Starting phenix.real_space_refine
on Sat Aug 23 12:45:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8s8p_19811/08_2025/8s8p_19811.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8s8p_19811/08_2025/8s8p_19811.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.11
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2025/8s8p_19811.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2025/8s8p_19811.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2025/8s8p_19811.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8s8p_19811/08_2025/8s8p_19811.map"
  }
  resolution = 3.11
  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=   0.018
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: 5
    Type Number    sf(0)   Gaussians
     P      40      5.49       5
     S      43      5.16       5
     C    7564      2.51       5
     N    2057      2.21       5
     O    2430      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 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: 12134
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "C"
      Number of atoms: 414
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 414
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
    Chain: "D"
      Number of atoms: 441
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 441
          Classifications: {'DNA': 21}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 20}
    Chain: "K"
      Number of atoms: 4617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 557, 4617
          Classifications: {'peptide': 557}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 20, 'TRANS': 535}
    Chain: "L"
      Number of atoms: 4658
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 587, 4658
          Classifications: {'peptide': 587}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 559}
    Chain: "R"
      Number of atoms: 2004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 242, 2004
          Classifications: {'peptide': 242}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 6, 'PCIS': 1, 'PTRANS': 15, 'TRANS': 219}
  Time building chain proxies: 3.29, per 1000 atoms: 0.27
  Number of scatterers: 12134
  At special positions: 0
  Unit cell: (103.806, 96.579, 159.651, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      43     16.00
     P      40     15.00
     O    2430      8.00
     N    2057      7.00
     C    7564      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 579.3 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2668

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 11 sheets defined
      37.9% alpha, 15.9% beta
      19 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 1.43
  Creating SS restraints...
    Processing helix  chain 'K' and resid 39 through 44
    Processing helix  chain 'K' and resid 53 through 73
      removed outlier: 3.966A  pdb=" N   ILE K  71 " --> pdb=" O   SER K  67 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 90 through 94
      removed outlier: 3.689A  pdb=" N   GLY K  93 " --> pdb=" O   ALA K  90 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   ILE K  94 " --> pdb=" O   LYS K  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 90 through 94'
    Processing helix  chain 'K' and resid 104 through 120
      removed outlier: 3.518A  pdb=" N   MET K 108 " --> pdb=" O   ASN K 104 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 124 through 130
    Processing helix  chain 'K' and resid 141 through 153
      removed outlier: 3.652A  pdb=" N   PHE K 153 " --> pdb=" O   MET K 149 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 177 through 181
    Processing helix  chain 'K' and resid 183 through 199
    Processing helix  chain 'K' and resid 217 through 225
    Processing helix  chain 'K' and resid 252 through 259
    Processing helix  chain 'K' and resid 345 through 354
    Processing helix  chain 'K' and resid 396 through 409
      removed outlier: 3.795A  pdb=" N   THR K 400 " --> pdb=" O   GLY K 396 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 470 through 488
      removed outlier: 3.912A  pdb=" N   TYR K 487 " --> pdb=" O   SER K 483 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE K 488 " --> pdb=" O   ILE K 484 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 495 through 499
    Processing helix  chain 'K' and resid 501 through 516
    Processing helix  chain 'K' and resid 527 through 539
    Processing helix  chain 'K' and resid 539 through 558
      removed outlier: 3.636A  pdb=" N   ARG K 543 " --> pdb=" O   ASP K 539 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   LYS K 544 " --> pdb=" O   ASP K 540 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLU K 556 " --> pdb=" O   ILE K 552 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 564 through 584
      removed outlier: 3.711A  pdb=" N   LYS K 568 " --> pdb=" O   GLN K 564 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE K 580 " --> pdb=" O   PHE K 576 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASN K 581 " --> pdb=" O   TYR K 577 " (cutoff:3.500A)
      removed outlier: 4.310A  pdb=" N   ASP K 582 " --> pdb=" O   LYS K 578 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 13 through 19
    Processing helix  chain 'L' and resid 20 through 38
      removed outlier: 3.580A  pdb=" N   LYS L  38 " --> pdb=" O   LEU L  34 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 76 through 94
    Processing helix  chain 'L' and resid 106 through 121
      removed outlier: 3.557A  pdb=" N   LEU L 110 " --> pdb=" O   MET L 106 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 143 through 154
    Processing helix  chain 'L' and resid 175 through 183
      removed outlier: 4.243A  pdb=" N   LEU L 179 " --> pdb=" O   ASN L 175 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 191 through 200
    Processing helix  chain 'L' and resid 327 through 334
      removed outlier: 3.534A  pdb=" N   ASP L 332 " --> pdb=" O   SER L 328 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 354 through 358
      removed outlier: 3.605A  pdb=" N   LEU L 358 " --> pdb=" O   ARG L 355 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 373 through 391
      removed outlier: 3.632A  pdb=" N   LEU L 377 " --> pdb=" O   CYS L 373 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 467 through 481
      removed outlier: 3.881A  pdb=" N   ASP L 471 " --> pdb=" O   GLY L 467 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   GLU L 472 " --> pdb=" O   HIS L 468 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   MET L 481 " --> pdb=" O   PHE L 477 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 497 through 501
    Processing helix  chain 'L' and resid 513 through 517
      removed outlier: 3.775A  pdb=" N   GLN L 516 " --> pdb=" O   ASN L 513 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 529 through 547
    Processing helix  chain 'L' and resid 559 through 566
      removed outlier: 4.183A  pdb=" N   LYS L 565 " --> pdb=" O   SER L 561 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE L 566 " --> pdb=" O   LEU L 562 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 576 through 584
    Processing helix  chain 'R' and resid 365 through 378
    Processing helix  chain 'R' and resid 379 through 382
      removed outlier: 3.706A  pdb=" N   ARG R 382 " --> pdb=" O   PRO R 379 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'R' and resid 379 through 382'
    Processing helix  chain 'R' and resid 385 through 395
      removed outlier: 3.530A  pdb=" N   ASP R 389 " --> pdb=" O   HIS R 385 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 399 through 410
    Processing helix  chain 'R' and resid 411 through 415
      removed outlier: 3.891A  pdb=" N   LEU R 415 " --> pdb=" O   SER R 412 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 450 through 471
    Processing helix  chain 'R' and resid 521 through 534
      removed outlier: 3.795A  pdb=" N   PHE R 525 " --> pdb=" O   ILE R 521 " (cutoff:3.500A)
      removed outlier: 4.351A  pdb=" N   PHE R 526 " --> pdb=" O   ALA R 522 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 537 through 553
      removed outlier: 3.618A  pdb=" N   TRP R 541 " --> pdb=" O   THR R 537 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   LEU R 550 " --> pdb=" O   ARG R 546 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   ALA R 551 " --> pdb=" O   LYS R 547 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 553 through 567
    Processing sheet with id=AA1, first strand: chain 'K' and resid 95 through 102
      removed outlier: 6.846A  pdb=" N   CYS K  80 " --> pdb=" O   LEU K  97 " (cutoff:3.500A)
      removed outlier: 5.497A  pdb=" N   ILE K  78 " --> pdb=" O   PRO K  99 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ARG K 101 " --> pdb=" O   THR K  76 " (cutoff:3.500A)
      removed outlier: 7.318A  pdb=" N   THR K  76 " --> pdb=" O   ARG K 101 " (cutoff:3.500A)
      removed outlier: 6.146A  pdb=" N   GLU K  30 " --> pdb=" O   ALA K  77 " (cutoff:3.500A)
      removed outlier: 7.847A  pdb=" N   GLY K  79 " --> pdb=" O   GLU K  30 " (cutoff:3.500A)
      removed outlier: 6.607A  pdb=" N   ILE K  32 " --> pdb=" O   GLY K  79 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   TYR K  81 " --> pdb=" O   ILE K  32 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   PHE K  34 " --> pdb=" O   TYR K  81 " (cutoff:3.500A)
      removed outlier: 7.832A  pdb=" N   TYR K  83 " --> pdb=" O   PHE K  34 " (cutoff:3.500A)
      removed outlier: 5.932A  pdb=" N   ILE K  36 " --> pdb=" O   TYR K  83 " (cutoff:3.500A)
      removed outlier: 6.397A  pdb=" N   GLY K  31 " --> pdb=" O   ARG K 167 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   PHE K 169 " --> pdb=" O   GLY K  31 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   LEU K  33 " --> pdb=" O   PHE K 169 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   PHE K 171 " --> pdb=" O   LEU K  33 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   CYS K  35 " --> pdb=" O   PHE K 171 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LYS K 166 " --> pdb=" O   ASN K 202 " (cutoff:3.500A)
      removed outlier: 7.508A  pdb=" N   ALA K 204 " --> pdb=" O   LYS K 166 " (cutoff:3.500A)
      removed outlier: 5.952A  pdb=" N   VAL K 168 " --> pdb=" O   ALA K 204 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   PHE K 206 " --> pdb=" O   VAL K 168 " (cutoff:3.500A)
      removed outlier: 6.974A  pdb=" N   LEU K 170 " --> pdb=" O   PHE K 206 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   ILE K 208 " --> pdb=" O   LEU K 170 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   THR K 172 " --> pdb=" O   ILE K 208 " (cutoff:3.500A)
      removed outlier: 6.912A  pdb=" N   ILE K 248 " --> pdb=" O   THR K 205 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   PHE K 207 " --> pdb=" O   ILE K 248 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'K' and resid 266 through 269
      removed outlier: 6.606A  pdb=" N   GLY K 286 " --> pdb=" O   MET K 267 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   GLN K 269 " --> pdb=" O   VAL K 284 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL K 284 " --> pdb=" O   GLN K 269 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER K 385 " --> pdb=" O   LEU K 446 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   TYR K 447 " --> pdb=" O   THR K 431 " (cutoff:3.500A)
      removed outlier: 4.806A  pdb=" N   LEU K 429 " --> pdb=" O   VAL K 449 " (cutoff:3.500A)
      removed outlier: 7.919A  pdb=" N   LYS K 413 " --> pdb=" O   PRO K 434 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   TRP K 418 " --> pdb=" O   ILE K 365 " (cutoff:3.500A)
      removed outlier: 5.624A  pdb=" N   ILE K 365 " --> pdb=" O   TRP K 418 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   LYS K 420 " --> pdb=" O   LEU K 363 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   LEU K 363 " --> pdb=" O   LYS K 420 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   ASP K 275 " --> pdb=" O   ILE K 365 " (cutoff:3.500A)
      removed outlier: 11.921A  pdb=" N   GLY K 367 " --> pdb=" O   ASP K 275 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   PHE K 280 " --> pdb=" O   LEU K 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'K' and resid 308 through 311
      removed outlier: 3.789A  pdb=" N   GLN K 310 " --> pdb=" O   TYR K 303 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'K' and resid 313 through 319
      removed outlier: 4.201A  pdb=" N   TYR L 282 " --> pdb=" O   ILE L 308 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ASN L 286 " --> pdb=" O   ILE L 304 " (cutoff:3.500A)
      removed outlier: 4.485A  pdb=" N   ILE L 304 " --> pdb=" O   ASN L 286 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'K' and resid 341 through 342
      removed outlier: 3.750A  pdb=" N   VAL L 274 " --> pdb=" O   VAL L 262 " (cutoff:3.500A)
      removed outlier: 4.433A  pdb=" N   ARG L 272 " --> pdb=" O   VAL L 264 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'K' and resid 394 through 395
    Processing sheet with id=AA7, first strand: chain 'L' and resid 65 through 72
      removed outlier: 6.635A  pdb=" N   CYS L  48 " --> pdb=" O   ILE L  68 " (cutoff:3.500A)
      removed outlier: 5.874A  pdb=" N   SER L  70 " --> pdb=" O   ILE L  46 " (cutoff:3.500A)
      removed outlier: 5.904A  pdb=" N   ILE L  46 " --> pdb=" O   SER L  70 " (cutoff:3.500A)
      removed outlier: 6.152A  pdb=" N   LEU L  72 " --> pdb=" O   ASP L  44 " (cutoff:3.500A)
      removed outlier: 6.008A  pdb=" N   ASP L  44 " --> pdb=" O   LEU L  72 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   GLU L   4 " --> pdb=" O   TRP L  45 " (cutoff:3.500A)
      removed outlier: 9.144A  pdb=" N   SER L  47 " --> pdb=" O   GLU L   4 " (cutoff:3.500A)
      removed outlier: 6.852A  pdb=" N   THR L   6 " --> pdb=" O   SER L  47 " (cutoff:3.500A)
      removed outlier: 8.332A  pdb=" N   TYR L  49 " --> pdb=" O   THR L   6 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   PHE L   8 " --> pdb=" O   TYR L  49 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   ALA L  51 " --> pdb=" O   PHE L   8 " (cutoff:3.500A)
      removed outlier: 6.303A  pdb=" N   VAL L  10 " --> pdb=" O   ALA L  51 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   SER L   5 " --> pdb=" O   GLN L 129 " (cutoff:3.500A)
      removed outlier: 7.608A  pdb=" N   VAL L 131 " --> pdb=" O   SER L   5 " (cutoff:3.500A)
      removed outlier: 6.291A  pdb=" N   THR L   7 " --> pdb=" O   VAL L 131 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   PHE L 133 " --> pdb=" O   THR L   7 " (cutoff:3.500A)
      removed outlier: 6.572A  pdb=" N   ILE L   9 " --> pdb=" O   PHE L 133 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   LYS L 128 " --> pdb=" O   ARG L 157 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ILE L 159 " --> pdb=" O   LYS L 128 " (cutoff:3.500A)
      removed outlier: 6.631A  pdb=" N   ILE L 130 " --> pdb=" O   ILE L 159 " (cutoff:3.500A)
      removed outlier: 7.406A  pdb=" N   ILE L 161 " --> pdb=" O   ILE L 130 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL L 132 " --> pdb=" O   ILE L 161 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 248 through 250
      removed outlier: 6.389A  pdb=" N   SER L 362 " --> pdb=" O   ALA L 249 " (cutoff:3.500A)
      removed outlier: 5.733A  pdb=" N   ALA L 367 " --> pdb=" O   LYS L 429 " (cutoff:3.500A)
      removed outlier: 9.892A  pdb=" N   LYS L 429 " --> pdb=" O   ALA L 367 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   MET L 408 " --> pdb=" O   LEU L 436 " (cutoff:3.500A)
      removed outlier: 7.542A  pdb=" N   LYS L 392 " --> pdb=" O   PRO L 413 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY L 346 " --> pdb=" O   VAL L 395 " (cutoff:3.500A)
      removed outlier: 6.141A  pdb=" N   ARG L 397 " --> pdb=" O   LEU L 344 " (cutoff:3.500A)
      removed outlier: 5.839A  pdb=" N   LEU L 344 " --> pdb=" O   ARG L 397 " (cutoff:3.500A)
      removed outlier: 7.794A  pdb=" N   VAL L 399 " --> pdb=" O   LEU L 342 " (cutoff:3.500A)
      removed outlier: 5.385A  pdb=" N   LEU L 342 " --> pdb=" O   VAL L 399 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   LEU L 342 " --> pdb=" O   SER L 213 " (cutoff:3.500A)
      removed outlier: 6.157A  pdb=" N   GLU L 215 " --> pdb=" O   LEU L 342 " (cutoff:3.500A)
      removed outlier: 7.212A  pdb=" N   LEU L 344 " --> pdb=" O   GLU L 215 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   ARG L 217 " --> pdb=" O   LEU L 344 " (cutoff:3.500A)
      removed outlier: 8.503A  pdb=" N   GLY L 346 " --> pdb=" O   ARG L 217 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 317 through 319
    Processing sheet with id=AB1, first strand: chain 'R' and resid 418 through 419
    Processing sheet with id=AB2, first strand: chain 'R' and resid 478 through 479
      removed outlier: 3.585A  pdb=" N   THR R 496 " --> pdb=" O   ARG R 478 " (cutoff:3.500A)

    429 hydrogen bonds defined for protein.
    1200 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      50 hydrogen bonds
      100 hydrogen bond angles
      0 basepair planarities
      19 basepair parallelities
      32 stacking parallelities
  Total time for adding SS restraints: 2.40

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3489
        1.34 -     1.45: 2062
        1.45 -     1.57: 6763
        1.57 -     1.69: 80
        1.69 -     1.81: 71
  Bond restraints: 12465
  Sorted by residual:
  bond pdb=" C   ASP R 498 "
       pdb=" N   PRO R 499 "
    ideal  model  delta    sigma   weight residual
    1.334  1.371 -0.037 2.34e-02 1.83e+03 2.47e+00
  bond pdb=" CG1 ILE K 407 "
       pdb=" CD1 ILE K 407 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.84e+00
  bond pdb=" C3'  DC C  16 "
       pdb=" O3'  DC C  16 "
    ideal  model  delta    sigma   weight residual
    1.422  1.461 -0.039 3.00e-02 1.11e+03 1.65e+00
  bond pdb=" N   LYS R 597 "
       pdb=" CA  LYS R 597 "
    ideal  model  delta    sigma   weight residual
    1.458  1.479 -0.021 1.90e-02 2.77e+03 1.24e+00
  bond pdb=" O4'  DT D  21 "
       pdb=" C1'  DT D  21 "
    ideal  model  delta    sigma   weight residual
    1.414  1.393  0.021 2.00e-02 2.50e+03 1.14e+00
  ... (remaining 12460 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 16720
        1.89 -     3.78: 270
        3.78 -     5.67: 22
        5.67 -     7.55: 5
        7.55 -     9.44: 1
  Bond angle restraints: 17018
  Sorted by residual:
  angle pdb=" C   GLU L 464 "
        pdb=" CA  GLU L 464 "
        pdb=" CB  GLU L 464 "
      ideal   model   delta    sigma   weight residual
     116.34  110.54    5.80 1.40e+00 5.10e-01 1.72e+01
  angle pdb=" C   ALA R 596 "
        pdb=" N   LYS R 597 "
        pdb=" CA  LYS R 597 "
      ideal   model   delta    sigma   weight residual
     121.70  128.93   -7.23 1.80e+00 3.09e-01 1.62e+01
  angle pdb=" C   VAL K 388 "
        pdb=" CA  VAL K 388 "
        pdb=" CB  VAL K 388 "
      ideal   model   delta    sigma   weight residual
     109.33  112.93   -3.60 9.80e-01 1.04e+00 1.35e+01
  angle pdb=" C   ARG K 409 "
        pdb=" N   LYS K 410 "
        pdb=" CA  LYS K 410 "
      ideal   model   delta    sigma   weight residual
     121.54  128.05   -6.51 1.91e+00 2.74e-01 1.16e+01
  angle pdb=" N   VAL K 388 "
        pdb=" CA  VAL K 388 "
        pdb=" C   VAL K 388 "
      ideal   model   delta    sigma   weight residual
     109.19  106.55    2.64 8.20e-01 1.49e+00 1.04e+01
  ... (remaining 17013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.87: 7085
       34.87 -    69.75: 423
       69.75 -   104.62: 24
      104.62 -   139.49: 0
      139.49 -   174.37: 1
  Dihedral angle restraints: 7533
    sinusoidal: 3417
      harmonic: 4116
  Sorted by residual:
  dihedral pdb=" CA  PHE R 363 "
           pdb=" C   PHE R 363 "
           pdb=" N   THR R 364 "
           pdb=" CA  THR R 364 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.46   23.54     0      5.00e+00 4.00e-02 2.22e+01
  dihedral pdb=" CA  THR R 364 "
           pdb=" C   THR R 364 "
           pdb=" N   ASP R 365 "
           pdb=" CA  ASP R 365 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.84  -23.16     0      5.00e+00 4.00e-02 2.15e+01
  dihedral pdb=" C4'  DC C  16 "
           pdb=" C3'  DC C  16 "
           pdb=" O3'  DC C  16 "
           pdb=" P    DA C  17 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   45.63  174.37     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1154
       0.028 -    0.057: 467
       0.057 -    0.085: 155
       0.085 -    0.113: 85
       0.113 -    0.142: 23
  Chirality restraints: 1884
  Sorted by residual:
  chirality pdb=" CA  PHE R 363 "
            pdb=" N   PHE R 363 "
            pdb=" C   PHE R 363 "
            pdb=" CB  PHE R 363 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.01e-01
  chirality pdb=" CA  ILE L 188 "
            pdb=" N   ILE L 188 "
            pdb=" C   ILE L 188 "
            pdb=" CB  ILE L 188 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  VAL K 388 "
            pdb=" N   VAL K 388 "
            pdb=" C   VAL K 388 "
            pdb=" CB  VAL K 388 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.36e-01
  ... (remaining 1881 not shown)

  Planarity restraints: 2055
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU L 558 "   -0.034 5.00e-02 4.00e+02   5.22e-02 4.36e+00
        pdb=" N   PRO L 559 "    0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO L 559 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO L 559 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL K 388 "   -0.030 5.00e-02 4.00e+02   4.47e-02 3.20e+00
        pdb=" N   PRO K 389 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO K 389 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO K 389 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE L 489 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO L 490 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO L 490 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO L 490 "    0.022 5.00e-02 4.00e+02
  ... (remaining 2052 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 419
        2.71 -     3.26: 11661
        3.26 -     3.80: 19419
        3.80 -     4.35: 25064
        4.35 -     4.90: 41126
  Nonbonded interactions: 97689
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU K  37 "
            pdb=" OG1 THR K 172 "
     model   vdw
     2.162 3.040
  nonbonded pdb=" O   ARG R 382 "
            pdb=" OH  TYR R 388 "
     model   vdw
     2.192 3.040
  nonbonded pdb=" OH  TYR K 494 "
            pdb=" O   PRO L 437 "
     model   vdw
     2.207 3.040
  nonbonded pdb=" O   PRO R 487 "
            pdb=" OG1 THR R 488 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" O   ILE L  68 "
            pdb=" NH1 ARG L  86 "
     model   vdw
     2.267 3.120
  ... (remaining 97684 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             11.050
  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:          0.290
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.450
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.020
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7608
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   0.053  12465  Z= 0.126
  Angle     :  0.573   9.443  17018  Z= 0.323
  Chirality :  0.039   0.142   1884
  Planarity :  0.004   0.052   2055
  Dihedral  : 19.608 174.366   4865
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.71 %
    Favored  : 95.14 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 21.52 %
    Favored  : 78.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.64 (0.22), residues: 1380
  helix:  1.26 (0.24), residues: 465
  sheet: -1.16 (0.38), residues: 170
  loop : -1.38 (0.22), residues: 745

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 543 
 TYR   0.014   0.001   TYR K 394 
 PHE   0.009   0.001   PHE K  98 
 TRP   0.014   0.001   TRP K 418 
 HIS   0.003   0.001   HIS L 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (12465)
  covalent geometry    : angle       0.57291 (17018)
  hydrogen bonds       : bond        0.16772 (  479)
  hydrogen bonds       : angle       6.50329 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 129
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
REVERT: K  213 LYS cc_start: 0.7622 (tttm) cc_final: 0.7082 (tmtt)
REVERT: R  412 SER cc_start: 0.7887 (p) cc_final: 0.7584 (p)
  outliers start: 4
  outliers final: 3
  residues processed: 132
  average time/residue: 0.1300
  time to fit residues: 24.2826
Evaluate side-chains
  120 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 117
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   29 HIS
Chi-restraints excluded: chain K residue  273 ILE
Chi-restraints excluded: chain L residue  111 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    0.2980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.0040
   chunk 124 optimal weight:   20.0000
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.0598

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

Flipped N/Q/H residues before XYZ refinement:
K 225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.214637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.170028 restraints weight = 13712.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.4043 rms_B_bonded: 2.62
r_work: 0.3698 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.0885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12465  Z= 0.188
  Angle     :  0.600   8.088  17018  Z= 0.322
  Chirality :  0.043   0.166   1884
  Planarity :  0.005   0.048   2055
  Dihedral  : 16.697 174.011   1978
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.14 %
    Favored  : 94.86 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 20.11 %
    Favored  : 76.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.73 (0.22), residues: 1380
  helix:  1.23 (0.24), residues: 474
  sheet: -1.29 (0.38), residues: 171
  loop : -1.48 (0.21), residues: 735

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG K 543 
 TYR   0.014   0.002   TYR K 577 
 PHE   0.017   0.002   PHE K  98 
 TRP   0.010   0.002   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 (12465)
  covalent geometry    : angle       0.59997 (17018)
  hydrogen bonds       : bond        0.04278 (  479)
  hydrogen bonds       : angle       5.21785 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 124
  time to evaluate  : 0.475 
Fit side-chains
   revert: symmetry clash
REVERT: K  216 ASP cc_start: 0.7256 (m-30) cc_final: 0.6952 (t0)
REVERT: L  142 ILE cc_start: 0.4169 (OUTLIER) cc_final: 0.3780 (mt)
REVERT: L  181 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7838 (pt0)
REVERT: R  543 ASP cc_start: 0.6502 (OUTLIER) cc_final: 0.6292 (t0)
  outliers start: 45
  outliers final: 26
  residues processed: 158
  average time/residue: 0.1071
  time to fit residues: 25.0290
Evaluate side-chains
  140 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 111
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue   29 HIS
Chi-restraints excluded: chain K residue  164 SER
Chi-restraints excluded: chain K residue  176 LYS
Chi-restraints excluded: chain K residue  255 SER
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  281 ILE
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  485 MET
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   15 SER
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  181 GLU
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  245 GLU
Chi-restraints excluded: chain L residue  313 VAL
Chi-restraints excluded: chain L residue  314 THR
Chi-restraints excluded: chain L residue  324 VAL
Chi-restraints excluded: chain L residue  331 VAL
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  404 SER
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain L residue  505 THR
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  543 ASP
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 7 optimal weight:    0.8980
   chunk 10 optimal weight:    0.0040
   chunk 82 optimal weight:    0.0070
   chunk 29 optimal weight:    0.0070
   chunk 26 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 122 optimal weight:    5.9990
   chunk 97 optimal weight:    0.9980
   chunk 89 optimal weight:   10.0000
   overall best weight:    0.3828

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

Flipped N/Q/H residues before XYZ refinement:
K 225 GLN
L 333 GLN
L 513 ASN
** R 405 HIS ** 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 = 0.4503 r_free = 0.4503 target = 0.218598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.174206 restraints weight = 13758.801|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 2.56
r_work: 0.3757 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7630
moved from start:          0.1142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  12465  Z= 0.117
  Angle     :  0.525   8.257  17018  Z= 0.282
  Chirality :  0.040   0.160   1884
  Planarity :  0.004   0.047   2055
  Dihedral  : 16.556 177.184   1976
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 21.13 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.55 (0.22), residues: 1380
  helix:  1.39 (0.24), residues: 480
  sheet: -1.17 (0.38), residues: 176
  loop : -1.41 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 543 
 TYR   0.012   0.001   TYR K  83 
 PHE   0.019   0.001   PHE K 197 
 TRP   0.009   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (12465)
  covalent geometry    : angle       0.52498 (17018)
  hydrogen bonds       : bond        0.03427 (  479)
  hydrogen bonds       : angle       4.84808 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 140
  time to evaluate  : 0.479 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7820 (t80) cc_final: 0.7400 (m-80)
REVERT: K  213 LYS cc_start: 0.7691 (tttm) cc_final: 0.7118 (tmtt)
REVERT: K  216 ASP cc_start: 0.7191 (m-30) cc_final: 0.6942 (t0)
REVERT: K  353 MET cc_start: 0.7561 (ttm) cc_final: 0.7337 (ttm)
REVERT: L  142 ILE cc_start: 0.3877 (OUTLIER) cc_final: 0.3546 (mt)
REVERT: L  181 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.7871 (pt0)
REVERT: L  324 VAL cc_start: 0.7321 (OUTLIER) cc_final: 0.7064 (m)
REVERT: R  543 ASP cc_start: 0.6457 (OUTLIER) cc_final: 0.6229 (t0)
  outliers start: 39
  outliers final: 20
  residues processed: 169
  average time/residue: 0.1133
  time to fit residues: 27.9509
Evaluate side-chains
  147 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  284 VAL
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  181 GLU
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  245 GLU
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  314 THR
Chi-restraints excluded: chain L residue  324 VAL
Chi-restraints excluded: chain L residue  333 GLN
Chi-restraints excluded: chain L residue  362 SER
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain L residue  561 SER
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  537 THR
Chi-restraints excluded: chain R residue  543 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 11 optimal weight:    0.0020
   chunk 20 optimal weight:    0.6980
   chunk 114 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   chunk 108 optimal weight:    0.0670
   chunk 49 optimal weight:    0.8980
   chunk 42 optimal weight:    0.6980
   chunk 84 optimal weight:    2.9990
   chunk 65 optimal weight:    0.0970
   chunk 120 optimal weight:    1.9990
   overall best weight:    0.3124

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

Flipped N/Q/H residues before XYZ refinement:
K 567 ASN
L 333 GLN
R 405 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4510 r_free = 0.4510 target = 0.219345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.175630 restraints weight = 13737.075|
|-----------------------------------------------------------------------------|
r_work (start): 0.4097 rms_B_bonded: 2.50
r_work: 0.3768 rms_B_bonded: 3.58 restraints_weight: 0.5000
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1351

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  12465  Z= 0.112
  Angle     :  0.519   8.040  17018  Z= 0.279
  Chirality :  0.040   0.148   1884
  Planarity :  0.004   0.044   2055
  Dihedral  : 16.460 176.948   1974
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.60 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.47 (0.22), residues: 1380
  helix:  1.48 (0.24), residues: 479
  sheet: -1.07 (0.39), residues: 175
  loop : -1.39 (0.21), residues: 726

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG K 543 
 TYR   0.015   0.001   TYR K  83 
 PHE   0.013   0.001   PHE L 133 
 TRP   0.007   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (12465)
  covalent geometry    : angle       0.51859 (17018)
  hydrogen bonds       : bond        0.03194 (  479)
  hydrogen bonds       : angle       4.70672 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7811 (t80) cc_final: 0.7481 (m-80)
REVERT: K  213 LYS cc_start: 0.7723 (tttm) cc_final: 0.7184 (tmtt)
REVERT: L  142 ILE cc_start: 0.3838 (OUTLIER) cc_final: 0.3531 (mt)
REVERT: L  324 VAL cc_start: 0.7254 (OUTLIER) cc_final: 0.6998 (m)
REVERT: R  412 SER cc_start: 0.8004 (p) cc_final: 0.7683 (p)
  outliers start: 35
  outliers final: 22
  residues processed: 160
  average time/residue: 0.1163
  time to fit residues: 27.1980
Evaluate side-chains
  148 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  164 SER
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  314 THR
Chi-restraints excluded: chain L residue  324 VAL
Chi-restraints excluded: chain L residue  329 VAL
Chi-restraints excluded: chain L residue  334 THR
Chi-restraints excluded: chain L residue  362 SER
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  537 THR
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 123 optimal weight:    0.0770
   chunk 15 optimal weight:    0.6980
   chunk 100 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 125 optimal weight:    0.5980
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 50 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
L 333 GLN
L 349 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.216610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.172132 restraints weight = 13745.285|
|-----------------------------------------------------------------------------|
r_work (start): 0.4066 rms_B_bonded: 2.58
r_work: 0.3721 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12465  Z= 0.140
  Angle     :  0.540   7.945  17018  Z= 0.288
  Chirality :  0.040   0.157   1884
  Planarity :  0.004   0.043   2055
  Dihedral  : 16.564 176.284   1974
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 5.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  3.13 %
    Allowed  : 21.75 %
    Favored  : 75.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.45 (0.22), residues: 1380
  helix:  1.51 (0.24), residues: 480
  sheet: -1.14 (0.38), residues: 169
  loop : -1.37 (0.22), residues: 731

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 272 
 TYR   0.015   0.001   TYR K 394 
 PHE   0.014   0.001   PHE K  98 
 TRP   0.007   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (12465)
  covalent geometry    : angle       0.54037 (17018)
  hydrogen bonds       : bond        0.03362 (  479)
  hydrogen bonds       : angle       4.65762 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 126
  time to evaluate  : 0.491 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7823 (t80) cc_final: 0.7457 (m-80)
REVERT: K  300 LYS cc_start: 0.8723 (OUTLIER) cc_final: 0.8375 (mtpt)
REVERT: L  142 ILE cc_start: 0.3821 (OUTLIER) cc_final: 0.3518 (mt)
REVERT: L  181 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.7933 (pt0)
  outliers start: 40
  outliers final: 29
  residues processed: 162
  average time/residue: 0.1081
  time to fit residues: 25.8244
Evaluate side-chains
  148 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 116
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  266 ILE
Chi-restraints excluded: chain K residue  281 ILE
Chi-restraints excluded: chain K residue  284 VAL
Chi-restraints excluded: chain K residue  300 LYS
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  461 LEU
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  181 GLU
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  260 THR
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  278 SER
Chi-restraints excluded: chain L residue  314 THR
Chi-restraints excluded: chain L residue  324 VAL
Chi-restraints excluded: chain L residue  329 VAL
Chi-restraints excluded: chain L residue  334 THR
Chi-restraints excluded: chain L residue  362 SER
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  537 THR
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 33 optimal weight:    2.9990
   chunk 64 optimal weight:    6.9990
   chunk 72 optimal weight:    0.2980
   chunk 101 optimal weight:    0.7980
   chunk 120 optimal weight:    0.7980
   chunk 122 optimal weight:    0.1980
   chunk 34 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 103 optimal weight:    4.9990
   chunk 31 optimal weight:    3.9990
   chunk 130 optimal weight:   20.0000
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
K  29 HIS
L 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.217220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.172440 restraints weight = 13640.593|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 2.56
r_work: 0.3731 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12465  Z= 0.128
  Angle     :  0.528   8.134  17018  Z= 0.282
  Chirality :  0.040   0.158   1884
  Planarity :  0.004   0.044   2055
  Dihedral  : 16.540 177.892   1974
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 21.44 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.42 (0.22), residues: 1380
  helix:  1.53 (0.24), residues: 480
  sheet: -1.10 (0.38), residues: 170
  loop : -1.35 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG L 272 
 TYR   0.015   0.001   TYR K  83 
 PHE   0.012   0.001   PHE K  98 
 TRP   0.006   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12465)
  covalent geometry    : angle       0.52814 (17018)
  hydrogen bonds       : bond        0.03219 (  479)
  hydrogen bonds       : angle       4.61230 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 128
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7842 (t80) cc_final: 0.7518 (m-80)
REVERT: K  216 ASP cc_start: 0.7168 (m-30) cc_final: 0.6854 (t0)
REVERT: K  300 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8262 (mtpt)
REVERT: L   17 MET cc_start: 0.6741 (mmt) cc_final: 0.6500 (mmm)
REVERT: L  142 ILE cc_start: 0.3738 (OUTLIER) cc_final: 0.3440 (mt)
REVERT: R  412 SER cc_start: 0.7979 (p) cc_final: 0.7657 (p)
  outliers start: 42
  outliers final: 30
  residues processed: 163
  average time/residue: 0.1089
  time to fit residues: 25.5590
Evaluate side-chains
  150 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 118
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  266 ILE
Chi-restraints excluded: chain K residue  281 ILE
Chi-restraints excluded: chain K residue  284 VAL
Chi-restraints excluded: chain K residue  300 LYS
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  461 LEU
Chi-restraints excluded: chain K residue  535 MET
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  260 THR
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  278 SER
Chi-restraints excluded: chain L residue  313 VAL
Chi-restraints excluded: chain L residue  324 VAL
Chi-restraints excluded: chain L residue  329 VAL
Chi-restraints excluded: chain L residue  362 SER
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain L residue  505 THR
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  537 THR
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9990
   chunk 139 optimal weight:    9.9990
   chunk 85 optimal weight:    0.0670
   chunk 110 optimal weight:    0.0870
   chunk 109 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0170
   chunk 12 optimal weight:    0.5980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.2734

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

Flipped N/Q/H residues before XYZ refinement:
K  29 HIS
L 333 GLN
L 390 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.218563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.174551 restraints weight = 13592.298|
|-----------------------------------------------------------------------------|
r_work (start): 0.4109 rms_B_bonded: 2.45
r_work: 0.3788 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7594
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.053  12465  Z= 0.104
  Angle     :  0.504   7.747  17018  Z= 0.270
  Chirality :  0.039   0.145   1884
  Planarity :  0.004   0.043   2055
  Dihedral  : 16.414 179.353   1974
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.35 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.52 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.31 (0.22), residues: 1380
  helix:  1.60 (0.24), residues: 481
  sheet: -0.94 (0.39), residues: 169
  loop : -1.31 (0.22), residues: 730

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG K 543 
 TYR   0.017   0.001   TYR K 394 
 PHE   0.008   0.001   PHE K  98 
 TRP   0.007   0.001   TRP K 418 
 HIS   0.003   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (12465)
  covalent geometry    : angle       0.50437 (17018)
  hydrogen bonds       : bond        0.02947 (  479)
  hydrogen bonds       : angle       4.46359 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7799 (t80) cc_final: 0.7522 (m-80)
REVERT: K  267 MET cc_start: 0.7387 (ptp) cc_final: 0.7130 (ptt)
REVERT: K  466 ASP cc_start: 0.7624 (OUTLIER) cc_final: 0.7248 (p0)
REVERT: K  556 GLU cc_start: 0.7276 (tt0) cc_final: 0.6931 (pt0)
REVERT: L  142 ILE cc_start: 0.3675 (OUTLIER) cc_final: 0.3391 (mt)
REVERT: R  412 SER cc_start: 0.7879 (p) cc_final: 0.7592 (p)
REVERT: R  413 LYS cc_start: 0.8150 (OUTLIER) cc_final: 0.7898 (ptpt)
  outliers start: 32
  outliers final: 20
  residues processed: 155
  average time/residue: 0.0889
  time to fit residues: 20.1789
Evaluate side-chains
  143 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  266 ILE
Chi-restraints excluded: chain K residue  284 VAL
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  260 THR
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  324 VAL
Chi-restraints excluded: chain L residue  329 VAL
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  413 LYS
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 104 optimal weight:    6.9990
   chunk 116 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 78 optimal weight:    0.7980
   chunk 101 optimal weight:    1.9990
   chunk 114 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0010
   chunk 117 optimal weight:    0.1980
   chunk 67 optimal weight:    0.9990
   chunk 118 optimal weight:    0.9990
   overall best weight:    0.5388

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

Flipped N/Q/H residues before XYZ refinement:
L 333 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4500 r_free = 0.4500 target = 0.217919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.173211 restraints weight = 13694.178|
|-----------------------------------------------------------------------------|
r_work (start): 0.4070 rms_B_bonded: 2.53
r_work: 0.3753 rms_B_bonded: 3.56 restraints_weight: 0.5000
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12465  Z= 0.126
  Angle     :  0.522   7.528  17018  Z= 0.276
  Chirality :  0.039   0.149   1884
  Planarity :  0.004   0.042   2055
  Dihedral  : 16.469 178.654   1972
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.60 %
    Favored  : 75.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.31 (0.22), residues: 1380
  helix:  1.59 (0.24), residues: 482
  sheet: -0.88 (0.39), residues: 170
  loop : -1.31 (0.21), residues: 728

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG K 543 
 TYR   0.016   0.001   TYR K 394 
 PHE   0.012   0.001   PHE K  98 
 TRP   0.006   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (12465)
  covalent geometry    : angle       0.52236 (17018)
  hydrogen bonds       : bond        0.03071 (  479)
  hydrogen bonds       : angle       4.45380 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 119
  time to evaluate  : 0.294 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7811 (t80) cc_final: 0.7438 (m-80)
REVERT: K  300 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8222 (mtpt)
REVERT: K  466 ASP cc_start: 0.7778 (OUTLIER) cc_final: 0.7455 (p0)
REVERT: L   15 SER cc_start: 0.8286 (OUTLIER) cc_final: 0.7789 (t)
REVERT: L  142 ILE cc_start: 0.3789 (OUTLIER) cc_final: 0.3507 (mt)
REVERT: R  412 SER cc_start: 0.7881 (p) cc_final: 0.7581 (p)
REVERT: R  413 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7930 (ptpt)
  outliers start: 36
  outliers final: 24
  residues processed: 151
  average time/residue: 0.0969
  time to fit residues: 21.6921
Evaluate side-chains
  142 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 113
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  266 ILE
Chi-restraints excluded: chain K residue  284 VAL
Chi-restraints excluded: chain K residue  300 LYS
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain K residue  466 ASP
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   15 SER
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  260 THR
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  278 SER
Chi-restraints excluded: chain L residue  329 VAL
Chi-restraints excluded: chain L residue  362 SER
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  413 LYS
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  537 THR
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 13 optimal weight:    5.9990
   chunk 66 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 101 optimal weight:    0.9990
   chunk 120 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
K 350 GLN
L 333 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4479 r_free = 0.4479 target = 0.215815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.171447 restraints weight = 13615.131|
|-----------------------------------------------------------------------------|
r_work (start): 0.4052 rms_B_bonded: 2.59
r_work: 0.3707 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.1916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12465  Z= 0.147
  Angle     :  0.545   7.338  17018  Z= 0.288
  Chirality :  0.040   0.156   1884
  Planarity :  0.004   0.041   2055
  Dihedral  : 16.606 178.586   1972
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.44 %
    Favored  : 75.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.34 (0.22), residues: 1380
  helix:  1.55 (0.24), residues: 481
  sheet: -0.96 (0.39), residues: 170
  loop : -1.31 (0.22), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 543 
 TYR   0.017   0.001   TYR K  83 
 PHE   0.014   0.001   PHE K  98 
 TRP   0.007   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (12465)
  covalent geometry    : angle       0.54462 (17018)
  hydrogen bonds       : bond        0.03277 (  479)
  hydrogen bonds       : angle       4.53666 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.480 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7871 (t80) cc_final: 0.7509 (m-80)
REVERT: K  300 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8243 (mtpt)
REVERT: L  142 ILE cc_start: 0.3945 (OUTLIER) cc_final: 0.3646 (mt)
REVERT: L  506 THR cc_start: 0.7989 (m) cc_final: 0.7743 (t)
REVERT: R  412 SER cc_start: 0.7937 (p) cc_final: 0.7625 (p)
REVERT: R  413 LYS cc_start: 0.8252 (OUTLIER) cc_final: 0.7944 (ptpt)
  outliers start: 35
  outliers final: 28
  residues processed: 155
  average time/residue: 0.1086
  time to fit residues: 24.7200
Evaluate side-chains
  146 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 115
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  266 ILE
Chi-restraints excluded: chain K residue  281 ILE
Chi-restraints excluded: chain K residue  284 VAL
Chi-restraints excluded: chain K residue  300 LYS
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   15 SER
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  111 LEU
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  260 THR
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  278 SER
Chi-restraints excluded: chain L residue  313 VAL
Chi-restraints excluded: chain L residue  329 VAL
Chi-restraints excluded: chain L residue  362 SER
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  413 LYS
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  537 THR
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 86 optimal weight:    0.0570
   chunk 98 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 76 optimal weight:    4.9990
   chunk 38 optimal weight:    0.8980
   chunk 132 optimal weight:   20.0000
   chunk 19 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0870
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
L 333 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4488 r_free = 0.4488 target = 0.216883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.172413 restraints weight = 13666.423|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 2.55
r_work: 0.3737 rms_B_bonded: 3.59 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12465  Z= 0.130
  Angle     :  0.534   7.951  17018  Z= 0.283
  Chirality :  0.040   0.156   1884
  Planarity :  0.004   0.042   2055
  Dihedral  : 16.577 179.663   1972
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  Rotamer:
    Outliers :  2.82 %
    Allowed  : 21.67 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.31 (0.22), residues: 1380
  helix:  1.58 (0.24), residues: 481
  sheet: -0.96 (0.39), residues: 170
  loop : -1.29 (0.22), residues: 729

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG K 543 
 TYR   0.016   0.001   TYR K 394 
 PHE   0.012   0.001   PHE K  98 
 TRP   0.006   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 (12465)
  covalent geometry    : angle       0.53355 (17018)
  hydrogen bonds       : bond        0.03111 (  479)
  hydrogen bonds       : angle       4.47474 ( 1300)

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

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

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2760 Ramachandran restraints generated.
    1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 121
  time to evaluate  : 0.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: K  197 PHE cc_start: 0.7861 (t80) cc_final: 0.7505 (m-80)
REVERT: K  300 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.8206 (mtpt)
REVERT: L   15 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7768 (t)
REVERT: L  142 ILE cc_start: 0.3983 (OUTLIER) cc_final: 0.3693 (mt)
REVERT: R  412 SER cc_start: 0.7891 (p) cc_final: 0.7583 (p)
REVERT: R  413 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.7971 (ptpt)
  outliers start: 36
  outliers final: 28
  residues processed: 154
  average time/residue: 0.1077
  time to fit residues: 24.2166
Evaluate side-chains
  146 residues out of total 1278 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 114
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain K residue  100 LEU
Chi-restraints excluded: chain K residue  148 PHE
Chi-restraints excluded: chain K residue  263 VAL
Chi-restraints excluded: chain K residue  266 ILE
Chi-restraints excluded: chain K residue  281 ILE
Chi-restraints excluded: chain K residue  284 VAL
Chi-restraints excluded: chain K residue  300 LYS
Chi-restraints excluded: chain K residue  302 VAL
Chi-restraints excluded: chain K residue  371 SER
Chi-restraints excluded: chain L residue    6 THR
Chi-restraints excluded: chain L residue   15 SER
Chi-restraints excluded: chain L residue   92 ASP
Chi-restraints excluded: chain L residue  130 ILE
Chi-restraints excluded: chain L residue  142 ILE
Chi-restraints excluded: chain L residue  236 ASP
Chi-restraints excluded: chain L residue  260 THR
Chi-restraints excluded: chain L residue  269 LYS
Chi-restraints excluded: chain L residue  278 SER
Chi-restraints excluded: chain L residue  313 VAL
Chi-restraints excluded: chain L residue  329 VAL
Chi-restraints excluded: chain L residue  362 SER
Chi-restraints excluded: chain L residue  388 LEU
Chi-restraints excluded: chain L residue  403 ASP
Chi-restraints excluded: chain L residue  501 VAL
Chi-restraints excluded: chain R residue  373 ASP
Chi-restraints excluded: chain R residue  383 THR
Chi-restraints excluded: chain R residue  399 THR
Chi-restraints excluded: chain R residue  413 LYS
Chi-restraints excluded: chain R residue  440 VAL
Chi-restraints excluded: chain R residue  514 THR
Chi-restraints excluded: chain R residue  537 THR
Chi-restraints excluded: chain R residue  578 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 141
   random chunks:
   chunk 15 optimal weight:    0.8980
   chunk 126 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9980
   chunk 52 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 85 optimal weight:    0.0870
   chunk 140 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 77 optimal weight:    0.0970
   chunk 136 optimal weight:    4.9990
   overall best weight:    0.5156

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

Flipped N/Q/H residues before XYZ refinement:
L 333 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4490 r_free = 0.4490 target = 0.217090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.172916 restraints weight = 13672.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 2.59
r_work: 0.3739 rms_B_bonded: 3.65 restraints_weight: 0.5000
r_work (final): 0.3739
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12465  Z= 0.126
  Angle     :  0.540   7.790  17018  Z= 0.285
  Chirality :  0.040   0.159   1884
  Planarity :  0.004   0.042   2055
  Dihedral  : 16.551 179.823   1972
  Min Nonbonded Distance : 2.339

Molprobity Statistics.
  All-atom Clashscore : 5.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  : 21.75 %
    Favored  : 75.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.17 %
    Cis-general     : 0.53 %
    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: -0.35 (0.22), residues: 1380
  helix:  1.53 (0.24), residues: 487
  sheet: -0.92 (0.39), residues: 170
  loop : -1.33 (0.22), residues: 723

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG K 543 
 TYR   0.017   0.001   TYR K  83 
 PHE   0.011   0.001   PHE K  98 
 TRP   0.006   0.001   TRP K 418 
 HIS   0.004   0.001   HIS K 512 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (12465)
  covalent geometry    : angle       0.54004 (17018)
  hydrogen bonds       : bond        0.03089 (  479)
  hydrogen bonds       : angle       4.48558 ( 1300)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3141.08 seconds
wall clock time: 54 minutes 32.35 seconds (3272.35 seconds total)