Starting phenix.real_space_refine
on Sat Jul 26 01:16:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gs4_34220/07_2025/8gs4_34220.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gs4_34220/07_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_34220/07_2025/8gs4_34220.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gs4_34220/07_2025/8gs4_34220.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gs4_34220/07_2025/8gs4_34220.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gs4_34220/07_2025/8gs4_34220.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 7.61, per 1000 atoms: 0.92
  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: 1.85
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.85
  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: 2.00

  Time building geometry restraints manager: 2.23 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: 0.04
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:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     23.990
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.960
-------------------------------------------------------------------------------
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 : 11.71
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.054   0.004   TRP B 298 
 HIS   0.006   0.001   HIS B 582 
 PHE   0.026   0.002   PHE B 262 
 TYR   0.017   0.002   TYR B 580 
 ARG   0.003   0.000   ARG A 447 

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

*********************** 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  : 0.889 
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: 0.1883
  time to fit residues: 30.4458
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  : 0.930 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    0.2980
   chunk 78 optimal weight:    5.9990
   chunk 43 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 53 optimal weight:    9.9990
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 49 optimal weight:    5.9990
   chunk 60 optimal weight:    1.9990
   chunk 94 optimal weight:    4.9990
   overall best weight:    2.4588

-------------------------------------------------------------------------------
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 = 0.4217 r_free = 0.4217 target = 0.195734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.158689 restraints weight = 10789.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.158960 restraints weight = 8857.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160404 restraints weight = 8610.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3849
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7443
moved from start:          0.1129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   8486  Z= 0.224
  Angle     :  0.802   9.355  11564  Z= 0.408
  Chirality :  0.049   0.151   1236
  Planarity :  0.007   0.100   1518
  Dihedral  :  6.787  40.136   1140
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 13.73 %
    Favored  : 86.27 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.89 %
    Favored  : 88.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.41 (0.22), residues: 1034
  helix: -3.09 (0.24), residues: 258
  sheet: -3.71 (0.42), residues: 122
  loop : -2.82 (0.22), residues: 654

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.003   TRP B 298 
 HIS   0.007   0.001   HIS A 458 
 PHE   0.024   0.002   PHE A 262 
 TYR   0.018   0.002   TYR B 214 
 ARG   0.003   0.001   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04893 (  151)
  hydrogen bonds       : angle       6.45036 (  411)
  SS BOND              : bond        0.00138 (    6)
  SS BOND              : angle       1.62893 (   12)
  covalent geometry    : bond        0.00530 ( 8480)
  covalent geometry    : angle       0.80054 (11552)

*********************** 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
  111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 0.909 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1724
  time to fit residues: 26.9984
Evaluate side-chains
  105 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 0.940 
-------------------------------------------------------------------------------
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 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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 32 optimal weight:    5.9990
   chunk 34 optimal weight:    8.9990
   chunk 8 optimal weight:    3.9990
   chunk 59 optimal weight:    0.8980
   chunk 87 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 75 optimal weight:    3.9990
   chunk 43 optimal weight:    0.0040
   overall best weight:    0.8996

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.200624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.164757 restraints weight = 10891.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.165343 restraints weight = 8895.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.166984 restraints weight = 8404.982|
|-----------------------------------------------------------------------------|
r_work (final): 0.3920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.1449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8486  Z= 0.129
  Angle     :  0.679   7.745  11564  Z= 0.344
  Chirality :  0.045   0.134   1236
  Planarity :  0.006   0.089   1518
  Dihedral  :  6.119  39.480   1140
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.93 %
    Favored  : 89.07 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 13.91 %
    Favored  : 84.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.94 (0.24), residues: 1034
  helix: -2.62 (0.28), residues: 260
  sheet: -3.11 (0.47), residues: 106
  loop : -2.66 (0.22), residues: 668

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 298 
 HIS   0.003   0.001   HIS B 609 
 PHE   0.013   0.001   PHE A 262 
 TYR   0.010   0.001   TYR B 481 
 ARG   0.002   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03706 (  151)
  hydrogen bonds       : angle       5.76975 (  411)
  SS BOND              : bond        0.00237 (    6)
  SS BOND              : angle       1.04189 (   12)
  covalent geometry    : bond        0.00300 ( 8480)
  covalent geometry    : angle       0.67808 (11552)

*********************** 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
  124 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 108
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 TYR cc_start: 0.8576 (m-80) cc_final: 0.8237 (m-10)
REVERT: A  503 GLU cc_start: 0.6922 (pm20) cc_final: 0.5734 (tm-30)
REVERT: B  147 TYR cc_start: 0.8576 (m-80) cc_final: 0.8237 (m-10)
REVERT: B  503 GLU cc_start: 0.6929 (pm20) cc_final: 0.5734 (tm-30)
  outliers start: 16
  outliers final: 10
  residues processed: 120
  average time/residue: 0.1932
  time to fit residues: 32.6886
Evaluate side-chains
  108 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.878 
-------------------------------------------------------------------------------
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  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  295 ILE
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  585 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 65 optimal weight:    4.9990
   chunk 79 optimal weight:    9.9990
   chunk 99 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 56 optimal weight:    4.9990
   chunk 80 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 95 optimal weight:    0.0770
   chunk 40 optimal weight:    3.9990
   chunk 83 optimal weight:    3.9990
   overall best weight:    1.7142

-------------------------------------------------------------------------------
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 = 0.198411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.161950 restraints weight = 10785.508|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.163039 restraints weight = 9068.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.164168 restraints weight = 8548.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3895
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8486  Z= 0.172
  Angle     :  0.712   8.273  11564  Z= 0.358
  Chirality :  0.046   0.161   1236
  Planarity :  0.006   0.092   1518
  Dihedral  :  6.182  39.926   1140
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.86 %
    Favored  : 81.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.81 (0.24), residues: 1034
  helix: -2.36 (0.29), residues: 254
  sheet: -3.23 (0.45), residues: 106
  loop : -2.61 (0.23), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B 570 
 HIS   0.006   0.001   HIS B 458 
 PHE   0.019   0.002   PHE A 262 
 TYR   0.015   0.001   TYR B 481 
 ARG   0.003   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03967 (  151)
  hydrogen bonds       : angle       5.66147 (  411)
  SS BOND              : bond        0.00210 (    6)
  SS BOND              : angle       1.12354 (   12)
  covalent geometry    : bond        0.00412 ( 8480)
  covalent geometry    : angle       0.71125 (11552)

*********************** 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
  118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 99
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8373 (mm) cc_final: 0.7998 (mt)
REVERT: A  133 TYR cc_start: 0.7314 (OUTLIER) cc_final: 0.6688 (t80)
REVERT: B  102 LEU cc_start: 0.8360 (mm) cc_final: 0.7982 (mt)
REVERT: B  133 TYR cc_start: 0.7316 (OUTLIER) cc_final: 0.6684 (t80)
  outliers start: 19
  outliers final: 15
  residues processed: 111
  average time/residue: 0.2239
  time to fit residues: 35.1628
Evaluate side-chains
  112 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
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  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  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  440 ASP
Chi-restraints excluded: chain B residue  529 MET
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 4 optimal weight:    0.0270
   chunk 22 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 68 optimal weight:    8.9990
   chunk 9 optimal weight:    0.9990
   chunk 55 optimal weight:    6.9990
   chunk 60 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.2042

-------------------------------------------------------------------------------
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 = 0.4257 r_free = 0.4257 target = 0.199958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.162503 restraints weight = 10838.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.161433 restraints weight = 9111.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.163040 restraints weight = 9942.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7412
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8486  Z= 0.141
  Angle     :  0.678   8.642  11564  Z= 0.342
  Chirality :  0.044   0.142   1236
  Planarity :  0.006   0.087   1518
  Dihedral  :  5.916  39.791   1140
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.80 %
    Favored  : 88.20 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 16.90 %
    Favored  : 79.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.61 (0.24), residues: 1034
  helix: -2.15 (0.31), residues: 250
  sheet: -3.19 (0.45), residues: 106
  loop : -2.48 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 460 
 HIS   0.006   0.001   HIS A 471 
 PHE   0.015   0.001   PHE A 262 
 TYR   0.012   0.001   TYR B 481 
 ARG   0.002   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03592 (  151)
  hydrogen bonds       : angle       5.42692 (  411)
  SS BOND              : bond        0.00269 (    6)
  SS BOND              : angle       0.94151 (   12)
  covalent geometry    : bond        0.00337 ( 8480)
  covalent geometry    : angle       0.67748 (11552)

*********************** 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
  128 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 100
  time to evaluate  : 0.877 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8326 (mm) cc_final: 0.8033 (mt)
REVERT: A  133 TYR cc_start: 0.7299 (OUTLIER) cc_final: 0.6557 (t80)
REVERT: A  570 TRP cc_start: 0.4666 (t-100) cc_final: 0.4004 (t-100)
REVERT: B  102 LEU cc_start: 0.8328 (mm) cc_final: 0.8035 (mt)
REVERT: B  133 TYR cc_start: 0.7296 (OUTLIER) cc_final: 0.6553 (t80)
REVERT: B  570 TRP cc_start: 0.4679 (t-100) cc_final: 0.4039 (t-100)
  outliers start: 28
  outliers final: 20
  residues processed: 120
  average time/residue: 0.1906
  time to fit residues: 33.4785
Evaluate side-chains
  118 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 1.028 
-------------------------------------------------------------------------------
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  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  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  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 19 optimal weight:    3.9990
   chunk 14 optimal weight:    0.0270
   chunk 57 optimal weight:   10.0000
   chunk 50 optimal weight:    4.9990
   chunk 98 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 35 optimal weight:    0.8980
   chunk 52 optimal weight:   10.0000
   chunk 5 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:    7.9990
   overall best weight:    2.9844

-------------------------------------------------------------------------------
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 = 0.4207 r_free = 0.4207 target = 0.194687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.156821 restraints weight = 10863.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.156228 restraints weight = 9414.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.157797 restraints weight = 9679.661|
|-----------------------------------------------------------------------------|
r_work (final): 0.3819
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7482
moved from start:          0.1933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.052   8486  Z= 0.262
  Angle     :  0.796   9.099  11564  Z= 0.405
  Chirality :  0.049   0.158   1236
  Planarity :  0.006   0.096   1518
  Dihedral  :  6.549  40.792   1140
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.70 %
    Favored  : 85.30 %
  Rotamer:
    Outliers :  4.94 %
    Allowed  : 17.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.82 (0.24), residues: 1034
  helix: -2.37 (0.29), residues: 250
  sheet: -3.66 (0.41), residues: 118
  loop : -2.50 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B 570 
 HIS   0.010   0.002   HIS A 458 
 PHE   0.027   0.002   PHE A 262 
 TYR   0.021   0.002   TYR B 481 
 ARG   0.004   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04598 (  151)
  hydrogen bonds       : angle       5.80660 (  411)
  SS BOND              : bond        0.00161 (    6)
  SS BOND              : angle       1.33694 (   12)
  covalent geometry    : bond        0.00625 ( 8480)
  covalent geometry    : angle       0.79524 (11552)

*********************** 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
  140 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 97
  time to evaluate  : 0.928 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8493 (mm) cc_final: 0.8156 (mt)
REVERT: A  133 TYR cc_start: 0.7357 (OUTLIER) cc_final: 0.6527 (t80)
REVERT: A  311 LEU cc_start: 0.6279 (OUTLIER) cc_final: 0.6079 (pt)
REVERT: A  446 MET cc_start: 0.6570 (OUTLIER) cc_final: 0.6130 (ttt)
REVERT: A  535 MET cc_start: 0.8082 (mtp) cc_final: 0.7750 (mtp)
REVERT: B  102 LEU cc_start: 0.8483 (mm) cc_final: 0.8142 (mt)
REVERT: B  133 TYR cc_start: 0.7354 (OUTLIER) cc_final: 0.6526 (t80)
REVERT: B  311 LEU cc_start: 0.6264 (OUTLIER) cc_final: 0.6063 (pt)
REVERT: B  446 MET cc_start: 0.6565 (OUTLIER) cc_final: 0.6120 (ttt)
REVERT: B  535 MET cc_start: 0.8091 (mtp) cc_final: 0.7753 (mtp)
  outliers start: 43
  outliers final: 31
  residues processed: 123
  average time/residue: 0.2353
  time to fit residues: 42.2605
Evaluate side-chains
  131 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 94
  time to evaluate  : 1.914 
-------------------------------------------------------------------------------
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  190 GLU
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  311 LEU
Chi-restraints excluded: chain A residue  363 ASP
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  486 HIS
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  585 LEU
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  190 GLU
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  311 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  486 HIS
Chi-restraints excluded: chain B residue  551 VAL
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  585 LEU
Chi-restraints excluded: chain B residue  602 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 39 optimal weight:    0.7980
   chunk 21 optimal weight:    1.9990
   chunk 52 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   chunk 10 optimal weight:    3.9990
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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 = 0.4240 r_free = 0.4240 target = 0.198351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.160919 restraints weight = 10867.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.159401 restraints weight = 9163.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.160990 restraints weight = 10004.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.2056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8486  Z= 0.161
  Angle     :  0.713   9.048  11564  Z= 0.360
  Chirality :  0.045   0.138   1236
  Planarity :  0.006   0.088   1518
  Dihedral  :  6.164  40.136   1140
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.61 %
    Favored  : 88.39 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 18.74 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.70 (0.24), residues: 1034
  helix: -2.18 (0.31), residues: 248
  sheet: -3.60 (0.41), residues: 120
  loop : -2.45 (0.23), residues: 666

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 570 
 HIS   0.005   0.001   HIS A 471 
 PHE   0.023   0.002   PHE B 523 
 TYR   0.017   0.001   TYR A 418 
 ARG   0.003   0.000   ARG B  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03736 (  151)
  hydrogen bonds       : angle       5.48436 (  411)
  SS BOND              : bond        0.00246 (    6)
  SS BOND              : angle       1.03761 (   12)
  covalent geometry    : bond        0.00386 ( 8480)
  covalent geometry    : angle       0.71252 (11552)

*********************** 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
  141 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 103
  time to evaluate  : 1.043 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8378 (mm) cc_final: 0.8015 (mt)
REVERT: A  133 TYR cc_start: 0.7435 (OUTLIER) cc_final: 0.6649 (t80)
REVERT: A  446 MET cc_start: 0.5423 (OUTLIER) cc_final: 0.4885 (ttt)
REVERT: A  503 GLU cc_start: 0.7342 (pm20) cc_final: 0.6205 (tm-30)
REVERT: B  102 LEU cc_start: 0.8377 (mm) cc_final: 0.8012 (mt)
REVERT: B  133 TYR cc_start: 0.7436 (OUTLIER) cc_final: 0.6654 (t80)
REVERT: B  446 MET cc_start: 0.5411 (OUTLIER) cc_final: 0.4878 (ttt)
REVERT: B  503 GLU cc_start: 0.7351 (pm20) cc_final: 0.6220 (tm-30)
  outliers start: 38
  outliers final: 26
  residues processed: 130
  average time/residue: 0.2028
  time to fit residues: 39.1268
Evaluate side-chains
  128 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 98
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
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  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  446 MET
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  585 LEU
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  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  533 VAL
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  585 LEU
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 71 optimal weight:    0.8980
   chunk 20 optimal weight:    0.0040
   chunk 4 optimal weight:    0.0670
   chunk 85 optimal weight:    0.5980
   chunk 76 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 94 optimal weight:    8.9990
   chunk 7 optimal weight:    0.0570
   overall best weight:    0.2848

-------------------------------------------------------------------------------
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 = 0.205400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.168574 restraints weight = 10925.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3911 r_free = 0.3911 target = 0.166960 restraints weight = 9062.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.168195 restraints weight = 9492.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7330
moved from start:          0.2421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8486  Z= 0.113
  Angle     :  0.650  10.558  11564  Z= 0.326
  Chirality :  0.044   0.177   1236
  Planarity :  0.005   0.079   1518
  Dihedral  :  5.429  38.596   1140
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.83 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.38 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.25), residues: 1034
  helix: -1.88 (0.32), residues: 250
  sheet: -3.11 (0.45), residues: 106
  loop : -2.36 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 609 
 PHE   0.013   0.001   PHE B 523 
 TYR   0.015   0.001   TYR A 418 
 ARG   0.002   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03079 (  151)
  hydrogen bonds       : angle       5.07345 (  411)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       0.68994 (   12)
  covalent geometry    : bond        0.00263 ( 8480)
  covalent geometry    : angle       0.65009 (11552)

*********************** 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
  114 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 92
  time to evaluate  : 0.934 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8172 (mm) cc_final: 0.7894 (mt)
REVERT: A  133 TYR cc_start: 0.7258 (OUTLIER) cc_final: 0.6534 (t80)
REVERT: A  147 TYR cc_start: 0.8515 (m-80) cc_final: 0.8247 (m-10)
REVERT: A  503 GLU cc_start: 0.7089 (pm20) cc_final: 0.5908 (tm-30)
REVERT: B  102 LEU cc_start: 0.8172 (mm) cc_final: 0.7893 (mt)
REVERT: B  133 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.6525 (t80)
REVERT: B  147 TYR cc_start: 0.8522 (m-80) cc_final: 0.8250 (m-10)
REVERT: B  503 GLU cc_start: 0.7084 (pm20) cc_final: 0.5915 (tm-30)
  outliers start: 22
  outliers final: 20
  residues processed: 112
  average time/residue: 0.1678
  time to fit residues: 28.0133
Evaluate side-chains
  105 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
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  264 SER
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  382 VAL
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  533 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  585 LEU
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  293 THR
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  311 LEU
Chi-restraints excluded: chain B residue  382 VAL
Chi-restraints excluded: chain B residue  440 ASP
Chi-restraints excluded: chain B residue  533 VAL
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  585 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 82 optimal weight:    0.0980
   chunk 0 optimal weight:   20.0000
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 47 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.5980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4297 r_free = 0.4297 target = 0.204492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.167510 restraints weight = 10954.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.166399 restraints weight = 9107.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.167870 restraints weight = 9894.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7337
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8486  Z= 0.116
  Angle     :  0.665  11.780  11564  Z= 0.327
  Chirality :  0.043   0.158   1236
  Planarity :  0.005   0.083   1518
  Dihedral  :  5.353  38.473   1140
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.54 %
    Favored  : 89.46 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.84 %
    Favored  : 74.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.27 (0.25), residues: 1034
  helix: -1.72 (0.32), residues: 250
  sheet: -3.09 (0.45), residues: 106
  loop : -2.30 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 122 
 HIS   0.003   0.001   HIS A 609 
 PHE   0.013   0.001   PHE A 523 
 TYR   0.019   0.001   TYR A 418 
 ARG   0.002   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  151)
  hydrogen bonds       : angle       5.03577 (  411)
  SS BOND              : bond        0.00351 (    6)
  SS BOND              : angle       0.74113 (   12)
  covalent geometry    : bond        0.00275 ( 8480)
  covalent geometry    : angle       0.66490 (11552)

*********************** 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
  119 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 91
  time to evaluate  : 0.857 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8208 (mm) cc_final: 0.7934 (mt)
REVERT: A  133 TYR cc_start: 0.7255 (OUTLIER) cc_final: 0.6535 (t80)
REVERT: A  147 TYR cc_start: 0.8529 (m-80) cc_final: 0.8258 (m-10)
REVERT: B  102 LEU cc_start: 0.8198 (mm) cc_final: 0.7925 (mt)
REVERT: B  133 TYR cc_start: 0.7251 (OUTLIER) cc_final: 0.6524 (t80)
REVERT: B  147 TYR cc_start: 0.8530 (m-80) cc_final: 0.8256 (m-10)
  outliers start: 28
  outliers final: 20
  residues processed: 117
  average time/residue: 0.1646
  time to fit residues: 28.1656
Evaluate side-chains
  111 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.920 
-------------------------------------------------------------------------------
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  293 THR
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  533 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  585 LEU
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  293 THR
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  533 VAL
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  585 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 94 optimal weight:    5.9990
   chunk 98 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   chunk 58 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 45 optimal weight:    8.9990
   chunk 49 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 42 optimal weight:    5.9990
   overall best weight:    1.3788

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.200604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.163832 restraints weight = 10924.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.165172 restraints weight = 9177.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.166322 restraints weight = 8562.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.3907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8486  Z= 0.153
  Angle     :  0.715  11.271  11564  Z= 0.351
  Chirality :  0.045   0.165   1236
  Planarity :  0.006   0.088   1518
  Dihedral  :  5.604  40.202   1140
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.19 %
    Favored  : 87.81 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 22.53 %
    Favored  : 74.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.24 (0.25), residues: 1034
  helix: -1.61 (0.32), residues: 250
  sheet: -3.16 (0.44), residues: 106
  loop : -2.30 (0.23), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 570 
 HIS   0.005   0.001   HIS B 458 
 PHE   0.018   0.002   PHE A  69 
 TYR   0.018   0.001   TYR A 418 
 ARG   0.002   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03631 (  151)
  hydrogen bonds       : angle       5.32100 (  411)
  SS BOND              : bond        0.00256 (    6)
  SS BOND              : angle       0.94728 (   12)
  covalent geometry    : bond        0.00365 ( 8480)
  covalent geometry    : angle       0.71449 (11552)

********************** 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
  116 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.891 
Fit side-chains
REVERT: A  102 LEU cc_start: 0.8291 (mm) cc_final: 0.8044 (mt)
REVERT: A  133 TYR cc_start: 0.7293 (OUTLIER) cc_final: 0.6569 (t80)
REVERT: A  523 PHE cc_start: 0.5585 (m-80) cc_final: 0.5161 (m-80)
REVERT: B  102 LEU cc_start: 0.8285 (mm) cc_final: 0.8037 (mt)
REVERT: B  133 TYR cc_start: 0.7295 (OUTLIER) cc_final: 0.6571 (t80)
  outliers start: 23
  outliers final: 20
  residues processed: 113
  average time/residue: 0.1736
  time to fit residues: 28.6744
Evaluate side-chains
  115 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
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  293 THR
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  533 VAL
Chi-restraints excluded: chain A residue  568 VAL
Chi-restraints excluded: chain A residue  585 LEU
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  293 THR
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  533 VAL
Chi-restraints excluded: chain B residue  568 VAL
Chi-restraints excluded: chain B residue  585 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 95 optimal weight:    0.0670
   chunk 85 optimal weight:    2.9990
   chunk 17 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 92 optimal weight:    0.3980
   chunk 26 optimal weight:    0.9980
   chunk 34 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.4297 r_free = 0.4297 target = 0.204360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.166839 restraints weight = 11040.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3895 r_free = 0.3895 target = 0.165960 restraints weight = 9402.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.167181 restraints weight = 9590.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7345
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8486  Z= 0.115
  Angle     :  0.676  11.897  11564  Z= 0.328
  Chirality :  0.043   0.155   1236
  Planarity :  0.005   0.081   1518
  Dihedral  :  5.233  39.237   1140
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.22 %
    Favored  : 88.78 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 22.99 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.16 (0.25), residues: 1034
  helix: -1.65 (0.32), residues: 262
  sheet: -2.98 (0.45), residues: 110
  loop : -2.22 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 122 
 HIS   0.003   0.001   HIS A 609 
 PHE   0.012   0.001   PHE B 523 
 TYR   0.015   0.001   TYR A 418 
 ARG   0.002   0.000   ARG A  83 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03129 (  151)
  hydrogen bonds       : angle       5.10478 (  411)
  SS BOND              : bond        0.00344 (    6)
  SS BOND              : angle       0.71715 (   12)
  covalent geometry    : bond        0.00273 ( 8480)
  covalent geometry    : angle       0.67634 (11552)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2669.62 seconds
wall clock time: 48 minutes 29.83 seconds (2909.83 seconds total)