Starting phenix.real_space_refine
on Fri Aug 22 22:05:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gs4_34220/08_2025/8gs4_34220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gs4_34220/08_2025/8gs4_34220.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/8gs4_34220/08_2025/8gs4_34220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gs4_34220/08_2025/8gs4_34220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gs4_34220/08_2025/8gs4_34220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gs4_34220/08_2025/8gs4_34220.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.085
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      36      5.16       5
     C    5288      2.51       5
     N    1412      2.21       5
     O    1514      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8250
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 525, 4125
          Classifications: {'peptide': 525}
          Link IDs: {'PTRANS': 34, 'TRANS': 490}
          Chain breaks: 3
  Restraints were copied for chains:
    B
  Time building chain proxies: 2.48, per 1000 atoms: 0.30
  Number of scatterers: 8250
  At special positions: 0
  Unit cell: (65.32, 153.64, 81.88, 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      36     16.00
     O    1514      8.00
     N    1412      7.00
     C    5288      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 106 " - pdb=" SG  CYS A 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 317 " - pdb=" SG  CYS A 328 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 487 " - pdb=" SG  CYS A 521 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 106 " - pdb=" SG  CYS B 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 317 " - pdb=" SG  CYS B 328 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 487 " - pdb=" SG  CYS B 521 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.45
  Conformation dependent library (CDL) restraints added in 311.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1932

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 12 sheets defined
      34.1% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 126
      removed outlier: 3.564A  pdb=" N   THR A 124 " --> pdb=" O   PRO A 120 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ASN A 126 " --> pdb=" O   TRP A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 132
      removed outlier: 3.716A  pdb=" N   THR A 132 " --> pdb=" O   GLU A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 197
      removed outlier: 3.859A  pdb=" N   ASP A 197 " --> pdb=" O   ASN A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 205
      removed outlier: 3.981A  pdb=" N   GLY A 205 " --> pdb=" O   LEU A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 221
      removed outlier: 3.893A  pdb=" N   GLY A 220 " --> pdb=" O   GLY A 217 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   PHE A 221 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 217 through 221'
    Processing helix  chain 'A' and resid 232 through 248
      removed outlier: 3.598A  pdb=" N   LEU A 236 " --> pdb=" O   ASN A 232 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 267
      No H-bonds generated for 'chain 'A' and resid 265 through 267'
    Processing helix  chain 'A' and resid 268 through 273
      removed outlier: 3.799A  pdb=" N   ASN A 272 " --> pdb=" O   ALA A 268 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU A 273 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 268 through 273'
    Processing helix  chain 'A' and resid 303 through 309
      removed outlier: 3.759A  pdb=" N   TYR A 307 " --> pdb=" O   GLN A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 330
    Processing helix  chain 'A' and resid 363 through 368
    Processing helix  chain 'A' and resid 405 through 417
      removed outlier: 4.100A  pdb=" N   VAL A 410 " --> pdb=" O   PHE A 406 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   SER A 411 " --> pdb=" O   ASP A 407 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ASN A 412 " --> pdb=" O   PHE A 408 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   VAL A 414 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 435
      removed outlier: 4.596A  pdb=" N   LEU A 427 " --> pdb=" O   GLY A 423 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   GLU A 429 " --> pdb=" O   ASP A 425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 437 through 441
      removed outlier: 4.163A  pdb=" N   ARG A 441 " --> pdb=" O   TRP A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 453
    Processing helix  chain 'A' and resid 454 through 460
      removed outlier: 3.923A  pdb=" N   HIS A 458 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN A 459 " --> pdb=" O   PHE A 455 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TRP A 460 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 454 through 460'
    Processing helix  chain 'A' and resid 463 through 474
      removed outlier: 3.536A  pdb=" N   LEU A 470 " --> pdb=" O   ALA A 466 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   TYR A 474 " --> pdb=" O   LEU A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 509
    Processing helix  chain 'A' and resid 510 through 514
      removed outlier: 3.635A  pdb=" N   VAL A 513 " --> pdb=" O   VAL A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 545
      removed outlier: 4.160A  pdb=" N   LEU A 530 " --> pdb=" O   ASN A 526 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER A 531 " --> pdb=" O   ASP A 527 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA A 532 " --> pdb=" O   VAL A 528 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL A 533 " --> pdb=" O   MET A 529 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   TRP A 538 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR A 539 " --> pdb=" O   MET A 535 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   ALA A 542 " --> pdb=" O   TRP A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 604
      removed outlier: 3.628A  pdb=" N   LEU A 604 " --> pdb=" O   PHE A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 609
      removed outlier: 3.971A  pdb=" N   LEU A 608 " --> pdb=" O   LEU A 604 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   HIS A 609 " --> pdb=" O   VAL A 605 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 604 through 609'
    Processing helix  chain 'B' and resid 120 through 126
      removed outlier: 3.564A  pdb=" N   THR B 124 " --> pdb=" O   PRO B 120 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN B 126 " --> pdb=" O   TRP B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 132
      removed outlier: 3.716A  pdb=" N   THR B 132 " --> pdb=" O   GLU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 193 through 197
      removed outlier: 3.859A  pdb=" N   ASP B 197 " --> pdb=" O   ASN B 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 199 through 205
      removed outlier: 3.981A  pdb=" N   GLY B 205 " --> pdb=" O   LEU B 201 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 221
      removed outlier: 3.892A  pdb=" N   GLY B 220 " --> pdb=" O   GLY B 217 " (cutoff:3.500A)
      removed outlier: 4.247A  pdb=" N   PHE B 221 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 217 through 221'
    Processing helix  chain 'B' and resid 232 through 248
      removed outlier: 3.599A  pdb=" N   LEU B 236 " --> pdb=" O   ASN B 232 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 267
      No H-bonds generated for 'chain 'B' and resid 265 through 267'
    Processing helix  chain 'B' and resid 268 through 273
      removed outlier: 3.799A  pdb=" N   ASN B 272 " --> pdb=" O   ALA B 268 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LEU B 273 " --> pdb=" O   SER B 269 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 268 through 273'
    Processing helix  chain 'B' and resid 303 through 309
      removed outlier: 3.758A  pdb=" N   TYR B 307 " --> pdb=" O   GLN B 303 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 330
    Processing helix  chain 'B' and resid 363 through 368
      removed outlier: 3.504A  pdb=" N   MET B 368 " --> pdb=" O   PRO B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 417
      removed outlier: 4.091A  pdb=" N   VAL B 410 " --> pdb=" O   PHE B 406 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   SER B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ASN B 412 " --> pdb=" O   PHE B 408 " (cutoff:3.500A)
      removed outlier: 4.502A  pdb=" N   VAL B 414 " --> pdb=" O   VAL B 410 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 423 through 435
      removed outlier: 4.596A  pdb=" N   LEU B 427 " --> pdb=" O   GLY B 423 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   GLU B 429 " --> pdb=" O   ASP B 425 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 437 through 441
      removed outlier: 4.163A  pdb=" N   ARG B 441 " --> pdb=" O   TRP B 438 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 450 through 453
    Processing helix  chain 'B' and resid 454 through 460
      removed outlier: 3.924A  pdb=" N   HIS B 458 " --> pdb=" O   LEU B 454 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLN B 459 " --> pdb=" O   PHE B 455 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TRP B 460 " --> pdb=" O   THR B 456 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 454 through 460'
    Processing helix  chain 'B' and resid 463 through 474
      removed outlier: 3.534A  pdb=" N   LEU B 470 " --> pdb=" O   ALA B 466 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   TYR B 474 " --> pdb=" O   LEU B 470 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 509
    Processing helix  chain 'B' and resid 510 through 514
      removed outlier: 3.636A  pdb=" N   VAL B 513 " --> pdb=" O   VAL B 510 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 526 through 545
      removed outlier: 4.160A  pdb=" N   LEU B 530 " --> pdb=" O   ASN B 526 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   SER B 531 " --> pdb=" O   ASP B 527 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ALA B 532 " --> pdb=" O   VAL B 528 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   VAL B 533 " --> pdb=" O   MET B 529 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   TRP B 538 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   THR B 539 " --> pdb=" O   MET B 535 " (cutoff:3.500A)
      removed outlier: 4.232A  pdb=" N   ALA B 542 " --> pdb=" O   TRP B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 594 through 604
      removed outlier: 3.626A  pdb=" N   LEU B 604 " --> pdb=" O   PHE B 600 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 604 through 609
      removed outlier: 3.966A  pdb=" N   LEU B 608 " --> pdb=" O   LEU B 604 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   HIS B 609 " --> pdb=" O   VAL B 605 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 604 through 609'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 46
    Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 57
      removed outlier: 3.720A  pdb=" N   VAL A  66 " --> pdb=" O   ARG A  56 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 72 through 73
    Processing sheet with id=AA4, first strand: chain 'A' and resid 208 through 210
      removed outlier: 4.213A  pdb=" N   ALA A 210 " --> pdb=" O   MET A 180 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LYS A 177 " --> pdb=" O   ASP A 255 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   GLU A 257 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   VAL A 179 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   ILE A 259 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU A 181 " --> pdb=" O   ILE A 259 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 210
      removed outlier: 4.213A  pdb=" N   ALA A 210 " --> pdb=" O   MET A 180 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   PHE A 262 " --> pdb=" O   VAL A 179 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   LEU A 181 " --> pdb=" O   PHE A 262 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 289 through 290
      removed outlier: 8.448A  pdb=" N   PHE A 483 " --> pdb=" O   ILE A 380 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   VAL A 382 " --> pdb=" O   PHE A 483 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 46
    Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 57
      removed outlier: 3.720A  pdb=" N   VAL B  66 " --> pdb=" O   ARG B  56 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 72 through 73
    Processing sheet with id=AB1, first strand: chain 'B' and resid 208 through 210
      removed outlier: 4.213A  pdb=" N   ALA B 210 " --> pdb=" O   MET B 180 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   LYS B 177 " --> pdb=" O   ASP B 255 " (cutoff:3.500A)
      removed outlier: 7.263A  pdb=" N   GLU B 257 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 8.177A  pdb=" N   VAL B 179 " --> pdb=" O   GLU B 257 " (cutoff:3.500A)
      removed outlier: 4.906A  pdb=" N   ILE B 259 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   LEU B 181 " --> pdb=" O   ILE B 259 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 210
      removed outlier: 4.213A  pdb=" N   ALA B 210 " --> pdb=" O   MET B 180 " (cutoff:3.500A)
      removed outlier: 7.169A  pdb=" N   PHE B 262 " --> pdb=" O   VAL B 179 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   LEU B 181 " --> pdb=" O   PHE B 262 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 289 through 290
      removed outlier: 8.448A  pdb=" N   PHE B 483 " --> pdb=" O   ILE B 380 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   VAL B 382 " --> pdb=" O   PHE B 483 " (cutoff:3.500A)

    157 hydrogen bonds defined for protein.
    411 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: 0.95

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2713
        1.34 -     1.46: 2003
        1.46 -     1.58: 3706
        1.58 -     1.70: 0
        1.70 -     1.82: 58
  Bond restraints: 8480
  Sorted by residual:
  bond pdb=" CG  LEU A 581 "
       pdb=" CD1 LEU A 581 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.46e+00
  bond pdb=" CG  LEU B 581 "
       pdb=" CD1 LEU B 581 "
    ideal  model  delta    sigma   weight residual
    1.521  1.469  0.052 3.30e-02 9.18e+02 2.46e+00
  bond pdb=" C   GLN B 549 "
       pdb=" N   PRO B 550 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.56e+00
  bond pdb=" C   GLN A 549 "
       pdb=" N   PRO A 550 "
    ideal  model  delta    sigma   weight residual
    1.334  1.363 -0.029 2.34e-02 1.83e+03 1.56e+00
  bond pdb=" CA  ASP A 440 "
       pdb=" CB  ASP A 440 "
    ideal  model  delta    sigma   weight residual
    1.524  1.540 -0.016 1.62e-02 3.81e+03 9.59e-01
  ... (remaining 8475 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.03: 11175
        2.03 -     4.07: 319
        4.07 -     6.10: 46
        6.10 -     8.14: 6
        8.14 -    10.17: 6
  Bond angle restraints: 11552
  Sorted by residual:
  angle pdb=" N   VAL B 359 "
        pdb=" CA  VAL B 359 "
        pdb=" C   VAL B 359 "
      ideal   model   delta    sigma   weight residual
     113.53  108.90    4.63 9.80e-01 1.04e+00 2.23e+01
  angle pdb=" N   VAL A 359 "
        pdb=" CA  VAL A 359 "
        pdb=" C   VAL A 359 "
      ideal   model   delta    sigma   weight residual
     113.53  108.90    4.63 9.80e-01 1.04e+00 2.23e+01
  angle pdb=" C   VAL A 461 "
        pdb=" N   ALA A 462 "
        pdb=" CA  ALA A 462 "
      ideal   model   delta    sigma   weight residual
     121.80  112.76    9.04 2.44e+00 1.68e-01 1.37e+01
  angle pdb=" C   VAL B 461 "
        pdb=" N   ALA B 462 "
        pdb=" CA  ALA B 462 "
      ideal   model   delta    sigma   weight residual
     121.80  112.76    9.04 2.44e+00 1.68e-01 1.37e+01
  angle pdb=" C   GLY A 545 "
        pdb=" N   ASP A 546 "
        pdb=" CA  ASP A 546 "
      ideal   model   delta    sigma   weight residual
     120.69  110.52   10.17 2.95e+00 1.15e-01 1.19e+01
  ... (remaining 11547 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.56: 4370
       15.56 -    31.11: 496
       31.11 -    46.67: 108
       46.67 -    62.22: 14
       62.22 -    77.78: 4
  Dihedral angle restraints: 4992
    sinusoidal: 1970
      harmonic: 3022
  Sorted by residual:
  dihedral pdb=" CA  ALA A 462 "
           pdb=" C   ALA A 462 "
           pdb=" N   PRO A 463 "
           pdb=" CA  PRO A 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.19   38.81     0      5.00e+00 4.00e-02 6.02e+01
  dihedral pdb=" CA  ALA B 462 "
           pdb=" C   ALA B 462 "
           pdb=" N   PRO B 463 "
           pdb=" CA  PRO B 463 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.19   38.81     0      5.00e+00 4.00e-02 6.02e+01
  dihedral pdb=" CB  CYS B 317 "
           pdb=" SG  CYS B 317 "
           pdb=" SG  CYS B 328 "
           pdb=" CB  CYS B 328 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  153.84  -60.84     1      1.00e+01 1.00e-02 4.92e+01
  ... (remaining 4989 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 637
       0.031 -    0.063: 383
       0.063 -    0.094: 127
       0.094 -    0.126: 74
       0.126 -    0.157: 15
  Chirality restraints: 1236
  Sorted by residual:
  chirality pdb=" CB  THR A 101 "
            pdb=" CA  THR A 101 "
            pdb=" OG1 THR A 101 "
            pdb=" CG2 THR A 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.15e-01
  chirality pdb=" CB  THR B 101 "
            pdb=" CA  THR B 101 "
            pdb=" OG1 THR B 101 "
            pdb=" CG2 THR B 101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.39    0.16 2.00e-01 2.50e+01 6.15e-01
  chirality pdb=" CA  LEU A 581 "
            pdb=" N   LEU A 581 "
            pdb=" C   LEU A 581 "
            pdb=" CB  LEU A 581 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.14e-01
  ... (remaining 1233 not shown)

  Planarity restraints: 1518
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 462 "    0.064 5.00e-02 4.00e+02   9.73e-02 1.51e+01
        pdb=" N   PRO A 463 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO A 463 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO A 463 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 462 "    0.064 5.00e-02 4.00e+02   9.73e-02 1.51e+01
        pdb=" N   PRO B 463 "   -0.168 5.00e-02 4.00e+02
        pdb=" CA  PRO B 463 "    0.051 5.00e-02 4.00e+02
        pdb=" CD  PRO B 463 "    0.053 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 298 "    0.021 2.00e-02 2.50e+03   2.04e-02 1.04e+01
        pdb=" CG  TRP B 298 "   -0.054 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 298 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 298 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 298 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 298 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 298 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 298 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 298 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 298 "    0.003 2.00e-02 2.50e+03
  ... (remaining 1515 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2002
        2.78 -     3.31: 7699
        3.31 -     3.84: 12585
        3.84 -     4.37: 14988
        4.37 -     4.90: 25900
  Nonbonded interactions: 63174
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 269 "
            pdb=" OG  SER A 299 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER B 269 "
            pdb=" OG  SER B 299 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   GLU A 327 "
            pdb=" NH2 ARG A 331 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   GLU B 327 "
            pdb=" NH2 ARG B 331 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   SER B 575 "
            pdb=" NZ  LYS B 578 "
     model   vdw
     2.271 3.120
  ... (remaining 63169 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain '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:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     8.100
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
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      :  0.004   0.052   8486  Z= 0.184
  Angle     :  0.838  10.174  11564  Z= 0.443
  Chirality :  0.048   0.157   1236
  Planarity :  0.007   0.097   1518
  Dihedral  : 13.581  77.781   3042
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.35 %
    Favored  : 86.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.70 (0.22), residues: 1034
  helix: -3.64 (0.23), residues: 266
  sheet: -3.45 (0.45), residues: 110
  loop : -2.97 (0.21), residues: 658

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 447 
 TYR   0.017   0.002   TYR B 580 
 PHE   0.026   0.002   PHE B 262 
 TRP   0.054   0.004   TRP B 298 
 HIS   0.006   0.001   HIS B 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8480)
  covalent geometry    : angle       0.83280 (11552)
  SS BOND              : bond        0.00182 (    6)
  SS BOND              : angle       2.88898 (   12)
  hydrogen bonds       : bond        0.22035 (  151)
  hydrogen bonds       : angle       8.76489 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  260 THR cc_start: 0.8752 (m) cc_final: 0.8511 (p)
REVERT: B  260 THR cc_start: 0.8739 (m) cc_final: 0.8499 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 114
  average time/residue: 0.0757
  time to fit residues: 12.2441
Evaluate side-chains
  94 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    6.9990
   overall best weight:    1.9788

-------------------------------------------------------------------------------
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 = 0.4232 r_free = 0.4232 target = 0.197313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.160333 restraints weight = 10851.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.160486 restraints weight = 8873.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.161985 restraints weight = 8561.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.163097 restraints weight = 6596.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.163630 restraints weight = 6066.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.1096

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8486  Z= 0.193
  Angle     :  0.770   8.860  11564  Z= 0.391
  Chirality :  0.048   0.149   1236
  Planarity :  0.007   0.098   1518
  Dihedral  :  6.595  39.811   1140
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.96 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  8.85 %
    Favored  : 90.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -4.32 (0.23), residues: 1034
  helix: -2.99 (0.25), residues: 258
  sheet: -3.67 (0.42), residues: 122
  loop : -2.77 (0.22), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  83 
 TYR   0.015   0.002   TYR B 214 
 PHE   0.021   0.002   PHE B 262 
 TRP   0.031   0.002   TRP A 298 
 HIS   0.005   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 8480)
  covalent geometry    : angle       0.76913 (11552)
  SS BOND              : bond        0.00145 (    6)
  SS BOND              : angle       1.50723 (   12)
  hydrogen bonds       : bond        0.04455 (  151)
  hydrogen bonds       : angle       6.27569 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 102
  time to evaluate  : 0.223 
Fit side-chains
REVERT: A  335 ARG cc_start: 0.8114 (tpp-160) cc_final: 0.7871 (tpt170)
REVERT: B  335 ARG cc_start: 0.8116 (tpp-160) cc_final: 0.7869 (tpt170)
  outliers start: 10
  outliers final: 10
  residues processed: 108
  average time/residue: 0.0661
  time to fit residues: 10.3051
Evaluate side-chains
  110 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  529 MET
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  529 MET
Chi-restraints excluded: chain B residue  585 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 78 optimal weight:    0.1980
   chunk 6 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 72 optimal weight:    2.9990
   chunk 66 optimal weight:    6.9990
   chunk 95 optimal weight:    0.0470
   chunk 84 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 73 optimal weight:    5.9990
   chunk 52 optimal weight:   20.0000
   overall best weight:    0.8082

-------------------------------------------------------------------------------
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 = 0.4278 r_free = 0.4278 target = 0.202046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3915 r_free = 0.3915 target = 0.166092 restraints weight = 10650.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.165247 restraints weight = 9497.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.166997 restraints weight = 9642.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.168133 restraints weight = 7264.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.168992 restraints weight = 6684.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7326
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8486  Z= 0.122
  Angle     :  0.662   7.504  11564  Z= 0.335
  Chirality :  0.044   0.150   1236
  Planarity :  0.006   0.087   1518
  Dihedral  :  5.896  39.172   1140
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.93 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 13.33 %
    Favored  : 85.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.78 (0.24), residues: 1034
  helix: -2.49 (0.29), residues: 256
  sheet: -3.02 (0.47), residues: 106
  loop : -2.55 (0.23), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  83 
 TYR   0.011   0.001   TYR A 481 
 PHE   0.013   0.001   PHE A 483 
 TRP   0.013   0.001   TRP A 298 
 HIS   0.003   0.001   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 8480)
  covalent geometry    : angle       0.66177 (11552)
  SS BOND              : bond        0.00285 (    6)
  SS BOND              : angle       0.93022 (   12)
  hydrogen bonds       : bond        0.03512 (  151)
  hydrogen bonds       : angle       5.61753 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 108
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 TYR cc_start: 0.8525 (m-80) cc_final: 0.8227 (m-10)
REVERT: B  147 TYR cc_start: 0.8526 (m-80) cc_final: 0.8223 (m-10)
  outliers start: 14
  outliers final: 8
  residues processed: 120
  average time/residue: 0.0735
  time to fit residues: 12.4871
Evaluate side-chains
  103 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 95
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  440 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 6 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 4 optimal weight:    0.0970
   chunk 57 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 30 optimal weight:    6.9990
   chunk 15 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 60 optimal weight:    2.9990
   chunk 63 optimal weight:    5.9990
   overall best weight:    1.3582

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

Flipped N/Q/H residues before XYZ refinement:
A 383 ASN
B 383 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.200052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.163904 restraints weight = 11050.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.164919 restraints weight = 9066.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.166487 restraints weight = 8305.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.167470 restraints weight = 6191.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.168107 restraints weight = 5780.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8486  Z= 0.149
  Angle     :  0.686   8.140  11564  Z= 0.344
  Chirality :  0.045   0.154   1236
  Planarity :  0.006   0.089   1518
  Dihedral  :  5.920  39.516   1140
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.70 %
    Favored  : 88.30 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 15.86 %
    Favored  : 82.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.61 (0.24), residues: 1034
  helix: -2.22 (0.30), residues: 250
  sheet: -3.13 (0.45), residues: 106
  loop : -2.47 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.013   0.001   TYR A 481 
 PHE   0.016   0.002   PHE B 262 
 TRP   0.011   0.001   TRP A 570 
 HIS   0.004   0.001   HIS B 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 8480)
  covalent geometry    : angle       0.68607 (11552)
  SS BOND              : bond        0.00250 (    6)
  SS BOND              : angle       0.98725 (   12)
  hydrogen bonds       : bond        0.03706 (  151)
  hydrogen bonds       : angle       5.49096 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8328 (mm) cc_final: 0.7972 (mt)
REVERT: A  133 TYR cc_start: 0.7165 (OUTLIER) cc_final: 0.6515 (t80)
REVERT: B  102 LEU cc_start: 0.8318 (mm) cc_final: 0.7962 (mt)
REVERT: B  133 TYR cc_start: 0.7169 (OUTLIER) cc_final: 0.6515 (t80)
  outliers start: 18
  outliers final: 12
  residues processed: 114
  average time/residue: 0.0696
  time to fit residues: 11.4417
Evaluate side-chains
  102 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 88
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  585 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 101 optimal weight:    4.9990
   chunk 46 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 11 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 90 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 87 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0050
   chunk 86 optimal weight:    4.9990
   overall best weight:    2.1400

-------------------------------------------------------------------------------
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 = 0.4231 r_free = 0.4231 target = 0.196970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.159382 restraints weight = 10960.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.157725 restraints weight = 9363.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.159303 restraints weight = 9299.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.160762 restraints weight = 7184.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.161498 restraints weight = 6467.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7463
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8486  Z= 0.201
  Angle     :  0.737   8.745  11564  Z= 0.373
  Chirality :  0.047   0.154   1236
  Planarity :  0.006   0.093   1518
  Dihedral  :  6.250  40.685   1140
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.96 %
    Favored  : 87.04 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 17.36 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.71 (0.24), residues: 1034
  helix: -2.29 (0.30), residues: 250
  sheet: -3.53 (0.41), residues: 118
  loop : -2.43 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  83 
 TYR   0.017   0.002   TYR A 481 
 PHE   0.022   0.002   PHE A 262 
 TRP   0.012   0.002   TRP B 460 
 HIS   0.008   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00480 ( 8480)
  covalent geometry    : angle       0.73681 (11552)
  SS BOND              : bond        0.00196 (    6)
  SS BOND              : angle       1.20285 (   12)
  hydrogen bonds       : bond        0.04153 (  151)
  hydrogen bonds       : angle       5.64625 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.193 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8422 (mm) cc_final: 0.8045 (mt)
REVERT: A  133 TYR cc_start: 0.7344 (OUTLIER) cc_final: 0.6564 (t80)
REVERT: A  570 TRP cc_start: 0.4784 (t-100) cc_final: 0.4167 (t-100)
REVERT: B  102 LEU cc_start: 0.8414 (mm) cc_final: 0.8034 (mt)
REVERT: B  133 TYR cc_start: 0.7346 (OUTLIER) cc_final: 0.6563 (t80)
REVERT: B  570 TRP cc_start: 0.4787 (t-100) cc_final: 0.4174 (t-100)
  outliers start: 28
  outliers final: 17
  residues processed: 115
  average time/residue: 0.0524
  time to fit residues: 9.0254
Evaluate side-chains
  113 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  585 LEU
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  363 ASP
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  585 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 81 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0010
   chunk 21 optimal weight:    6.9990
   chunk 6 optimal weight:    3.9990
   chunk 58 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   overall best weight:    0.9190

-------------------------------------------------------------------------------
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 = 0.4272 r_free = 0.4272 target = 0.201230 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.164398 restraints weight = 10834.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.166549 restraints weight = 10786.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.167772 restraints weight = 9378.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3934 r_free = 0.3934 target = 0.169542 restraints weight = 6789.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.169942 restraints weight = 5884.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8486  Z= 0.126
  Angle     :  0.661   8.542  11564  Z= 0.332
  Chirality :  0.044   0.134   1236
  Planarity :  0.006   0.085   1518
  Dihedral  :  5.742  39.570   1140
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.41 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 18.74 %
    Favored  : 78.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.55 (0.25), residues: 1034
  helix: -2.08 (0.32), residues: 248
  sheet: -3.31 (0.43), residues: 108
  loop : -2.42 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  83 
 TYR   0.017   0.001   TYR B 418 
 PHE   0.012   0.001   PHE B 262 
 TRP   0.007   0.001   TRP B 122 
 HIS   0.004   0.001   HIS A 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8480)
  covalent geometry    : angle       0.66104 (11552)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       0.85849 (   12)
  hydrogen bonds       : bond        0.03342 (  151)
  hydrogen bonds       : angle       5.27220 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 98
  time to evaluate  : 0.190 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8243 (mm) cc_final: 0.7955 (mt)
REVERT: A  133 TYR cc_start: 0.7281 (OUTLIER) cc_final: 0.6546 (t80)
REVERT: A  448 ARG cc_start: 0.6360 (ttt180) cc_final: 0.6059 (ttm-80)
REVERT: A  570 TRP cc_start: 0.4691 (t-100) cc_final: 0.4166 (t-100)
REVERT: B  102 LEU cc_start: 0.8247 (mm) cc_final: 0.7959 (mt)
REVERT: B  133 TYR cc_start: 0.7283 (OUTLIER) cc_final: 0.6549 (t80)
REVERT: B  448 ARG cc_start: 0.6353 (ttt180) cc_final: 0.6053 (ttm-80)
REVERT: B  570 TRP cc_start: 0.4699 (t-100) cc_final: 0.4174 (t-100)
  outliers start: 25
  outliers final: 18
  residues processed: 117
  average time/residue: 0.0616
  time to fit residues: 10.6705
Evaluate side-chains
  114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  446 MET
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  446 MET
Chi-restraints excluded: chain B residue  568 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 94 optimal weight:    6.9990
   chunk 5 optimal weight:    9.9990
   chunk 72 optimal weight:    0.6980
   chunk 82 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   chunk 95 optimal weight:    0.6980
   chunk 96 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   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 = 0.4264 r_free = 0.4264 target = 0.200780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.163806 restraints weight = 10890.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.162251 restraints weight = 9039.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.163930 restraints weight = 9680.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.165172 restraints weight = 7033.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.165821 restraints weight = 6233.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3904
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7380
moved from start:          0.2265

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8486  Z= 0.135
  Angle     :  0.678   9.738  11564  Z= 0.339
  Chirality :  0.044   0.137   1236
  Planarity :  0.005   0.085   1518
  Dihedral  :  5.708  39.598   1140
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.32 %
    Favored  : 88.68 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 18.74 %
    Favored  : 77.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.49 (0.25), residues: 1034
  helix: -2.02 (0.32), residues: 248
  sheet: -3.25 (0.43), residues: 108
  loop : -2.39 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  83 
 TYR   0.014   0.001   TYR B 418 
 PHE   0.018   0.002   PHE B 541 
 TRP   0.007   0.001   TRP B 460 
 HIS   0.004   0.001   HIS B 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8480)
  covalent geometry    : angle       0.67816 (11552)
  SS BOND              : bond        0.00274 (    6)
  SS BOND              : angle       0.90706 (   12)
  hydrogen bonds       : bond        0.03394 (  151)
  hydrogen bonds       : angle       5.20143 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 90
  time to evaluate  : 0.210 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8280 (mm) cc_final: 0.7999 (mt)
REVERT: A  133 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6546 (t80)
REVERT: A  448 ARG cc_start: 0.6451 (ttt180) cc_final: 0.6199 (ttm-80)
REVERT: B  102 LEU cc_start: 0.8272 (mm) cc_final: 0.7992 (mt)
REVERT: B  133 TYR cc_start: 0.7276 (OUTLIER) cc_final: 0.6546 (t80)
REVERT: B  448 ARG cc_start: 0.6443 (ttt180) cc_final: 0.6189 (ttm-80)
  outliers start: 34
  outliers final: 22
  residues processed: 116
  average time/residue: 0.0593
  time to fit residues: 10.1983
Evaluate side-chains
  105 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 81
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  446 MET
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  446 MET
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    8.9990
   chunk 81 optimal weight:    0.6980
   chunk 11 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 96 optimal weight:    0.7980
   chunk 98 optimal weight:    3.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.8986

-------------------------------------------------------------------------------
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 = 0.4242 r_free = 0.4242 target = 0.198340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.160611 restraints weight = 11006.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.158982 restraints weight = 9472.985|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.160461 restraints weight = 10052.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.161777 restraints weight = 7472.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.162507 restraints weight = 6702.550|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7446
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8486  Z= 0.184
  Angle     :  0.735  10.470  11564  Z= 0.367
  Chirality :  0.046   0.180   1236
  Planarity :  0.006   0.090   1518
  Dihedral  :  5.973  40.445   1140
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  3.45 %
    Allowed  : 19.31 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.51 (0.24), residues: 1034
  helix: -2.08 (0.31), residues: 250
  sheet: -3.16 (0.45), residues: 106
  loop : -2.41 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  83 
 TYR   0.016   0.002   TYR A 481 
 PHE   0.020   0.002   PHE B 262 
 TRP   0.010   0.001   TRP B 570 
 HIS   0.007   0.001   HIS A 458 

Details of bonding type rmsd
  covalent geometry    : bond        0.00442 ( 8480)
  covalent geometry    : angle       0.73429 (11552)
  SS BOND              : bond        0.00227 (    6)
  SS BOND              : angle       1.06742 (   12)
  hydrogen bonds       : bond        0.03786 (  151)
  hydrogen bonds       : angle       5.44242 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.284 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8328 (mm) cc_final: 0.8077 (mt)
REVERT: A  133 TYR cc_start: 0.7382 (OUTLIER) cc_final: 0.6587 (t80)
REVERT: A  368 MET cc_start: 0.5941 (OUTLIER) cc_final: 0.5726 (ttt)
REVERT: B  102 LEU cc_start: 0.8321 (mm) cc_final: 0.8070 (mt)
REVERT: B  133 TYR cc_start: 0.7379 (OUTLIER) cc_final: 0.6583 (t80)
  outliers start: 30
  outliers final: 27
  residues processed: 108
  average time/residue: 0.0575
  time to fit residues: 9.3208
Evaluate side-chains
  118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 88
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 THR
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  368 MET
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  446 MET
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain B residue   46 THR
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  293 THR
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  305 LEU
Chi-restraints excluded: chain B residue  363 ASP
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  446 MET
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 34 optimal weight:    8.9990
   chunk 82 optimal weight:    7.9990
   chunk 70 optimal weight:    0.1980
   chunk 37 optimal weight:    3.9990
   chunk 51 optimal weight:    0.8980
   chunk 23 optimal weight:    0.0870
   chunk 78 optimal weight:    8.9990
   chunk 4 optimal weight:    0.0670
   chunk 17 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.2696

-------------------------------------------------------------------------------
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 = 0.4308 r_free = 0.4308 target = 0.205343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.172526 restraints weight = 10944.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.171921 restraints weight = 9571.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.173672 restraints weight = 8305.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.174198 restraints weight = 6739.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.174549 restraints weight = 6817.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8486  Z= 0.111
  Angle     :  0.664  11.879  11564  Z= 0.327
  Chirality :  0.043   0.156   1236
  Planarity :  0.005   0.077   1518
  Dihedral  :  5.260  38.995   1140
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.35 %
    Favored  : 89.65 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 19.43 %
    Favored  : 77.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.48 (0.24), residues: 1034
  helix: -2.10 (0.30), residues: 274
  sheet: -3.02 (0.45), residues: 106
  loop : -2.37 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.011   0.001   TYR A 418 
 PHE   0.010   0.001   PHE A 541 
 TRP   0.010   0.001   TRP B 122 
 HIS   0.003   0.001   HIS B 609 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 8480)
  covalent geometry    : angle       0.66415 (11552)
  SS BOND              : bond        0.00380 (    6)
  SS BOND              : angle       0.66424 (   12)
  hydrogen bonds       : bond        0.03000 (  151)
  hydrogen bonds       : angle       5.05031 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 94
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8133 (mm) cc_final: 0.7852 (mt)
REVERT: A  133 TYR cc_start: 0.7274 (OUTLIER) cc_final: 0.6550 (t80)
REVERT: B  102 LEU cc_start: 0.8131 (mm) cc_final: 0.7853 (mt)
REVERT: B  133 TYR cc_start: 0.7269 (OUTLIER) cc_final: 0.6543 (t80)
  outliers start: 31
  outliers final: 18
  residues processed: 118
  average time/residue: 0.0592
  time to fit residues: 10.7254
Evaluate side-chains
  103 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  118 MET
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  568 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 101 optimal weight:    0.0980
   chunk 90 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 86 optimal weight:    0.1980
   chunk 29 optimal weight:    4.9990
   chunk 1 optimal weight:    0.5980
   chunk 53 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 99 optimal weight:    5.9990
   overall best weight:    0.5582

-------------------------------------------------------------------------------
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 = 0.4296 r_free = 0.4296 target = 0.204649 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.167359 restraints weight = 10827.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.165717 restraints weight = 9203.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.166932 restraints weight = 9599.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.168735 restraints weight = 7367.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.169350 restraints weight = 6409.204|
|-----------------------------------------------------------------------------|
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7305
moved from start:          0.2766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8486  Z= 0.117
  Angle     :  0.689  11.583  11564  Z= 0.333
  Chirality :  0.043   0.155   1236
  Planarity :  0.005   0.082   1518
  Dihedral  :  5.195  38.718   1140
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.54 %
    Favored  : 89.46 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.46 %
    Favored  : 77.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.30 (0.24), residues: 1034
  helix: -1.87 (0.30), residues: 274
  sheet: -2.97 (0.44), residues: 106
  loop : -2.28 (0.23), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.012   0.001   TYR A 418 
 PHE   0.008   0.001   PHE B 541 
 TRP   0.017   0.001   TRP A 244 
 HIS   0.003   0.001   HIS B 471 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8480)
  covalent geometry    : angle       0.68865 (11552)
  SS BOND              : bond        0.00325 (    6)
  SS BOND              : angle       0.77359 (   12)
  hydrogen bonds       : bond        0.02956 (  151)
  hydrogen bonds       : angle       5.06071 (  411)

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

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

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2068 Ramachandran restraints generated.
    1034 Oldfield, 0 Emsley, 1034 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.183 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8169 (mm) cc_final: 0.7906 (mt)
REVERT: A  133 TYR cc_start: 0.7155 (OUTLIER) cc_final: 0.6412 (t80)
REVERT: A  335 ARG cc_start: 0.8082 (tpm170) cc_final: 0.7490 (tpp-160)
REVERT: A  368 MET cc_start: 0.5808 (ttt) cc_final: 0.5589 (mtt)
REVERT: A  448 ARG cc_start: 0.6368 (ttt180) cc_final: 0.6050 (ttm-80)
REVERT: B  102 LEU cc_start: 0.8175 (mm) cc_final: 0.7914 (mt)
REVERT: B  133 TYR cc_start: 0.7149 (OUTLIER) cc_final: 0.6404 (t80)
REVERT: B  335 ARG cc_start: 0.8077 (tpm170) cc_final: 0.7489 (tpp-160)
REVERT: B  448 ARG cc_start: 0.6364 (ttt180) cc_final: 0.6047 (ttm-80)
  outliers start: 21
  outliers final: 16
  residues processed: 107
  average time/residue: 0.0593
  time to fit residues: 9.3634
Evaluate side-chains
  106 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  106 CYS
Chi-restraints excluded: chain A residue  133 TYR
Chi-restraints excluded: chain A residue  224 THR
Chi-restraints excluded: chain A residue  264 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain B residue  106 CYS
Chi-restraints excluded: chain B residue  133 TYR
Chi-restraints excluded: chain B residue  224 THR
Chi-restraints excluded: chain B residue  264 SER
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  355 VAL
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  568 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0870
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0470
   chunk 63 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0870
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.4434

-------------------------------------------------------------------------------
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 = 0.4315 r_free = 0.4315 target = 0.206738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.169713 restraints weight = 10991.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.168265 restraints weight = 9100.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.169309 restraints weight = 9672.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.170932 restraints weight = 7466.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.171512 restraints weight = 6611.746|
|-----------------------------------------------------------------------------|
r_work (final): 0.3959
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7290
moved from start:          0.2983

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8486  Z= 0.114
  Angle     :  0.696  12.459  11564  Z= 0.334
  Chirality :  0.043   0.151   1236
  Planarity :  0.005   0.079   1518
  Dihedral  :  5.029  39.124   1140
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.86 %
    Favored  : 90.14 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 20.80 %
    Favored  : 76.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.15 (0.25), residues: 1034
  helix: -1.74 (0.30), residues: 274
  sheet: -2.96 (0.43), residues: 122
  loop : -2.13 (0.24), residues: 638

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  83 
 TYR   0.009   0.001   TYR A 147 
 PHE   0.018   0.001   PHE B 541 
 TRP   0.015   0.001   TRP B 244 
 HIS   0.003   0.001   HIS B 500 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 8480)
  covalent geometry    : angle       0.69601 (11552)
  SS BOND              : bond        0.00354 (    6)
  SS BOND              : angle       0.69250 (   12)
  hydrogen bonds       : bond        0.02859 (  151)
  hydrogen bonds       : angle       4.97334 (  411)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1085.85 seconds
wall clock time: 19 minutes 25.34 seconds (1165.34 seconds total)