Starting phenix.real_space_refine
on Wed Mar  4 02:21:34 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7x07_32919/03_2026/7x07_32919.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7x07_32919/03_2026/7x07_32919.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7x07_32919/03_2026/7x07_32919.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7x07_32919/03_2026/7x07_32919.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7x07_32919/03_2026/7x07_32919.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7x07_32919/03_2026/7x07_32919.map"
  }
  resolution = 3.78
  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=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      48      5.16       5
     C    6489      2.51       5
     N    1782      2.21       5
     O    1806      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 100 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10125
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 633, 5046
          Classifications: {'peptide': 633}
          Link IDs: {'PTRANS': 22, 'TRANS': 610}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5051
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 633, 5051
          Classifications: {'peptide': 633}
          Link IDs: {'PTRANS': 22, 'TRANS': 610}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'7PO': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.40, per 1000 atoms: 0.24
  Number of scatterers: 10125
  At special positions: 0
  Unit cell: (74.7, 118.69, 147.74, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      48     16.00
     O    1806      8.00
     N    1782      7.00
     C    6489      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: 0.78
  Conformation dependent library (CDL) restraints added in 465.7 milliseconds
  

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2370

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 4 sheets defined
      51.6% alpha, 3.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 68 through 83
      removed outlier: 3.913A  pdb=" N   LEU A  72 " --> pdb=" O   ASN A  68 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   GLN A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 96
      removed outlier: 3.741A  pdb=" N   LEU A  93 " --> pdb=" O   ARG A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 106
    Processing helix  chain 'A' and resid 106 through 111
      removed outlier: 3.574A  pdb=" N   TYR A 110 " --> pdb=" O   PHE A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 124
      removed outlier: 4.397A  pdb=" N   CYS A 121 " --> pdb=" O   ARG A 117 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   VAL A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG A 124 " --> pdb=" O   ARG A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 140
      removed outlier: 3.650A  pdb=" N   GLY A 131 " --> pdb=" O   PRO A 127 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   TRP A 132 " --> pdb=" O   ARG A 128 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   GLN A 133 " --> pdb=" O   ALA A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 168
      removed outlier: 3.872A  pdb=" N   ARG A 152 " --> pdb=" O   ASN A 148 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   LEU A 154 " --> pdb=" O   ALA A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 175
    Processing helix  chain 'A' and resid 178 through 186
      removed outlier: 4.055A  pdb=" N   SER A 184 " --> pdb=" O   TYR A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 198
    Processing helix  chain 'A' and resid 201 through 206
    Processing helix  chain 'A' and resid 217 through 232
      removed outlier: 4.089A  pdb=" N   ALA A 223 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER A 226 " --> pdb=" O   VAL A 222 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   TYR A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 229 " --> pdb=" O   THR A 225 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   LEU A 230 " --> pdb=" O   SER A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 246
      removed outlier: 3.574A  pdb=" N   ILE A 246 " --> pdb=" O   TRP A 242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
      removed outlier: 3.632A  pdb=" N   PHE A 265 " --> pdb=" O   PHE A 261 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   GLU A 267 " --> pdb=" O   PRO A 263 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   LEU A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 296
      removed outlier: 3.856A  pdb=" N   TYR A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 302 through 306
      removed outlier: 3.706A  pdb=" N   LEU A 306 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 347 through 353
      removed outlier: 4.003A  pdb=" N   ILE A 351 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 371
      removed outlier: 3.825A  pdb=" N   GLU A 371 " --> pdb=" O   LYS A 367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 394
      removed outlier: 3.908A  pdb=" N   ALA A 384 " --> pdb=" O   GLU A 380 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   PHE A 385 " --> pdb=" O   ARG A 381 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A 392 " --> pdb=" O   ALA A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 404
      removed outlier: 4.320A  pdb=" N   ILE A 402 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 431
      removed outlier: 3.647A  pdb=" N   LEU A 412 " --> pdb=" O   GLU A 408 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLU A 427 " --> pdb=" O   PHE A 423 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLN A 430 " --> pdb=" O   PHE A 426 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ARG A 431 " --> pdb=" O   GLU A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 511
    Processing helix  chain 'A' and resid 512 through 521
    Processing helix  chain 'A' and resid 552 through 557
      removed outlier: 4.169A  pdb=" N   VAL A 557 " --> pdb=" O   LEU A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 583
      removed outlier: 3.606A  pdb=" N   ALA A 578 " --> pdb=" O   GLN A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 591
    Processing helix  chain 'A' and resid 606 through 608
      No H-bonds generated for 'chain 'A' and resid 606 through 608'
    Processing helix  chain 'A' and resid 609 through 621
    Processing helix  chain 'A' and resid 639 through 650
    Processing helix  chain 'A' and resid 660 through 667
      removed outlier: 3.794A  pdb=" N   LEU A 663 " --> pdb=" O   ARG A 660 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS A 665 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 690 through 701
      removed outlier: 4.476A  pdb=" N   LYS A 696 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 708 through 718
    Processing helix  chain 'A' and resid 719 through 721
      No H-bonds generated for 'chain 'A' and resid 719 through 721'
    Processing helix  chain 'B' and resid 68 through 83
      removed outlier: 3.830A  pdb=" N   LEU B  72 " --> pdb=" O   ASN B  68 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   GLN B  73 " --> pdb=" O   ARG B  69 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   TRP B  77 " --> pdb=" O   GLN B  73 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   LEU B  78 " --> pdb=" O   ARG B  74 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   ARG B  80 " --> pdb=" O   LEU B  76 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU B  81 " --> pdb=" O   TRP B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 88 through 92
    Processing helix  chain 'B' and resid 118 through 123
      removed outlier: 3.741A  pdb=" N   ILE B 122 " --> pdb=" O   LEU B 118 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 118 through 123'
    Processing helix  chain 'B' and resid 127 through 139
      removed outlier: 3.715A  pdb=" N   TRP B 132 " --> pdb=" O   ARG B 128 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   GLN B 133 " --> pdb=" O   ALA B 129 " (cutoff:3.500A)
      removed outlier: 4.366A  pdb=" N   GLN B 136 " --> pdb=" O   TRP B 132 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP B 137 " --> pdb=" O   GLN B 133 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LEU B 139 " --> pdb=" O   LEU B 135 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 141 through 146
    Processing helix  chain 'B' and resid 155 through 160
    Processing helix  chain 'B' and resid 181 through 186
    Processing helix  chain 'B' and resid 192 through 199
      removed outlier: 3.688A  pdb=" N   SER B 196 " --> pdb=" O   ASN B 192 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   THR B 198 " --> pdb=" O   ASP B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 206
    Processing helix  chain 'B' and resid 220 through 225
    Processing helix  chain 'B' and resid 227 through 237
    Processing helix  chain 'B' and resid 250 through 255
    Processing helix  chain 'B' and resid 267 through 289
    Processing helix  chain 'B' and resid 289 through 297
      removed outlier: 3.922A  pdb=" N   ILE B 293 " --> pdb=" O   ASN B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 300 through 312
    Processing helix  chain 'B' and resid 318 through 323
      removed outlier: 4.121A  pdb=" N   LEU B 322 " --> pdb=" O   ASN B 318 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLU B 323 " --> pdb=" O   LEU B 319 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 318 through 323'
    Processing helix  chain 'B' and resid 327 through 337
      removed outlier: 3.946A  pdb=" N   LEU B 334 " --> pdb=" O   LEU B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 353
      removed outlier: 4.319A  pdb=" N   LEU B 345 " --> pdb=" O   ALA B 341 " (cutoff:3.500A)
      removed outlier: 4.058A  pdb=" N   MET B 346 " --> pdb=" O   SER B 342 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   VAL B 349 " --> pdb=" O   LEU B 345 " (cutoff:3.500A)
      Proline residue:  B 350  - end of helix
    Processing helix  chain 'B' and resid 362 through 371
    Processing helix  chain 'B' and resid 373 through 378
    Processing helix  chain 'B' and resid 382 through 391
      removed outlier: 4.218A  pdb=" N   ALA B 388 " --> pdb=" O   ALA B 384 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 407 through 426
      removed outlier: 4.350A  pdb=" N   ALA B 413 " --> pdb=" O   VAL B 409 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B 414 " --> pdb=" O   THR B 410 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   TYR B 415 " --> pdb=" O   GLU B 411 " (cutoff:3.500A)
      removed outlier: 4.551A  pdb=" N   PHE B 423 " --> pdb=" O   VAL B 419 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   GLN B 424 " --> pdb=" O   HIS B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 428 through 432
    Processing helix  chain 'B' and resid 512 through 522
      removed outlier: 4.224A  pdb=" N   LEU B 516 " --> pdb=" O   GLY B 512 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE B 517 " --> pdb=" O   LYS B 513 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ARG B 518 " --> pdb=" O   SER B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 552 through 556
    Processing helix  chain 'B' and resid 564 through 568
    Processing helix  chain 'B' and resid 572 through 574
      No H-bonds generated for 'chain 'B' and resid 572 through 574'
    Processing helix  chain 'B' and resid 575 through 583
      removed outlier: 3.799A  pdb=" N   VAL B 583 " --> pdb=" O   ILE B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 608 through 621
      removed outlier: 3.658A  pdb=" N   ARG B 612 " --> pdb=" O   GLY B 608 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET B 618 " --> pdb=" O   GLY B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 640 through 649
    Processing helix  chain 'B' and resid 661 through 665
      removed outlier: 3.737A  pdb=" N   LYS B 665 " --> pdb=" O   SER B 662 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 686 through 706
      removed outlier: 3.874A  pdb=" N   LEU B 690 " --> pdb=" O   SER B 686 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER B 691 " --> pdb=" O   ALA B 687 " (cutoff:3.500A)
      removed outlier: 4.464A  pdb=" N   ILE B 706 " --> pdb=" O   GLN B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 709 through 721
      removed outlier: 3.548A  pdb=" N   LEU B 713 " --> pdb=" O   MET B 709 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLN B 714 " --> pdb=" O   GLN B 710 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   GLU B 715 " --> pdb=" O   ARG B 711 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE B 719 " --> pdb=" O   GLU B 715 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 469
      removed outlier: 4.836A  pdb=" N   LEU A 493 " --> pdb=" O   ASN A 478 " (cutoff:3.500A)
      removed outlier: 7.192A  pdb=" N   ALA A 491 " --> pdb=" O   PRO A 480 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   VAL A 482 " --> pdb=" O   VAL A 489 " (cutoff:3.500A)
      removed outlier: 6.565A  pdb=" N   VAL A 489 " --> pdb=" O   VAL A 482 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 467 through 469
      removed outlier: 3.844A  pdb=" N   TYR B 532 " --> pdb=" O   ILE B 475 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 539 through 543
      removed outlier: 6.466A  pdb=" N   PHE B 540 " --> pdb=" O   LEU B 627 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   ASP B 629 " --> pdb=" O   PHE B 540 " (cutoff:3.500A)
      removed outlier: 6.610A  pdb=" N   ILE B 542 " --> pdb=" O   ASP B 629 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 670 through 671

    330 hydrogen bonds defined for protein.
    915 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.43

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1626
        1.30 -     1.43: 2748
        1.43 -     1.56: 5880
        1.56 -     1.69: 0
        1.69 -     1.83: 80
  Bond restraints: 10334
  Sorted by residual:
  bond pdb=" C   PRO B 143 "
       pdb=" O   PRO B 143 "
    ideal  model  delta    sigma   weight residual
    1.238  1.170  0.068 1.37e-02 5.33e+03 2.48e+01
  bond pdb=" N   ARG B 236 "
       pdb=" CA  ARG B 236 "
    ideal  model  delta    sigma   weight residual
    1.459  1.519 -0.060 1.23e-02 6.61e+03 2.38e+01
  bond pdb=" C   VAL A 224 "
       pdb=" O   VAL A 224 "
    ideal  model  delta    sigma   weight residual
    1.231  1.278 -0.047 1.02e-02 9.61e+03 2.11e+01
  bond pdb=" C   ALA B 626 "
       pdb=" O   ALA B 626 "
    ideal  model  delta    sigma   weight residual
    1.235  1.184  0.051 1.15e-02 7.56e+03 1.99e+01
  bond pdb=" N   THR B 506 "
       pdb=" CA  THR B 506 "
    ideal  model  delta    sigma   weight residual
    1.455  1.510 -0.055 1.27e-02 6.20e+03 1.86e+01
  ... (remaining 10329 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.46: 13410
        3.46 -     6.92: 549
        6.92 -    10.39: 10
       10.39 -    13.85: 0
       13.85 -    17.31: 1
  Bond angle restraints: 13970
  Sorted by residual:
  angle pdb=" N   ILE B 637 "
        pdb=" CA  ILE B 637 "
        pdb=" C   ILE B 637 "
      ideal   model   delta    sigma   weight residual
     109.34   92.03   17.31 2.08e+00 2.31e-01 6.93e+01
  angle pdb=" N   ILE A 320 "
        pdb=" CA  ILE A 320 "
        pdb=" C   ILE A 320 "
      ideal   model   delta    sigma   weight residual
     112.17  105.61    6.56 9.50e-01 1.11e+00 4.77e+01
  angle pdb=" N   ILE B 151 "
        pdb=" CA  ILE B 151 "
        pdb=" C   ILE B 151 "
      ideal   model   delta    sigma   weight residual
     112.90  106.87    6.03 9.60e-01 1.09e+00 3.95e+01
  angle pdb=" N   ALA B 168 "
        pdb=" CA  ALA B 168 "
        pdb=" C   ALA B 168 "
      ideal   model   delta    sigma   weight residual
     112.68  104.44    8.24 1.33e+00 5.65e-01 3.84e+01
  angle pdb=" N   VAL B 102 "
        pdb=" CA  VAL B 102 "
        pdb=" C   VAL B 102 "
      ideal   model   delta    sigma   weight residual
     111.91  106.50    5.41 8.90e-01 1.26e+00 3.70e+01
  ... (remaining 13965 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 5475
       17.58 -    35.15: 605
       35.15 -    52.73: 113
       52.73 -    70.30: 19
       70.30 -    87.88: 14
  Dihedral angle restraints: 6226
    sinusoidal: 2544
      harmonic: 3682
  Sorted by residual:
  dihedral pdb=" CA  LEU B  96 "
           pdb=" C   LEU B  96 "
           pdb=" N   HIS B  97 "
           pdb=" CA  HIS B  97 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.40   28.60     0      5.00e+00 4.00e-02 3.27e+01
  dihedral pdb=" CA  ALA B 170 "
           pdb=" C   ALA B 170 "
           pdb=" N   TYR B 171 "
           pdb=" CA  TYR B 171 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.04   26.96     0      5.00e+00 4.00e-02 2.91e+01
  dihedral pdb=" CA  SER B 636 "
           pdb=" C   SER B 636 "
           pdb=" N   ILE B 637 "
           pdb=" CA  ILE B 637 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.47   26.53     0      5.00e+00 4.00e-02 2.81e+01
  ... (remaining 6223 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 921
       0.067 -    0.134: 511
       0.134 -    0.201: 119
       0.201 -    0.267: 7
       0.267 -    0.334: 1
  Chirality restraints: 1559
  Sorted by residual:
  chirality pdb=" CA  ILE B 637 "
            pdb=" N   ILE B 637 "
            pdb=" C   ILE B 637 "
            pdb=" CB  ILE B 637 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.77   -0.33 2.00e-01 2.50e+01 2.79e+00
  chirality pdb=" CB  THR A 225 "
            pdb=" CA  THR A 225 "
            pdb=" OG1 THR A 225 "
            pdb=" CG2 THR A 225 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.47e+00
  chirality pdb=" CA  ILE A 657 "
            pdb=" N   ILE A 657 "
            pdb=" C   ILE A 657 "
            pdb=" CB  ILE A 657 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1556 not shown)

  Planarity restraints: 1774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO B 143 "   -0.018 2.00e-02 2.50e+03   3.75e-02 1.41e+01
        pdb=" C   PRO B 143 "    0.065 2.00e-02 2.50e+03
        pdb=" O   PRO B 143 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   ALA B 144 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY B 641 "   -0.018 2.00e-02 2.50e+03   3.54e-02 1.25e+01
        pdb=" C   GLY B 641 "    0.061 2.00e-02 2.50e+03
        pdb=" O   GLY B 641 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   LYS B 642 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 622 "   -0.018 2.00e-02 2.50e+03   3.53e-02 1.24e+01
        pdb=" C   ARG B 622 "    0.061 2.00e-02 2.50e+03
        pdb=" O   ARG B 622 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   PRO B 623 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1771 not shown)

  Histogram of nonbonded interaction distances:
        2.14 -     2.70: 298
        2.70 -     3.25: 9979
        3.25 -     3.80: 14719
        3.80 -     4.35: 20324
        4.35 -     4.90: 32170
  Nonbonded interactions: 77490
  Sorted by model distance:
  nonbonded pdb=" N   ILE B 637 "
            pdb=" O   ILE B 637 "
     model   vdw
     2.145 2.496
  nonbonded pdb=" C   SER B 636 "
            pdb=" O   ILE B 637 "
     model   vdw
     2.211 3.270
  nonbonded pdb=" NH1 ARG B 275 "
            pdb=" O   ASP B 312 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   GLY A 188 "
            pdb=" NH2 ARG A 191 "
     model   vdw
     2.325 3.120
  nonbonded pdb=" OE2 GLU B 155 "
            pdb=" OG  SER B 213 "
     model   vdw
     2.335 3.040
  ... (remaining 77485 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 67 through 721)
  selection = (chain 'B' and resid 67 through 721)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.360
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.790
  Find NCS groups from input model:        0.110
  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:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
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      :  0.013   0.068  10334  Z= 0.947
  Angle     :  1.657  17.311  13970  Z= 1.222
  Chirality :  0.077   0.334   1559
  Planarity :  0.008   0.046   1774
  Dihedral  : 15.382  87.879   3856
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.72 %
    Allowed  :  8.11 %
    Favored  : 91.18 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  5.53 %
    Favored  : 92.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.75 (0.20), residues: 1258
  helix: -3.09 (0.15), residues: 739
  sheet: -3.69 (0.77), residues: 40
  loop : -2.93 (0.26), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.002   ARG B 418 
 TYR   0.036   0.006   TYR B 174 
 PHE   0.042   0.005   PHE B 204 
 TRP   0.029   0.005   TRP B 524 
 HIS   0.020   0.004   HIS B 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.01267 (10334)
  covalent geometry    : angle       1.65724 (13970)
  hydrogen bonds       : bond        0.22326 (  330)
  hydrogen bonds       : angle       8.65644 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 147
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  114 LEU cc_start: 0.9135 (tp) cc_final: 0.8910 (tt)
REVERT: B  160 LEU cc_start: 0.8819 (tp) cc_final: 0.8435 (tt)
REVERT: B  493 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7653 (mp)
REVERT: B  501 MET cc_start: 0.7923 (tpp) cc_final: 0.7207 (mmm)
REVERT: B  615 MET cc_start: 0.7873 (mtt) cc_final: 0.7389 (mtt)
REVERT: B  663 LEU cc_start: 0.9145 (tp) cc_final: 0.8941 (tt)
  outliers start: 21
  outliers final: 8
  residues processed: 161
  average time/residue: 0.0967
  time to fit residues: 22.0184
Evaluate side-chains
  120 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 111
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue  175 PHE
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  504 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    6.9990
   chunk 97 optimal weight:    0.5980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:    6.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:   10.0000
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
B 430 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4447 r_free = 0.4447 target = 0.222729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.177120 restraints weight = 12120.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.173457 restraints weight = 20099.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.169138 restraints weight = 14866.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.162352 restraints weight = 20336.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.160320 restraints weight = 22354.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7444
moved from start:          0.1718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  10334  Z= 0.191
  Angle     :  0.729  10.548  13970  Z= 0.387
  Chirality :  0.044   0.142   1559
  Planarity :  0.005   0.041   1774
  Dihedral  :  8.042  58.667   1454
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  7.00 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.97 %
    Favored  : 87.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -4.07 (0.21), residues: 1258
  helix: -2.46 (0.17), residues: 776
  sheet: -2.75 (0.94), residues: 34
  loop : -2.84 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 660 
 TYR   0.016   0.002   TYR A 559 
 PHE   0.016   0.002   PHE A 146 
 TRP   0.039   0.002   TRP B 664 
 HIS   0.010   0.002   HIS B 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (10334)
  covalent geometry    : angle       0.72879 (13970)
  hydrogen bonds       : bond        0.03943 (  330)
  hydrogen bonds       : angle       5.40585 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 125
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.5834 (tpt) cc_final: 0.5614 (mmm)
REVERT: A  505 ILE cc_start: 0.5656 (OUTLIER) cc_final: 0.5331 (mt)
REVERT: A  537 GLN cc_start: 0.5686 (mm-40) cc_final: 0.5337 (tp40)
REVERT: A  674 ASP cc_start: 0.5324 (p0) cc_final: 0.4925 (p0)
REVERT: B  114 LEU cc_start: 0.9187 (tp) cc_final: 0.8873 (tt)
REVERT: B  380 GLU cc_start: 0.7942 (mm-30) cc_final: 0.7326 (tt0)
REVERT: B  493 LEU cc_start: 0.8314 (OUTLIER) cc_final: 0.7554 (mp)
REVERT: B  501 MET cc_start: 0.8121 (tpp) cc_final: 0.7609 (mmt)
REVERT: B  621 HIS cc_start: 0.8536 (OUTLIER) cc_final: 0.7862 (m-70)
REVERT: B  663 LEU cc_start: 0.9182 (tp) cc_final: 0.8957 (tp)
  outliers start: 17
  outliers final: 12
  residues processed: 136
  average time/residue: 0.0997
  time to fit residues: 19.4778
Evaluate side-chains
  127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  322 LEU
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  324 ARG
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 123 optimal weight:    6.9990
   chunk 78 optimal weight:    0.9990
   chunk 61 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 40 optimal weight:    7.9990
   chunk 99 optimal weight:    0.0980
   chunk 38 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 46 optimal weight:   20.0000
   chunk 121 optimal weight:    2.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
A 256 ASN
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 584 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.227754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.176574 restraints weight = 11868.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.174378 restraints weight = 18096.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.168518 restraints weight = 15502.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.165541 restraints weight = 19608.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.162220 restraints weight = 19877.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.2178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.060  10334  Z= 0.290
  Angle     :  0.764  12.036  13970  Z= 0.398
  Chirality :  0.047   0.145   1559
  Planarity :  0.005   0.056   1774
  Dihedral  :  8.090  52.832   1445
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  9.46 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 13.87 %
    Favored  : 82.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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 are not related in a simple way.
  whole: -3.97 (0.22), residues: 1258
  helix: -2.39 (0.17), residues: 768
  sheet: -3.14 (0.82), residues: 42
  loop : -2.72 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 280 
 TYR   0.019   0.002   TYR B 180 
 PHE   0.016   0.002   PHE B 204 
 TRP   0.014   0.002   TRP B 664 
 HIS   0.013   0.002   HIS B 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00686 (10334)
  covalent geometry    : angle       0.76396 (13970)
  hydrogen bonds       : bond        0.03903 (  330)
  hydrogen bonds       : angle       5.26986 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 112
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9281 (tp) cc_final: 0.9039 (tp)
REVERT: A  319 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8715 (tt)
REVERT: A  338 VAL cc_start: 0.8987 (OUTLIER) cc_final: 0.8153 (m)
REVERT: A  537 GLN cc_start: 0.5843 (mm-40) cc_final: 0.5340 (tp40)
REVERT: A  680 LYS cc_start: 0.7643 (pttm) cc_final: 0.7397 (mtmm)
REVERT: B  335 MET cc_start: 0.7311 (tmm) cc_final: 0.7104 (tmm)
REVERT: B  380 GLU cc_start: 0.8076 (mm-30) cc_final: 0.7429 (tt0)
REVERT: B  493 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.7707 (mp)
REVERT: B  501 MET cc_start: 0.8282 (tpp) cc_final: 0.7598 (mmt)
REVERT: B  642 LYS cc_start: 0.8449 (ttpt) cc_final: 0.8071 (pttm)
  outliers start: 34
  outliers final: 22
  residues processed: 138
  average time/residue: 0.0833
  time to fit residues: 17.3693
Evaluate side-chains
  130 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  161 SER
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  256 ASN
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  347 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 81 optimal weight:    9.9990
   chunk 51 optimal weight:    0.4980
   chunk 118 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9980
   chunk 6 optimal weight:    0.2980
   chunk 9 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 92 optimal weight:    9.9990
   chunk 36 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 621 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 701 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4586 r_free = 0.4586 target = 0.232271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.181255 restraints weight = 11986.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.178280 restraints weight = 18092.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.175040 restraints weight = 15532.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.173669 restraints weight = 15679.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.172107 restraints weight = 15028.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  10334  Z= 0.162
  Angle     :  0.657  10.911  13970  Z= 0.346
  Chirality :  0.043   0.215   1559
  Planarity :  0.004   0.049   1774
  Dihedral  :  7.469  54.311   1443
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.63 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 17.34 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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 are not related in a simple way.
  whole: -3.62 (0.22), residues: 1258
  helix: -2.13 (0.18), residues: 767
  sheet: -2.58 (0.95), residues: 34
  loop : -2.62 (0.27), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 280 
 TYR   0.018   0.001   TYR B 571 
 PHE   0.038   0.002   PHE A 681 
 TRP   0.012   0.001   TRP B 664 
 HIS   0.009   0.001   HIS B 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (10334)
  covalent geometry    : angle       0.65671 (13970)
  hydrogen bonds       : bond        0.03295 (  330)
  hydrogen bonds       : angle       4.88924 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 119
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9252 (tp) cc_final: 0.8983 (tp)
REVERT: A  319 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8700 (tt)
REVERT: B   81 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8929 (tp)
REVERT: B  380 GLU cc_start: 0.7951 (mm-30) cc_final: 0.7253 (tt0)
REVERT: B  501 MET cc_start: 0.8103 (tpp) cc_final: 0.7538 (mmt)
REVERT: B  618 MET cc_start: 0.7660 (ttp) cc_final: 0.7388 (ttt)
  outliers start: 26
  outliers final: 18
  residues processed: 141
  average time/residue: 0.0773
  time to fit residues: 16.6422
Evaluate side-chains
  124 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  495 ILE
Chi-restraints excluded: chain B residue  503 LEU
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 27 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9990
   chunk 87 optimal weight:   10.0000
   chunk 105 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 81 optimal weight:   10.0000
   chunk 50 optimal weight:    7.9990
   chunk 71 optimal weight:    0.1980
   chunk 58 optimal weight:   20.0000
   chunk 78 optimal weight:    0.0570
   overall best weight:    0.5098

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 178 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4465 r_free = 0.4465 target = 0.224709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.179064 restraints weight = 11957.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.176707 restraints weight = 19522.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.174963 restraints weight = 17264.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.173431 restraints weight = 16715.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.171974 restraints weight = 17222.092|
|-----------------------------------------------------------------------------|
r_work (final): 0.3894
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7271
moved from start:          0.2673

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10334  Z= 0.122
  Angle     :  0.612  10.078  13970  Z= 0.323
  Chirality :  0.041   0.170   1559
  Planarity :  0.004   0.039   1774
  Dihedral  :  6.879  58.131   1441
  Min Nonbonded Distance : 2.582

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  7.39 %
    Favored  : 92.53 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 18.18 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -3.52 (0.22), residues: 1258
  helix: -1.98 (0.18), residues: 780
  sheet: -2.54 (0.93), residues: 34
  loop : -2.71 (0.27), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 280 
 TYR   0.013   0.001   TYR B 181 
 PHE   0.016   0.001   PHE A 252 
 TRP   0.011   0.001   TRP B 664 
 HIS   0.007   0.001   HIS B 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10334)
  covalent geometry    : angle       0.61188 (13970)
  hydrogen bonds       : bond        0.02976 (  330)
  hydrogen bonds       : angle       4.58651 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 116
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9228 (tp) cc_final: 0.8952 (tp)
REVERT: A  319 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8756 (tt)
REVERT: A  548 MET cc_start: 0.5557 (tmm) cc_final: 0.5337 (tmm)
REVERT: B   81 LEU cc_start: 0.9146 (OUTLIER) cc_final: 0.8893 (tp)
REVERT: B  380 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7167 (tt0)
REVERT: B  501 MET cc_start: 0.8000 (tpp) cc_final: 0.7246 (mmm)
REVERT: B  618 MET cc_start: 0.7768 (ttp) cc_final: 0.7511 (ttt)
  outliers start: 26
  outliers final: 14
  residues processed: 139
  average time/residue: 0.0790
  time to fit residues: 16.6806
Evaluate side-chains
  118 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 50 optimal weight:    8.9990
   chunk 125 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 67 optimal weight:    0.3980
   chunk 86 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   chunk 115 optimal weight:    0.6980
   overall best weight:    0.8186

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

Flipped N/Q/H residues before XYZ refinement:
A 148 ASN
** B 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4449 r_free = 0.4449 target = 0.222804 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.177426 restraints weight = 12082.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.175371 restraints weight = 19285.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.170832 restraints weight = 14669.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.164545 restraints weight = 20256.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.162496 restraints weight = 24345.775|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.2874

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10334  Z= 0.151
  Angle     :  0.635  11.103  13970  Z= 0.328
  Chirality :  0.043   0.261   1559
  Planarity :  0.004   0.037   1774
  Dihedral  :  6.828  56.252   1441
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  8.19 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  3.47 %
    Allowed  : 18.56 %
    Favored  : 77.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -3.38 (0.23), residues: 1258
  helix: -1.87 (0.18), residues: 779
  sheet: -2.57 (0.92), residues: 34
  loop : -2.65 (0.27), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 163 
 TYR   0.010   0.001   TYR B 541 
 PHE   0.024   0.001   PHE A 295 
 TRP   0.048   0.001   TRP B 664 
 HIS   0.013   0.001   HIS B 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 (10334)
  covalent geometry    : angle       0.63490 (13970)
  hydrogen bonds       : bond        0.02966 (  330)
  hydrogen bonds       : angle       4.53237 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 111
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9246 (tp) cc_final: 0.8941 (tp)
REVERT: A  319 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8593 (tt)
REVERT: A  505 ILE cc_start: 0.5713 (OUTLIER) cc_final: 0.5448 (mt)
REVERT: A  548 MET cc_start: 0.5735 (tmm) cc_final: 0.5511 (tmm)
REVERT: B   81 LEU cc_start: 0.9142 (OUTLIER) cc_final: 0.8875 (tp)
REVERT: B  114 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8944 (tp)
REVERT: B  380 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7200 (tt0)
REVERT: B  493 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.7569 (mp)
REVERT: B  501 MET cc_start: 0.8210 (tpp) cc_final: 0.7925 (tpp)
REVERT: B  618 MET cc_start: 0.7894 (ttp) cc_final: 0.7577 (ttt)
REVERT: B  663 LEU cc_start: 0.9131 (tp) cc_final: 0.8846 (tp)
  outliers start: 37
  outliers final: 24
  residues processed: 142
  average time/residue: 0.0830
  time to fit residues: 17.6262
Evaluate side-chains
  129 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 100
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  505 ILE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  495 ILE
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 114 optimal weight:    1.9990
   chunk 123 optimal weight:    0.7980
   chunk 104 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    4.9990
   chunk 71 optimal weight:    0.3980
   chunk 111 optimal weight:    3.9990
   chunk 100 optimal weight:    4.9990
   chunk 21 optimal weight:    1.9990
   chunk 17 optimal weight:    8.9990
   overall best weight:    1.2386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4437 r_free = 0.4437 target = 0.220687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.174978 restraints weight = 12027.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.172553 restraints weight = 20463.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.165987 restraints weight = 19485.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.161652 restraints weight = 23899.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.159751 restraints weight = 24383.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  10334  Z= 0.200
  Angle     :  0.657  11.586  13970  Z= 0.340
  Chirality :  0.044   0.192   1559
  Planarity :  0.004   0.040   1774
  Dihedral  :  6.988  57.463   1441
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.30 %
    Favored  : 90.70 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 18.74 %
    Favored  : 76.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -3.37 (0.23), residues: 1258
  helix: -1.85 (0.18), residues: 781
  sheet: -2.84 (0.79), residues: 42
  loop : -2.64 (0.28), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 163 
 TYR   0.011   0.001   TYR B 174 
 PHE   0.026   0.002   PHE A 295 
 TRP   0.076   0.002   TRP B 664 
 HIS   0.009   0.001   HIS B 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00473 (10334)
  covalent geometry    : angle       0.65698 (13970)
  hydrogen bonds       : bond        0.03066 (  330)
  hydrogen bonds       : angle       4.58277 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 101
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9280 (tp) cc_final: 0.8948 (tp)
REVERT: A  253 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6533 (tp)
REVERT: A  319 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8733 (tt)
REVERT: A  338 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.7888 (m)
REVERT: A  548 MET cc_start: 0.5777 (tmm) cc_final: 0.5564 (tmm)
REVERT: B   81 LEU cc_start: 0.9145 (OUTLIER) cc_final: 0.8896 (tp)
REVERT: B  114 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8557 (tt)
REVERT: B  380 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7304 (tt0)
REVERT: B  493 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.7595 (mp)
REVERT: B  618 MET cc_start: 0.7921 (ttp) cc_final: 0.7611 (ttt)
  outliers start: 47
  outliers final: 31
  residues processed: 141
  average time/residue: 0.0766
  time to fit residues: 16.7475
Evaluate side-chains
  136 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 99
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  208 VAL
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  227 TYR
Chi-restraints excluded: chain B residue  338 VAL
Chi-restraints excluded: chain B residue  349 VAL
Chi-restraints excluded: chain B residue  409 VAL
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  495 ILE
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Chi-restraints excluded: chain B residue  643 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 60 optimal weight:    0.9980
   chunk 82 optimal weight:    6.9990
   chunk 53 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    7.9990
   chunk 99 optimal weight:    0.6980
   chunk 73 optimal weight:    0.4980
   chunk 78 optimal weight:    0.0980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.224689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.178964 restraints weight = 11894.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.176623 restraints weight = 18998.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.174916 restraints weight = 16620.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.172993 restraints weight = 18103.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.171682 restraints weight = 17284.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3888
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7270
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10334  Z= 0.124
  Angle     :  0.617  11.251  13970  Z= 0.319
  Chirality :  0.042   0.193   1559
  Planarity :  0.004   0.037   1774
  Dihedral  :  6.578  59.692   1441
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 6.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.55 %
    Favored  : 92.45 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.24 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -3.17 (0.23), residues: 1258
  helix: -1.67 (0.18), residues: 781
  sheet: -2.47 (0.91), residues: 34
  loop : -2.67 (0.27), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  74 
 TYR   0.008   0.001   TYR B 181 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.069   0.002   TRP B 664 
 HIS   0.010   0.001   HIS B 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10334)
  covalent geometry    : angle       0.61668 (13970)
  hydrogen bonds       : bond        0.02815 (  330)
  hydrogen bonds       : angle       4.40343 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 106
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9220 (tp) cc_final: 0.8897 (tp)
REVERT: A  319 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8653 (tt)
REVERT: A  517 PHE cc_start: 0.6117 (OUTLIER) cc_final: 0.5761 (t80)
REVERT: B   81 LEU cc_start: 0.9161 (OUTLIER) cc_final: 0.8900 (tp)
REVERT: B  114 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8675 (tt)
REVERT: B  380 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7177 (tt0)
REVERT: B  406 TYR cc_start: 0.7379 (t80) cc_final: 0.7148 (t80)
REVERT: B  493 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7465 (mp)
REVERT: B  618 MET cc_start: 0.7906 (ttp) cc_final: 0.7639 (ttt)
  outliers start: 33
  outliers final: 24
  residues processed: 133
  average time/residue: 0.0769
  time to fit residues: 15.7207
Evaluate side-chains
  127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  495 ILE
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  523 LEU
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 107 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 111 optimal weight:    0.0970
   chunk 39 optimal weight:    0.0670
   chunk 89 optimal weight:    4.9990
   chunk 125 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.4916

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

Flipped N/Q/H residues before XYZ refinement:
** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4474 r_free = 0.4474 target = 0.225488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.178724 restraints weight = 11945.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.176642 restraints weight = 18646.700|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.175008 restraints weight = 17084.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.170821 restraints weight = 18462.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.169695 restraints weight = 20363.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10334  Z= 0.118
  Angle     :  0.627  12.484  13970  Z= 0.320
  Chirality :  0.042   0.222   1559
  Planarity :  0.004   0.038   1774
  Dihedral  :  6.415  58.188   1441
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.81 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -3.01 (0.23), residues: 1258
  helix: -1.54 (0.19), residues: 781
  sheet: -2.25 (0.93), residues: 34
  loop : -2.61 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 152 
 TYR   0.022   0.001   TYR B 620 
 PHE   0.012   0.001   PHE A 517 
 TRP   0.061   0.001   TRP B 664 
 HIS   0.008   0.001   HIS B 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (10334)
  covalent geometry    : angle       0.62679 (13970)
  hydrogen bonds       : bond        0.02718 (  330)
  hydrogen bonds       : angle       4.32279 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 102
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9214 (tp) cc_final: 0.8883 (tp)
REVERT: A  319 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8646 (tt)
REVERT: A  517 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.5743 (t80)
REVERT: A  548 MET cc_start: 0.5493 (tmm) cc_final: 0.4577 (mmt)
REVERT: A  559 TYR cc_start: 0.7788 (t80) cc_final: 0.7565 (t80)
REVERT: B   81 LEU cc_start: 0.9148 (OUTLIER) cc_final: 0.8903 (tp)
REVERT: B  114 LEU cc_start: 0.9154 (OUTLIER) cc_final: 0.8640 (tt)
REVERT: B  380 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7159 (tt0)
REVERT: B  406 TYR cc_start: 0.7361 (t80) cc_final: 0.7114 (t80)
REVERT: B  493 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7471 (mp)
REVERT: B  618 MET cc_start: 0.7865 (ttp) cc_final: 0.7594 (ttt)
  outliers start: 31
  outliers final: 24
  residues processed: 126
  average time/residue: 0.0802
  time to fit residues: 15.7568
Evaluate side-chains
  127 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.309 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain A residue  517 PHE
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  495 ILE
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Chi-restraints excluded: chain B residue  643 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 105 optimal weight:    0.5980
   chunk 13 optimal weight:    6.9990
   chunk 118 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9990
   chunk 42 optimal weight:   10.0000
   chunk 85 optimal weight:    4.9990
   chunk 92 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4464 r_free = 0.4464 target = 0.224065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.176871 restraints weight = 11951.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.174871 restraints weight = 20766.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.172661 restraints weight = 19841.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.171463 restraints weight = 19106.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.169487 restraints weight = 19427.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7312
moved from start:          0.3364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10334  Z= 0.147
  Angle     :  0.661  12.887  13970  Z= 0.333
  Chirality :  0.043   0.222   1559
  Planarity :  0.004   0.038   1774
  Dihedral  :  6.450  56.774   1441
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 7.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.19 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 21.18 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -2.93 (0.23), residues: 1258
  helix: -1.47 (0.19), residues: 781
  sheet: -2.00 (0.96), residues: 34
  loop : -2.59 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 152 
 TYR   0.019   0.001   TYR B 620 
 PHE   0.013   0.001   PHE B 644 
 TRP   0.087   0.002   TRP B 664 
 HIS   0.007   0.001   HIS B 669 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (10334)
  covalent geometry    : angle       0.66139 (13970)
  hydrogen bonds       : bond        0.02841 (  330)
  hydrogen bonds       : angle       4.30630 (  915)

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

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

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2516 Ramachandran restraints generated.
    1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 104
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 LEU cc_start: 0.9226 (tp) cc_final: 0.8896 (tp)
REVERT: A  319 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8717 (tt)
REVERT: A  548 MET cc_start: 0.5517 (tmm) cc_final: 0.4638 (mmt)
REVERT: A  559 TYR cc_start: 0.7807 (t80) cc_final: 0.7527 (t80)
REVERT: B   81 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8920 (tp)
REVERT: B  114 LEU cc_start: 0.9182 (OUTLIER) cc_final: 0.8670 (tt)
REVERT: B  380 GLU cc_start: 0.7919 (mm-30) cc_final: 0.7192 (tt0)
REVERT: B  493 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7475 (mp)
  outliers start: 33
  outliers final: 27
  residues processed: 132
  average time/residue: 0.0737
  time to fit residues: 15.0774
Evaluate side-chains
  132 residues out of total 1067 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 101
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 LEU
Chi-restraints excluded: chain A residue   91 THR
Chi-restraints excluded: chain A residue  105 THR
Chi-restraints excluded: chain A residue  140 ILE
Chi-restraints excluded: chain A residue  224 VAL
Chi-restraints excluded: chain A residue  278 GLU
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 VAL
Chi-restraints excluded: chain A residue  382 THR
Chi-restraints excluded: chain A residue  403 MET
Chi-restraints excluded: chain A residue  406 TYR
Chi-restraints excluded: chain B residue   81 LEU
Chi-restraints excluded: chain B residue  109 VAL
Chi-restraints excluded: chain B residue  114 LEU
Chi-restraints excluded: chain B residue  123 VAL
Chi-restraints excluded: chain B residue  208 VAL
Chi-restraints excluded: chain B residue  216 THR
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  230 LEU
Chi-restraints excluded: chain B residue  410 THR
Chi-restraints excluded: chain B residue  429 VAL
Chi-restraints excluded: chain B residue  483 THR
Chi-restraints excluded: chain B residue  493 LEU
Chi-restraints excluded: chain B residue  495 ILE
Chi-restraints excluded: chain B residue  497 VAL
Chi-restraints excluded: chain B residue  575 ASP
Chi-restraints excluded: chain B residue  580 LEU
Chi-restraints excluded: chain B residue  604 VAL
Chi-restraints excluded: chain B residue  621 HIS
Chi-restraints excluded: chain B residue  643 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 119 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 22 optimal weight:    0.1980
   chunk 35 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 90 optimal weight:    0.5980
   chunk 111 optimal weight:    0.9980
   chunk 1 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 57 optimal weight:    8.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** A 669 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 702 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.223258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.176976 restraints weight = 11961.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.175501 restraints weight = 19103.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.174026 restraints weight = 19070.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.167767 restraints weight = 18958.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.164313 restraints weight = 23249.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7394
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10334  Z= 0.163
  Angle     :  0.667  12.758  13970  Z= 0.337
  Chirality :  0.044   0.209   1559
  Planarity :  0.004   0.038   1774
  Dihedral  :  6.501  55.441   1441
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 20.81 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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 are not related in a simple way.
  whole: -2.90 (0.23), residues: 1258
  helix: -1.45 (0.19), residues: 781
  sheet: -1.95 (0.97), residues: 34
  loop : -2.57 (0.28), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 152 
 TYR   0.018   0.001   TYR B 620 
 PHE   0.014   0.001   PHE B 644 
 TRP   0.085   0.002   TRP B 664 
 HIS   0.007   0.001   HIS B 621 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 (10334)
  covalent geometry    : angle       0.66685 (13970)
  hydrogen bonds       : bond        0.02854 (  330)
  hydrogen bonds       : angle       4.31230 (  915)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1603.72 seconds
wall clock time: 28 minutes 25.40 seconds (1705.40 seconds total)