Starting phenix.real_space_refine
on Thu Mar 13 03:02:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vxf_21436/03_2025/6vxf_21436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vxf_21436/03_2025/6vxf_21436.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2025/6vxf_21436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2025/6vxf_21436.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2025/6vxf_21436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vxf_21436/03_2025/6vxf_21436.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
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.017
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      58      5.16       5
     C    5700      2.51       5
     N    1450      2.21       5
     O    1578      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 8786
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4393
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 565, 4393
          Classifications: {'peptide': 565}
          Link IDs: {'PTRANS': 18, 'TRANS': 546}
          Chain breaks: 3
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.88, per 1000 atoms: 0.90
  Number of scatterers: 8786
  At special positions: 0
  Unit cell: (99.63, 73.8, 127.92, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      58     16.00
     O    1578      8.00
     N    1450      7.00
     C    5700      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 592 " - pdb=" SG  CYS B 608 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.86
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      60.2% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'B' and resid 87 through 94
      removed outlier: 3.656A  pdb=" N   ASP B  91 " --> pdb=" O   SER B  87 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 98 through 102
      removed outlier: 3.668A  pdb=" N   GLY B 101 " --> pdb=" O   ASP B  98 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU B 102 " --> pdb=" O   PRO B  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 98 through 102'
    Processing helix  chain 'B' and resid 135 through 148
      removed outlier: 3.784A  pdb=" N   PHE B 142 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 153 through 169
    Processing helix  chain 'B' and resid 170 through 174
    Processing helix  chain 'B' and resid 188 through 199
      removed outlier: 3.877A  pdb=" N   GLU B 199 " --> pdb=" O   SER B 195 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 217 through 232
    Processing helix  chain 'B' and resid 233 through 235
      No H-bonds generated for 'chain 'B' and resid 233 through 235'
    Processing helix  chain 'B' and resid 247 through 251
      removed outlier: 3.815A  pdb=" N   PHE B 250 " --> pdb=" O   TYR B 247 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   LYS B 251 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 247 through 251'
    Processing helix  chain 'B' and resid 272 through 278
      removed outlier: 4.057A  pdb=" N   PHE B 277 " --> pdb=" O   ALA B 273 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 289 through 299
      removed outlier: 3.735A  pdb=" N   LEU B 295 " --> pdb=" O   ALA B 291 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE B 298 " --> pdb=" O   PHE B 294 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 338
      removed outlier: 3.780A  pdb=" N   GLU B 334 " --> pdb=" O   GLU B 330 " (cutoff:3.500A)
      removed outlier: 4.236A  pdb=" N   ILE B 335 " --> pdb=" O   LYS B 331 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR B 336 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL B 337 " --> pdb=" O   ALA B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 354
      removed outlier: 4.120A  pdb=" N   LYS B 343 " --> pdb=" O   SER B 339 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU B 348 " --> pdb=" O   GLU B 344 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLN B 351 " --> pdb=" O   ALA B 347 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 372 through 391
    Processing helix  chain 'B' and resid 395 through 415
      removed outlier: 3.941A  pdb=" N   GLY B 415 " --> pdb=" O   ALA B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 435
      removed outlier: 3.861A  pdb=" N   GLY B 428 " --> pdb=" O   GLN B 424 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LEU B 430 " --> pdb=" O   ARG B 426 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE B 431 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 436 through 445
      removed outlier: 4.714A  pdb=" N   PHE B 439 " --> pdb=" O   ASN B 436 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER B 440 " --> pdb=" O   GLN B 437 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   SER B 441 " --> pdb=" O   CYS B 438 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   VAL B 442 " --> pdb=" O   PHE B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 452 through 461
      removed outlier: 3.583A  pdb=" N   HIS B 457 " --> pdb=" O   LYS B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 465 through 475
    Processing helix  chain 'B' and resid 477 through 482
    Processing helix  chain 'B' and resid 483 through 494
    Processing helix  chain 'B' and resid 495 through 497
      No H-bonds generated for 'chain 'B' and resid 495 through 497'
    Processing helix  chain 'B' and resid 504 through 528
      removed outlier: 3.670A  pdb=" N   ALA B 528 " --> pdb=" O   ALA B 524 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 532 through 546
      removed outlier: 3.912A  pdb=" N   ALA B 537 " --> pdb=" O   VAL B 533 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS B 544 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 557 through 561
      removed outlier: 3.562A  pdb=" N   ILE B 561 " --> pdb=" O   LEU B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 565 through 571
      removed outlier: 3.653A  pdb=" N   LEU B 568 " --> pdb=" O   LEU B 565 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 572 through 586
      removed outlier: 4.237A  pdb=" N   TYR B 576 " --> pdb=" O   SER B 572 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLY B 577 " --> pdb=" O   ILE B 573 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN B 584 " --> pdb=" O   ALA B 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 610 through 618
      removed outlier: 3.800A  pdb=" N   VAL B 615 " --> pdb=" O   GLU B 611 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   LYS B 616 " --> pdb=" O   GLU B 612 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 650
      removed outlier: 3.717A  pdb=" N   TRP B 627 " --> pdb=" O   PRO B 623 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   ASN B 629 " --> pdb=" O   GLY B 625 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   HIS B 630 " --> pdb=" O   LEU B 626 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU B 648 " --> pdb=" O   ALA B 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 94
      removed outlier: 3.657A  pdb=" N   ASP A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 98 through 102
      removed outlier: 3.668A  pdb=" N   GLY A 101 " --> pdb=" O   ASP A  98 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   LEU A 102 " --> pdb=" O   PRO A  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 98 through 102'
    Processing helix  chain 'A' and resid 135 through 148
      removed outlier: 3.784A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 170 through 174
    Processing helix  chain 'A' and resid 188 through 199
      removed outlier: 3.877A  pdb=" N   GLU A 199 " --> pdb=" O   SER A 195 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 217 through 232
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 247 through 251
      removed outlier: 3.814A  pdb=" N   PHE A 250 " --> pdb=" O   TYR A 247 " (cutoff:3.500A)
      removed outlier: 4.275A  pdb=" N   LYS A 251 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 247 through 251'
    Processing helix  chain 'A' and resid 272 through 278
      removed outlier: 4.057A  pdb=" N   PHE A 277 " --> pdb=" O   ALA A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 299
      removed outlier: 3.736A  pdb=" N   LEU A 295 " --> pdb=" O   ALA A 291 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   ILE A 298 " --> pdb=" O   PHE A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 338
      removed outlier: 3.780A  pdb=" N   GLU A 334 " --> pdb=" O   GLU A 330 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   ILE A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
      removed outlier: 4.524A  pdb=" N   TYR A 336 " --> pdb=" O   LEU A 332 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   VAL A 337 " --> pdb=" O   ALA A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 354
      removed outlier: 4.120A  pdb=" N   LYS A 343 " --> pdb=" O   SER A 339 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLN A 351 " --> pdb=" O   ALA A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 372 through 391
    Processing helix  chain 'A' and resid 395 through 415
      removed outlier: 3.942A  pdb=" N   GLY A 415 " --> pdb=" O   ALA A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 435
      removed outlier: 3.860A  pdb=" N   GLY A 428 " --> pdb=" O   GLN A 424 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 430 " --> pdb=" O   ARG A 426 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   PHE A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 445
      removed outlier: 4.714A  pdb=" N   PHE A 439 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   SER A 440 " --> pdb=" O   GLN A 437 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   SER A 441 " --> pdb=" O   CYS A 438 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL A 442 " --> pdb=" O   PHE A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 461
      removed outlier: 3.584A  pdb=" N   HIS A 457 " --> pdb=" O   LYS A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 475
    Processing helix  chain 'A' and resid 477 through 482
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 495 through 497
      No H-bonds generated for 'chain 'A' and resid 495 through 497'
    Processing helix  chain 'A' and resid 504 through 528
      removed outlier: 3.671A  pdb=" N   ALA A 528 " --> pdb=" O   ALA A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 546
      removed outlier: 3.912A  pdb=" N   ALA A 537 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   CYS A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 561
      removed outlier: 3.562A  pdb=" N   ILE A 561 " --> pdb=" O   LEU A 558 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 571
      removed outlier: 3.654A  pdb=" N   LEU A 568 " --> pdb=" O   LEU A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 586
      removed outlier: 4.237A  pdb=" N   TYR A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   GLY A 577 " --> pdb=" O   ILE A 573 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ASN A 584 " --> pdb=" O   ALA A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 618
      removed outlier: 3.801A  pdb=" N   VAL A 615 " --> pdb=" O   GLU A 611 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   LYS A 616 " --> pdb=" O   GLU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 650
      removed outlier: 3.718A  pdb=" N   TRP A 627 " --> pdb=" O   PRO A 623 " (cutoff:3.500A)
      removed outlier: 4.976A  pdb=" N   ASN A 629 " --> pdb=" O   GLY A 625 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   HIS A 630 " --> pdb=" O   LEU A 626 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 648 " --> pdb=" O   ALA A 644 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 68 through 71
    Processing sheet with id=AA2, first strand: chain 'B' and resid 121 through 123
      removed outlier: 5.788A  pdb=" N   GLY B 122 " --> pdb=" O   PHE B 208 " (cutoff:3.500A)
      removed outlier: 7.796A  pdb=" N   THR B 257 " --> pdb=" O   LEU B  75 " (cutoff:3.500A)
      removed outlier: 6.170A  pdb=" N   ALA B  77 " --> pdb=" O   THR B 257 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU B 259 " --> pdb=" O   ALA B  77 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   LEU B  79 " --> pdb=" O   LEU B 259 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU B 256 " --> pdb=" O   HIS B 267 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   HIS B 267 " --> pdb=" O   LEU B 256 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   LEU B 258 " --> pdb=" O   MET B 265 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 68 through 71
    Processing sheet with id=AA4, first strand: chain 'A' and resid 121 through 123
      removed outlier: 5.788A  pdb=" N   GLY A 122 " --> pdb=" O   PHE A 208 " (cutoff:3.500A)
      removed outlier: 7.795A  pdb=" N   THR A 257 " --> pdb=" O   LEU A  75 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ALA A  77 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   LEU A 259 " --> pdb=" O   ALA A  77 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   LEU A  79 " --> pdb=" O   LEU A 259 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   LEU A 256 " --> pdb=" O   HIS A 267 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   HIS A 267 " --> pdb=" O   LEU A 256 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU A 258 " --> pdb=" O   MET A 265 " (cutoff:3.500A)

    416 hydrogen bonds defined for protein.
    1170 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.49

  Time building geometry restraints manager: 2.28 seconds

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

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

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

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 4658
       17.86 -    35.73: 531
       35.73 -    53.59: 94
       53.59 -    71.45: 20
       71.45 -    89.32: 6
  Dihedral angle restraints: 5309
    sinusoidal: 2057
      harmonic: 3252
  Sorted by residual:
  dihedral pdb=" CA  LEU B 555 "
           pdb=" C   LEU B 555 "
           pdb=" N   VAL B 556 "
           pdb=" CA  VAL B 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.34   28.66     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  LEU A 555 "
           pdb=" C   LEU A 555 "
           pdb=" N   VAL A 556 "
           pdb=" CA  VAL A 556 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.36   28.64     0      5.00e+00 4.00e-02 3.28e+01
  dihedral pdb=" CA  GLU A 138 "
           pdb=" C   GLU A 138 "
           pdb=" N   ASN A 139 "
           pdb=" CA  ASN A 139 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.60   25.40     0      5.00e+00 4.00e-02 2.58e+01
  ... (remaining 5306 not shown)

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

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

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 72
        2.60 -     3.18: 7230
        3.18 -     3.75: 13732
        3.75 -     4.33: 18935
        4.33 -     4.90: 31710
  Nonbonded interactions: 71679
  Sorted by model distance:
  nonbonded pdb=" SG  CYS B 603 "
            pdb=" SG  CYS A 603 "
     model   vdw
     2.025 3.760
  nonbonded pdb=" SG  CYS A 592 "
            pdb=" SG  CYS A 608 "
     model   vdw
     2.039 3.760
  nonbonded pdb=" O   SER A 552 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   SER B 552 "
            pdb=" OG  SER B 552 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   MET A 548 "
            pdb=" OG  SER A 552 "
     model   vdw
     2.333 3.040
  ... (remaining 71674 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:             0.300
  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:          0.340
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.630
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.077   8968  Z= 0.604
  Angle     :  1.040  11.230  12134  Z= 0.550
  Chirality :  0.059   0.239   1408
  Planarity :  0.006   0.053   1514
  Dihedral  : 15.362  89.316   3218
  Min Nonbonded Distance : 2.025

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

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

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

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 153
  time to evaluate  : 0.913 
Fit side-chains
REVERT: B  163 ARG cc_start: 0.7050 (ttp-170) cc_final: 0.6795 (ttm170)
REVERT: B  246 ARG cc_start: 0.8063 (ptp-170) cc_final: 0.7705 (ptp-110)
REVERT: B  515 MET cc_start: 0.8633 (mmm) cc_final: 0.8156 (mmp)
REVERT: B  628 LYS cc_start: 0.7596 (tttt) cc_final: 0.7302 (ttpp)
REVERT: A  126 GLN cc_start: 0.8247 (tt0) cc_final: 0.7945 (tt0)
REVERT: A  194 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8323 (t)
REVERT: A  382 LYS cc_start: 0.8972 (ttmt) cc_final: 0.8742 (ttmm)
REVERT: A  515 MET cc_start: 0.8640 (mmm) cc_final: 0.7832 (mmp)
REVERT: A  541 MET cc_start: 0.9071 (tpp) cc_final: 0.8813 (tpt)
REVERT: A  623 PRO cc_start: 0.8755 (Cg_exo) cc_final: 0.8507 (Cg_endo)
REVERT: A  628 LYS cc_start: 0.7452 (tttt) cc_final: 0.7213 (ttmt)
  outliers start: 12
  outliers final: 2
  residues processed: 161
  average time/residue: 0.2906
  time to fit residues: 66.6390
Evaluate side-chains
  121 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 118
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  609 THR
Chi-restraints excluded: chain A residue  194 THR
Chi-restraints excluded: chain A residue  609 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.5980
   chunk 84 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 87 optimal weight:    0.6980
   chunk 33 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 65 optimal weight:    0.9990
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.165544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.127378 restraints weight = 11092.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.129478 restraints weight = 7938.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.130989 restraints weight = 6547.333|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8968  Z= 0.170
  Angle     :  0.608   7.631  12134  Z= 0.312
  Chirality :  0.041   0.137   1408
  Planarity :  0.004   0.032   1514
  Dihedral  :  5.742  42.825   1207
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 7.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 16.53 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.23), residues: 1114
  helix: -0.76 (0.20), residues: 596
  sheet: -2.01 (0.58), residues: 70
  loop : -2.77 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 379 
 HIS   0.008   0.001   HIS B 155 
 PHE   0.016   0.001   PHE A 470 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.005   0.000   ARG B 378 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 142
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
REVERT: B  163 ARG cc_start: 0.7046 (ttp-170) cc_final: 0.6643 (ttm170)
REVERT: B  342 TYR cc_start: 0.6728 (t80) cc_final: 0.6524 (t80)
REVERT: B  514 MET cc_start: 0.8224 (mtt) cc_final: 0.8015 (mtm)
REVERT: B  515 MET cc_start: 0.8543 (mmm) cc_final: 0.8193 (mmp)
REVERT: B  628 LYS cc_start: 0.7532 (tttt) cc_final: 0.7276 (ttpp)
REVERT: A  168 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8482 (tp)
REVERT: A  272 GLU cc_start: 0.7139 (pm20) cc_final: 0.6777 (pm20)
REVERT: A  382 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8721 (ttmm)
REVERT: A  458 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7950 (mt-10)
REVERT: A  471 LEU cc_start: 0.8672 (mp) cc_final: 0.8364 (mt)
REVERT: A  515 MET cc_start: 0.8478 (mmm) cc_final: 0.7694 (mmp)
REVERT: A  570 TYR cc_start: 0.8682 (m-80) cc_final: 0.8150 (m-80)
REVERT: A  628 LYS cc_start: 0.7378 (tttt) cc_final: 0.7070 (ttmt)
  outliers start: 9
  outliers final: 7
  residues processed: 148
  average time/residue: 0.2111
  time to fit residues: 43.6905
Evaluate side-chains
  132 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 124
  time to evaluate  : 0.908 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  168 LEU
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  609 THR
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  609 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 3 optimal weight:    9.9990
   chunk 1 optimal weight:    5.9990
   chunk 108 optimal weight:    3.9990
   chunk 8 optimal weight:    1.9990
   chunk 82 optimal weight:    2.9990
   chunk 30 optimal weight:    0.3980
   chunk 63 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    2.0788

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

Flipped N/Q/H residues before XYZ refinement:
B 437 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.161761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.123459 restraints weight = 11401.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.125720 restraints weight = 8144.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.126989 restraints weight = 6676.721|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.1899

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8968  Z= 0.305
  Angle     :  0.651   7.623  12134  Z= 0.331
  Chirality :  0.044   0.195   1408
  Planarity :  0.004   0.030   1514
  Dihedral  :  5.235  22.216   1206
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.40
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  7.54 %
    Favored  : 92.28 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.78 %
    Favored  : 79.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.81 (0.25), residues: 1114
  helix: -0.08 (0.21), residues: 596
  sheet: -2.30 (0.53), residues: 70
  loop : -2.57 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 379 
 HIS   0.005   0.001   HIS A 267 
 PHE   0.012   0.002   PHE B 208 
 TYR   0.014   0.002   TYR A 459 
 ARG   0.010   0.001   ARG A 193 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.947 
Fit side-chains
REVERT: B  258 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7708 (tp)
REVERT: B  487 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8360 (mt)
REVERT: B  515 MET cc_start: 0.8644 (mmm) cc_final: 0.7621 (mmp)
REVERT: B  541 MET cc_start: 0.8458 (tpt) cc_final: 0.8053 (tpt)
REVERT: B  628 LYS cc_start: 0.7563 (tttt) cc_final: 0.7305 (ttpp)
REVERT: A  193 ARG cc_start: 0.8224 (ttm110) cc_final: 0.7385 (mmm-85)
REVERT: A  246 ARG cc_start: 0.7851 (ptp-170) cc_final: 0.7620 (ptp-170)
REVERT: A  258 LEU cc_start: 0.8313 (OUTLIER) cc_final: 0.7970 (tt)
REVERT: A  272 GLU cc_start: 0.7127 (pm20) cc_final: 0.6895 (pm20)
REVERT: A  382 LYS cc_start: 0.9011 (ttmt) cc_final: 0.8762 (ttmm)
REVERT: A  487 ILE cc_start: 0.8744 (OUTLIER) cc_final: 0.8540 (mt)
REVERT: A  515 MET cc_start: 0.8489 (mmm) cc_final: 0.7575 (mmp)
  outliers start: 23
  outliers final: 15
  residues processed: 152
  average time/residue: 0.2294
  time to fit residues: 47.3220
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 128
  time to evaluate  : 0.976 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  487 ILE
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 105 optimal weight:    4.9990
   chunk 78 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 26 optimal weight:    0.9980
   chunk 86 optimal weight:    6.9990
   chunk 67 optimal weight:    0.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
B  76 ASN
A  76 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.162759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.124066 restraints weight = 11246.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.126353 restraints weight = 8001.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.127789 restraints weight = 6550.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   8968  Z= 0.183
  Angle     :  0.579   7.750  12134  Z= 0.290
  Chirality :  0.041   0.176   1408
  Planarity :  0.003   0.027   1514
  Dihedral  :  4.883  22.607   1204
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 19.33 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.26), residues: 1114
  helix:  0.54 (0.22), residues: 598
  sheet: -2.27 (0.51), residues: 70
  loop : -2.44 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 155 
 PHE   0.015   0.001   PHE B 506 
 TYR   0.024   0.001   TYR A 247 
 ARG   0.006   0.000   ARG B 184 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 134
  time to evaluate  : 0.872 
Fit side-chains
REVERT: B  258 LEU cc_start: 0.8109 (OUTLIER) cc_final: 0.7768 (tt)
REVERT: B  515 MET cc_start: 0.8587 (mmm) cc_final: 0.7850 (mmp)
REVERT: B  541 MET cc_start: 0.8108 (tpt) cc_final: 0.7762 (tpt)
REVERT: A  193 ARG cc_start: 0.8135 (ttm110) cc_final: 0.7905 (ttm110)
REVERT: A  258 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.7841 (tt)
REVERT: A  272 GLU cc_start: 0.7095 (pm20) cc_final: 0.6832 (pm20)
REVERT: A  382 LYS cc_start: 0.8971 (ttmt) cc_final: 0.8736 (ttmm)
REVERT: A  487 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8517 (mt)
REVERT: A  515 MET cc_start: 0.8525 (mmm) cc_final: 0.7633 (mmp)
REVERT: A  554 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7604 (pt)
  outliers start: 27
  outliers final: 14
  residues processed: 154
  average time/residue: 0.2097
  time to fit residues: 44.5957
Evaluate side-chains
  140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 122
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  554 LEU
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:   10.0000
   chunk 105 optimal weight:    6.9990
   chunk 95 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 25 optimal weight:    6.9990
   chunk 17 optimal weight:    4.9990
   chunk 75 optimal weight:    5.9990
   chunk 89 optimal weight:   10.0000
   chunk 4 optimal weight:    0.5980
   chunk 93 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    3.9188

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.155929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.117010 restraints weight = 11434.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.119277 restraints weight = 8209.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.120494 restraints weight = 6734.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.083   8968  Z= 0.516
  Angle     :  0.765   9.314  12134  Z= 0.386
  Chirality :  0.049   0.153   1408
  Planarity :  0.004   0.032   1514
  Dihedral  :  5.341  21.372   1204
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.89 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 19.75 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.70 (0.25), residues: 1114
  helix:  0.12 (0.21), residues: 598
  sheet: -2.76 (0.45), residues: 70
  loop : -2.60 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP B 379 
 HIS   0.006   0.002   HIS A 267 
 PHE   0.014   0.002   PHE A  39 
 TYR   0.018   0.002   TYR B 342 
 ARG   0.005   0.001   ARG B 246 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 133
  time to evaluate  : 0.938 
Fit side-chains
REVERT: B  107 LEU cc_start: 0.8341 (tt) cc_final: 0.8019 (mp)
REVERT: B  258 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7760 (tp)
REVERT: B  515 MET cc_start: 0.8653 (mmm) cc_final: 0.8145 (mmp)
REVERT: A  246 ARG cc_start: 0.8174 (ptp-170) cc_final: 0.7945 (ptp-110)
REVERT: A  258 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8073 (tt)
REVERT: A  272 GLU cc_start: 0.7142 (pm20) cc_final: 0.6921 (pm20)
REVERT: A  487 ILE cc_start: 0.8750 (OUTLIER) cc_final: 0.8539 (mt)
REVERT: A  515 MET cc_start: 0.8602 (mmm) cc_final: 0.7527 (mmp)
  outliers start: 35
  outliers final: 26
  residues processed: 162
  average time/residue: 0.2045
  time to fit residues: 46.1872
Evaluate side-chains
  153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  175 ASP
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  226 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  255 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  226 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  490 THR
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 79 optimal weight:    7.9990
   chunk 48 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 77 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 50 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.160823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.122618 restraints weight = 11162.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.124985 restraints weight = 7950.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.126370 restraints weight = 6499.093|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
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   0.025   8968  Z= 0.190
  Angle     :  0.597   8.858  12134  Z= 0.300
  Chirality :  0.041   0.184   1408
  Planarity :  0.003   0.026   1514
  Dihedral  :  4.931  21.664   1204
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.41 %
    Favored  : 75.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.10 (0.26), residues: 1114
  helix:  0.68 (0.22), residues: 598
  sheet: -2.49 (0.48), residues: 70
  loop : -2.44 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 379 
 HIS   0.005   0.001   HIS A 155 
 PHE   0.017   0.001   PHE B 506 
 TYR   0.021   0.001   TYR B 342 
 ARG   0.004   0.000   ARG B 193 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.977 
Fit side-chains
REVERT: B  181 GLN cc_start: 0.5046 (mp10) cc_final: 0.4782 (mp10)
REVERT: B  246 ARG cc_start: 0.7698 (ptp-110) cc_final: 0.7060 (mtp85)
REVERT: B  258 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7859 (tt)
REVERT: B  515 MET cc_start: 0.8582 (mmm) cc_final: 0.7594 (mmp)
REVERT: B  541 MET cc_start: 0.8099 (tpt) cc_final: 0.7598 (tpt)
REVERT: A  252 LEU cc_start: 0.6221 (mp) cc_final: 0.5939 (mp)
REVERT: A  258 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.8074 (tt)
REVERT: A  272 GLU cc_start: 0.7225 (pm20) cc_final: 0.7015 (pm20)
REVERT: A  487 ILE cc_start: 0.8690 (OUTLIER) cc_final: 0.8454 (mt)
REVERT: A  515 MET cc_start: 0.8571 (mmm) cc_final: 0.7596 (mmp)
  outliers start: 27
  outliers final: 19
  residues processed: 148
  average time/residue: 0.2171
  time to fit residues: 44.2863
Evaluate side-chains
  140 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 118
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  108 ILE
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 99 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 82 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 13 optimal weight:    4.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
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 = 0.3708 r_free = 0.3708 target = 0.157986 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.119069 restraints weight = 11399.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.121354 restraints weight = 8091.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.122562 restraints weight = 6642.600|
|-----------------------------------------------------------------------------|
r_work (final): 0.3257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8968  Z= 0.317
  Angle     :  0.640   7.879  12134  Z= 0.325
  Chirality :  0.043   0.138   1408
  Planarity :  0.004   0.028   1514
  Dihedral  :  4.962  20.708   1204
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  8.17 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 21.83 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.25), residues: 1114
  helix:  0.61 (0.22), residues: 598
  sheet: -2.56 (0.47), residues: 70
  loop : -2.41 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 379 
 HIS   0.005   0.002   HIS A 155 
 PHE   0.012   0.002   PHE A 506 
 TYR   0.022   0.002   TYR B 342 
 ARG   0.008   0.000   ARG A 193 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.896 
Fit side-chains
REVERT: B  107 LEU cc_start: 0.8318 (tt) cc_final: 0.8035 (mp)
REVERT: B  258 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7960 (tp)
REVERT: B  515 MET cc_start: 0.8572 (mmm) cc_final: 0.7560 (mmp)
REVERT: A  191 ARG cc_start: 0.6678 (ttt180) cc_final: 0.6451 (ttp80)
REVERT: A  193 ARG cc_start: 0.8219 (ttm110) cc_final: 0.7334 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.8087 (tt)
REVERT: A  265 MET cc_start: 0.7963 (mmp) cc_final: 0.7758 (mmp)
REVERT: A  272 GLU cc_start: 0.7135 (pm20) cc_final: 0.6883 (pm20)
REVERT: A  487 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8515 (mt)
REVERT: A  515 MET cc_start: 0.8560 (mmm) cc_final: 0.8038 (mmp)
  outliers start: 27
  outliers final: 22
  residues processed: 146
  average time/residue: 0.2019
  time to fit residues: 41.3608
Evaluate side-chains
  148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 123
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  476 SER
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  492 ILE
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 54 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 50 optimal weight:    9.9990
   chunk 90 optimal weight:    0.9990
   chunk 92 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.9382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.160970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.122380 restraints weight = 11427.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.124797 restraints weight = 7940.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.126354 restraints weight = 6435.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7866
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   8968  Z= 0.186
  Angle     :  0.574   7.514  12134  Z= 0.291
  Chirality :  0.040   0.132   1408
  Planarity :  0.003   0.026   1514
  Dihedral  :  4.755  21.576   1204
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 22.35 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.26), residues: 1114
  helix:  0.94 (0.22), residues: 598
  sheet: -2.35 (0.48), residues: 70
  loop : -2.27 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 379 
 HIS   0.006   0.001   HIS A 155 
 PHE   0.018   0.001   PHE A 506 
 TYR   0.025   0.001   TYR B 342 
 ARG   0.006   0.000   ARG A 193 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.903 
Fit side-chains
REVERT: B  107 LEU cc_start: 0.8261 (tt) cc_final: 0.8002 (mp)
REVERT: B  246 ARG cc_start: 0.7844 (ptp-110) cc_final: 0.7183 (mtp85)
REVERT: B  258 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7897 (tp)
REVERT: B  515 MET cc_start: 0.8578 (mmm) cc_final: 0.7589 (mmp)
REVERT: A  193 ARG cc_start: 0.8168 (ttm110) cc_final: 0.7289 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8448 (OUTLIER) cc_final: 0.8141 (tt)
REVERT: A  487 ILE cc_start: 0.8688 (OUTLIER) cc_final: 0.8444 (mt)
REVERT: A  515 MET cc_start: 0.8565 (mmm) cc_final: 0.8074 (mmp)
  outliers start: 25
  outliers final: 20
  residues processed: 151
  average time/residue: 0.2104
  time to fit residues: 44.6095
Evaluate side-chains
  145 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 122
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 69 optimal weight:    9.9990
   chunk 58 optimal weight:    8.9990
   chunk 34 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 74 optimal weight:    4.9990
   chunk 47 optimal weight:    0.7980
   chunk 66 optimal weight:   10.0000
   chunk 102 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    1.1182

-------------------------------------------------------------------------------
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 = 0.3745 r_free = 0.3745 target = 0.161611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.122633 restraints weight = 11291.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.125047 restraints weight = 7964.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.126222 restraints weight = 6500.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2848

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8968  Z= 0.203
  Angle     :  0.585   7.179  12134  Z= 0.295
  Chirality :  0.041   0.175   1408
  Planarity :  0.003   0.030   1514
  Dihedral  :  4.677  21.410   1204
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.93 %
    Favored  : 75.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.62 (0.26), residues: 1114
  helix:  1.04 (0.22), residues: 598
  sheet: -2.24 (0.48), residues: 70
  loop : -2.17 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 379 
 HIS   0.007   0.001   HIS A 155 
 PHE   0.016   0.001   PHE A 506 
 TYR   0.023   0.001   TYR B 342 
 ARG   0.008   0.001   ARG A 191 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.899 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.7891 (ptp-110) cc_final: 0.7185 (mtp85)
REVERT: B  258 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7945 (tt)
REVERT: B  424 GLN cc_start: 0.7464 (tp40) cc_final: 0.7258 (mm-40)
REVERT: B  515 MET cc_start: 0.8595 (mmm) cc_final: 0.7607 (mmp)
REVERT: A  193 ARG cc_start: 0.8282 (ttm110) cc_final: 0.7430 (mtt-85)
REVERT: A  216 LEU cc_start: 0.7562 (mt) cc_final: 0.7346 (mt)
REVERT: A  258 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8125 (tt)
REVERT: A  272 GLU cc_start: 0.7043 (pm20) cc_final: 0.6839 (pm20)
REVERT: A  487 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8466 (mt)
REVERT: A  515 MET cc_start: 0.8546 (mmm) cc_final: 0.8059 (mmp)
  outliers start: 26
  outliers final: 23
  residues processed: 149
  average time/residue: 0.2041
  time to fit residues: 42.7293
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 125
  time to evaluate  : 0.950 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  496 MET
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  255 SER
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  496 MET
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  536 VAL
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.0470
   chunk 34 optimal weight:    0.6980
   chunk 68 optimal weight:    2.9990
   chunk 85 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 73 optimal weight:    7.9990
   chunk 98 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 70 optimal weight:    0.6980
   chunk 87 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9990
   overall best weight:    0.6880

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.163059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.124446 restraints weight = 11226.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.126884 restraints weight = 7968.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.128310 restraints weight = 6485.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8968  Z= 0.166
  Angle     :  0.560   7.371  12134  Z= 0.282
  Chirality :  0.040   0.157   1408
  Planarity :  0.003   0.042   1514
  Dihedral  :  4.541  21.860   1204
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.10 %
    Favored  : 93.90 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.35 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.26), residues: 1114
  helix:  1.19 (0.23), residues: 596
  sheet: -2.03 (0.50), residues: 70
  loop : -2.16 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 379 
 HIS   0.007   0.001   HIS A 155 
 PHE   0.020   0.001   PHE A 506 
 TYR   0.022   0.001   TYR B 342 
 ARG   0.006   0.001   ARG A 193 

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

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

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

  2228 Ramachandran restraints generated.
    1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 1.029 
Fit side-chains
REVERT: B  246 ARG cc_start: 0.7844 (ptp-110) cc_final: 0.7172 (mtp85)
REVERT: B  258 LEU cc_start: 0.8286 (OUTLIER) cc_final: 0.7953 (tp)
REVERT: B  454 LEU cc_start: 0.9307 (tp) cc_final: 0.9051 (tp)
REVERT: B  515 MET cc_start: 0.8580 (mmm) cc_final: 0.7623 (mmp)
REVERT: A  193 ARG cc_start: 0.8302 (ttm110) cc_final: 0.7371 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8116 (tt)
REVERT: A  272 GLU cc_start: 0.7148 (pm20) cc_final: 0.6940 (pm20)
REVERT: A  454 LEU cc_start: 0.9281 (tp) cc_final: 0.9008 (tp)
REVERT: A  487 ILE cc_start: 0.8618 (OUTLIER) cc_final: 0.8378 (mt)
REVERT: A  515 MET cc_start: 0.8507 (mmm) cc_final: 0.7645 (mmp)
  outliers start: 23
  outliers final: 19
  residues processed: 153
  average time/residue: 0.2038
  time to fit residues: 43.5874
Evaluate side-chains
  148 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.997 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  225 LEU
Chi-restraints excluded: chain B residue  237 THR
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  555 LEU
Chi-restraints excluded: chain B residue  556 VAL
Chi-restraints excluded: chain B residue  615 VAL
Chi-restraints excluded: chain A residue  225 LEU
Chi-restraints excluded: chain A residue  237 THR
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  420 SER
Chi-restraints excluded: chain A residue  445 VAL
Chi-restraints excluded: chain A residue  487 ILE
Chi-restraints excluded: chain A residue  491 CYS
Chi-restraints excluded: chain A residue  496 MET
Chi-restraints excluded: chain A residue  499 LEU
Chi-restraints excluded: chain A residue  544 CYS
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Chi-restraints excluded: chain A residue  615 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0670
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 43 optimal weight:    3.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 47 optimal weight:    0.8980
   chunk 49 optimal weight:    5.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    1.1720

-------------------------------------------------------------------------------
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 = 0.3781 r_free = 0.3781 target = 0.165309 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.127625 restraints weight = 11181.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.129948 restraints weight = 7943.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.131408 restraints weight = 6505.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.3003

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8968  Z= 0.205
  Angle     :  0.578   7.247  12134  Z= 0.293
  Chirality :  0.041   0.138   1408
  Planarity :  0.003   0.045   1514
  Dihedral  :  4.545  21.578   1204
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.87 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.26), residues: 1114
  helix:  1.16 (0.22), residues: 596
  sheet: -2.05 (0.50), residues: 70
  loop : -2.09 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 379 
 HIS   0.008   0.001   HIS A 155 
 PHE   0.018   0.001   PHE A 506 
 TYR   0.021   0.001   TYR B 342 
 ARG   0.006   0.000   ARG A 193 

===============================================================================
Job complete
usr+sys time: 2700.72 seconds
wall clock time: 48 minutes 58.06 seconds (2938.06 seconds total)