   8.622  11691  Z= 0.291
  Chirality :  0.036   0.147   1391
  Planarity :  0.004   0.060   1447
  Dihedral  : 13.728 174.860   1281
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 25.55 %
    Favored  : 71.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.27), residues: 1085
  helix:  1.59 (0.19), residues: 809
  sheet: -1.53 (0.67), residues: 60
  loop : -2.75 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  25 
 TYR   0.009   0.001   TYR A 201 
 PHE   0.011   0.001   PHE B 303 
 TRP   0.009   0.001   TRP A  44 
 HIS   0.004   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 8651)
  covalent geometry    : angle       0.58117 (11691)
  hydrogen bonds       : bond        0.05067 (  558)
  hydrogen bonds       : angle       4.03777 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  153 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 129
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5906 (OUTLIER) cc_final: 0.5427 (m-70)
REVERT: A  507 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.8460 (mmm160)
REVERT: B  412 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8641 (mt0)
  outliers start: 24
  outliers final: 17
  residues processed: 146
  average time/residue: 0.1316
  time to fit residues: 29.8676
Evaluate side-chains
  147 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  412 GLN
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  481 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:    0.9990
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 55 optimal weight:    4.9990
   chunk 92 optimal weight:    4.9990
   chunk 19 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0980
   chunk 58 optimal weight:    0.7980
   chunk 106 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   overall best weight:    0.9786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.127175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.109354 restraints weight = 37118.704|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 2.00
r_work: 0.3230 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3089 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.3089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.0550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   8651  Z= 0.110
  Angle     :  0.531   6.755  11691  Z= 0.258
  Chirality :  0.034   0.150   1391
  Planarity :  0.004   0.055   1447
  Dihedral  : 13.143 174.807   1281
  Min Nonbonded Distance : 2.340

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 25.78 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.26 (0.28), residues: 1085
  helix:  1.90 (0.19), residues: 808
  sheet: -1.56 (0.67), residues: 60
  loop : -2.66 (0.42), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  25 
 TYR   0.007   0.001   TYR B 503 
 PHE   0.010   0.001   PHE A 154 
 TRP   0.006   0.001   TRP A  44 
 HIS   0.004   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00230 ( 8651)
  covalent geometry    : angle       0.53133 (11691)
  hydrogen bonds       : bond        0.04125 (  558)
  hydrogen bonds       : angle       3.80698 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  153 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 133
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8162 (pm20)
REVERT: A  434 HIS cc_start: 0.5699 (OUTLIER) cc_final: 0.5287 (m-70)
REVERT: A  507 ARG cc_start: 0.8722 (OUTLIER) cc_final: 0.8431 (mmm160)
REVERT: B  135 ASN cc_start: 0.8956 (m-40) cc_final: 0.8657 (m-40)
REVERT: B  412 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8646 (mt0)
  outliers start: 20
  outliers final: 14
  residues processed: 146
  average time/residue: 0.1227
  time to fit residues: 27.8386
Evaluate side-chains
  148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 130
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 ASP
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  348 MET
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  412 GLN
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 54 optimal weight:    3.9990
   chunk 105 optimal weight:    2.9990
   chunk 1 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 49 optimal weight:    0.9990
   chunk 73 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.126523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108761 restraints weight = 37134.172|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 1.99
r_work: 0.3225 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3088 rms_B_bonded: 4.28 restraints_weight: 0.2500
r_work (final): 0.3088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.0627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8651  Z= 0.130
  Angle     :  0.533   7.153  11691  Z= 0.260
  Chirality :  0.035   0.145   1391
  Planarity :  0.004   0.052   1447
  Dihedral  : 12.784 175.114   1281
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 3.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 26.01 %
    Favored  : 71.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.28), residues: 1085
  helix:  1.90 (0.19), residues: 809
  sheet: -1.58 (0.67), residues: 60
  loop : -2.65 (0.41), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  25 
 TYR   0.007   0.001   TYR B 503 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.007   0.001   TRP A  44 
 HIS   0.004   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 8651)
  covalent geometry    : angle       0.53292 (11691)
  hydrogen bonds       : bond        0.04152 (  558)
  hydrogen bonds       : angle       3.82003 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  152 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.467 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5780 (OUTLIER) cc_final: 0.5411 (m-70)
REVERT: A  507 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8431 (mmm160)
REVERT: B  412 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8649 (mt0)
  outliers start: 18
  outliers final: 13
  residues processed: 147
  average time/residue: 0.1537
  time to fit residues: 34.3531
Evaluate side-chains
  146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 130
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  412 GLN
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 48 optimal weight:    4.9990
   chunk 105 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9990
   chunk 98 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 72 optimal weight:    5.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.5586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.126190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.108405 restraints weight = 37276.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 2.00
r_work: 0.3217 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.0587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   8651  Z= 0.137
  Angle     :  0.538   7.159  11691  Z= 0.263
  Chirality :  0.035   0.146   1391
  Planarity :  0.004   0.051   1447
  Dihedral  : 12.668 174.903   1281
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 25.78 %
    Favored  : 71.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.27), residues: 1085
  helix:  1.88 (0.19), residues: 809
  sheet: -1.61 (0.67), residues: 60
  loop : -2.63 (0.42), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  25 
 TYR   0.007   0.001   TYR B 503 
 PHE   0.008   0.001   PHE A 154 
 TRP   0.007   0.001   TRP A  44 
 HIS   0.004   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8651)
  covalent geometry    : angle       0.53847 (11691)
  hydrogen bonds       : bond        0.04212 (  558)
  hydrogen bonds       : angle       3.83156 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  151 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 130
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5694 (OUTLIER) cc_final: 0.5256 (m-70)
REVERT: A  507 ARG cc_start: 0.8717 (OUTLIER) cc_final: 0.8432 (mmm160)
REVERT: B  412 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8652 (mt0)
  outliers start: 21
  outliers final: 17
  residues processed: 146
  average time/residue: 0.1394
  time to fit residues: 31.3250
Evaluate side-chains
  148 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 128
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 ASP
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  412 GLN
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 106 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9980
   chunk 41 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 72 optimal weight:    5.9990
   chunk 5 optimal weight:    4.9990
   chunk 103 optimal weight:    0.4980
   chunk 64 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.127659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.110009 restraints weight = 37197.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3365 rms_B_bonded: 2.00
r_work: 0.3243 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3104 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8089
moved from start:          0.0634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   8651  Z= 0.105
  Angle     :  0.523   6.692  11691  Z= 0.252
  Chirality :  0.034   0.145   1391
  Planarity :  0.004   0.049   1447
  Dihedral  : 12.465 174.361   1281
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 2.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 25.89 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.28), residues: 1085
  helix:  2.01 (0.19), residues: 808
  sheet: -1.58 (0.67), residues: 60
  loop : -2.75 (0.40), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  25 
 TYR   0.007   0.001   TYR B 503 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.006   0.001   TRP A  44 
 HIS   0.004   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 8651)
  covalent geometry    : angle       0.52254 (11691)
  hydrogen bonds       : bond        0.03761 (  558)
  hydrogen bonds       : angle       3.73226 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  155 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 137
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5705 (OUTLIER) cc_final: 0.5364 (m-70)
REVERT: A  507 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8418 (mmm160)
REVERT: B  412 GLN cc_start: 0.8854 (OUTLIER) cc_final: 0.8628 (mt0)
  outliers start: 18
  outliers final: 13
  residues processed: 149
  average time/residue: 0.1285
  time to fit residues: 29.6869
Evaluate side-chains
  145 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  285 ASP
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  412 GLN
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 15 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 92 optimal weight:    4.9990
   chunk 55 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    5.9990
   chunk 41 optimal weight:    0.8980
   chunk 82 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 69 optimal weight:    2.9990
   chunk 105 optimal weight:    3.9990
   overall best weight:    2.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.125802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.107853 restraints weight = 37407.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.01
r_work: 0.3206 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.0670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8651  Z= 0.184
  Angle     :  0.566   7.763  11691  Z= 0.278
  Chirality :  0.035   0.144   1391
  Planarity :  0.004   0.050   1447
  Dihedral  : 12.572 174.711   1281
  Min Nonbonded Distance : 2.271

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.00 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 26.47 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.27), residues: 1085
  helix:  1.82 (0.19), residues: 810
  sheet: -1.61 (0.67), residues: 60
  loop : -2.64 (0.42), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 216 
 TYR   0.008   0.001   TYR A 201 
 PHE   0.011   0.001   PHE B 303 
 TRP   0.008   0.001   TRP A  44 
 HIS   0.006   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 8651)
  covalent geometry    : angle       0.56627 (11691)
  hydrogen bonds       : bond        0.04531 (  558)
  hydrogen bonds       : angle       3.90704 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5844 (OUTLIER) cc_final: 0.5447 (m-70)
REVERT: A  507 ARG cc_start: 0.8730 (OUTLIER) cc_final: 0.8446 (mmm160)
REVERT: B  412 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8649 (mt0)
  outliers start: 17
  outliers final: 14
  residues processed: 138
  average time/residue: 0.1247
  time to fit residues: 26.5768
Evaluate side-chains
  143 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 126
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  198 LEU
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  412 GLN
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 17 optimal weight:    9.9990
   chunk 60 optimal weight:    3.9990
   chunk 63 optimal weight:    2.9990
   chunk 94 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 89 optimal weight:    2.9990
   chunk 87 optimal weight:    2.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    2.1188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108043 restraints weight = 37108.659|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 1.99
r_work: 0.3206 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.3067 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8131
moved from start:          0.0719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8651  Z= 0.173
  Angle     :  0.565   8.362  11691  Z= 0.277
  Chirality :  0.035   0.145   1391
  Planarity :  0.004   0.050   1447
  Dihedral  : 12.390 174.173   1281
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 26.35 %
    Favored  : 71.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.96 (0.27), residues: 1085
  helix:  1.68 (0.19), residues: 815
  sheet: -1.68 (0.67), residues: 60
  loop : -2.90 (0.41), residues: 210

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 216 
 TYR   0.008   0.001   TYR A 503 
 PHE   0.008   0.001   PHE B 286 
 TRP   0.007   0.001   TRP A  44 
 HIS   0.006   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 8651)
  covalent geometry    : angle       0.56525 (11691)
  hydrogen bonds       : bond        0.04585 (  558)
  hydrogen bonds       : angle       3.93071 ( 1644)

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

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

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2170 Ramachandran restraints generated.
    1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  127 is missing expected H atoms. Skipping.
Residue THR  127 is missing expected H atoms. Skipping.
Evaluate side-chains
  146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  434 HIS cc_start: 0.5751 (OUTLIER) cc_final: 0.5422 (m-70)
REVERT: A  507 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.8442 (mmm160)
REVERT: B  412 GLN cc_start: 0.8872 (OUTLIER) cc_final: 0.8649 (mt0)
  outliers start: 19
  outliers final: 16
  residues processed: 141
  average time/residue: 0.1539
  time to fit residues: 33.4526
Evaluate side-chains
  146 residues out of total 869 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 127
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 MET
Chi-restraints excluded: chain A residue  135 ASN
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  282 MET
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  434 HIS
Chi-restraints excluded: chain A residue  507 ARG
Chi-restraints excluded: chain B residue   86 VAL
Chi-restraints excluded: chain B residue  142 THR
Chi-restraints excluded: chain B residue  186 LEU
Chi-restraints excluded: chain B residue  196 VAL
Chi-restraints excluded: chain B residue  250 VAL
Chi-restraints excluded: chain B residue  285 ASP
Chi-restraints excluded: chain B residue  297 VAL
Chi-restraints excluded: chain B residue  367 SER
Chi-restraints excluded: chain B residue  412 GLN
Chi-restraints excluded: chain B residue  433 ASP
Chi-restraints excluded: chain B residue  455 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 97 optimal weight:    0.4980
   chunk 66 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 100 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.126577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.108677 restraints weight = 37442.177|
|-----------------------------------------------------------------------------|
r_work (start): 0.3349 rms_B_bonded: 2.01
r_work: 0.3226 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3085 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.0668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   8651  Z= 0.119
  Angle     :  0.540   7.633  11691  Z= 0.261
  Chirality :  0.035   0.144   1391
  Planarity :  0.004   0.049   1447
  Dihedral  : 12.262 174.075   1281
  Min Nonbonded Distance : 2.315

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 26.12 %
    Favored  : 71.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.18 (0.27), residues: 1085
  helix:  1.83 (0.19), residues: 816
  sheet: -1.66 (0.67), residues: 60
  loop : -2.79 (0.41), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 216 
 TYR   0.007   0.001   TYR B 503 
 PHE   0.009   0.001   PHE A 154 
 TRP   0.006   0.001   TRP A  44 
 HIS   0.005   0.001   HIS A 430 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 8651)
  covalent geometry    : angle       0.53959 (11691)
  hydrogen bonds       : bond        0.04113 (  558)
  hydrogen bonds       : angle       3.81981 ( 1644)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3960.89 seconds
wall clock time: 67 minutes 47.50 seconds (4067.50 seconds total)