Starting phenix.real_space_refine
on Sat Aug 23 05:32:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nq1_0478/08_2025/6nq1_0478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nq1_0478/08_2025/6nq1_0478.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/6nq1_0478/08_2025/6nq1_0478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nq1_0478/08_2025/6nq1_0478.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nq1_0478/08_2025/6nq1_0478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nq1_0478/08_2025/6nq1_0478.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
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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      60      5.16       5
     C    6674      2.51       5
     N    1622      2.21       5
     O    1690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10046
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5023
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 621, 5023
          Classifications: {'peptide': 621}
          Link IDs: {'PTRANS': 21, 'TRANS': 599}
          Chain breaks: 4
  Restraints were copied for chains:
    B
  Time building chain proxies: 3.83, per 1000 atoms: 0.38
  Number of scatterers: 10046
  At special positions: 0
  Unit cell: (118.77, 127.33, 107, 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      60     16.00
     O    1690      8.00
     N    1622      7.00
     C    6674      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 122 " - pdb=" SG  CYS A 180 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 623 " - pdb=" SG  CYS B 623 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 122 " - pdb=" SG  CYS B 180 " distance=2.03

  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 370.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2380

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 0 sheets defined
      78.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 39 through 58
      removed outlier: 3.515A  pdb=" N   PHE A  52 " --> pdb=" O   GLN A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 78
      removed outlier: 3.507A  pdb=" N   TYR A  78 " --> pdb=" O   TYR A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 94
      removed outlier: 3.560A  pdb=" N   GLN A  83 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 100
      removed outlier: 3.863A  pdb=" N   GLU A 100 " --> pdb=" O   ALA A  97 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 147
      removed outlier: 3.503A  pdb=" N   VAL A 130 " --> pdb=" O   GLU A 126 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   CYS A 132 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 155
    Processing helix  chain 'A' and resid 155 through 178
    Processing helix  chain 'A' and resid 185 through 190
    Processing helix  chain 'A' and resid 191 through 198
      removed outlier: 3.985A  pdb=" N   LEU A 195 " --> pdb=" O   ARG A 191 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ASN A 198 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 212
      removed outlier: 3.521A  pdb=" N   LYS A 207 " --> pdb=" O   LYS A 203 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 239
      removed outlier: 3.818A  pdb=" N   SER A 218 " --> pdb=" O   PRO A 214 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   PHE A 230 " --> pdb=" O   HIS A 226 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   MET A 232 " --> pdb=" O   CYS A 228 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 237 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ALA A 239 " --> pdb=" O   MET A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 270
      removed outlier: 3.636A  pdb=" N   THR A 270 " --> pdb=" O   LEU A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 285
    Processing helix  chain 'A' and resid 288 through 300
      removed outlier: 3.910A  pdb=" N   PHE A 292 " --> pdb=" O   TYR A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 313
      removed outlier: 3.657A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR A 308 " --> pdb=" O   MET A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 343
      removed outlier: 3.702A  pdb=" N   THR A 325 " --> pdb=" O   LYS A 321 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A 343 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 369
      removed outlier: 3.823A  pdb=" N   GLN A 364 " --> pdb=" O   GLN A 360 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   VAL A 365 " --> pdb=" O   ASN A 361 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLN A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS A 368 " --> pdb=" O   GLN A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 386
    Processing helix  chain 'A' and resid 392 through 398
    Processing helix  chain 'A' and resid 399 through 405
      removed outlier: 3.683A  pdb=" N   GLU A 402 " --> pdb=" O   LEU A 399 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A 403 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ASP A 404 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 433 through 459
      removed outlier: 3.679A  pdb=" N   SER A 448 " --> pdb=" O   ALA A 444 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP A 456 " --> pdb=" O   PHE A 452 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ASP A 458 " --> pdb=" O   VAL A 454 " (cutoff:3.500A)
      removed outlier: 4.752A  pdb=" N   VAL A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 489
      removed outlier: 4.105A  pdb=" N   GLY A 470 " --> pdb=" O   ASP A 466 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ILE A 471 " --> pdb=" O   PHE A 467 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   MET A 484 " --> pdb=" O   TYR A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 498
      removed outlier: 3.898A  pdb=" N   LEU A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER A 498 " --> pdb=" O   ARG A 494 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 523
      removed outlier: 3.841A  pdb=" N   VAL A 514 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 553
      removed outlier: 3.794A  pdb=" N   PHE A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 558
    Processing helix  chain 'A' and resid 565 through 577
      removed outlier: 3.854A  pdb=" N   ALA A 569 " --> pdb=" O   MET A 565 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 601
      removed outlier: 3.661A  pdb=" N   ILE A 595 " --> pdb=" O   TYR A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
      removed outlier: 4.538A  pdb=" N   ALA A 633 " --> pdb=" O   GLU A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 638 through 651
      removed outlier: 3.530A  pdb=" N   VAL A 644 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 667
    Processing helix  chain 'A' and resid 670 through 682
      removed outlier: 3.552A  pdb=" N   PHE A 674 " --> pdb=" O   SER A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 698
      removed outlier: 3.588A  pdb=" N   ASN A 687 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 58
      removed outlier: 3.515A  pdb=" N   PHE B  52 " --> pdb=" O   GLN B  48 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 69 through 78
      removed outlier: 3.507A  pdb=" N   TYR B  78 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 94
      removed outlier: 3.560A  pdb=" N   GLN B  83 " --> pdb=" O   SER B  79 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 95 through 100
      removed outlier: 3.862A  pdb=" N   GLU B 100 " --> pdb=" O   ALA B  97 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 147
      removed outlier: 3.503A  pdb=" N   VAL B 130 " --> pdb=" O   GLU B 126 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   CYS B 132 " --> pdb=" O   VAL B 128 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   VAL B 135 " --> pdb=" O   LEU B 131 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 155
    Processing helix  chain 'B' and resid 155 through 178
    Processing helix  chain 'B' and resid 185 through 190
    Processing helix  chain 'B' and resid 191 through 198
      removed outlier: 3.985A  pdb=" N   LEU B 195 " --> pdb=" O   ARG B 191 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   ASN B 198 " --> pdb=" O   PHE B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 201 through 212
      removed outlier: 3.520A  pdb=" N   LYS B 207 " --> pdb=" O   LYS B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 212 through 239
      removed outlier: 3.818A  pdb=" N   SER B 218 " --> pdb=" O   PRO B 214 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   PHE B 230 " --> pdb=" O   HIS B 226 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   MET B 232 " --> pdb=" O   CYS B 228 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU B 237 " --> pdb=" O   PHE B 233 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA B 239 " --> pdb=" O   MET B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 270
      removed outlier: 3.637A  pdb=" N   THR B 270 " --> pdb=" O   LEU B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 278 through 285
    Processing helix  chain 'B' and resid 288 through 300
      removed outlier: 3.911A  pdb=" N   PHE B 292 " --> pdb=" O   TYR B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 301 through 313
      removed outlier: 3.658A  pdb=" N   ASN B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   THR B 308 " --> pdb=" O   MET B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 317 through 343
      removed outlier: 3.702A  pdb=" N   THR B 325 " --> pdb=" O   LYS B 321 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   SER B 343 " --> pdb=" O   GLU B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 369
      removed outlier: 3.823A  pdb=" N   GLN B 364 " --> pdb=" O   GLN B 360 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL B 365 " --> pdb=" O   ASN B 361 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   LYS B 368 " --> pdb=" O   GLN B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 386
    Processing helix  chain 'B' and resid 392 through 398
    Processing helix  chain 'B' and resid 399 through 405
      removed outlier: 3.683A  pdb=" N   GLU B 402 " --> pdb=" O   LEU B 399 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU B 403 " --> pdb=" O   PHE B 400 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ASP B 404 " --> pdb=" O   ASN B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 428
    Processing helix  chain 'B' and resid 433 through 459
      removed outlier: 3.679A  pdb=" N   SER B 448 " --> pdb=" O   ALA B 444 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ASP B 456 " --> pdb=" O   PHE B 452 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ALA B 457 " --> pdb=" O   LEU B 453 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ASP B 458 " --> pdb=" O   VAL B 454 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   VAL B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 489
      removed outlier: 4.105A  pdb=" N   GLY B 470 " --> pdb=" O   ASP B 466 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   ILE B 471 " --> pdb=" O   PHE B 467 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   MET B 484 " --> pdb=" O   TYR B 480 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 492 through 498
      removed outlier: 3.898A  pdb=" N   LEU B 497 " --> pdb=" O   LEU B 493 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   SER B 498 " --> pdb=" O   ARG B 494 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 499 through 523
      removed outlier: 3.841A  pdb=" N   VAL B 514 " --> pdb=" O   VAL B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 553
      removed outlier: 3.794A  pdb=" N   PHE B 553 " --> pdb=" O   MET B 549 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 554 through 558
    Processing helix  chain 'B' and resid 565 through 577
      removed outlier: 3.854A  pdb=" N   ALA B 569 " --> pdb=" O   MET B 565 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   THR B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 579 through 601
      removed outlier: 3.661A  pdb=" N   ILE B 595 " --> pdb=" O   TYR B 591 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 630 through 634
      removed outlier: 4.539A  pdb=" N   ALA B 633 " --> pdb=" O   GLU B 630 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 638 through 651
      removed outlier: 3.529A  pdb=" N   VAL B 644 " --> pdb=" O   ALA B 640 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 667
    Processing helix  chain 'B' and resid 670 through 682
      removed outlier: 3.552A  pdb=" N   PHE B 674 " --> pdb=" O   SER B 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 683 through 698
      removed outlier: 3.588A  pdb=" N   ASN B 687 " --> pdb=" O   VAL B 683 " (cutoff:3.500A)

    621 hydrogen bonds defined for protein.
    1809 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: 1.73

  Time building geometry restraints manager: 0.94 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: 3010
        1.34 -     1.46: 2540
        1.46 -     1.58: 4652
        1.58 -     1.70: 0
        1.70 -     1.82: 100
  Bond restraints: 10302
  Sorted by residual:
  bond pdb=" CB  PHE B 582 "
       pdb=" CG  PHE B 582 "
    ideal  model  delta    sigma   weight residual
    1.502  1.453  0.049 2.30e-02 1.89e+03 4.53e+00
  bond pdb=" CB  TRP A 655 "
       pdb=" CG  TRP A 655 "
    ideal  model  delta    sigma   weight residual
    1.498  1.433  0.065 3.10e-02 1.04e+03 4.43e+00
  bond pdb=" CB  PHE A 582 "
       pdb=" CG  PHE A 582 "
    ideal  model  delta    sigma   weight residual
    1.502  1.454  0.048 2.30e-02 1.89e+03 4.40e+00
  bond pdb=" CB  TRP B 655 "
       pdb=" CG  TRP B 655 "
    ideal  model  delta    sigma   weight residual
    1.498  1.434  0.064 3.10e-02 1.04e+03 4.20e+00
  bond pdb=" CB  MET A 650 "
       pdb=" CG  MET A 650 "
    ideal  model  delta    sigma   weight residual
    1.520  1.466  0.054 3.00e-02 1.11e+03 3.29e+00
  ... (remaining 10297 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.84: 13279
        1.84 -     3.69: 585
        3.69 -     5.53: 88
        5.53 -     7.38: 33
        7.38 -     9.22: 29
  Bond angle restraints: 14014
  Sorted by residual:
  angle pdb=" C   HIS A 431 "
        pdb=" N   TYR A 432 "
        pdb=" CA  TYR A 432 "
      ideal   model   delta    sigma   weight residual
     121.54  129.83   -8.29 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" C   HIS B 431 "
        pdb=" N   TYR B 432 "
        pdb=" CA  TYR B 432 "
      ideal   model   delta    sigma   weight residual
     121.54  129.82   -8.28 1.91e+00 2.74e-01 1.88e+01
  angle pdb=" N   ILE A 279 "
        pdb=" CA  ILE A 279 "
        pdb=" C   ILE A 279 "
      ideal   model   delta    sigma   weight residual
     108.88  116.61   -7.73 2.16e+00 2.14e-01 1.28e+01
  angle pdb=" N   ILE B 279 "
        pdb=" CA  ILE B 279 "
        pdb=" C   ILE B 279 "
      ideal   model   delta    sigma   weight residual
     108.88  116.61   -7.73 2.16e+00 2.14e-01 1.28e+01
  angle pdb=" CA  ILE B 279 "
        pdb=" C   ILE B 279 "
        pdb=" N   PRO B 280 "
      ideal   model   delta    sigma   weight residual
     118.88  123.59   -4.71 1.54e+00 4.22e-01 9.37e+00
  ... (remaining 14009 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 5382
       17.87 -    35.74: 539
       35.74 -    53.61: 75
       53.61 -    71.48: 18
       71.48 -    89.36: 9
  Dihedral angle restraints: 6023
    sinusoidal: 2355
      harmonic: 3668
  Sorted by residual:
  dihedral pdb=" CB  CYS A 623 "
           pdb=" SG  CYS A 623 "
           pdb=" SG  CYS B 623 "
           pdb=" CB  CYS B 623 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00    3.36  -89.36     1      1.00e+01 1.00e-02 9.49e+01
  dihedral pdb=" CB  CYS B 122 "
           pdb=" SG  CYS B 122 "
           pdb=" SG  CYS B 180 "
           pdb=" CB  CYS B 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.84  -81.84     1      1.00e+01 1.00e-02 8.24e+01
  dihedral pdb=" CB  CYS A 122 "
           pdb=" SG  CYS A 122 "
           pdb=" SG  CYS A 180 "
           pdb=" CB  CYS A 180 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  174.83  -81.83     1      1.00e+01 1.00e-02 8.24e+01
  ... (remaining 6020 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1172
       0.054 -    0.108: 380
       0.108 -    0.162: 58
       0.162 -    0.216: 20
       0.216 -    0.270: 4
  Chirality restraints: 1634
  Sorted by residual:
  chirality pdb=" CB  VAL A 652 "
            pdb=" CA  VAL A 652 "
            pdb=" CG1 VAL A 652 "
            pdb=" CG2 VAL A 652 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  VAL B 652 "
            pdb=" CA  VAL B 652 "
            pdb=" CG1 VAL B 652 "
            pdb=" CG2 VAL B 652 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.81e+00
  chirality pdb=" CB  VAL B 179 "
            pdb=" CA  VAL B 179 "
            pdb=" CG1 VAL B 179 "
            pdb=" CG2 VAL B 179 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 1631 not shown)

  Planarity restraints: 1702
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 101 "   -0.051 5.00e-02 4.00e+02   7.66e-02 9.38e+00
        pdb=" N   PRO B 102 "    0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO B 102 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO B 102 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 101 "    0.051 5.00e-02 4.00e+02   7.63e-02 9.31e+00
        pdb=" N   PRO A 102 "   -0.132 5.00e-02 4.00e+02
        pdb=" CA  PRO A 102 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 102 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 655 "    0.021 2.00e-02 2.50e+03   1.70e-02 7.24e+00
        pdb=" CG  TRP B 655 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 655 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 655 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 655 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 655 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 655 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 655 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 655 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 655 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1699 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 3266
        2.82 -     3.34: 9233
        3.34 -     3.86: 15727
        3.86 -     4.38: 18242
        4.38 -     4.90: 30536
  Nonbonded interactions: 77004
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 334 "
            pdb=" OE1 GLN A 397 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" OG1 THR B 334 "
            pdb=" OE1 GLN B 397 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   ASN B 445 "
            pdb=" OG  SER B 448 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   ASN A 445 "
            pdb=" OG  SER A 448 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" O   VAL B 174 "
            pdb=" OG  SER B 177 "
     model   vdw
     2.340 3.040
  ... (remaining 76999 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.730
  Find NCS groups from input model:        0.050
  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:1.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8233
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      :  0.008   0.083  10305  Z= 0.365
  Angle     :  0.974   9.223  14020  Z= 0.500
  Chirality :  0.056   0.270   1634
  Planarity :  0.006   0.077   1702
  Dihedral  : 14.326  82.260   3634
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 3.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  9.80 %
    Favored  : 90.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.53 (0.17), residues: 1222
  helix: -3.85 (0.09), residues: 886
  sheet:  None (None), residues: 0
  loop : -2.30 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  60 
 TYR   0.017   0.002   TYR A  74 
 PHE   0.018   0.002   PHE B 626 
 TRP   0.045   0.003   TRP B 655 
 HIS   0.010   0.002   HIS A 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00826 (10302)
  covalent geometry    : angle       0.97291 (14014)
  SS BOND              : bond        0.00792 (    3)
  SS BOND              : angle       2.09401 (    6)
  hydrogen bonds       : bond        0.30632 (  621)
  hydrogen bonds       : angle       8.88541 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 152
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
REVERT: A  379 MET cc_start: 0.7338 (mmt) cc_final: 0.6724 (mtp)
REVERT: A  446 LEU cc_start: 0.9209 (tt) cc_final: 0.9004 (tp)
REVERT: A  545 ARG cc_start: 0.7244 (mtm110) cc_final: 0.7024 (ptt180)
REVERT: A  653 ASN cc_start: 0.9141 (t0) cc_final: 0.8555 (t0)
REVERT: B  379 MET cc_start: 0.7309 (mmt) cc_final: 0.6701 (mtp)
REVERT: B  446 LEU cc_start: 0.9213 (tt) cc_final: 0.9005 (tp)
REVERT: B  545 ARG cc_start: 0.7300 (mtm110) cc_final: 0.7073 (ptt180)
REVERT: B  653 ASN cc_start: 0.9145 (t0) cc_final: 0.8705 (t0)
  outliers start: 2
  outliers final: 0
  residues processed: 154
  average time/residue: 0.1038
  time to fit residues: 21.8641
Evaluate side-chains
  94 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:   10.0000
   chunk 97 optimal weight:    9.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.0970
   chunk 123 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A  58 GLN
A 153 GLN
A 305 ASN
A 375 HIS
A 431 HIS
A 653 ASN
B  58 GLN
B 305 ASN
B 375 HIS
B 431 HIS
B 653 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.101488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.075870 restraints weight = 27724.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.075993 restraints weight = 15525.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.076098 restraints weight = 12027.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.076292 restraints weight = 12068.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.076833 restraints weight = 10732.512|
|-----------------------------------------------------------------------------|
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10305  Z= 0.146
  Angle     :  0.677   8.447  14020  Z= 0.346
  Chirality :  0.040   0.166   1634
  Planarity :  0.005   0.043   1702
  Dihedral  :  5.150  27.320   1352
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 13.88 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.23), residues: 1222
  helix: -0.88 (0.16), residues: 888
  sheet:  None (None), residues: 0
  loop : -2.20 (0.36), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 554 
 TYR   0.025   0.001   TYR B 479 
 PHE   0.019   0.001   PHE A 338 
 TRP   0.032   0.002   TRP A 685 
 HIS   0.002   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10302)
  covalent geometry    : angle       0.67727 (14014)
  SS BOND              : bond        0.00189 (    3)
  SS BOND              : angle       0.88745 (    6)
  hydrogen bonds       : bond        0.05980 (  621)
  hydrogen bonds       : angle       4.07408 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 121
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 CYS cc_start: 0.8958 (t) cc_final: 0.8526 (p)
REVERT: A   92 LEU cc_start: 0.9113 (tp) cc_final: 0.8894 (tp)
REVERT: A  153 GLN cc_start: 0.8479 (OUTLIER) cc_final: 0.7879 (mp10)
REVERT: A  344 MET cc_start: 0.7045 (tpt) cc_final: 0.6451 (tpt)
REVERT: A  379 MET cc_start: 0.7416 (mmt) cc_final: 0.6951 (mtt)
REVERT: A  549 MET cc_start: 0.8258 (mtm) cc_final: 0.8049 (ptm)
REVERT: A  653 ASN cc_start: 0.8864 (t0) cc_final: 0.8633 (t0)
REVERT: A  690 LEU cc_start: 0.9362 (tp) cc_final: 0.9149 (tp)
REVERT: B   92 LEU cc_start: 0.9113 (tp) cc_final: 0.8885 (tp)
REVERT: B  320 MET cc_start: 0.8006 (tpp) cc_final: 0.7782 (tpp)
REVERT: B  370 GLN cc_start: 0.7509 (mp10) cc_final: 0.7213 (mp10)
REVERT: B  379 MET cc_start: 0.7433 (mmt) cc_final: 0.6965 (mtt)
REVERT: B  549 MET cc_start: 0.8327 (mtm) cc_final: 0.8022 (ptm)
REVERT: B  653 ASN cc_start: 0.8888 (t0) cc_final: 0.8656 (t0)
REVERT: B  690 LEU cc_start: 0.9340 (tp) cc_final: 0.9125 (tp)
  outliers start: 9
  outliers final: 3
  residues processed: 130
  average time/residue: 0.0792
  time to fit residues: 15.4974
Evaluate side-chains
  95 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 91
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  550 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 28 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 1 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0170
   chunk 116 optimal weight:    2.9990
   chunk 37 optimal weight:   10.0000
   chunk 78 optimal weight:    4.9990
   chunk 104 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   overall best weight:    2.2026

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

Flipped N/Q/H residues before XYZ refinement:
A 153 GLN
B 153 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.100442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.074998 restraints weight = 28222.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.074818 restraints weight = 16098.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.074825 restraints weight = 13115.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.075133 restraints weight = 13060.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.075422 restraints weight = 11384.777|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031  10305  Z= 0.159
  Angle     :  0.661  11.784  14020  Z= 0.328
  Chirality :  0.042   0.192   1634
  Planarity :  0.005   0.039   1702
  Dihedral  :  4.916  27.162   1352
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.34 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.24), residues: 1222
  helix:  0.11 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -2.18 (0.37), residues: 318

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 554 
 TYR   0.029   0.001   TYR A 479 
 PHE   0.013   0.001   PHE A 504 
 TRP   0.032   0.002   TRP B 685 
 HIS   0.003   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (10302)
  covalent geometry    : angle       0.66047 (14014)
  SS BOND              : bond        0.00362 (    3)
  SS BOND              : angle       0.95817 (    6)
  hydrogen bonds       : bond        0.05155 (  621)
  hydrogen bonds       : angle       3.75641 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.412 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9147 (tp) cc_final: 0.8930 (tp)
REVERT: A  332 LEU cc_start: 0.8875 (pp) cc_final: 0.8584 (mp)
REVERT: A  344 MET cc_start: 0.7163 (tpt) cc_final: 0.6880 (tpt)
REVERT: A  549 MET cc_start: 0.8330 (mtm) cc_final: 0.8041 (ptm)
REVERT: A  653 ASN cc_start: 0.9075 (t0) cc_final: 0.8674 (t0)
REVERT: B   92 LEU cc_start: 0.9126 (tp) cc_final: 0.8900 (tp)
REVERT: B  153 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7730 (mp10)
REVERT: B  229 LEU cc_start: 0.8794 (tt) cc_final: 0.8377 (mt)
REVERT: B  332 LEU cc_start: 0.8913 (pp) cc_final: 0.8602 (mp)
REVERT: B  549 MET cc_start: 0.8349 (mtm) cc_final: 0.8076 (ptm)
  outliers start: 24
  outliers final: 10
  residues processed: 132
  average time/residue: 0.0846
  time to fit residues: 16.6487
Evaluate side-chains
  107 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue  153 GLN
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 35 optimal weight:   10.0000
   chunk 103 optimal weight:    7.9990
   chunk 29 optimal weight:    0.0970
   chunk 65 optimal weight:    7.9990
   chunk 7 optimal weight:    0.1980
   chunk 91 optimal weight:    8.9990
   chunk 4 optimal weight:    0.9990
   chunk 94 optimal weight:    6.9990
   chunk 22 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0270
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.8640

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

Flipped N/Q/H residues before XYZ refinement:
B 153 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.102116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.074588 restraints weight = 28321.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.076424 restraints weight = 15368.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.077496 restraints weight = 10846.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.078106 restraints weight = 8996.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.078455 restraints weight = 8120.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8162
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      :  0.003   0.032  10305  Z= 0.118
  Angle     :  0.633  12.198  14020  Z= 0.308
  Chirality :  0.041   0.187   1634
  Planarity :  0.004   0.036   1702
  Dihedral  :  4.712  26.121   1352
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 16.52 %
    Favored  : 81.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.03 (0.25), residues: 1222
  helix:  0.71 (0.17), residues: 894
  sheet:  None (None), residues: 0
  loop : -2.00 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 554 
 TYR   0.028   0.001   TYR A 479 
 PHE   0.013   0.001   PHE B 452 
 TRP   0.034   0.001   TRP A 685 
 HIS   0.002   0.001   HIS A 226 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 (10302)
  covalent geometry    : angle       0.63283 (14014)
  SS BOND              : bond        0.00235 (    3)
  SS BOND              : angle       0.49605 (    6)
  hydrogen bonds       : bond        0.04332 (  621)
  hydrogen bonds       : angle       3.57667 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 112
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9112 (tp) cc_final: 0.8890 (tp)
REVERT: A  229 LEU cc_start: 0.8781 (tt) cc_final: 0.8385 (mt)
REVERT: A  344 MET cc_start: 0.7235 (tpt) cc_final: 0.6958 (tpt)
REVERT: A  549 MET cc_start: 0.8367 (mtm) cc_final: 0.8023 (ptm)
REVERT: A  653 ASN cc_start: 0.8970 (t0) cc_final: 0.8585 (t0)
REVERT: B   45 CYS cc_start: 0.8876 (t) cc_final: 0.8453 (p)
REVERT: B   92 LEU cc_start: 0.9114 (tp) cc_final: 0.8895 (tp)
REVERT: B  229 LEU cc_start: 0.8778 (tt) cc_final: 0.8386 (mt)
REVERT: B  370 GLN cc_start: 0.7631 (mp10) cc_final: 0.7313 (mp10)
REVERT: B  549 MET cc_start: 0.8380 (mtm) cc_final: 0.8020 (ptm)
REVERT: B  557 ARG cc_start: 0.8404 (OUTLIER) cc_final: 0.7404 (tpp-160)
  outliers start: 21
  outliers final: 14
  residues processed: 132
  average time/residue: 0.0718
  time to fit residues: 14.3221
Evaluate side-chains
  110 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  557 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 121 optimal weight:    6.9990
   chunk 2 optimal weight:    4.9990
   chunk 100 optimal weight:    5.9990
   chunk 6 optimal weight:    4.9990
   chunk 67 optimal weight:    0.0370
   chunk 47 optimal weight:    2.9990
   chunk 103 optimal weight:   20.0000
   chunk 51 optimal weight:    1.9990
   chunk 24 optimal weight:    2.9990
   chunk 61 optimal weight:    0.9980
   chunk 23 optimal weight:    5.9990
   overall best weight:    1.8064

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

Flipped N/Q/H residues before XYZ refinement:
B 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.101301 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.073779 restraints weight = 28539.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.075580 restraints weight = 15485.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.076631 restraints weight = 10994.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.077237 restraints weight = 9089.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.077596 restraints weight = 8209.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3044

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10305  Z= 0.139
  Angle     :  0.651  11.777  14020  Z= 0.317
  Chirality :  0.042   0.171   1634
  Planarity :  0.004   0.037   1702
  Dihedral  :  4.615  25.853   1352
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 18.24 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.37 (0.25), residues: 1222
  helix:  1.01 (0.18), residues: 892
  sheet:  None (None), residues: 0
  loop : -1.85 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 554 
 TYR   0.027   0.001   TYR B 479 
 PHE   0.011   0.001   PHE B 582 
 TRP   0.039   0.001   TRP A 685 
 HIS   0.003   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10302)
  covalent geometry    : angle       0.65054 (14014)
  SS BOND              : bond        0.00296 (    3)
  SS BOND              : angle       0.79076 (    6)
  hydrogen bonds       : bond        0.04260 (  621)
  hydrogen bonds       : angle       3.56637 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9150 (tp) cc_final: 0.8930 (tp)
REVERT: A  229 LEU cc_start: 0.8745 (tt) cc_final: 0.8355 (mt)
REVERT: A  344 MET cc_start: 0.7272 (tpt) cc_final: 0.6978 (tpt)
REVERT: A  549 MET cc_start: 0.8375 (mtm) cc_final: 0.8051 (ptm)
REVERT: A  653 ASN cc_start: 0.9050 (t0) cc_final: 0.8685 (t0)
REVERT: B   45 CYS cc_start: 0.8885 (t) cc_final: 0.8450 (p)
REVERT: B   92 LEU cc_start: 0.9153 (tp) cc_final: 0.8935 (tp)
REVERT: B  229 LEU cc_start: 0.8766 (tt) cc_final: 0.8394 (mt)
REVERT: B  370 GLN cc_start: 0.7604 (mp10) cc_final: 0.7307 (mp10)
REVERT: B  549 MET cc_start: 0.8395 (mtm) cc_final: 0.8045 (ptm)
  outliers start: 23
  outliers final: 17
  residues processed: 126
  average time/residue: 0.0721
  time to fit residues: 13.9323
Evaluate side-chains
  113 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 96
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  486 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 76 optimal weight:    9.9990
   chunk 60 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9980
   chunk 101 optimal weight:    6.9990
   chunk 58 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 17 optimal weight:    0.7980
   chunk 91 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3684 r_free = 0.3684 target = 0.101914 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.074341 restraints weight = 28581.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.076105 restraints weight = 15750.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.077149 restraints weight = 11351.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.077730 restraints weight = 9462.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.077924 restraints weight = 8593.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8183
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10305  Z= 0.129
  Angle     :  0.635  10.839  14020  Z= 0.308
  Chirality :  0.041   0.171   1634
  Planarity :  0.004   0.036   1702
  Dihedral  :  4.515  25.269   1352
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 18.42 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.26), residues: 1222
  helix:  1.23 (0.18), residues: 894
  sheet:  None (None), residues: 0
  loop : -1.74 (0.38), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 554 
 TYR   0.026   0.001   TYR A 479 
 PHE   0.013   0.001   PHE A 504 
 TRP   0.036   0.001   TRP A 685 
 HIS   0.003   0.001   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10302)
  covalent geometry    : angle       0.63493 (14014)
  SS BOND              : bond        0.00242 (    3)
  SS BOND              : angle       0.64171 (    6)
  hydrogen bonds       : bond        0.04031 (  621)
  hydrogen bonds       : angle       3.51738 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 106
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9124 (tp) cc_final: 0.8911 (tp)
REVERT: A  229 LEU cc_start: 0.8761 (tt) cc_final: 0.8348 (mt)
REVERT: A  344 MET cc_start: 0.7276 (tpt) cc_final: 0.6976 (tpt)
REVERT: A  549 MET cc_start: 0.8350 (mtm) cc_final: 0.8072 (ptm)
REVERT: A  653 ASN cc_start: 0.9048 (t0) cc_final: 0.8708 (t0)
REVERT: B   45 CYS cc_start: 0.8826 (t) cc_final: 0.8403 (p)
REVERT: B   92 LEU cc_start: 0.9128 (tp) cc_final: 0.8906 (tp)
REVERT: B  229 LEU cc_start: 0.8768 (tt) cc_final: 0.8358 (mt)
REVERT: B  370 GLN cc_start: 0.7585 (mp10) cc_final: 0.7253 (mp10)
REVERT: B  452 PHE cc_start: 0.8641 (m-80) cc_final: 0.8410 (m-10)
REVERT: B  549 MET cc_start: 0.8378 (mtm) cc_final: 0.8081 (ptm)
  outliers start: 25
  outliers final: 19
  residues processed: 127
  average time/residue: 0.0733
  time to fit residues: 14.3924
Evaluate side-chains
  114 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 81 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9990
   chunk 85 optimal weight:    0.3980
   chunk 120 optimal weight:    5.9990
   chunk 108 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 123 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 69 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   overall best weight:    2.6586

-------------------------------------------------------------------------------
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 = 0.3662 r_free = 0.3662 target = 0.100677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.072738 restraints weight = 28539.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.074503 restraints weight = 15569.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.075554 restraints weight = 11189.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.076163 restraints weight = 9331.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.076387 restraints weight = 8445.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10305  Z= 0.173
  Angle     :  0.661  10.696  14020  Z= 0.325
  Chirality :  0.043   0.198   1634
  Planarity :  0.004   0.037   1702
  Dihedral  :  4.564  24.943   1352
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 19.42 %
    Favored  : 78.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.25), residues: 1222
  helix:  1.14 (0.18), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.87 (0.38), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 554 
 TYR   0.024   0.001   TYR B 479 
 PHE   0.016   0.001   PHE A 582 
 TRP   0.037   0.002   TRP B 685 
 HIS   0.003   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 (10302)
  covalent geometry    : angle       0.66042 (14014)
  SS BOND              : bond        0.00362 (    3)
  SS BOND              : angle       1.01409 (    6)
  hydrogen bonds       : bond        0.04316 (  621)
  hydrogen bonds       : angle       3.60282 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 95
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  344 MET cc_start: 0.7260 (tpt) cc_final: 0.7030 (tpt)
REVERT: A  549 MET cc_start: 0.8392 (mtm) cc_final: 0.8138 (ptm)
REVERT: B   45 CYS cc_start: 0.8808 (t) cc_final: 0.8387 (p)
REVERT: B  370 GLN cc_start: 0.7494 (mp10) cc_final: 0.7273 (mp10)
REVERT: B  549 MET cc_start: 0.8385 (mtm) cc_final: 0.8119 (ptm)
  outliers start: 28
  outliers final: 23
  residues processed: 119
  average time/residue: 0.0739
  time to fit residues: 13.4017
Evaluate side-chains
  114 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  504 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 75 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 118 optimal weight:    0.7980
   chunk 34 optimal weight:    8.9990
   chunk 56 optimal weight:    0.9980
   chunk 27 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   overall best weight:    2.3584

-------------------------------------------------------------------------------
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 = 0.3666 r_free = 0.3666 target = 0.101003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.073322 restraints weight = 28508.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.075092 restraints weight = 15564.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.076126 restraints weight = 11168.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.076754 restraints weight = 9335.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.077021 restraints weight = 8454.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3207
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  10305  Z= 0.159
  Angle     :  0.656  11.268  14020  Z= 0.322
  Chirality :  0.043   0.193   1634
  Planarity :  0.004   0.037   1702
  Dihedral  :  4.553  24.755   1352
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.24 %
    Favored  : 77.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.25), residues: 1222
  helix:  1.20 (0.18), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.82 (0.38), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 554 
 TYR   0.025   0.001   TYR A 479 
 PHE   0.013   0.001   PHE A 452 
 TRP   0.041   0.002   TRP B 685 
 HIS   0.002   0.001   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 (10302)
  covalent geometry    : angle       0.65576 (14014)
  SS BOND              : bond        0.00300 (    3)
  SS BOND              : angle       0.85012 (    6)
  hydrogen bonds       : bond        0.04272 (  621)
  hydrogen bonds       : angle       3.59314 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.8751 (tt) cc_final: 0.8395 (mt)
REVERT: A  344 MET cc_start: 0.7238 (tpt) cc_final: 0.6948 (tpt)
REVERT: A  549 MET cc_start: 0.8333 (mtm) cc_final: 0.8084 (ptm)
REVERT: B   45 CYS cc_start: 0.8804 (t) cc_final: 0.8352 (p)
REVERT: B  229 LEU cc_start: 0.8749 (tt) cc_final: 0.8391 (mt)
REVERT: B  370 GLN cc_start: 0.7494 (mp10) cc_final: 0.7262 (mp10)
REVERT: B  549 MET cc_start: 0.8368 (mtm) cc_final: 0.8112 (ptm)
  outliers start: 33
  outliers final: 27
  residues processed: 123
  average time/residue: 0.0753
  time to fit residues: 14.3809
Evaluate side-chains
  119 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue   94 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  223 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  504 PHE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  651 VAL
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  223 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  446 LEU
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  556 LEU
Chi-restraints excluded: chain B residue  651 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 85 optimal weight:    0.7980
   chunk 118 optimal weight:    0.8980
   chunk 38 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 123 optimal weight:    3.9990
   chunk 52 optimal weight:    5.9990
   chunk 43 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   chunk 65 optimal weight:    6.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A 274 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.102197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.074645 restraints weight = 28244.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.076472 restraints weight = 15268.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.077558 restraints weight = 10850.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3242 r_free = 0.3242 target = 0.078100 restraints weight = 9006.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.078500 restraints weight = 8214.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10305  Z= 0.120
  Angle     :  0.638  11.237  14020  Z= 0.308
  Chirality :  0.042   0.198   1634
  Planarity :  0.004   0.041   1702
  Dihedral  :  4.422  23.539   1352
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.96 %
    Favored  : 77.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.83 (0.25), residues: 1222
  helix:  1.33 (0.18), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.76 (0.38), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 554 
 TYR   0.024   0.001   TYR B 479 
 PHE   0.014   0.001   PHE A 489 
 TRP   0.042   0.001   TRP A 685 
 HIS   0.001   0.000   HIS B 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10302)
  covalent geometry    : angle       0.63787 (14014)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.49360 (    6)
  hydrogen bonds       : bond        0.03845 (  621)
  hydrogen bonds       : angle       3.49113 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.8826 (tt) cc_final: 0.8529 (mt)
REVERT: A  344 MET cc_start: 0.7310 (tpt) cc_final: 0.7061 (tpt)
REVERT: A  549 MET cc_start: 0.8327 (mtm) cc_final: 0.8083 (ptm)
REVERT: B   45 CYS cc_start: 0.8776 (t) cc_final: 0.8391 (p)
REVERT: B  229 LEU cc_start: 0.8849 (tt) cc_final: 0.8535 (mt)
REVERT: B  370 GLN cc_start: 0.7575 (mp10) cc_final: 0.7274 (mp10)
REVERT: B  549 MET cc_start: 0.8337 (mtm) cc_final: 0.8058 (ptm)
  outliers start: 23
  outliers final: 19
  residues processed: 124
  average time/residue: 0.0708
  time to fit residues: 13.7951
Evaluate side-chains
  107 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  504 PHE
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 56 optimal weight:    0.1980
   chunk 111 optimal weight:    8.9990
   chunk 88 optimal weight:    0.9980
   chunk 60 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 121 optimal weight:    5.9990
   chunk 95 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 52 optimal weight:    0.7980
   chunk 76 optimal weight:    7.9990
   overall best weight:    1.1984

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.101978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.074675 restraints weight = 27716.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.076491 restraints weight = 15076.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.077556 restraints weight = 10730.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.078188 restraints weight = 8981.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.078188 restraints weight = 8107.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10305  Z= 0.121
  Angle     :  0.648  11.205  14020  Z= 0.310
  Chirality :  0.042   0.202   1634
  Planarity :  0.004   0.042   1702
  Dihedral  :  4.389  23.252   1352
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 20.60 %
    Favored  : 77.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.26), residues: 1222
  helix:  1.30 (0.18), residues: 924
  sheet:  None (None), residues: 0
  loop : -1.70 (0.40), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 554 
 TYR   0.024   0.001   TYR A 479 
 PHE   0.014   0.001   PHE A 489 
 TRP   0.044   0.001   TRP A 685 
 HIS   0.001   0.000   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10302)
  covalent geometry    : angle       0.64758 (14014)
  SS BOND              : bond        0.00227 (    3)
  SS BOND              : angle       0.53841 (    6)
  hydrogen bonds       : bond        0.03782 (  621)
  hydrogen bonds       : angle       3.44089 ( 1809)

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

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

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2444 Ramachandran restraints generated.
    1222 Oldfield, 0 Emsley, 1222 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  229 LEU cc_start: 0.8807 (tt) cc_final: 0.8525 (mt)
REVERT: A  344 MET cc_start: 0.7263 (tpt) cc_final: 0.6986 (tpt)
REVERT: A  549 MET cc_start: 0.8299 (mtm) cc_final: 0.8051 (ptm)
REVERT: B   45 CYS cc_start: 0.8747 (t) cc_final: 0.8358 (p)
REVERT: B  229 LEU cc_start: 0.8860 (tt) cc_final: 0.8538 (mt)
REVERT: B  370 GLN cc_start: 0.7550 (mp10) cc_final: 0.7170 (mp10)
REVERT: B  508 LEU cc_start: 0.9008 (mp) cc_final: 0.8797 (mm)
REVERT: B  549 MET cc_start: 0.8336 (mtm) cc_final: 0.8061 (ptm)
  outliers start: 21
  outliers final: 19
  residues processed: 112
  average time/residue: 0.0779
  time to fit residues: 13.4630
Evaluate side-chains
  105 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  189 LEU
Chi-restraints excluded: chain A residue  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  504 PHE
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 LEU
Chi-restraints excluded: chain B residue  357 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 117 optimal weight:    5.9990
   chunk 75 optimal weight:    1.9990
   chunk 95 optimal weight:    8.9990
   chunk 12 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 53 optimal weight:    7.9990
   chunk 82 optimal weight:    0.1980
   chunk 3 optimal weight:    7.9990
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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 = 0.3683 r_free = 0.3683 target = 0.101939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.076724 restraints weight = 28371.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.076549 restraints weight = 15951.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.076553 restraints weight = 13237.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.076948 restraints weight = 12902.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.077025 restraints weight = 11838.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3199
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.3692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10305  Z= 0.126
  Angle     :  0.658  12.284  14020  Z= 0.314
  Chirality :  0.042   0.197   1634
  Planarity :  0.005   0.103   1702
  Dihedral  :  4.379  22.998   1352
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 21.05 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.26), residues: 1222
  helix:  1.29 (0.18), residues: 930
  sheet:  None (None), residues: 0
  loop : -1.74 (0.40), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 554 
 TYR   0.022   0.001   TYR B 479 
 PHE   0.014   0.001   PHE A 489 
 TRP   0.046   0.001   TRP A 685 
 HIS   0.001   0.000   HIS A 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10302)
  covalent geometry    : angle       0.65818 (14014)
  SS BOND              : bond        0.00226 (    3)
  SS BOND              : angle       0.57523 (    6)
  hydrogen bonds       : bond        0.03784 (  621)
  hydrogen bonds       : angle       3.42522 ( 1809)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1504.87 seconds
wall clock time: 26 minutes 43.17 seconds (1603.17 seconds total)