Starting phenix.real_space_refine
on Thu Feb 13 01:26:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6vxf_21436/02_2025/6vxf_21436.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6vxf_21436/02_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_21436/02_2025/6vxf_21436.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6vxf_21436/02_2025/6vxf_21436.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6vxf_21436/02_2025/6vxf_21436.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6vxf_21436/02_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-5592/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: 7.39, per 1000 atoms: 0.84
  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: 2.12
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.05
  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: 2.61

  Time building geometry restraints manager: 2.48 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: 0.05
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.550
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     24.960
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.130
-------------------------------------------------------------------------------
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  : 0.941 
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: 0.2152
  time to fit residues: 48.2919
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  : 1.042 
-------------------------------------------------------------------------------
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 = 61)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.127378 restraints weight = 11092.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.129636 restraints weight = 7938.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.131004 restraints weight = 6523.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7832
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  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: B  163 ARG cc_start: 0.7045 (ttp-170) cc_final: 0.6642 (ttm170)
REVERT: B  342 TYR cc_start: 0.6725 (t80) cc_final: 0.6522 (t80)
REVERT: B  514 MET cc_start: 0.8225 (mtt) cc_final: 0.8016 (mtm)
REVERT: B  515 MET cc_start: 0.8542 (mmm) cc_final: 0.8192 (mmp)
REVERT: B  628 LYS cc_start: 0.7532 (tttt) cc_final: 0.7274 (ttpp)
REVERT: A  168 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8483 (tp)
REVERT: A  272 GLU cc_start: 0.7137 (pm20) cc_final: 0.6778 (pm20)
REVERT: A  382 LYS cc_start: 0.8933 (ttmt) cc_final: 0.8721 (ttmm)
REVERT: A  458 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7949 (mt-10)
REVERT: A  471 LEU cc_start: 0.8671 (mp) cc_final: 0.8362 (mt)
REVERT: A  515 MET cc_start: 0.8481 (mmm) cc_final: 0.7691 (mmp)
REVERT: A  570 TYR cc_start: 0.8683 (m-80) cc_final: 0.8150 (m-80)
REVERT: A  628 LYS cc_start: 0.7378 (tttt) cc_final: 0.7071 (ttmt)
  outliers start: 9
  outliers final: 7
  residues processed: 148
  average time/residue: 0.2165
  time to fit residues: 44.4799
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  : 1.045 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 108 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0060
   chunk 63 optimal weight:    7.9990
   chunk 53 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.6802

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.163194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.125073 restraints weight = 11362.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.127334 restraints weight = 8101.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.128696 restraints weight = 6644.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8968  Z= 0.260
  Angle     :  0.619   7.044  12134  Z= 0.315
  Chirality :  0.042   0.159   1408
  Planarity :  0.003   0.030   1514
  Dihedral  :  5.166  22.733   1206
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.45 %
    Favored  : 92.46 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.57 %
    Favored  : 80.15 %
  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: -1.74 (0.25), residues: 1114
  helix: -0.02 (0.21), residues: 596
  sheet: -2.16 (0.54), residues: 70
  loop : -2.55 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.004   0.001   HIS B 155 
 PHE   0.012   0.001   PHE B 470 
 TYR   0.013   0.001   TYR A 459 
 ARG   0.006   0.000   ARG B 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
  152 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 130
  time to evaluate  : 1.021 
Fit side-chains
REVERT: B   45 ARG cc_start: 0.5982 (ttt-90) cc_final: 0.5711 (ttt90)
REVERT: B  163 ARG cc_start: 0.7099 (ttp-170) cc_final: 0.6709 (ttm170)
REVERT: B  258 LEU cc_start: 0.8005 (OUTLIER) cc_final: 0.7675 (tt)
REVERT: B  487 ILE cc_start: 0.8605 (OUTLIER) cc_final: 0.8326 (mt)
REVERT: B  515 MET cc_start: 0.8639 (mmm) cc_final: 0.7619 (mmp)
REVERT: B  541 MET cc_start: 0.8416 (tpt) cc_final: 0.7972 (tpt)
REVERT: B  628 LYS cc_start: 0.7543 (tttt) cc_final: 0.7297 (ttpp)
REVERT: A  193 ARG cc_start: 0.8238 (ttm110) cc_final: 0.8029 (ttm110)
REVERT: A  258 LEU cc_start: 0.8282 (OUTLIER) cc_final: 0.7923 (tt)
REVERT: A  272 GLU cc_start: 0.7111 (pm20) cc_final: 0.6897 (pm20)
REVERT: A  487 ILE cc_start: 0.8752 (OUTLIER) cc_final: 0.8536 (mt)
REVERT: A  515 MET cc_start: 0.8518 (mmm) cc_final: 0.7676 (mmp)
  outliers start: 22
  outliers final: 15
  residues processed: 147
  average time/residue: 0.2372
  time to fit residues: 46.8232
Evaluate side-chains
  141 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 122
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 2 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 105 optimal weight:    6.9990
   chunk 78 optimal weight:    5.9990
   chunk 66 optimal weight:    8.9990
   chunk 26 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0270
   chunk 67 optimal weight:    0.9990
   overall best weight:    1.2044

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.162099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.123725 restraints weight = 11273.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.125978 restraints weight = 7990.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.127419 restraints weight = 6558.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8968  Z= 0.203
  Angle     :  0.581   8.008  12134  Z= 0.293
  Chirality :  0.041   0.180   1408
  Planarity :  0.003   0.028   1514
  Dihedral  :  4.882  22.563   1204
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 19.85 %
    Favored  : 77.75 %
  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: -1.25 (0.25), residues: 1114
  helix:  0.47 (0.22), residues: 598
  sheet: -2.20 (0.51), residues: 70
  loop : -2.45 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 379 
 HIS   0.003   0.001   HIS B 155 
 PHE   0.014   0.001   PHE B 506 
 TYR   0.012   0.001   TYR A 459 
 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
  158 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 0.955 
Fit side-chains
REVERT: B  193 ARG cc_start: 0.7956 (ttm110) cc_final: 0.7667 (ttm110)
REVERT: B  258 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7738 (tt)
REVERT: B  515 MET cc_start: 0.8595 (mmm) cc_final: 0.7860 (mmp)
REVERT: B  541 MET cc_start: 0.8403 (tpt) cc_final: 0.8044 (tpt)
REVERT: A  193 ARG cc_start: 0.8223 (ttm110) cc_final: 0.8020 (ttm110)
REVERT: A  258 LEU cc_start: 0.8246 (OUTLIER) cc_final: 0.7868 (tt)
REVERT: A  272 GLU cc_start: 0.7089 (pm20) cc_final: 0.6840 (pm20)
REVERT: A  487 ILE cc_start: 0.8726 (OUTLIER) cc_final: 0.8508 (mt)
REVERT: A  515 MET cc_start: 0.8525 (mmm) cc_final: 0.7686 (mmp)
REVERT: A  554 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7695 (pt)
  outliers start: 23
  outliers final: 15
  residues processed: 153
  average time/residue: 0.2173
  time to fit residues: 45.5636
Evaluate side-chains
  142 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 1.204 
-------------------------------------------------------------------------------
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   68 ASN
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  476 SER
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
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:    0.7980
   chunk 25 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 75 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 4 optimal weight:    1.9990
   chunk 93 optimal weight:    3.9990
   chunk 28 optimal weight:    5.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
B 166 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.159494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.120804 restraints weight = 11348.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.123065 restraints weight = 8122.812|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.123948 restraints weight = 6695.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7928
moved from start:          0.2319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   8968  Z= 0.304
  Angle     :  0.620   7.787  12134  Z= 0.316
  Chirality :  0.043   0.141   1408
  Planarity :  0.003   0.029   1514
  Dihedral  :  4.949  21.475   1204
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  7.99 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.85 %
    Favored  : 76.82 %
  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: -1.24 (0.25), residues: 1114
  helix:  0.50 (0.22), residues: 598
  sheet: -2.35 (0.48), residues: 70
  loop : -2.43 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 379 
 HIS   0.004   0.001   HIS A 267 
 PHE   0.014   0.002   PHE B 495 
 TYR   0.025   0.002   TYR A 247 
 ARG   0.007   0.001   ARG B 184 

*********************** 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
  163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 1.018 
Fit side-chains
REVERT: B  107 LEU cc_start: 0.8309 (tt) cc_final: 0.8049 (mp)
REVERT: B  258 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7889 (tp)
REVERT: B  343 LYS cc_start: 0.8014 (mptt) cc_final: 0.7813 (mmtt)
REVERT: B  475 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8401 (tt)
REVERT: B  515 MET cc_start: 0.8603 (mmm) cc_final: 0.7606 (mmp)
REVERT: A  191 ARG cc_start: 0.6850 (ttt180) cc_final: 0.6285 (ttt90)
REVERT: A  258 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8070 (tt)
REVERT: A  265 MET cc_start: 0.7914 (mmp) cc_final: 0.7698 (mmp)
REVERT: A  272 GLU cc_start: 0.7236 (pm20) cc_final: 0.6938 (pm20)
REVERT: A  487 ILE cc_start: 0.8732 (OUTLIER) cc_final: 0.8503 (mt)
REVERT: A  515 MET cc_start: 0.8551 (mmm) cc_final: 0.7566 (mmp)
  outliers start: 32
  outliers final: 21
  residues processed: 156
  average time/residue: 0.2165
  time to fit residues: 46.3922
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
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  255 SER
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  475 LEU
Chi-restraints excluded: chain B residue  476 SER
Chi-restraints excluded: chain B residue  544 CYS
Chi-restraints excluded: chain B residue  548 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   68 ASN
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  476 SER
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  548 MET
Chi-restraints excluded: chain A residue  555 LEU
Chi-restraints excluded: chain A residue  556 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 79 optimal weight:    0.8980
   chunk 48 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 77 optimal weight:    6.9990
   chunk 60 optimal weight:    0.7980
   chunk 3 optimal weight:    6.9990
   chunk 50 optimal weight:    9.9990
   chunk 103 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 72 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B  66 ASN
A 437 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.163485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.125841 restraints weight = 11176.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.128166 restraints weight = 7927.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.129609 restraints weight = 6481.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3324
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7858
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8968  Z= 0.192
  Angle     :  0.571   8.892  12134  Z= 0.288
  Chirality :  0.041   0.137   1408
  Planarity :  0.003   0.026   1514
  Dihedral  :  4.723  21.804   1204
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 20.27 %
    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: -0.87 (0.26), residues: 1114
  helix:  0.85 (0.22), residues: 596
  sheet: -2.21 (0.49), residues: 70
  loop : -2.34 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 379 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.017   0.001   PHE A 506 
 TYR   0.023   0.001   TYR A 247 
 ARG   0.007   0.000   ARG B 184 

*********************** 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
  163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.927 
Fit side-chains
REVERT: B  107 LEU cc_start: 0.8282 (tt) cc_final: 0.8010 (mp)
REVERT: B  258 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7879 (tt)
REVERT: B  454 LEU cc_start: 0.9294 (tp) cc_final: 0.8996 (tp)
REVERT: B  471 LEU cc_start: 0.8637 (mp) cc_final: 0.8375 (mt)
REVERT: B  475 LEU cc_start: 0.8541 (OUTLIER) cc_final: 0.8333 (tt)
REVERT: B  515 MET cc_start: 0.8595 (mmm) cc_final: 0.7663 (mmp)
REVERT: B  541 MET cc_start: 0.8084 (tpt) cc_final: 0.7597 (tpt)
REVERT: A  193 ARG cc_start: 0.8208 (ttm110) cc_final: 0.7586 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8403 (OUTLIER) cc_final: 0.8064 (tt)
REVERT: A  272 GLU cc_start: 0.7171 (pm20) cc_final: 0.6849 (pm20)
REVERT: A  487 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8457 (mt)
REVERT: A  515 MET cc_start: 0.8552 (mmm) cc_final: 0.7632 (mmp)
  outliers start: 30
  outliers final: 22
  residues processed: 159
  average time/residue: 0.2179
  time to fit residues: 47.8500
Evaluate side-chains
  150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 124
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ASN
Chi-restraints excluded: chain B residue  108 ILE
Chi-restraints excluded: chain B residue  175 ASP
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  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  475 LEU
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  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
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:    0.9980
   chunk 99 optimal weight:    2.9990
   chunk 60 optimal weight:    0.7980
   chunk 100 optimal weight:    0.1980
   chunk 35 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 54 optimal weight:    0.6980
   chunk 66 optimal weight:    0.9980
   chunk 13 optimal weight:    4.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3769 r_free = 0.3769 target = 0.163984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.125912 restraints weight = 11335.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.128253 restraints weight = 7973.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.129720 restraints weight = 6497.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8968  Z= 0.160
  Angle     :  0.549   8.201  12134  Z= 0.277
  Chirality :  0.040   0.138   1408
  Planarity :  0.003   0.026   1514
  Dihedral  :  4.514  21.986   1204
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 19.96 %
    Favored  : 77.03 %
  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: -0.52 (0.26), residues: 1114
  helix:  1.14 (0.23), residues: 596
  sheet: -1.99 (0.51), residues: 70
  loop : -2.19 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 379 
 HIS   0.003   0.001   HIS A 155 
 PHE   0.015   0.001   PHE B 506 
 TYR   0.025   0.001   TYR B 342 
 ARG   0.006   0.000   ARG B 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
  165 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 1.054 
Fit side-chains
REVERT: B  181 GLN cc_start: 0.5561 (mp10) cc_final: 0.5052 (mp10)
REVERT: B  193 ARG cc_start: 0.8170 (ttm110) cc_final: 0.7273 (mtt180)
REVERT: B  246 ARG cc_start: 0.7636 (ptp-110) cc_final: 0.7045 (mtp85)
REVERT: B  258 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7895 (tt)
REVERT: B  454 LEU cc_start: 0.9212 (tp) cc_final: 0.8961 (tp)
REVERT: B  471 LEU cc_start: 0.8528 (mp) cc_final: 0.8264 (mt)
REVERT: B  515 MET cc_start: 0.8602 (mmm) cc_final: 0.7635 (mmp)
REVERT: B  541 MET cc_start: 0.8116 (tpt) cc_final: 0.7713 (tpt)
REVERT: A  258 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8085 (tt)
REVERT: A  272 GLU cc_start: 0.7155 (pm20) cc_final: 0.6877 (pm20)
REVERT: A  487 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8417 (mt)
REVERT: A  515 MET cc_start: 0.8555 (mmm) cc_final: 0.7641 (mmp)
  outliers start: 29
  outliers final: 19
  residues processed: 158
  average time/residue: 0.2140
  time to fit residues: 46.9261
Evaluate side-chains
  151 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  108 ILE
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  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  108 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 54 optimal weight:    6.9990
   chunk 21 optimal weight:    3.9990
   chunk 59 optimal weight:    0.0040
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0970
   chunk 50 optimal weight:    9.9990
   chunk 90 optimal weight:    1.9990
   chunk 92 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    2.0196

-------------------------------------------------------------------------------
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 = 0.3729 r_free = 0.3729 target = 0.160315 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.121401 restraints weight = 11513.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.123790 restraints weight = 8136.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.125018 restraints weight = 6634.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7903
moved from start:          0.2733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   8968  Z= 0.291
  Angle     :  0.618   9.497  12134  Z= 0.311
  Chirality :  0.043   0.156   1408
  Planarity :  0.003   0.029   1514
  Dihedral  :  4.697  21.151   1204
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  2.91 %
    Allowed  : 21.10 %
    Favored  : 75.99 %
  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: -0.95 (0.26), residues: 1114
  helix:  0.73 (0.22), residues: 614
  sheet: -2.18 (0.50), residues: 70
  loop : -2.41 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 379 
 HIS   0.004   0.001   HIS A 155 
 PHE   0.011   0.002   PHE A 506 
 TYR   0.019   0.002   TYR B 342 
 ARG   0.007   0.001   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
  163 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 135
  time to evaluate  : 1.026 
Fit side-chains
REVERT: B  191 ARG cc_start: 0.6972 (ttt180) cc_final: 0.6741 (ttt-90)
REVERT: B  229 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8179 (tptm)
REVERT: B  246 ARG cc_start: 0.8025 (ptp-110) cc_final: 0.7502 (mtp85)
REVERT: B  258 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7988 (tp)
REVERT: B  515 MET cc_start: 0.8614 (mmm) cc_final: 0.7590 (mmp)
REVERT: A  191 ARG cc_start: 0.6845 (ttt180) cc_final: 0.6281 (ttt90)
REVERT: A  193 ARG cc_start: 0.8249 (ttm110) cc_final: 0.7410 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8213 (tt)
REVERT: A  487 ILE cc_start: 0.8720 (OUTLIER) cc_final: 0.8505 (mt)
REVERT: A  515 MET cc_start: 0.8563 (mmm) cc_final: 0.8051 (mmp)
  outliers start: 28
  outliers final: 22
  residues processed: 158
  average time/residue: 0.2269
  time to fit residues: 48.9697
Evaluate side-chains
  154 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 129
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   68 ASN
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  420 SER
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  476 SER
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 61 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0670
   chunk 58 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 65 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 102 optimal weight:    0.2980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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 = 0.3798 r_free = 0.3798 target = 0.166496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.128888 restraints weight = 11234.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.131286 restraints weight = 7879.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.132694 restraints weight = 6404.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7819
moved from start:          0.2912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8968  Z= 0.149
  Angle     :  0.566   9.127  12134  Z= 0.281
  Chirality :  0.040   0.142   1408
  Planarity :  0.003   0.026   1514
  Dihedral  :  4.512  21.816   1204
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.01 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 22.45 %
    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: -0.37 (0.26), residues: 1114
  helix:  1.21 (0.23), residues: 598
  sheet: -1.86 (0.52), residues: 70
  loop : -2.07 (0.29), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 379 
 HIS   0.005   0.001   HIS A 155 
 PHE   0.020   0.001   PHE A 506 
 TYR   0.022   0.001   TYR B 342 
 ARG   0.008   0.000   ARG B 193 

*********************** 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
  156 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.891 
Fit side-chains
REVERT: B  193 ARG cc_start: 0.8239 (ttm110) cc_final: 0.7300 (mtt180)
REVERT: B  229 LYS cc_start: 0.8545 (mmmm) cc_final: 0.8106 (tptm)
REVERT: B  246 ARG cc_start: 0.7638 (ptp-110) cc_final: 0.6931 (mtp85)
REVERT: B  258 LEU cc_start: 0.8287 (OUTLIER) cc_final: 0.7965 (tp)
REVERT: B  272 GLU cc_start: 0.6988 (pm20) cc_final: 0.6716 (pm20)
REVERT: B  454 LEU cc_start: 0.9187 (tp) cc_final: 0.8975 (tp)
REVERT: B  471 LEU cc_start: 0.8495 (mp) cc_final: 0.8281 (mt)
REVERT: B  515 MET cc_start: 0.8594 (mmm) cc_final: 0.7704 (mmp)
REVERT: B  541 MET cc_start: 0.8158 (tpt) cc_final: 0.7395 (tpt)
REVERT: A  191 ARG cc_start: 0.6763 (ttt180) cc_final: 0.6185 (ttt90)
REVERT: A  193 ARG cc_start: 0.8222 (ttm110) cc_final: 0.7397 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8107 (tt)
REVERT: A  265 MET cc_start: 0.7899 (mmp) cc_final: 0.7626 (mmp)
REVERT: A  272 GLU cc_start: 0.7021 (pm20) cc_final: 0.6809 (pm20)
REVERT: A  487 ILE cc_start: 0.8650 (OUTLIER) cc_final: 0.8413 (mt)
REVERT: A  515 MET cc_start: 0.8571 (mmm) cc_final: 0.7614 (mmp)
REVERT: A  541 MET cc_start: 0.8209 (tpt) cc_final: 0.6391 (tpt)
  outliers start: 21
  outliers final: 17
  residues processed: 153
  average time/residue: 0.2128
  time to fit residues: 45.0212
Evaluate side-chains
  147 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.947 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  420 SER
Chi-restraints excluded: chain B residue  445 VAL
Chi-restraints excluded: chain B residue  499 LEU
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  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  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:    0.9990
   chunk 34 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 85 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 87 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   overall best weight:    1.4986

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

Flipped N/Q/H residues before XYZ refinement:
B 391 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.164485 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.127087 restraints weight = 11258.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.129252 restraints weight = 8229.190|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.130509 restraints weight = 6816.996|
|-----------------------------------------------------------------------------|
r_work (final): 0.3297
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   8968  Z= 0.235
  Angle     :  0.593   9.061  12134  Z= 0.296
  Chirality :  0.042   0.158   1408
  Planarity :  0.003   0.027   1514
  Dihedral  :  4.550  21.381   1204
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 22.66 %
    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: -0.67 (0.26), residues: 1114
  helix:  0.95 (0.22), residues: 614
  sheet: -2.02 (0.51), residues: 70
  loop : -2.29 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 379 
 HIS   0.007   0.001   HIS A 155 
 PHE   0.014   0.001   PHE A 506 
 TYR   0.019   0.001   TYR B 342 
 ARG   0.008   0.001   ARG B 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
  155 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 133
  time to evaluate  : 0.932 
Fit side-chains
REVERT: B  181 GLN cc_start: 0.4734 (mp10) cc_final: 0.4429 (mp10)
REVERT: B  193 ARG cc_start: 0.8234 (ttm110) cc_final: 0.7335 (mtt180)
REVERT: B  229 LYS cc_start: 0.8656 (mmmm) cc_final: 0.8267 (tptm)
REVERT: B  246 ARG cc_start: 0.7740 (ptp-110) cc_final: 0.7137 (mtp85)
REVERT: B  258 LEU cc_start: 0.8326 (OUTLIER) cc_final: 0.8030 (tp)
REVERT: B  454 LEU cc_start: 0.9275 (tp) cc_final: 0.8992 (tp)
REVERT: B  515 MET cc_start: 0.8615 (mmm) cc_final: 0.7636 (mmp)
REVERT: B  541 MET cc_start: 0.8161 (tpt) cc_final: 0.7648 (tpt)
REVERT: A  191 ARG cc_start: 0.6859 (ttt180) cc_final: 0.6282 (ttt90)
REVERT: A  193 ARG cc_start: 0.8209 (ttm110) cc_final: 0.7411 (mtt-85)
REVERT: A  258 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8217 (tt)
REVERT: A  265 MET cc_start: 0.7885 (mmp) cc_final: 0.7623 (mmp)
REVERT: A  272 GLU cc_start: 0.7169 (pm20) cc_final: 0.6947 (pm20)
REVERT: A  487 ILE cc_start: 0.8658 (OUTLIER) cc_final: 0.8439 (mt)
REVERT: A  515 MET cc_start: 0.8589 (mmm) cc_final: 0.8100 (mmp)
  outliers start: 22
  outliers final: 16
  residues processed: 151
  average time/residue: 0.2126
  time to fit residues: 44.3104
Evaluate side-chains
  150 residues out of total 962 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  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  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:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 61 optimal weight:    0.4980
   chunk 47 optimal weight:    0.9980
   chunk 49 optimal weight:    6.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.9582

-------------------------------------------------------------------------------
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 = 0.3775 r_free = 0.3775 target = 0.164604 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.126861 restraints weight = 11231.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.129272 restraints weight = 7926.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.130447 restraints weight = 6449.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   8968  Z= 0.181
  Angle     :  0.568   8.821  12134  Z= 0.283
  Chirality :  0.041   0.145   1408
  Planarity :  0.003   0.027   1514
  Dihedral  :  4.489  21.736   1204
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 9.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.28 %
    Favored  : 93.72 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 22.56 %
    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: -0.34 (0.26), residues: 1114
  helix:  1.22 (0.22), residues: 598
  sheet: -1.88 (0.51), residues: 70
  loop : -2.03 (0.30), residues: 446

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 379 
 HIS   0.007   0.001   HIS B 155 
 PHE   0.017   0.001   PHE A 506 
 TYR   0.020   0.001   TYR B 342 
 ARG   0.008   0.000   ARG B 193 

===============================================================================
Job complete
usr+sys time: 2639.44 seconds
wall clock time: 48 minutes 30.01 seconds (2910.01 seconds total)