Starting phenix.real_space_refine
on Tue Mar  3 20:23:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vxf_21436/03_2026/6vxf_21436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vxf_21436/03_2026/6vxf_21436.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2026/6vxf_21436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2026/6vxf_21436.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2026/6vxf_21436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2026/6vxf_21436.map"
  }
  resolution = 3.5
  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
-------------------------------------------------------------------------------
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=   0.017
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      58      5.16       5
     C    5700      2.51       5
     N    1450      2.21       5
     O    1578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 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: 8786
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 4393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4393
          Classifications: {'peptide': 565}
          Link IDs: {'PTRANS': 18, 'TRANS': 546}
          Chain breaks: 3
  Restraints were copied for chains:
    A
  Time building chain proxies: 3.04, per 1000 atoms: 0.35
  Number of scatterers: 8786
  At special positions: 0
  Unit cell: (99.63, 73.8, 127.92, 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      58     16.00
     O    1578      8.00
     N    1450      7.00
     C    5700      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 592 " - pdb=" SG  CYS B 608 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 603 " - pdb=" SG  CYS A 603 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 592 " - pdb=" SG  CYS A 608 " distance=2.04

  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: 0.74
  Conformation dependent library (CDL) restraints added in 342.5 milliseconds
  

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2088

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      60.2% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'B' and resid 87 through 94
      removed outlier: 3.656A  pdb=" N   ASP B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 102
      removed outlier: 3.668A  pdb=" N   GLY B 101 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU B 102 " --> pdb=" O   PRO B  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 98 through 102'
    Processing helix  chain 'B' and resid 135 through 148
      removed outlier: 3.784A  pdb=" N   PHE B 142 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 169
    Processing helix  chain 'B' and resid 170 through 174
    Processing helix  chain 'B' and resid 188 through 199
      removed outlier: 3.877A  pdb=" N   GLU B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 232
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 3.815A  pdb=" N   PHE B 250 " --> pdb=" O   TYR B 247 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LYS B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 247 through 251'
    Processing helix  chain 'B' and resid 272 through 278
      removed outlier: 4.057A  pdb=" N   PHE B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 299
      removed outlier: 3.735A  pdb=" N   LEU B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 298 " --> pdb=" O   PHE B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 338
      removed outlier: 3.780A  pdb=" N   GLU B 334 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B 337 " --> pdb=" O   ALA B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 354
      removed outlier: 4.120A  pdb=" N   LYS B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 391
    Processing helix  chain 'B' and resid 395 through 415
      removed outlier: 3.941A  pdb=" N   GLY B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 435
      removed outlier: 3.861A  pdb=" N   GLY B 428 " --> pdb=" O   GLN B 424 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 430 " --> pdb=" O   ARG B 426 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE B 431 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 445
      removed outlier: 4.714A  pdb=" N   PHE B 439 " --> pdb=" O   ASN B 436 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER B 440 " --> pdb=" O   GLN B 437 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER B 441 " --> pdb=" O   CYS B 438 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   VAL B 442 " --> pdb=" O   PHE B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 461
      removed outlier: 3.583A  pdb=" N   HIS B 457 " --> pdb=" O   LYS B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 475
    Processing helix  chain 'B' and resid 477 through 482
    Processing helix  chain 'B' and resid 483 through 494
    Processing helix  chain 'B' and resid 495 through 497
      No H-bonds generated for 'chain 'B' and resid 495 through 497'
    Processing helix  chain 'B' and resid 504 through 528
      removed outlier: 3.670A  pdb=" N   ALA B 528 " --> pdb=" O   ALA B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 546
      removed outlier: 3.912A  pdb=" N   ALA B 537 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS B 544 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 561
      removed outlier: 3.562A  pdb=" N   ILE B 561 " --> pdb=" O   LEU B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 571
      removed outlier: 3.653A  pdb=" N   LEU B 568 " --> pdb=" O   LEU B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 586
      removed outlier: 4.237A  pdb=" N   TYR B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN B 584 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 618
      removed outlier: 3.800A  pdb=" N   VAL B 615 " --> pdb=" O   GLU B 611 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   LYS B 616 " --> pdb=" O   GLU B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 650
      removed outlier: 3.717A  pdb=" N   TRP B 627 " --> pdb=" O   PRO B 623 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   ASN B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   HIS B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B 648 " --> pdb=" O   ALA B 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 94
      removed outlier: 3.657A  pdb=" N   ASP A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.668A  pdb=" N   GLY A 101 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU A 102 " --> pdb=" O   PRO A  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 135 through 148
      removed outlier: 3.784A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 170 through 174
    Processing helix  chain 'A' and resid 188 through 199
      removed outlier: 3.877A  pdb=" N   GLU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 232
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 247 through 251
      removed outlier: 3.814A  pdb=" N   PHE A 250 " --> pdb=" O   TYR A 247 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LYS A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 247 through 251'
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 4.057A  pdb=" N   PHE A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 299
      removed outlier: 3.736A  pdb=" N   LEU A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 298 " --> pdb=" O   PHE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 338
      removed outlier: 3.780A  pdb=" N   GLU A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ILE A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 354
      removed outlier: 4.120A  pdb=" N   LYS A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLN A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'A' and resid 395 through 415
      removed outlier: 3.942A  pdb=" N   GLY A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 435
      removed outlier: 3.860A  pdb=" N   GLY A 428 " --> pdb=" O   GLN A 424 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 430 " --> pdb=" O   ARG A 426 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 445
      removed outlier: 4.714A  pdb=" N   PHE A 439 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 440 " --> pdb=" O   GLN A 437 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 441 " --> pdb=" O   CYS A 438 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL A 442 " --> pdb=" O   PHE A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 461
      removed outlier: 3.584A  pdb=" N   HIS A 457 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 475
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 495 through 497
      No H-bonds generated for 'chain 'A' and resid 495 through 497'
    Processing helix  chain 'A' and resid 504 through 528
      removed outlier: 3.671A  pdb=" N   ALA A 528 " --> pdb=" O   ALA A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 546
      removed outlier: 3.912A  pdb=" N   ALA A 537 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 561
      removed outlier: 3.562A  pdb=" N   ILE A 561 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.654A  pdb=" N   LEU A 568 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 586
      removed outlier: 4.237A  pdb=" N   TYR A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN A 584 " --> pdb=" O   ALA A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 618
      removed outlier: 3.801A  pdb=" N   VAL A 615 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   LYS A 616 " --> pdb=" O   GLU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 650
      removed outlier: 3.718A  pdb=" N   TRP A 627 " --> pdb=" O   PRO A 623 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   ASN A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   HIS A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 648 " --> pdb=" O   ALA A 644 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 68 through 71
    Processing sheet with id=AA2, first strand: chain 'B' and resid 121 through 123
      removed outlier: 5.788A  pdb=" N   GLY B 122 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   THR B 257 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ALA B  77 " --> pdb=" O   THR B 257 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU B 259 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU B 256 " --> pdb=" O   HIS B 267 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   HIS B 267 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU B 258 " --> pdb=" O   MET B 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123
      removed outlier: 5.788A  pdb=" N   GLY A 122 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   THR A 257 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ALA A  77 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU A 259 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   LEU A  79 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A 256 " --> pdb=" O   HIS A 267 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   HIS A 267 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU A 258 " --> pdb=" O   MET A 265 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    1170 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: 1.31

  Time building geometry restraints manager: 1.00 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2746
        1.34 -     1.46: 2171
        1.46 -     1.59: 3957
        1.59 -     1.71: 0
        1.71 -     1.83: 94
  Bond restraints: 8968
  Sorted by residual:
  bond pdb=" CA  LEU B 497 "
       pdb=" CB  LEU B 497 "
    ideal  model  delta    sigma   weight residual
    1.542  1.519  0.024 8.90e-03 1.26e+04 7.12e+00
  bond pdb=" CA  LEU A 497 "
       pdb=" CB  LEU A 497 "
    ideal  model  delta    sigma   weight residual
    1.542  1.519  0.023 8.90e-03 1.26e+04 6.74e+00
  bond pdb=" CG  LEU B 209 "
       pdb=" CD1 LEU B 209 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.93e+00
  bond pdb=" CG  LEU A 209 "
       pdb=" CD1 LEU A 209 "
    ideal  model  delta    sigma   weight residual
    1.521  1.456  0.065 3.30e-02 9.18e+02 3.93e+00
  bond pdb=" CG  LEU A 474 "
       pdb=" CD2 LEU A 474 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.41e+00
  ... (remaining 8963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 11620
        2.25 -     4.49: 415
        4.49 -     6.74: 75
        6.74 -     8.98: 20
        8.98 -    11.23: 4
  Bond angle restraints: 12134
  Sorted by residual:
  angle pdb=" N   LEU A 497 "
        pdb=" CA  LEU A 497 "
        pdb=" C   LEU A 497 "
      ideal   model   delta    sigma   weight residual
     108.49  114.24   -5.75 1.15e+00 7.56e-01 2.50e+01
  angle pdb=" N   LEU B 497 "
        pdb=" CA  LEU B 497 "
        pdb=" C   LEU B 497 "
      ideal   model   delta    sigma   weight residual
     108.49  114.23   -5.74 1.15e+00 7.56e-01 2.49e+01
  angle pdb=" C   ALA A  95 "
        pdb=" N   ARG A  96 "
        pdb=" CA  ARG A  96 "
      ideal   model   delta    sigma   weight residual
     121.54  129.77   -8.23 1.91e+00 2.74e-01 1.86e+01
  angle pdb=" C   ALA B  95 "
        pdb=" N   ARG B  96 "
        pdb=" CA  ARG B  96 "
      ideal   model   delta    sigma   weight residual
     121.54  129.77   -8.23 1.91e+00 2.74e-01 1.85e+01
  angle pdb=" C   LEU A 497 "
        pdb=" CA  LEU A 497 "
        pdb=" CB  LEU A 497 "
      ideal   model   delta    sigma   weight residual
     114.87  109.20    5.67 1.51e+00 4.39e-01 1.41e+01
  ... (remaining 12129 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4662
       17.86 -    35.73: 533
       35.73 -    53.59: 94
       53.59 -    71.45: 20
       71.45 -    89.32: 6
  Dihedral angle restraints: 5315
    sinusoidal: 2063
      harmonic: 3252
  Sorted by residual:
  dihedral pdb=" CA  LEU B 555 "
           pdb=" C   LEU B 555 "
           pdb=" N   VAL B 556 "
           pdb=" CA  VAL B 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.34   28.66     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  LEU A 555 "
           pdb=" C   LEU A 555 "
           pdb=" N   VAL A 556 "
           pdb=" CA  VAL A 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.36   28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  GLU A 138 "
           pdb=" C   GLU A 138 "
           pdb=" N   ASN A 139 "
           pdb=" CA  ASN A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.60   25.40     0      5.00e+00 4.00e-02 2.58e+01
  ... (remaining 5312 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.048: 878
       0.048 -    0.096: 404
       0.096 -    0.143: 92
       0.143 -    0.191: 22
       0.191 -    0.239: 12
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CG  LEU A  75 "
            pdb=" CB  LEU A  75 "
            pdb=" CD1 LEU A  75 "
            pdb=" CD2 LEU A  75 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.35   -0.24 2.00e-01 2.50e+01 1.43e+00
  chirality pdb=" CB  THR B 609 "
            pdb=" CA  THR B 609 "
            pdb=" OG1 THR B 609 "
            pdb=" CG2 THR B 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CB  THR A 609 "
            pdb=" CA  THR A 609 "
            pdb=" OG1 THR A 609 "
            pdb=" CG2 THR A 609 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1514
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B 545 "   -0.011 2.00e-02 2.50e+03   2.22e-02 4.95e+00
        pdb=" C   PHE B 545 "    0.038 2.00e-02 2.50e+03
        pdb=" O   PHE B 545 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   VAL B 546 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 545 "    0.011 2.00e-02 2.50e+03   2.21e-02 4.90e+00
        pdb=" C   PHE A 545 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   PHE A 545 "    0.014 2.00e-02 2.50e+03
        pdb=" N   VAL A 546 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 622 "    0.035 5.00e-02 4.00e+02   5.33e-02 4.55e+00
        pdb=" N   PRO B 623 "   -0.092 5.00e-02 4.00e+02
        pdb=" CA  PRO B 623 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO B 623 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1511 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2252
        2.78 -     3.31: 8118
        3.31 -     3.84: 14424
        3.84 -     4.37: 17119
        4.37 -     4.90: 29760
  Nonbonded interactions: 71673
  Sorted by model distance:
  nonbonded pdb=" O   SER A 552 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   SER B 552 "
            pdb=" OG  SER B 552 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   MET A 548 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" OG  SER A 187 "
            pdb=" OE1 GLU A 190 "
     model   vdw
     2.333 3.040
  nonbonded pdb=" O   MET B 548 "
            pdb=" OG  SER B 552 "
     model   vdw
     2.333 3.040
  ... (remaining 71668 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'A'
}

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:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     10.330
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
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      :  0.009   0.077   8971  Z= 0.395
  Angle     :  1.040  11.230  12140  Z= 0.550
  Chirality :  0.059   0.239   1408
  Planarity :  0.006   0.053   1514
  Dihedral  : 15.362  89.316   3218
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.72 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.50 %
    Favored  : 88.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -4.65 (0.18), residues: 1114
  helix: -2.83 (0.14), residues: 606
  sheet: -2.77 (0.70), residues: 50
  loop : -3.35 (0.24), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 193 
 TYR   0.026   0.003   TYR A 494 
 PHE   0.018   0.003   PHE A 182 
 TRP   0.011   0.002   TRP A 379 
 HIS   0.010   0.002   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00941 ( 8968)
  covalent geometry    : angle       1.03953 (12134)
  SS BOND              : bond        0.00715 (    3)
  SS BOND              : angle       1.30507 (    6)
  hydrogen bonds       : bond        0.14540 (  416)
  hydrogen bonds       : angle       6.57005 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 0.318 
Fit side-chains
REVERT: B  163 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6794 (ttm170)
REVERT: B  246 ARG cc_start: 0.8062 (ptp-170) cc_final: 0.7704 (ptp-110)
REVERT: B  515 MET cc_start: 0.8633 (mmm) cc_final: 0.8156 (mmp)
REVERT: B  628 LYS cc_start: 0.7596 (tttt) cc_final: 0.7302 (ttpp)
REVERT: A  126 GLN cc_start: 0.8247 (tt0) cc_final: 0.7949 (tt0)
REVERT: A  194 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8334 (t)
REVERT: A  382 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8742 (ttmm)
REVERT: A  515 MET cc_start: 0.8640 (mmm) cc_final: 0.7832 (mmp)
REVERT: A  541 MET cc_start: 0.9071 (tpp) cc_final: 0.8813 (tpt)
REVERT: A  623 PRO cc_start: 0.8755 (Cg_exo) cc_final: 0.8507 (Cg_endo)
REVERT: A  628 LYS cc_start: 0.7452 (tttt) cc_final: 0.7213 (ttmt)
  outliers start: 12
  outliers final: 2
  residues processed: 161
  average time/residue: 0.0881
  time to fit residues: 20.0739
Evaluate side-chains
  121 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  609 THR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  609 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0770
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0030
   chunk 100 optimal weight:    0.9980
   chunk 106 optimal weight:    7.9990
   overall best weight:    0.5348

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

Flipped N/Q/H residues before XYZ refinement:
B 158 ASN
B 271 GLN
B 629 ASN
A 158 ASN
A 166 GLN
A 629 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.166530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.128157 restraints weight = 11259.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.130465 restraints weight = 8037.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.131859 restraints weight = 6602.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.132515 restraints weight = 5890.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.133046 restraints weight = 5532.792|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7802
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8971  Z= 0.110
  Angle     :  0.602   7.634  12140  Z= 0.309
  Chirality :  0.040   0.142   1408
  Planarity :  0.004   0.031   1514
  Dihedral  :  5.697  42.524   1207
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 16.63 %
    Favored  : 82.64 %
  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: -2.43 (0.23), residues: 1114
  helix: -0.73 (0.20), residues: 596
  sheet: -2.00 (0.58), residues: 70
  loop : -2.73 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 246 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.016   0.001   PHE A 470 
 TRP   0.009   0.001   TRP A 379 
 HIS   0.008   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8968)
  covalent geometry    : angle       0.60161 (12134)
  SS BOND              : bond        0.00413 (    3)
  SS BOND              : angle       0.88478 (    6)
  hydrogen bonds       : bond        0.03506 (  416)
  hydrogen bonds       : angle       4.66278 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 147
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: B  163 ARG cc_start: 0.7024 (ttp-170) cc_final: 0.6638 (ttm170)
REVERT: B  515 MET cc_start: 0.8546 (mmm) cc_final: 0.8119 (mmp)
REVERT: B  628 LYS cc_start: 0.7513 (tttt) cc_final: 0.7264 (ttpp)
REVERT: A  272 GLU cc_start: 0.7111 (pm20) cc_final: 0.6776 (pm20)
REVERT: A  382 LYS cc_start: 0.8924 (ttmt) cc_final: 0.8717 (ttmm)
REVERT: A  471 LEU cc_start: 0.8670 (mp) cc_final: 0.8382 (mt)
REVERT: A  515 MET cc_start: 0.8485 (mmm) cc_final: 0.7687 (mmp)
REVERT: A  570 TYR cc_start: 0.8669 (m-80) cc_final: 0.8140 (m-80)
REVERT: A  628 LYS cc_start: 0.7355 (tttt) cc_final: 0.7048 (ttmt)
  outliers start: 7
  outliers final: 5
  residues processed: 152
  average time/residue: 0.0923
  time to fit residues: 19.8183
Evaluate side-chains
  131 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 126
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  609 THR
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  609 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 40 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 77 optimal weight:    5.9990
   chunk 46 optimal weight:    3.9990
   chunk 67 optimal weight:    6.9990
   chunk 59 optimal weight:    4.9990
   chunk 107 optimal weight:    9.9990
   chunk 55 optimal weight:    2.9990
   chunk 102 optimal weight:    5.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
B  76 ASN
B 338 ASN
B 351 GLN
B 437 GLN
A  76 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.160635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.122025 restraints weight = 11341.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.124208 restraints weight = 8148.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.125486 restraints weight = 6737.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.126345 restraints weight = 6031.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.126645 restraints weight = 5671.780|
|-----------------------------------------------------------------------------|
r_work (final): 0.3263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1949

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045   8971  Z= 0.264
  Angle     :  0.712   8.038  12140  Z= 0.362
  Chirality :  0.045   0.149   1408
  Planarity :  0.004   0.031   1514
  Dihedral  :  5.413  21.653   1206
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.14
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.63 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.46 %
    Favored  : 79.83 %
  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: -2.05 (0.24), residues: 1114
  helix: -0.31 (0.20), residues: 598
  sheet: -2.47 (0.53), residues: 70
  loop : -2.63 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 184 
 TYR   0.017   0.002   TYR A 459 
 PHE   0.015   0.002   PHE B 208 
 TRP   0.009   0.002   TRP B 379 
 HIS   0.005   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00628 ( 8968)
  covalent geometry    : angle       0.71147 (12134)
  SS BOND              : bond        0.00490 (    3)
  SS BOND              : angle       1.02310 (    6)
  hydrogen bonds       : bond        0.03832 (  416)
  hydrogen bonds       : angle       4.62288 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 0.314 
Fit side-chains
REVERT: B  193 ARG cc_start: 0.7987 (ttm110) cc_final: 0.7752 (ttm110)
REVERT: B  258 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7780 (tp)
REVERT: B  343 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7737 (mmtt)
REVERT: B  487 ILE cc_start: 0.8673 (OUTLIER) cc_final: 0.8424 (mt)
REVERT: B  515 MET cc_start: 0.8704 (mmm) cc_final: 0.7637 (mmp)
REVERT: B  541 MET cc_start: 0.8429 (tpt) cc_final: 0.8081 (tpt)
REVERT: A  193 ARG cc_start: 0.8369 (ttm110) cc_final: 0.8126 (ttm110)
REVERT: A  246 ARG cc_start: 0.7893 (ptp-170) cc_final: 0.7641 (ptp-170)
REVERT: A  258 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8012 (tp)
REVERT: A  272 GLU cc_start: 0.7146 (pm20) cc_final: 0.6911 (pm20)
REVERT: A  382 LYS cc_start: 0.9012 (ttmt) cc_final: 0.8768 (ttmm)
REVERT: A  458 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7930 (mt-10)
REVERT: A  515 MET cc_start: 0.8570 (mmm) cc_final: 0.7620 (mmp)
  outliers start: 26
  outliers final: 18
  residues processed: 158
  average time/residue: 0.1018
  time to fit residues: 22.0340
Evaluate side-chains
  155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  105 ASP
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  487 ILE
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  481 MET
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 64 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 70 optimal weight:    0.6980
   chunk 100 optimal weight:    0.8980
   chunk 75 optimal weight:    4.9990
   chunk 78 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  66 ASN
A  66 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.164544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.126263 restraints weight = 11335.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.128596 restraints weight = 8073.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.130035 restraints weight = 6603.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.130886 restraints weight = 5884.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.131009 restraints weight = 5503.241|
|-----------------------------------------------------------------------------|
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8971  Z= 0.113
  Angle     :  0.590   7.699  12140  Z= 0.293
  Chirality :  0.041   0.194   1408
  Planarity :  0.003   0.026   1514
  Dihedral  :  4.938  22.527   1204
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 19.85 %
    Favored  : 77.65 %
  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: -1.30 (0.25), residues: 1114
  helix:  0.45 (0.22), residues: 598
  sheet: -2.41 (0.51), residues: 70
  loop : -2.46 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 184 
 TYR   0.011   0.001   TYR A 459 
 PHE   0.024   0.001   PHE B 495 
 TRP   0.012   0.001   TRP B 379 
 HIS   0.005   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8968)
  covalent geometry    : angle       0.59038 (12134)
  SS BOND              : bond        0.00321 (    3)
  SS BOND              : angle       0.73448 (    6)
  hydrogen bonds       : bond        0.02935 (  416)
  hydrogen bonds       : angle       4.28892 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 137
  time to evaluate  : 0.299 
Fit side-chains
REVERT: B  163 ARG cc_start: 0.7137 (ttp-170) cc_final: 0.6777 (ttm170)
REVERT: B  258 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7810 (tt)
REVERT: B  343 LYS cc_start: 0.7798 (mmtt) cc_final: 0.7545 (mmtt)
REVERT: B  487 ILE cc_start: 0.8431 (OUTLIER) cc_final: 0.8133 (mt)
REVERT: B  515 MET cc_start: 0.8585 (mmm) cc_final: 0.7666 (mmp)
REVERT: B  541 MET cc_start: 0.8399 (tpt) cc_final: 0.8045 (tpt)
REVERT: A  258 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7933 (tt)
REVERT: A  272 GLU cc_start: 0.7084 (pm20) cc_final: 0.6850 (pm20)
REVERT: A  458 GLU cc_start: 0.8149 (mt-10) cc_final: 0.7858 (mt-10)
REVERT: A  515 MET cc_start: 0.8529 (mmm) cc_final: 0.7633 (mmp)
  outliers start: 24
  outliers final: 12
  residues processed: 157
  average time/residue: 0.0995
  time to fit residues: 21.5362
Evaluate side-chains
  138 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  487 ILE
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    0.5980
   chunk 54 optimal weight:    6.9990
   chunk 4 optimal weight:    0.8980
   chunk 109 optimal weight:    0.4980
   chunk 105 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 63 optimal weight:    4.9990
   chunk 81 optimal weight:   10.0000
   chunk 90 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
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 = 0.3774 r_free = 0.3774 target = 0.163974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.125438 restraints weight = 11212.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.127744 restraints weight = 7939.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.129236 restraints weight = 6488.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.130012 restraints weight = 5775.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.130285 restraints weight = 5417.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7809
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8971  Z= 0.104
  Angle     :  0.585   9.391  12140  Z= 0.288
  Chirality :  0.040   0.138   1408
  Planarity :  0.003   0.035   1514
  Dihedral  :  4.645  22.433   1204
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.69 %
    Favored  : 76.51 %
  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: -0.80 (0.26), residues: 1114
  helix:  0.92 (0.22), residues: 598
  sheet: -2.24 (0.52), residues: 70
  loop : -2.34 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 193 
 TYR   0.025   0.001   TYR B 342 
 PHE   0.019   0.001   PHE B 506 
 TRP   0.011   0.001   TRP B 379 
 HIS   0.004   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 8968)
  covalent geometry    : angle       0.58514 (12134)
  SS BOND              : bond        0.00219 (    3)
  SS BOND              : angle       0.55430 (    6)
  hydrogen bonds       : bond        0.02719 (  416)
  hydrogen bonds       : angle       4.10306 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 138
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
REVERT: B  258 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7795 (tt)
REVERT: B  343 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7543 (mmtt)
REVERT: B  454 LEU cc_start: 0.9210 (tp) cc_final: 0.8914 (tp)
REVERT: B  515 MET cc_start: 0.8571 (mmm) cc_final: 0.7876 (mmp)
REVERT: B  541 MET cc_start: 0.8377 (tpt) cc_final: 0.8000 (tpt)
REVERT: A  252 LEU cc_start: 0.5818 (mp) cc_final: 0.5614 (mp)
REVERT: A  258 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.8162 (tt)
REVERT: A  272 GLU cc_start: 0.7157 (pm20) cc_final: 0.6874 (pm20)
REVERT: A  515 MET cc_start: 0.8516 (mmm) cc_final: 0.7621 (mmp)
  outliers start: 27
  outliers final: 17
  residues processed: 160
  average time/residue: 0.0995
  time to fit residues: 22.0736
Evaluate side-chains
  142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 104 optimal weight:    1.9990
   chunk 54 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0980
   chunk 66 optimal weight:    6.9990
   chunk 17 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 32 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 59 optimal weight:    5.9990
   chunk 108 optimal weight:    0.8980
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3773 r_free = 0.3773 target = 0.163966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.125467 restraints weight = 11285.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.127814 restraints weight = 7976.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.129022 restraints weight = 6532.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.129920 restraints weight = 5829.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.130594 restraints weight = 5437.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7821
moved from start:          0.2636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8971  Z= 0.120
  Angle     :  0.572   8.168  12140  Z= 0.285
  Chirality :  0.040   0.145   1408
  Planarity :  0.003   0.027   1514
  Dihedral  :  4.560  21.914   1204
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 21.52 %
    Favored  : 75.88 %
  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: -0.64 (0.26), residues: 1114
  helix:  1.04 (0.22), residues: 598
  sheet: -2.07 (0.53), residues: 70
  loop : -2.25 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 193 
 TYR   0.020   0.001   TYR B 342 
 PHE   0.019   0.001   PHE B 506 
 TRP   0.010   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 8968)
  covalent geometry    : angle       0.57186 (12134)
  SS BOND              : bond        0.00230 (    3)
  SS BOND              : angle       0.53628 (    6)
  hydrogen bonds       : bond        0.02746 (  416)
  hydrogen bonds       : angle       4.05563 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.312 
Fit side-chains
REVERT: B  107 LEU cc_start: 0.8293 (tt) cc_final: 0.8003 (mp)
REVERT: B  193 ARG cc_start: 0.8199 (ttm110) cc_final: 0.7258 (mtt-85)
REVERT: B  246 ARG cc_start: 0.7742 (OUTLIER) cc_final: 0.7444 (ptp-110)
REVERT: B  258 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7901 (tt)
REVERT: B  343 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7546 (mmtt)
REVERT: B  454 LEU cc_start: 0.9184 (tp) cc_final: 0.8960 (tp)
REVERT: B  515 MET cc_start: 0.8599 (mmm) cc_final: 0.7624 (mmp)
REVERT: A  191 ARG cc_start: 0.6887 (ttt180) cc_final: 0.6400 (ttt90)
REVERT: A  193 ARG cc_start: 0.8215 (ttm110) cc_final: 0.7390 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8494 (OUTLIER) cc_final: 0.8174 (tt)
REVERT: A  272 GLU cc_start: 0.7110 (pm20) cc_final: 0.6842 (pm20)
REVERT: A  458 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7857 (mt-10)
REVERT: A  515 MET cc_start: 0.8581 (mmm) cc_final: 0.7645 (mmp)
  outliers start: 25
  outliers final: 20
  residues processed: 151
  average time/residue: 0.0983
  time to fit residues: 20.5458
Evaluate side-chains
  146 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 123
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    0.0980
   chunk 43 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 4 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 48 optimal weight:    0.5980
   chunk 70 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3780 r_free = 0.3780 target = 0.164568 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.125405 restraints weight = 11243.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.127772 restraints weight = 7958.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.128990 restraints weight = 6507.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.129908 restraints weight = 5847.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.130248 restraints weight = 5468.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3343
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8971  Z= 0.101
  Angle     :  0.557   7.441  12140  Z= 0.279
  Chirality :  0.039   0.157   1408
  Planarity :  0.003   0.027   1514
  Dihedral  :  4.451  21.918   1204
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 20.89 %
    Favored  : 76.51 %
  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: -0.46 (0.26), residues: 1114
  helix:  1.18 (0.23), residues: 596
  sheet: -1.98 (0.53), residues: 70
  loop : -2.13 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 184 
 TYR   0.025   0.001   TYR B 342 
 PHE   0.019   0.001   PHE A 506 
 TRP   0.011   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 8968)
  covalent geometry    : angle       0.55726 (12134)
  SS BOND              : bond        0.00204 (    3)
  SS BOND              : angle       0.49013 (    6)
  hydrogen bonds       : bond        0.02602 (  416)
  hydrogen bonds       : angle       4.00419 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 136
  time to evaluate  : 0.234 
Fit side-chains
REVERT: B  193 ARG cc_start: 0.8150 (ttm110) cc_final: 0.7181 (mtt-85)
REVERT: B  229 LYS cc_start: 0.8639 (mmmm) cc_final: 0.8167 (tptm)
REVERT: B  258 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7846 (tt)
REVERT: B  272 GLU cc_start: 0.7107 (pm20) cc_final: 0.6861 (pm20)
REVERT: B  343 LYS cc_start: 0.7782 (mmtt) cc_final: 0.7504 (mmtt)
REVERT: B  454 LEU cc_start: 0.9156 (tp) cc_final: 0.8904 (tp)
REVERT: B  515 MET cc_start: 0.8575 (mmm) cc_final: 0.7882 (mmp)
REVERT: B  541 MET cc_start: 0.8112 (tpt) cc_final: 0.7647 (tpt)
REVERT: A  191 ARG cc_start: 0.6804 (ttt180) cc_final: 0.6196 (ttt90)
REVERT: A  193 ARG cc_start: 0.8181 (ttm110) cc_final: 0.7387 (mtt-85)
REVERT: A  246 ARG cc_start: 0.7756 (ptp-110) cc_final: 0.7471 (ptp-110)
REVERT: A  258 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8204 (tt)
REVERT: A  272 GLU cc_start: 0.7119 (pm20) cc_final: 0.6849 (pm20)
REVERT: A  515 MET cc_start: 0.8572 (mmm) cc_final: 0.8080 (mmp)
  outliers start: 25
  outliers final: 21
  residues processed: 157
  average time/residue: 0.0952
  time to fit residues: 20.7690
Evaluate side-chains
  156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 133
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 94 optimal weight:    2.9990
   chunk 80 optimal weight:    6.9990
   chunk 45 optimal weight:    0.8980
   chunk 41 optimal weight:    0.0370
   chunk 8 optimal weight:    0.2980
   chunk 86 optimal weight:    0.3980
   chunk 106 optimal weight:    8.9990
   chunk 78 optimal weight:    6.9990
   chunk 30 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.4258

-------------------------------------------------------------------------------
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 = 0.3826 r_free = 0.3826 target = 0.169032 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.131253 restraints weight = 11157.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.133600 restraints weight = 7941.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.134985 restraints weight = 6538.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.135563 restraints weight = 5811.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.136212 restraints weight = 5467.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.3378
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2955

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   8971  Z= 0.094
  Angle     :  0.541   8.145  12140  Z= 0.270
  Chirality :  0.039   0.162   1408
  Planarity :  0.003   0.027   1514
  Dihedral  :  4.297  22.267   1204
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 21.10 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.27 (0.27), residues: 1114
  helix:  1.29 (0.23), residues: 600
  sheet: -1.80 (0.54), residues: 70
  loop : -2.03 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 193 
 TYR   0.023   0.001   TYR B 342 
 PHE   0.019   0.001   PHE A 506 
 TRP   0.010   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B  40 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 8968)
  covalent geometry    : angle       0.54069 (12134)
  SS BOND              : bond        0.00177 (    3)
  SS BOND              : angle       0.43446 (    6)
  hydrogen bonds       : bond        0.02501 (  416)
  hydrogen bonds       : angle       3.88152 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 148
  time to evaluate  : 0.343 
Fit side-chains
REVERT: B  191 ARG cc_start: 0.6611 (ttt-90) cc_final: 0.6341 (ttt90)
REVERT: B  193 ARG cc_start: 0.8173 (ttm110) cc_final: 0.7233 (mtt-85)
REVERT: B  229 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8000 (tptm)
REVERT: B  246 ARG cc_start: 0.7863 (ptp-110) cc_final: 0.7245 (mtp85)
REVERT: B  258 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.7944 (tt)
REVERT: B  454 LEU cc_start: 0.9152 (tp) cc_final: 0.8888 (tp)
REVERT: B  515 MET cc_start: 0.8558 (mmm) cc_final: 0.7892 (mmp)
REVERT: B  541 MET cc_start: 0.8159 (tpt) cc_final: 0.7719 (tpt)
REVERT: A  191 ARG cc_start: 0.6893 (ttt180) cc_final: 0.6310 (ttt90)
REVERT: A  258 LEU cc_start: 0.8550 (OUTLIER) cc_final: 0.8233 (tt)
REVERT: A  272 GLU cc_start: 0.7072 (pm20) cc_final: 0.6868 (pm20)
REVERT: A  515 MET cc_start: 0.8548 (mmm) cc_final: 0.8133 (mmp)
  outliers start: 21
  outliers final: 17
  residues processed: 164
  average time/residue: 0.0912
  time to fit residues: 21.0939
Evaluate side-chains
  153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 78 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 58 optimal weight:    2.9990
   chunk 59 optimal weight:    4.9990
   chunk 16 optimal weight:    5.9990
   chunk 50 optimal weight:    7.9990
   chunk 24 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 103 optimal weight:    3.9990
   overall best weight:    2.7588

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

Flipped N/Q/H residues before XYZ refinement:
B 391 ASN
** A  76 ASN ** 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 = 0.3736 r_free = 0.3736 target = 0.160545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.121507 restraints weight = 11215.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.123802 restraints weight = 8122.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.125096 restraints weight = 6704.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.125725 restraints weight = 6035.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.126303 restraints weight = 5680.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050   8971  Z= 0.247
  Angle     :  0.678   7.138  12140  Z= 0.343
  Chirality :  0.045   0.147   1408
  Planarity :  0.004   0.032   1514
  Dihedral  :  4.783  20.269   1204
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.72 %
    Favored  : 92.10 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 20.48 %
    Favored  : 76.61 %
  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: -0.93 (0.25), residues: 1114
  helix:  0.67 (0.21), residues: 614
  sheet: -2.05 (0.51), residues: 70
  loop : -2.29 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 246 
 TYR   0.015   0.002   TYR B 342 
 PHE   0.015   0.002   PHE B 507 
 TRP   0.005   0.001   TRP B 379 
 HIS   0.005   0.002   HIS A 267 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 ( 8968)
  covalent geometry    : angle       0.67803 (12134)
  SS BOND              : bond        0.00345 (    3)
  SS BOND              : angle       0.79748 (    6)
  hydrogen bonds       : bond        0.03380 (  416)
  hydrogen bonds       : angle       4.21569 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 0.341 
Fit side-chains
REVERT: B  258 LEU cc_start: 0.8334 (OUTLIER) cc_final: 0.8040 (tp)
REVERT: B  272 GLU cc_start: 0.7167 (pm20) cc_final: 0.6872 (pm20)
REVERT: B  515 MET cc_start: 0.8670 (mmm) cc_final: 0.8177 (mmp)
REVERT: A  191 ARG cc_start: 0.6899 (ttt180) cc_final: 0.6360 (ttt90)
REVERT: A  258 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8281 (tp)
REVERT: A  515 MET cc_start: 0.8594 (mmm) cc_final: 0.7555 (mmp)
  outliers start: 28
  outliers final: 23
  residues processed: 157
  average time/residue: 0.0935
  time to fit residues: 20.5205
Evaluate side-chains
  154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  246 ARG
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  424 GLN
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0570
   chunk 109 optimal weight:    6.9990
   chunk 13 optimal weight:    5.9990
   chunk 50 optimal weight:    9.9990
   chunk 21 optimal weight:    7.9990
   chunk 65 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 58 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.9100

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

Flipped N/Q/H residues before XYZ refinement:
** A  41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 437 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.164257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.125910 restraints weight = 11175.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.128228 restraints weight = 7955.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.129505 restraints weight = 6527.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.130388 restraints weight = 5832.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.130540 restraints weight = 5487.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3325
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.2981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8971  Z= 0.121
  Angle     :  0.589   8.966  12140  Z= 0.296
  Chirality :  0.040   0.171   1408
  Planarity :  0.003   0.028   1514
  Dihedral  :  4.608  21.196   1204
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.41 %
    Favored  : 76.09 %
  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: -0.61 (0.26), residues: 1114
  helix:  0.94 (0.22), residues: 608
  sheet: -1.89 (0.51), residues: 70
  loop : -2.14 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 193 
 TYR   0.025   0.001   TYR B 247 
 PHE   0.019   0.001   PHE A 506 
 TRP   0.011   0.001   TRP A 379 
 HIS   0.006   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8968)
  covalent geometry    : angle       0.58851 (12134)
  SS BOND              : bond        0.00262 (    3)
  SS BOND              : angle       0.63012 (    6)
  hydrogen bonds       : bond        0.02829 (  416)
  hydrogen bonds       : angle       4.02700 ( 1170)

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.315 
Fit side-chains
REVERT: B  181 GLN cc_start: 0.4647 (mp10) cc_final: 0.4237 (mp10)
REVERT: B  191 ARG cc_start: 0.6679 (ttt-90) cc_final: 0.6449 (ttt90)
REVERT: B  193 ARG cc_start: 0.8166 (ttm110) cc_final: 0.7258 (mtt-85)
REVERT: B  229 LYS cc_start: 0.8727 (mmmm) cc_final: 0.8246 (tptm)
REVERT: B  244 GLN cc_start: 0.6813 (mm-40) cc_final: 0.6540 (tp40)
REVERT: B  258 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.7987 (tt)
REVERT: B  515 MET cc_start: 0.8601 (mmm) cc_final: 0.7653 (mmp)
REVERT: B  541 MET cc_start: 0.8132 (tpt) cc_final: 0.7312 (tpt)
REVERT: A  191 ARG cc_start: 0.6902 (ttt180) cc_final: 0.6366 (ttt90)
REVERT: A  193 ARG cc_start: 0.8292 (ttm110) cc_final: 0.7388 (mtt-85)
REVERT: A  246 ARG cc_start: 0.7178 (ptp-110) cc_final: 0.6857 (ttm110)
REVERT: A  258 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8239 (tt)
REVERT: A  272 GLU cc_start: 0.7047 (pm20) cc_final: 0.6844 (pm20)
REVERT: A  515 MET cc_start: 0.8589 (mmm) cc_final: 0.7609 (mmp)
REVERT: A  541 MET cc_start: 0.8193 (tpt) cc_final: 0.6492 (tpt)
  outliers start: 24
  outliers final: 17
  residues processed: 150
  average time/residue: 0.0959
  time to fit residues: 19.9477
Evaluate side-chains
  149 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  560 THR
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 106 optimal weight:    0.0370
   chunk 101 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 44 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.7980
   chunk 108 optimal weight:    0.4980
   chunk 100 optimal weight:    6.9990
   overall best weight:    1.0662

-------------------------------------------------------------------------------
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 = 0.3779 r_free = 0.3779 target = 0.164703 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.126421 restraints weight = 11028.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.128761 restraints weight = 7953.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.130172 restraints weight = 6529.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.130820 restraints weight = 5829.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.130979 restraints weight = 5481.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8971  Z= 0.130
  Angle     :  0.583   7.518  12140  Z= 0.296
  Chirality :  0.041   0.145   1408
  Planarity :  0.003   0.031   1514
  Dihedral  :  4.513  21.443   1204
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 21.10 %
    Favored  : 76.40 %
  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: -0.48 (0.26), residues: 1114
  helix:  1.04 (0.22), residues: 614
  sheet: -1.77 (0.52), residues: 70
  loop : -2.13 (0.30), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 193 
 TYR   0.019   0.001   TYR B 342 
 PHE   0.019   0.001   PHE A 506 
 TRP   0.009   0.001   TRP B 379 
 HIS   0.007   0.001   HIS B 155 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 8968)
  covalent geometry    : angle       0.58336 (12134)
  SS BOND              : bond        0.00218 (    3)
  SS BOND              : angle       0.55319 (    6)
  hydrogen bonds       : bond        0.02801 (  416)
  hydrogen bonds       : angle       3.98562 ( 1170)

===============================================================================
Job complete
usr+sys time: 1464.06 seconds
wall clock time: 26 minutes 6.95 seconds (1566.95 seconds total)