Starting phenix.real_space_refine
on Wed Apr 30 23:30:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nq1_0478/04_2025/6nq1_0478.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nq1_0478/04_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nq1_0478/04_2025/6nq1_0478.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nq1_0478/04_2025/6nq1_0478.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nq1_0478/04_2025/6nq1_0478.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nq1_0478/04_2025/6nq1_0478.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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): 0.06s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 10.69, per 1000 atoms: 1.06
  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: 2.39
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.93
  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: 2.77

  Time building geometry restraints manager: 2.88 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: 0.05
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:             1.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.400
  Check model and map are aligned:         0.080
  Set scattering table:                    0.130
  Process input model:                     30.280
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.730
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  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
 TRP   0.045   0.003   TRP B 655 
 HIS   0.010   0.002   HIS A 411 
 PHE   0.018   0.002   PHE B 626 
 TYR   0.017   0.002   TYR A  74 
 ARG   0.004   0.001   ARG B  60 

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

*********************** 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  : 1.047 
Fit side-chains
   revert: symmetry clash
REVERT: A  379 MET cc_start: 0.7338 (mmt) cc_final: 0.6731 (mtp)
REVERT: A  446 LEU cc_start: 0.9209 (tt) cc_final: 0.9005 (tp)
REVERT: A  653 ASN cc_start: 0.9141 (t0) cc_final: 0.8554 (t0)
REVERT: B  379 MET cc_start: 0.7309 (mmt) cc_final: 0.6707 (mtp)
REVERT: B  446 LEU cc_start: 0.9213 (tt) cc_final: 0.9007 (tp)
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: 0.2534
  time to fit residues: 53.1473
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  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 104 optimal weight:    4.9990
   chunk 93 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 97 optimal weight:    0.2980
   chunk 37 optimal weight:    7.9990
   chunk 59 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 112 optimal weight:    1.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A  58 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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.100975 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.075041 restraints weight = 27589.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.075616 restraints weight = 15170.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.075532 restraints weight = 11641.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2157

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= 0.151
  Angle     :  0.688   8.377  14020  Z= 0.352
  Chirality :  0.041   0.163   1634
  Planarity :  0.006   0.044   1702
  Dihedral  :  5.175  27.558   1352
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 14.16 %
    Favored  : 85.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.23), residues: 1222
  helix: -0.95 (0.16), residues: 888
  sheet:  None (None), residues: 0
  loop : -2.18 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP A 685 
 HIS   0.003   0.001   HIS B 151 
 PHE   0.018   0.001   PHE A 338 
 TYR   0.023   0.001   TYR B 479 
 ARG   0.003   0.000   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06482 (  621)
  hydrogen bonds       : angle       4.14479 ( 1809)
  SS BOND              : bond        0.00216 (    3)
  SS BOND              : angle       0.97121 (    6)
  covalent geometry    : bond        0.00311 (10302)
  covalent geometry    : angle       0.68829 (14014)

*********************** 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
  128 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 120
  time to evaluate  : 1.046 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 CYS cc_start: 0.8948 (t) cc_final: 0.8519 (p)
REVERT: A   92 LEU cc_start: 0.9122 (tp) cc_final: 0.8912 (tp)
REVERT: A  320 MET cc_start: 0.8074 (tpp) cc_final: 0.7848 (tpp)
REVERT: A  379 MET cc_start: 0.7484 (mmt) cc_final: 0.6977 (mtt)
REVERT: A  549 MET cc_start: 0.8103 (mtp) cc_final: 0.7896 (ptm)
REVERT: A  653 ASN cc_start: 0.8932 (t0) cc_final: 0.8710 (t0)
REVERT: B   92 LEU cc_start: 0.9117 (tp) cc_final: 0.8908 (tp)
REVERT: B  320 MET cc_start: 0.8040 (tpp) cc_final: 0.7819 (tpp)
REVERT: B  370 GLN cc_start: 0.7558 (mp10) cc_final: 0.7289 (mp10)
REVERT: B  379 MET cc_start: 0.7436 (mmt) cc_final: 0.6976 (mtt)
REVERT: B  549 MET cc_start: 0.8134 (mtp) cc_final: 0.7922 (ptm)
REVERT: B  690 LEU cc_start: 0.9355 (tp) cc_final: 0.9155 (tp)
  outliers start: 8
  outliers final: 3
  residues processed: 128
  average time/residue: 0.1950
  time to fit residues: 36.8446
Evaluate side-chains
  94 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 61 optimal weight:    1.9990
   chunk 122 optimal weight:    0.9980
   chunk 101 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0980
   chunk 42 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   chunk 24 optimal weight:    6.9990
   chunk 64 optimal weight:    7.9990
   chunk 104 optimal weight:    1.9990
   overall best weight:    1.4186

-------------------------------------------------------------------------------
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 = 0.3672 r_free = 0.3672 target = 0.101200 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.075838 restraints weight = 28163.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.075729 restraints weight = 15862.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.075784 restraints weight = 12695.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.2633

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10305  Z= 0.130
  Angle     :  0.621  10.056  14020  Z= 0.312
  Chirality :  0.041   0.167   1634
  Planarity :  0.004   0.038   1702
  Dihedral  :  4.851  26.815   1352
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.52 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.24), residues: 1222
  helix:  0.22 (0.17), residues: 894
  sheet:  None (None), residues: 0
  loop : -2.10 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 685 
 HIS   0.002   0.001   HIS B 151 
 PHE   0.012   0.001   PHE A 504 
 TYR   0.025   0.001   TYR A 479 
 ARG   0.008   0.000   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04954 (  621)
  hydrogen bonds       : angle       3.69384 ( 1809)
  SS BOND              : bond        0.00293 (    3)
  SS BOND              : angle       0.77345 (    6)
  covalent geometry    : bond        0.00286 (10302)
  covalent geometry    : angle       0.62108 (14014)

*********************** 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
  131 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 1.099 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 CYS cc_start: 0.9023 (t) cc_final: 0.8514 (p)
REVERT: A   92 LEU cc_start: 0.9119 (tp) cc_final: 0.8884 (tp)
REVERT: A  229 LEU cc_start: 0.8784 (tt) cc_final: 0.8368 (mt)
REVERT: A  332 LEU cc_start: 0.8821 (pp) cc_final: 0.8552 (mp)
REVERT: A  549 MET cc_start: 0.8100 (mtp) cc_final: 0.7888 (ptm)
REVERT: B   45 CYS cc_start: 0.8964 (t) cc_final: 0.8474 (p)
REVERT: B   92 LEU cc_start: 0.9096 (tp) cc_final: 0.8875 (tp)
REVERT: B  229 LEU cc_start: 0.8763 (tt) cc_final: 0.8335 (mt)
REVERT: B  332 LEU cc_start: 0.8861 (pp) cc_final: 0.8621 (mp)
  outliers start: 22
  outliers final: 12
  residues processed: 130
  average time/residue: 0.1925
  time to fit residues: 36.9567
Evaluate side-chains
  111 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
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 A residue  550 LEU
Chi-restraints excluded: chain B residue  184 LEU
Chi-restraints excluded: chain B residue  189 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  550 LEU
Chi-restraints excluded: chain B residue  650 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 98 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 121 optimal weight:    2.9990
   chunk 32 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   chunk 2 optimal weight:   10.0000
   chunk 5 optimal weight:    1.9990
   chunk 46 optimal weight:    5.9990
   overall best weight:    3.9990

-------------------------------------------------------------------------------
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 = 0.3632 r_free = 0.3632 target = 0.099097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.073575 restraints weight = 28363.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.073473 restraints weight = 16652.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.073446 restraints weight = 13265.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10305  Z= 0.238
  Angle     :  0.704  10.401  14020  Z= 0.353
  Chirality :  0.045   0.209   1634
  Planarity :  0.005   0.039   1702
  Dihedral  :  4.969  27.571   1352
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 16.88 %
    Favored  : 80.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.24), residues: 1222
  helix:  0.49 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -2.01 (0.37), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP B 685 
 HIS   0.004   0.001   HIS A 151 
 PHE   0.015   0.002   PHE B 452 
 TYR   0.026   0.002   TYR B 479 
 ARG   0.006   0.001   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05087 (  621)
  hydrogen bonds       : angle       3.79647 ( 1809)
  SS BOND              : bond        0.00509 (    3)
  SS BOND              : angle       1.36527 (    6)
  covalent geometry    : bond        0.00549 (10302)
  covalent geometry    : angle       0.70370 (14014)

*********************** 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
  129 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  332 LEU cc_start: 0.8890 (pp) cc_final: 0.8643 (mp)
REVERT: B   45 CYS cc_start: 0.8998 (t) cc_final: 0.8483 (p)
REVERT: B  332 LEU cc_start: 0.8932 (pp) cc_final: 0.8660 (mp)
REVERT: B  370 GLN cc_start: 0.7575 (mp10) cc_final: 0.7271 (mp10)
  outliers start: 27
  outliers final: 18
  residues processed: 124
  average time/residue: 0.2125
  time to fit residues: 38.9448
Evaluate side-chains
  110 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 92
  time to evaluate  : 1.111 
-------------------------------------------------------------------------------
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  371 LEU
Chi-restraints excluded: chain A residue  446 LEU
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain B residue  146 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  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  550 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 107 optimal weight:    6.9990
   chunk 80 optimal weight:    6.9990
   chunk 101 optimal weight:    6.9990
   chunk 28 optimal weight:    9.9990
   chunk 74 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0770
   chunk 15 optimal weight:    4.9990
   chunk 51 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0170
   chunk 114 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   overall best weight:    0.9578

-------------------------------------------------------------------------------
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 = 0.3682 r_free = 0.3682 target = 0.101873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.076418 restraints weight = 28336.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.076160 restraints weight = 16665.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.076250 restraints weight = 13129.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3047

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     :  0.624   9.894  14020  Z= 0.306
  Chirality :  0.041   0.187   1634
  Planarity :  0.004   0.036   1702
  Dihedral  :  4.683  25.722   1352
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.51 %
    Favored  : 79.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1222
  helix:  1.01 (0.18), residues: 894
  sheet:  None (None), residues: 0
  loop : -1.76 (0.38), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.001   TRP A 685 
 HIS   0.002   0.001   HIS B 226 
 PHE   0.014   0.001   PHE A 504 
 TYR   0.023   0.001   TYR B 479 
 ARG   0.005   0.000   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04221 (  621)
  hydrogen bonds       : angle       3.52227 ( 1809)
  SS BOND              : bond        0.00232 (    3)
  SS BOND              : angle       0.49639 (    6)
  covalent geometry    : bond        0.00254 (10302)
  covalent geometry    : angle       0.62375 (14014)

*********************** 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
  142 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
REVERT: A   45 CYS cc_start: 0.8867 (t) cc_final: 0.8406 (p)
REVERT: A   92 LEU cc_start: 0.9110 (tp) cc_final: 0.8889 (tp)
REVERT: A  229 LEU cc_start: 0.8713 (tt) cc_final: 0.8349 (mt)
REVERT: B   45 CYS cc_start: 0.8962 (t) cc_final: 0.8445 (p)
REVERT: B   92 LEU cc_start: 0.9110 (tp) cc_final: 0.8890 (tp)
REVERT: B  229 LEU cc_start: 0.8712 (tt) cc_final: 0.8353 (mt)
REVERT: B  370 GLN cc_start: 0.7596 (mp10) cc_final: 0.7268 (mp10)
  outliers start: 28
  outliers final: 18
  residues processed: 137
  average time/residue: 0.1835
  time to fit residues: 37.4093
Evaluate side-chains
  119 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
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  486 LEU
Chi-restraints excluded: chain A residue  504 PHE
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
Chi-restraints excluded: chain B residue  550 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 75 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 118 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 81 optimal weight:    3.9990
   chunk 62 optimal weight:   10.0000
   chunk 89 optimal weight:    1.9990
   chunk 85 optimal weight:    4.9990
   chunk 77 optimal weight:    0.9980
   chunk 102 optimal weight:    6.9990
   chunk 79 optimal weight:    0.6980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
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 = 0.3670 r_free = 0.3670 target = 0.101237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.073280 restraints weight = 28046.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.075156 restraints weight = 15086.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.076244 restraints weight = 10624.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8229
moved from start:          0.3214

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= 0.144
  Angle     :  0.647   9.798  14020  Z= 0.317
  Chirality :  0.042   0.174   1634
  Planarity :  0.004   0.037   1702
  Dihedral  :  4.589  25.825   1352
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 7.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 18.24 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.25), residues: 1222
  helix:  1.14 (0.18), residues: 898
  sheet:  None (None), residues: 0
  loop : -1.82 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP B 685 
 HIS   0.002   0.001   HIS A 151 
 PHE   0.016   0.001   PHE A 504 
 TYR   0.020   0.001   TYR A 479 
 ARG   0.007   0.000   ARG A 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  621)
  hydrogen bonds       : angle       3.49184 ( 1809)
  SS BOND              : bond        0.00328 (    3)
  SS BOND              : angle       0.84142 (    6)
  covalent geometry    : bond        0.00331 (10302)
  covalent geometry    : angle       0.64641 (14014)

*********************** 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
  129 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9116 (tp) cc_final: 0.8906 (tp)
REVERT: A  153 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.7847 (mp10)
REVERT: A  229 LEU cc_start: 0.8711 (tt) cc_final: 0.8308 (mt)
REVERT: A  549 MET cc_start: 0.7684 (ptm) cc_final: 0.7418 (ptm)
REVERT: B   45 CYS cc_start: 0.8849 (t) cc_final: 0.8410 (p)
REVERT: B  153 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.7818 (mp10)
REVERT: B  229 LEU cc_start: 0.8716 (tt) cc_final: 0.8321 (mt)
REVERT: B  370 GLN cc_start: 0.7627 (mp10) cc_final: 0.7310 (mp10)
  outliers start: 27
  outliers final: 21
  residues processed: 126
  average time/residue: 0.2787
  time to fit residues: 52.5638
Evaluate side-chains
  119 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 96
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 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  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  153 GLN
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
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  556 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 119 optimal weight:    0.6980
   chunk 7 optimal weight:    7.9990
   chunk 1 optimal weight:    5.9990
   chunk 66 optimal weight:    0.9990
   chunk 96 optimal weight:    8.9990
   chunk 0 optimal weight:    5.9990
   chunk 120 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 108 optimal weight:    5.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3692 r_free = 0.3692 target = 0.102583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.074784 restraints weight = 28368.292|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.076714 restraints weight = 14979.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.077844 restraints weight = 10468.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3223
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.3402

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10305  Z= 0.119
  Angle     :  0.625  10.749  14020  Z= 0.306
  Chirality :  0.041   0.184   1634
  Planarity :  0.004   0.035   1702
  Dihedral  :  4.439  24.689   1352
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.88 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.26), residues: 1222
  helix:  1.26 (0.18), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.76 (0.39), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 685 
 HIS   0.001   0.001   HIS B 226 
 PHE   0.013   0.001   PHE A 504 
 TYR   0.023   0.001   TYR A 479 
 ARG   0.008   0.000   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03832 (  621)
  hydrogen bonds       : angle       3.41545 ( 1809)
  SS BOND              : bond        0.00209 (    3)
  SS BOND              : angle       0.44441 (    6)
  covalent geometry    : bond        0.00265 (10302)
  covalent geometry    : angle       0.62477 (14014)

*********************** 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
  141 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 110
  time to evaluate  : 1.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   92 LEU cc_start: 0.9087 (tp) cc_final: 0.8872 (tp)
REVERT: A  153 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7803 (mp10)
REVERT: A  229 LEU cc_start: 0.8735 (tt) cc_final: 0.8481 (mt)
REVERT: B   45 CYS cc_start: 0.8807 (t) cc_final: 0.8375 (p)
REVERT: B   92 LEU cc_start: 0.9083 (tp) cc_final: 0.8869 (tp)
REVERT: B  153 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7816 (mp10)
REVERT: B  229 LEU cc_start: 0.8742 (tt) cc_final: 0.8433 (mt)
REVERT: B  370 GLN cc_start: 0.7532 (mp10) cc_final: 0.7179 (mp10)
  outliers start: 31
  outliers final: 21
  residues processed: 136
  average time/residue: 0.2556
  time to fit residues: 52.4377
Evaluate side-chains
  117 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 1.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue  153 GLN
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  389 VAL
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  153 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
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  556 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 34 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 17 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 1 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 75 optimal weight:    3.9990
   chunk 84 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3681 r_free = 0.3681 target = 0.101965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.076794 restraints weight = 28418.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.076940 restraints weight = 15652.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.076925 restraints weight = 12199.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3196
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10305  Z= 0.129
  Angle     :  0.628   9.629  14020  Z= 0.308
  Chirality :  0.042   0.185   1634
  Planarity :  0.004   0.042   1702
  Dihedral  :  4.404  24.288   1352
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.24 %
    Favored  : 94.76 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.51 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.71 (0.25), residues: 1222
  helix:  1.24 (0.18), residues: 912
  sheet:  None (None), residues: 0
  loop : -1.81 (0.39), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 685 
 HIS   0.001   0.001   HIS B 151 
 PHE   0.016   0.001   PHE A 452 
 TYR   0.017   0.001   TYR A 479 
 ARG   0.007   0.000   ARG A 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03923 (  621)
  hydrogen bonds       : angle       3.45144 ( 1809)
  SS BOND              : bond        0.00251 (    3)
  SS BOND              : angle       0.68914 (    6)
  covalent geometry    : bond        0.00295 (10302)
  covalent geometry    : angle       0.62789 (14014)

*********************** 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
  128 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 1.040 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7832 (mp10)
REVERT: A  229 LEU cc_start: 0.8738 (tt) cc_final: 0.8521 (mt)
REVERT: B   45 CYS cc_start: 0.8845 (t) cc_final: 0.8399 (p)
REVERT: B  153 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7833 (mp10)
REVERT: B  229 LEU cc_start: 0.8743 (tt) cc_final: 0.8518 (mt)
REVERT: B  370 GLN cc_start: 0.7517 (mp10) cc_final: 0.7151 (mp10)
REVERT: B  549 MET cc_start: 0.8153 (ptm) cc_final: 0.7642 (ptp)
  outliers start: 33
  outliers final: 25
  residues processed: 124
  average time/residue: 0.1902
  time to fit residues: 34.8614
Evaluate side-chains
  118 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 91
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 GLN
Chi-restraints excluded: chain A residue  156 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  357 VAL
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  486 LEU
Chi-restraints excluded: chain A residue  504 PHE
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain B residue   48 GLN
Chi-restraints excluded: chain B residue  153 GLN
Chi-restraints excluded: chain B residue  156 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  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  550 LEU
Chi-restraints excluded: chain B residue  556 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 113 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   chunk 104 optimal weight:    7.9990
   chunk 44 optimal weight:    0.7980
   chunk 93 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 81 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 86 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 116 optimal weight:    0.0980
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.102839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.077992 restraints weight = 28116.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.077642 restraints weight = 16381.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.077726 restraints weight = 12847.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10305  Z= 0.114
  Angle     :  0.625   9.627  14020  Z= 0.307
  Chirality :  0.041   0.169   1634
  Planarity :  0.004   0.038   1702
  Dihedral  :  4.330  23.732   1352
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 20.24 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.25), residues: 1222
  helix:  1.23 (0.17), residues: 930
  sheet:  None (None), residues: 0
  loop : -1.78 (0.40), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP A 685 
 HIS   0.001   0.000   HIS A 226 
 PHE   0.015   0.001   PHE A 504 
 TYR   0.015   0.001   TYR A 479 
 ARG   0.009   0.000   ARG A 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03754 (  621)
  hydrogen bonds       : angle       3.43174 ( 1809)
  SS BOND              : bond        0.00188 (    3)
  SS BOND              : angle       0.46469 (    6)
  covalent geometry    : bond        0.00254 (10302)
  covalent geometry    : angle       0.62540 (14014)

*********************** 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
  134 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 1.039 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7730 (mp10)
REVERT: A  223 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9101 (mt)
REVERT: A  229 LEU cc_start: 0.8753 (tt) cc_final: 0.8489 (mt)
REVERT: B   45 CYS cc_start: 0.8789 (t) cc_final: 0.8347 (p)
REVERT: B  153 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.7724 (mp10)
REVERT: B  229 LEU cc_start: 0.8755 (tt) cc_final: 0.8486 (mt)
REVERT: B  370 GLN cc_start: 0.7590 (mp10) cc_final: 0.7250 (mp10)
REVERT: B  549 MET cc_start: 0.8200 (ptm) cc_final: 0.7682 (ptp)
  outliers start: 26
  outliers final: 22
  residues processed: 131
  average time/residue: 0.1783
  time to fit residues: 35.7674
Evaluate side-chains
  120 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 1.027 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue  153 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  389 VAL
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  153 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  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  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  550 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 93 optimal weight:    0.3980
   chunk 64 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 3 optimal weight:    9.9990
   chunk 32 optimal weight:    9.9990
   chunk 109 optimal weight:    5.9990
   chunk 45 optimal weight:    7.9990
   chunk 72 optimal weight:    4.9990
   chunk 63 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.102141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.076779 restraints weight = 28515.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.076536 restraints weight = 16556.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.076615 restraints weight = 12998.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3675

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= 0.130
  Angle     :  0.631   9.524  14020  Z= 0.310
  Chirality :  0.041   0.184   1634
  Planarity :  0.005   0.097   1702
  Dihedral  :  4.377  23.363   1352
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 20.87 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.25), residues: 1222
  helix:  1.37 (0.18), residues: 918
  sheet:  None (None), residues: 0
  loop : -1.74 (0.39), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.042   0.001   TRP B 685 
 HIS   0.001   0.000   HIS A 151 
 PHE   0.023   0.001   PHE A 582 
 TYR   0.014   0.001   TYR A 479 
 ARG   0.011   0.000   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  621)
  hydrogen bonds       : angle       3.40922 ( 1809)
  SS BOND              : bond        0.00243 (    3)
  SS BOND              : angle       0.62646 (    6)
  covalent geometry    : bond        0.00298 (10302)
  covalent geometry    : angle       0.63128 (14014)

********************** 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
  116 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 GLN cc_start: 0.8212 (OUTLIER) cc_final: 0.7755 (mp10)
REVERT: A  229 LEU cc_start: 0.8778 (tt) cc_final: 0.8531 (mt)
REVERT: B  153 GLN cc_start: 0.8215 (OUTLIER) cc_final: 0.7743 (mp10)
REVERT: B  229 LEU cc_start: 0.8775 (tt) cc_final: 0.8531 (mt)
REVERT: B  370 GLN cc_start: 0.7645 (mp10) cc_final: 0.7292 (mp10)
REVERT: B  549 MET cc_start: 0.8227 (ptm) cc_final: 0.7693 (ptp)
  outliers start: 25
  outliers final: 22
  residues processed: 113
  average time/residue: 0.1753
  time to fit residues: 30.0360
Evaluate side-chains
  111 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 87
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 GLN
Chi-restraints excluded: chain A residue  153 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  389 VAL
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  153 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  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  486 LEU
Chi-restraints excluded: chain B residue  504 PHE
Chi-restraints excluded: chain B residue  550 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 124
   random chunks:
   chunk 114 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 97 optimal weight:    4.9990
   chunk 103 optimal weight:    8.9990
   chunk 27 optimal weight:    2.9990
   chunk 43 optimal weight:    9.9990
   chunk 20 optimal weight:    5.9990
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    1.7988

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.101590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.076556 restraints weight = 28344.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.076310 restraints weight = 16439.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.076399 restraints weight = 13030.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3180
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3689

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= 0.137
  Angle     :  0.642   9.511  14020  Z= 0.317
  Chirality :  0.042   0.234   1634
  Planarity :  0.005   0.093   1702
  Dihedral  :  4.398  23.167   1352
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 21.05 %
    Favored  : 76.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.87 (0.25), residues: 1222
  helix:  1.30 (0.18), residues: 928
  sheet:  None (None), residues: 0
  loop : -1.75 (0.40), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP A 685 
 HIS   0.002   0.001   HIS A 151 
 PHE   0.017   0.001   PHE A 504 
 TYR   0.013   0.001   TYR A 479 
 ARG   0.009   0.000   ARG B 554 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03895 (  621)
  hydrogen bonds       : angle       3.45306 ( 1809)
  SS BOND              : bond        0.00253 (    3)
  SS BOND              : angle       0.66027 (    6)
  covalent geometry    : bond        0.00315 (10302)
  covalent geometry    : angle       0.64208 (14014)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3055.91 seconds
wall clock time: 54 minutes 52.93 seconds (3292.93 seconds total)