Starting phenix.real_space_refine
on Thu Mar  5 00:33:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7fho_31588/03_2026/7fho_31588.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7fho_31588/03_2026/7fho_31588.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7fho_31588/03_2026/7fho_31588.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7fho_31588/03_2026/7fho_31588.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7fho_31588/03_2026/7fho_31588.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7fho_31588/03_2026/7fho_31588.cif"
  }
  resolution = 2.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8728 atoms to isotropic.
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: 5
    Type Number    sf(0)   Gaussians
     Ca      6      9.91       5
     S      44      5.16       5
     C    7102      2.51       5
     N    1630      2.21       5
     O    1866      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10648
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 647, 5321
          Classifications: {'peptide': 647}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 626}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "C"
      Number of atoms: 5321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 647, 5321
          Classifications: {'peptide': 647}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 20, 'TRANS': 626}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "C"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' CA': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.79, per 1000 atoms: 0.26
  Number of scatterers: 10648
  At special positions: 0
  Unit cell: (108.498, 120.666, 100.386, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Ca      6     19.99
     S      44     16.00
     O    1866      8.00
     N    1630      7.00
     C    7102      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  93 " - pdb=" SG  CYS A 101 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  93 " - pdb=" SG  CYS C 101 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 500.1 milliseconds
  

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2472

  Finding SS restraints...
    Secondary structure from input PDB file:
      69 helices and 2 sheets defined
      79.3% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 29 through 43
      removed outlier: 3.594A  pdb=" N   ASP A  43 " --> pdb=" O   ASP A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 52
      removed outlier: 3.661A  pdb=" N   ILE A  51 " --> pdb=" O   PRO A  48 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   LEU A  52 " --> pdb=" O   VAL A  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 48 through 52'
    Processing helix  chain 'A' and resid 57 through 69
      removed outlier: 3.738A  pdb=" N   TYR A  63 " --> pdb=" O   GLU A  59 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 70 through 83
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.646A  pdb=" N   GLU A  88 " --> pdb=" O   ASN A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 90 through 95
      removed outlier: 3.589A  pdb=" N   GLU A  94 " --> pdb=" O   PRO A  90 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LYS A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 90 through 95'
    Processing helix  chain 'A' and resid 116 through 137
    Processing helix  chain 'A' and resid 146 through 149
    Processing helix  chain 'A' and resid 150 through 174
    Processing helix  chain 'A' and resid 186 through 198
    Processing helix  chain 'A' and resid 199 through 238
      removed outlier: 4.580A  pdb=" N   GLY A 214 " --> pdb=" O   SER A 210 " (cutoff:3.500A)
      removed outlier: 4.711A  pdb=" N   THR A 215 " --> pdb=" O   GLY A 211 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 250 through 263
      removed outlier: 3.843A  pdb=" N   THR A 263 " --> pdb=" O   PHE A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 271
      removed outlier: 4.146A  pdb=" N   TRP A 271 " --> pdb=" O   ASN A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 281 through 295
      removed outlier: 3.665A  pdb=" N   PHE A 285 " --> pdb=" O   SER A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 335
      removed outlier: 3.535A  pdb=" N   ALA A 313 " --> pdb=" O   LYS A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 355
      removed outlier: 3.770A  pdb=" N   PHE A 351 " --> pdb=" O   CYS A 347 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   GLU A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   GLN A 353 " --> pdb=" O   LYS A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 376
      removed outlier: 3.703A  pdb=" N   LEU A 370 " --> pdb=" O   GLU A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 391 through 396
      removed outlier: 3.931A  pdb=" N   ALA A 396 " --> pdb=" O   CYS A 392 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 410
      removed outlier: 3.679A  pdb=" N   GLU A 409 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   HIS A 410 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 406 through 410'
    Processing helix  chain 'A' and resid 417 through 429
      removed outlier: 3.760A  pdb=" N   GLN A 422 " --> pdb=" O   ALA A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 453
      removed outlier: 3.776A  pdb=" N   TYR A 434 " --> pdb=" O   PRO A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 487
      removed outlier: 4.183A  pdb=" N   TRP A 464 " --> pdb=" O   ALA A 460 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   TRP A 473 " --> pdb=" O   PHE A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 494
      removed outlier: 4.623A  pdb=" N   GLU A 494 " --> pdb=" O   ASN A 490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 517
      removed outlier: 3.780A  pdb=" N   ARG A 498 " --> pdb=" O   GLU A 494 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLY A 510 " --> pdb=" O   VAL A 506 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE A 515 " --> pdb=" O   GLU A 511 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR A 517 " --> pdb=" O   ALA A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 526 through 542
      removed outlier: 3.566A  pdb=" N   ILE A 542 " --> pdb=" O   MET A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 547
    Processing helix  chain 'A' and resid 548 through 587
      removed outlier: 4.244A  pdb=" N   PHE A 554 " --> pdb=" O   ARG A 550 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE A 562 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
      Proline residue:  A 563  - end of helix
      Proline residue:  A 567  - end of helix
    Processing helix  chain 'A' and resid 601 through 606
    Processing helix  chain 'A' and resid 615 through 628
      removed outlier: 3.668A  pdb=" N   PHE A 624 " --> pdb=" O   MET A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 644
      removed outlier: 3.876A  pdb=" N   MET A 636 " --> pdb=" O   TRP A 632 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP A 641 " --> pdb=" O   GLU A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 647
      No H-bonds generated for 'chain 'A' and resid 645 through 647'
    Processing helix  chain 'A' and resid 648 through 659
      removed outlier: 4.195A  pdb=" N   PHE A 652 " --> pdb=" O   SER A 648 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 662 through 684
      removed outlier: 3.937A  pdb=" N   GLU A 682 " --> pdb=" O   GLU A 678 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   GLU A 683 " --> pdb=" O   LEU A 679 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLU A 684 " --> pdb=" O   ASP A 680 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 29 through 43
      removed outlier: 3.599A  pdb=" N   ASP C  43 " --> pdb=" O   ASP C  39 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 48 through 52
      removed outlier: 3.630A  pdb=" N   ILE C  51 " --> pdb=" O   PRO C  48 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU C  52 " --> pdb=" O   VAL C  49 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 48 through 52'
    Processing helix  chain 'C' and resid 57 through 69
      removed outlier: 3.734A  pdb=" N   TYR C  63 " --> pdb=" O   GLU C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 70 through 83
    Processing helix  chain 'C' and resid 84 through 88
      removed outlier: 3.634A  pdb=" N   GLU C  88 " --> pdb=" O   ASN C  85 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 95
      removed outlier: 3.577A  pdb=" N   GLU C  94 " --> pdb=" O   PRO C  90 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   LYS C  95 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 90 through 95'
    Processing helix  chain 'C' and resid 116 through 137
    Processing helix  chain 'C' and resid 146 through 149
    Processing helix  chain 'C' and resid 150 through 174
    Processing helix  chain 'C' and resid 186 through 198
    Processing helix  chain 'C' and resid 199 through 238
      removed outlier: 4.779A  pdb=" N   GLY C 214 " --> pdb=" O   SER C 210 " (cutoff:3.500A)
      removed outlier: 5.150A  pdb=" N   THR C 215 " --> pdb=" O   GLY C 211 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU C 222 " --> pdb=" O   ASN C 218 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 263
    Processing helix  chain 'C' and resid 266 through 271
      removed outlier: 4.199A  pdb=" N   TRP C 271 " --> pdb=" O   ASN C 267 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 271 through 278
    Processing helix  chain 'C' and resid 280 through 335
      removed outlier: 4.412A  pdb=" N   PHE C 284 " --> pdb=" O   TRP C 280 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   PHE C 285 " --> pdb=" O   SER C 281 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 343 through 355
      removed outlier: 3.613A  pdb=" N   CYS C 347 " --> pdb=" O   ASP C 343 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 376
      removed outlier: 3.513A  pdb=" N   PHE C 368 " --> pdb=" O   SER C 364 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   GLY C 369 " --> pdb=" O   LYS C 365 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP C 376 " --> pdb=" O   PHE C 372 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 386 through 389
    Processing helix  chain 'C' and resid 390 through 396
      removed outlier: 3.546A  pdb=" N   ALA C 394 " --> pdb=" O   ASP C 390 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ALA C 396 " --> pdb=" O   CYS C 392 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 406 through 410
      removed outlier: 3.710A  pdb=" N   GLU C 409 " --> pdb=" O   SER C 406 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   HIS C 410 " --> pdb=" O   LEU C 407 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 406 through 410'
    Processing helix  chain 'C' and resid 417 through 429
    Processing helix  chain 'C' and resid 430 through 453
      removed outlier: 3.756A  pdb=" N   TYR C 434 " --> pdb=" O   PRO C 430 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU C 453 " --> pdb=" O   VAL C 449 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 460 through 487
      removed outlier: 4.484A  pdb=" N   TRP C 464 " --> pdb=" O   ALA C 460 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 488 through 494
      removed outlier: 4.669A  pdb=" N   GLU C 494 " --> pdb=" O   ASN C 490 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 494 through 516
      removed outlier: 3.714A  pdb=" N   ARG C 498 " --> pdb=" O   GLU C 494 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 526 through 541
    Processing helix  chain 'C' and resid 542 through 547
    Processing helix  chain 'C' and resid 548 through 565
      removed outlier: 3.700A  pdb=" N   PHE C 554 " --> pdb=" O   ARG C 550 " (cutoff:3.500A)
      Proline residue:  C 563  - end of helix
    Processing helix  chain 'C' and resid 565 through 587
    Processing helix  chain 'C' and resid 601 through 606
    Processing helix  chain 'C' and resid 615 through 628
      removed outlier: 3.562A  pdb=" N   PHE C 624 " --> pdb=" O   MET C 620 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 632 through 644
      removed outlier: 3.890A  pdb=" N   MET C 636 " --> pdb=" O   TRP C 632 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS C 640 " --> pdb=" O   MET C 636 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   ASP C 641 " --> pdb=" O   GLU C 637 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 645 through 647
      No H-bonds generated for 'chain 'C' and resid 645 through 647'
    Processing helix  chain 'C' and resid 648 through 659
      removed outlier: 4.119A  pdb=" N   PHE C 652 " --> pdb=" O   SER C 648 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 662 through 683
    Processing sheet with id=AA1, first strand: chain 'A' and resid 341 through 342
      removed outlier: 3.532A  pdb=" N   ILE A 383 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 341 through 342

    686 hydrogen bonds defined for protein.
    2025 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: 1.73

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3192
        1.34 -     1.46: 2416
        1.46 -     1.58: 5254
        1.58 -     1.69: 0
        1.69 -     1.81: 72
  Bond restraints: 10934
  Sorted by residual:
  bond pdb=" C   ALA A 187 "
       pdb=" N   PRO A 188 "
    ideal  model  delta    sigma   weight residual
    1.334  1.365 -0.031 1.51e-02 4.39e+03 4.08e+00
  bond pdb=" C   ALA C 187 "
       pdb=" N   PRO C 188 "
    ideal  model  delta    sigma   weight residual
    1.335  1.361 -0.026 1.38e-02 5.25e+03 3.48e+00
  bond pdb=" CG  GLU C 352 "
       pdb=" CD  GLU C 352 "
    ideal  model  delta    sigma   weight residual
    1.516  1.486  0.030 2.50e-02 1.60e+03 1.41e+00
  bond pdb=" C   PHE A 137 "
       pdb=" N   PRO A 138 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.25e+00
  bond pdb=" C   PHE C 137 "
       pdb=" N   PRO C 138 "
    ideal  model  delta    sigma   weight residual
    1.334  1.360 -0.026 2.34e-02 1.83e+03 1.24e+00
  ... (remaining 10929 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 14600
        1.76 -     3.51: 233
        3.51 -     5.27: 34
        5.27 -     7.02: 5
        7.02 -     8.78: 4
  Bond angle restraints: 14876
  Sorted by residual:
  angle pdb=" C   GLU C 111 "
        pdb=" N   LEU C 112 "
        pdb=" CA  LEU C 112 "
      ideal   model   delta    sigma   weight residual
     122.21  113.43    8.78 2.87e+00 1.21e-01 9.35e+00
  angle pdb=" C   GLU A 111 "
        pdb=" N   LEU A 112 "
        pdb=" CA  LEU A 112 "
      ideal   model   delta    sigma   weight residual
     122.21  113.51    8.70 2.87e+00 1.21e-01 9.19e+00
  angle pdb=" N   GLY A 110 "
        pdb=" CA  GLY A 110 "
        pdb=" C   GLY A 110 "
      ideal   model   delta    sigma   weight residual
     113.18  120.35   -7.17 2.37e+00 1.78e-01 9.16e+00
  angle pdb=" N   GLY C 110 "
        pdb=" CA  GLY C 110 "
        pdb=" C   GLY C 110 "
      ideal   model   delta    sigma   weight residual
     113.18  120.34   -7.16 2.37e+00 1.78e-01 9.12e+00
  angle pdb=" C   ILE C 186 "
        pdb=" N   ALA C 187 "
        pdb=" CA  ALA C 187 "
      ideal   model   delta    sigma   weight residual
     120.58  124.36   -3.78 1.32e+00 5.74e-01 8.19e+00
  ... (remaining 14871 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 5691
       16.90 -    33.79: 518
       33.79 -    50.69: 79
       50.69 -    67.58: 21
       67.58 -    84.48: 3
  Dihedral angle restraints: 6312
    sinusoidal: 2484
      harmonic: 3828
  Sorted by residual:
  dihedral pdb=" CB  CYS C  93 "
           pdb=" SG  CYS C  93 "
           pdb=" SG  CYS C 101 "
           pdb=" CB  CYS C 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  148.41  -55.41     1      1.00e+01 1.00e-02 4.15e+01
  dihedral pdb=" CB  CYS A  93 "
           pdb=" SG  CYS A  93 "
           pdb=" SG  CYS A 101 "
           pdb=" CB  CYS A 101 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  147.57  -54.57     1      1.00e+01 1.00e-02 4.04e+01
  dihedral pdb=" CA  GLY A 110 "
           pdb=" C   GLY A 110 "
           pdb=" N   GLU A 111 "
           pdb=" CA  GLU A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.54   21.46     0      5.00e+00 4.00e-02 1.84e+01
  ... (remaining 6309 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1107
       0.032 -    0.064: 443
       0.064 -    0.096: 105
       0.096 -    0.128: 28
       0.128 -    0.159: 3
  Chirality restraints: 1686
  Sorted by residual:
  chirality pdb=" CA  GLU C 111 "
            pdb=" N   GLU C 111 "
            pdb=" C   GLU C 111 "
            pdb=" CB  GLU C 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.35e-01
  chirality pdb=" CA  GLU A 111 "
            pdb=" N   GLU A 111 "
            pdb=" C   GLU A 111 "
            pdb=" CB  GLU A 111 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.34e-01
  chirality pdb=" CA  ILE C 542 "
            pdb=" N   ILE C 542 "
            pdb=" C   ILE C 542 "
            pdb=" CB  ILE C 542 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.91e-01
  ... (remaining 1683 not shown)

  Planarity restraints: 1832
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 562 "    0.032 5.00e-02 4.00e+02   4.88e-02 3.81e+00
        pdb=" N   PRO A 563 "   -0.084 5.00e-02 4.00e+02
        pdb=" CA  PRO A 563 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 563 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE C 562 "    0.031 5.00e-02 4.00e+02   4.71e-02 3.55e+00
        pdb=" N   PRO C 563 "   -0.082 5.00e-02 4.00e+02
        pdb=" CA  PRO C 563 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO C 563 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 293 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   VAL C 293 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL C 293 "    0.011 2.00e-02 2.50e+03
        pdb=" N   TYR C 294 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1829 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 366
        2.72 -     3.27: 11324
        3.27 -     3.81: 17529
        3.81 -     4.36: 21125
        4.36 -     4.90: 35713
  Nonbonded interactions: 86057
  Sorted by model distance:
  nonbonded pdb=" OG  SER C 265 "
            pdb=" OE1 GLN C 633 "
     model   vdw
     2.179 3.040
  nonbonded pdb=" OG  SER A 265 "
            pdb=" OE1 GLN A 633 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OH  TYR C 114 "
            pdb=" OD1 ASP C 615 "
     model   vdw
     2.198 3.040
  nonbonded pdb=" OH  TYR A 114 "
            pdb=" OD1 ASP A 615 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OH  TYR C 216 "
            pdb=" O   VAL C 657 "
     model   vdw
     2.236 3.040
  ... (remaining 86052 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
}

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 individual isotropic
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:             0.950
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.430
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.430
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
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      :  0.002   0.031  10936  Z= 0.124
  Angle     :  0.572   8.776  14880  Z= 0.329
  Chirality :  0.036   0.159   1686
  Planarity :  0.004   0.049   1832
  Dihedral  : 12.957  84.477   3834
  Min Nonbonded Distance : 2.179

Molprobity Statistics.
  All-atom Clashscore : 6.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.52 %
    Favored  : 99.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.34 (0.24), residues: 1282
  helix:  1.43 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -0.59 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 185 
 TYR   0.012   0.001   TYR A 294 
 PHE   0.023   0.001   PHE A 331 
 TRP   0.011   0.001   TRP C 271 
 HIS   0.001   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 (10934)
  covalent geometry    : angle       0.57229 (14876)
  SS BOND              : bond        0.00215 (    2)
  SS BOND              : angle       0.93929 (    4)
  hydrogen bonds       : bond        0.18333 (  686)
  hydrogen bonds       : angle       5.58980 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 160
  time to evaluate  : 0.387 
Fit side-chains
REVERT: A  543 ARG cc_start: 0.8548 (OUTLIER) cc_final: 0.6714 (mmp-170)
REVERT: A  670 PHE cc_start: 0.7673 (m-10) cc_final: 0.7312 (t80)
REVERT: C  258 MET cc_start: 0.8705 (mmm) cc_final: 0.8455 (mmp)
REVERT: C  469 PHE cc_start: 0.6942 (t80) cc_final: 0.6621 (t80)
  outliers start: 2
  outliers final: 1
  residues processed: 161
  average time/residue: 0.5812
  time to fit residues: 100.5027
Evaluate side-chains
  103 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 101
  time to evaluate  : 0.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  543 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 98 optimal weight:    0.0980
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0040
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9980
   chunk 55 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    0.6194

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

Flipped N/Q/H residues before XYZ refinement:
A 497 ASN
** C 267 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 497 ASN
C 547 ASN
C 585 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.169800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.112783 restraints weight = 13088.479|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.93
r_work: 0.3191 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10936  Z= 0.126
  Angle     :  0.525   6.955  14880  Z= 0.274
  Chirality :  0.037   0.172   1686
  Planarity :  0.004   0.045   1832
  Dihedral  :  3.759  23.691   1412
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.35 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  8.75 %
    Favored  : 90.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.11 (0.24), residues: 1282
  helix:  1.98 (0.17), residues: 948
  sheet:  None (None), residues: 0
  loop : -0.23 (0.37), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 379 
 TYR   0.012   0.001   TYR A 294 
 PHE   0.020   0.001   PHE C 331 
 TRP   0.011   0.001   TRP A 271 
 HIS   0.001   0.000   HIS C 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 (10934)
  covalent geometry    : angle       0.52412 (14876)
  SS BOND              : bond        0.00622 (    2)
  SS BOND              : angle       1.65167 (    4)
  hydrogen bonds       : bond        0.05074 (  686)
  hydrogen bonds       : angle       3.99667 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 123
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A  390 ASP cc_start: 0.7868 (t70) cc_final: 0.7409 (t0)
REVERT: C  390 ASP cc_start: 0.7884 (t70) cc_final: 0.7294 (t0)
REVERT: C  469 PHE cc_start: 0.7035 (t80) cc_final: 0.6688 (t80)
REVERT: C  526 ASN cc_start: 0.5762 (t0) cc_final: 0.5523 (t0)
REVERT: C  566 MET cc_start: 0.9241 (OUTLIER) cc_final: 0.9031 (mmm)
  outliers start: 13
  outliers final: 4
  residues processed: 131
  average time/residue: 0.5166
  time to fit residues: 73.8745
Evaluate side-chains
  105 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 100
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain C residue  483 ILE
Chi-restraints excluded: chain C residue  542 ILE
Chi-restraints excluded: chain C residue  566 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 90 optimal weight:    0.5980
   chunk 127 optimal weight:    3.9990
   chunk 122 optimal weight:    0.8980
   chunk 93 optimal weight:    7.9990
   chunk 39 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 101 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 218 ASN
A 497 ASN
C 585 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.169334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.111971 restraints weight = 13161.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.95
r_work: 0.3163 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.1664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10936  Z= 0.133
  Angle     :  0.520   7.105  14880  Z= 0.268
  Chirality :  0.038   0.216   1686
  Planarity :  0.004   0.044   1832
  Dihedral  :  3.621  22.380   1406
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 5.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.31 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.16 (0.24), residues: 1282
  helix:  2.04 (0.17), residues: 952
  sheet:  None (None), residues: 0
  loop : -0.34 (0.36), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 537 
 TYR   0.013   0.001   TYR C 294 
 PHE   0.016   0.001   PHE A 164 
 TRP   0.012   0.001   TRP A 271 
 HIS   0.001   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10934)
  covalent geometry    : angle       0.51994 (14876)
  SS BOND              : bond        0.00319 (    2)
  SS BOND              : angle       0.44051 (    4)
  hydrogen bonds       : bond        0.04579 (  686)
  hydrogen bonds       : angle       3.80136 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 118
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  351 PHE cc_start: 0.8096 (m-80) cc_final: 0.7790 (m-80)
REVERT: A  390 ASP cc_start: 0.7837 (t70) cc_final: 0.7324 (t0)
REVERT: A  499 PHE cc_start: 0.7649 (t80) cc_final: 0.7312 (t80)
REVERT: C  331 PHE cc_start: 0.7845 (t80) cc_final: 0.7594 (t80)
REVERT: C  352 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8462 (pm20)
REVERT: C  390 ASP cc_start: 0.7927 (t70) cc_final: 0.7282 (t0)
  outliers start: 15
  outliers final: 1
  residues processed: 128
  average time/residue: 0.4701
  time to fit residues: 66.2047
Evaluate side-chains
  101 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 99
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain C residue  352 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 102 optimal weight:    5.9990
   chunk 44 optimal weight:    6.9990
   chunk 86 optimal weight:    1.9990
   chunk 115 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 98 optimal weight:    5.9990
   chunk 62 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
C 585 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.167645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.109674 restraints weight = 13290.471|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 1.95
r_work: 0.3132 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 4.14 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10936  Z= 0.150
  Angle     :  0.528   7.379  14880  Z= 0.271
  Chirality :  0.039   0.243   1686
  Planarity :  0.004   0.046   1832
  Dihedral  :  3.685  22.555   1406
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 11.96 %
    Favored  : 86.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.25 (0.24), residues: 1282
  helix:  2.07 (0.17), residues: 954
  sheet:  None (None), residues: 0
  loop : -0.18 (0.36), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 537 
 TYR   0.017   0.001   TYR C 294 
 PHE   0.015   0.001   PHE C 469 
 TRP   0.012   0.001   TRP A 271 
 HIS   0.001   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (10934)
  covalent geometry    : angle       0.52775 (14876)
  SS BOND              : bond        0.00170 (    2)
  SS BOND              : angle       0.87693 (    4)
  hydrogen bonds       : bond        0.04623 (  686)
  hydrogen bonds       : angle       3.77837 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 118
  time to evaluate  : 0.423 
Fit side-chains
REVERT: A  351 PHE cc_start: 0.8126 (m-80) cc_final: 0.7911 (m-80)
REVERT: A  390 ASP cc_start: 0.7840 (t70) cc_final: 0.7290 (t0)
REVERT: A  499 PHE cc_start: 0.7624 (t80) cc_final: 0.7302 (t80)
REVERT: A  585 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7749 (tm-30)
REVERT: A  637 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7749 (mp0)
REVERT: C  331 PHE cc_start: 0.7941 (t80) cc_final: 0.7708 (t80)
REVERT: C  352 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8450 (pp20)
REVERT: C  390 ASP cc_start: 0.8010 (t70) cc_final: 0.7368 (t0)
REVERT: C  469 PHE cc_start: 0.7104 (t80) cc_final: 0.6813 (t80)
  outliers start: 16
  outliers final: 5
  residues processed: 130
  average time/residue: 0.4538
  time to fit residues: 65.0300
Evaluate side-chains
  115 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 107
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  474 ILE
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain A residue  637 GLU
Chi-restraints excluded: chain C residue   49 VAL
Chi-restraints excluded: chain C residue  170 ASP
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain C residue  483 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 114 optimal weight:    0.6980
   chunk 119 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 127 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0050
   chunk 0 optimal weight:   10.0000
   chunk 48 optimal weight:    0.0170
   chunk 22 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 113 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    0.4232

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

Flipped N/Q/H residues before XYZ refinement:
C 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.171008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.113918 restraints weight = 13063.886|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 1.96
r_work: 0.3186 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3064 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.2047

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  10936  Z= 0.105
  Angle     :  0.476   7.662  14880  Z= 0.246
  Chirality :  0.037   0.260   1686
  Planarity :  0.004   0.048   1832
  Dihedral  :  3.492  21.341   1406
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  : 13.52 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.64 (0.24), residues: 1282
  helix:  2.35 (0.17), residues: 940
  sheet:  None (None), residues: 0
  loop :  0.06 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 537 
 TYR   0.013   0.001   TYR C 256 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.010   0.001   TRP A 223 
 HIS   0.001   0.000   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 (10934)
  covalent geometry    : angle       0.47611 (14876)
  SS BOND              : bond        0.00103 (    2)
  SS BOND              : angle       0.17731 (    4)
  hydrogen bonds       : bond        0.03829 (  686)
  hydrogen bonds       : angle       3.61163 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 124
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
REVERT: A  351 PHE cc_start: 0.8207 (m-80) cc_final: 0.7976 (m-80)
REVERT: A  390 ASP cc_start: 0.7857 (t70) cc_final: 0.7273 (t0)
REVERT: A  499 PHE cc_start: 0.7616 (t80) cc_final: 0.7291 (t80)
REVERT: C  331 PHE cc_start: 0.7822 (t80) cc_final: 0.7567 (t80)
REVERT: C  352 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.8473 (pm20)
REVERT: C  390 ASP cc_start: 0.7961 (t70) cc_final: 0.7270 (t0)
  outliers start: 9
  outliers final: 2
  residues processed: 130
  average time/residue: 0.4486
  time to fit residues: 64.3328
Evaluate side-chains
  108 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 105
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  637 GLU
Chi-restraints excluded: chain C residue  352 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 101 optimal weight:   20.0000
   chunk 14 optimal weight:    7.9990
   chunk 123 optimal weight:    1.9990
   chunk 122 optimal weight:    0.6980
   chunk 119 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 22 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
C 298 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.165160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.105225 restraints weight = 13072.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3187 rms_B_bonded: 1.91
r_work: 0.3065 rms_B_bonded: 2.50 restraints_weight: 0.5000
r_work: 0.2944 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2186

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10936  Z= 0.176
  Angle     :  0.548   8.060  14880  Z= 0.281
  Chirality :  0.040   0.272   1686
  Planarity :  0.004   0.048   1832
  Dihedral  :  3.693  21.331   1406
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 14.82 %
    Favored  : 83.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.42 (0.24), residues: 1282
  helix:  2.16 (0.16), residues: 954
  sheet:  None (None), residues: 0
  loop : -0.02 (0.37), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 279 
 TYR   0.022   0.002   TYR C 256 
 PHE   0.027   0.002   PHE A 331 
 TRP   0.014   0.001   TRP C 271 
 HIS   0.001   0.001   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00427 (10934)
  covalent geometry    : angle       0.54788 (14876)
  SS BOND              : bond        0.00140 (    2)
  SS BOND              : angle       0.66340 (    4)
  hydrogen bonds       : bond        0.04697 (  686)
  hydrogen bonds       : angle       3.76691 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  390 ASP cc_start: 0.7915 (t70) cc_final: 0.7312 (t0)
REVERT: A  499 PHE cc_start: 0.7521 (t80) cc_final: 0.7219 (t80)
REVERT: A  585 GLN cc_start: 0.8489 (OUTLIER) cc_final: 0.7572 (tm-30)
REVERT: C  331 PHE cc_start: 0.7729 (t80) cc_final: 0.7484 (t80)
REVERT: C  352 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8401 (pm20)
REVERT: C  390 ASP cc_start: 0.7902 (t70) cc_final: 0.7239 (t0)
  outliers start: 15
  outliers final: 2
  residues processed: 118
  average time/residue: 0.5179
  time to fit residues: 66.6927
Evaluate side-chains
  104 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  585 GLN
Chi-restraints excluded: chain C residue  352 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 27 optimal weight:    0.9980
   chunk 84 optimal weight:    0.0980
   chunk 75 optimal weight:    0.9990
   chunk 101 optimal weight:   20.0000
   chunk 98 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 78 optimal weight:    7.9990
   chunk 115 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
C 218 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.167901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.108627 restraints weight = 12945.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.3235 rms_B_bonded: 1.97
r_work: 0.3111 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2988 rms_B_bonded: 4.13 restraints_weight: 0.2500
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.2238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10936  Z= 0.116
  Angle     :  0.498   8.564  14880  Z= 0.255
  Chirality :  0.038   0.286   1686
  Planarity :  0.004   0.049   1832
  Dihedral  :  3.584  20.843   1406
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 14.99 %
    Favored  : 84.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.67 (0.24), residues: 1282
  helix:  2.34 (0.17), residues: 940
  sheet:  None (None), residues: 0
  loop :  0.20 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  69 
 TYR   0.017   0.001   TYR C 256 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.010   0.001   TRP A 271 
 HIS   0.000   0.000   HIS C 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (10934)
  covalent geometry    : angle       0.49792 (14876)
  SS BOND              : bond        0.00077 (    2)
  SS BOND              : angle       0.31924 (    4)
  hydrogen bonds       : bond        0.04035 (  686)
  hydrogen bonds       : angle       3.64462 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 109
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A  331 PHE cc_start: 0.7703 (t80) cc_final: 0.7378 (t80)
REVERT: A  390 ASP cc_start: 0.7955 (t70) cc_final: 0.7311 (t0)
REVERT: A  499 PHE cc_start: 0.7571 (t80) cc_final: 0.7237 (t80)
REVERT: A  637 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8124 (mm-30)
REVERT: C  103 ASP cc_start: 0.7911 (t70) cc_final: 0.7566 (p0)
REVERT: C  331 PHE cc_start: 0.7710 (t80) cc_final: 0.7462 (t80)
REVERT: C  352 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8423 (pm20)
REVERT: C  390 ASP cc_start: 0.7929 (t70) cc_final: 0.7239 (t0)
REVERT: C  511 GLU cc_start: 0.6743 (tp30) cc_final: 0.6277 (tm-30)
  outliers start: 10
  outliers final: 4
  residues processed: 118
  average time/residue: 0.5044
  time to fit residues: 65.0661
Evaluate side-chains
  108 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  637 GLU
Chi-restraints excluded: chain C residue  352 GLU
Chi-restraints excluded: chain C residue  483 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 69 optimal weight:    0.6980
   chunk 41 optimal weight:    0.4980
   chunk 117 optimal weight:    0.5980
   chunk 99 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 103 optimal weight:    4.9990
   chunk 123 optimal weight:    0.8980
   chunk 7 optimal weight:    0.0270
   chunk 16 optimal weight:    0.6980
   chunk 122 optimal weight:    0.9980
   chunk 102 optimal weight:    3.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A  96 ASN
C 585 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.170494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.114083 restraints weight = 13134.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3315 rms_B_bonded: 1.92
r_work: 0.3188 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3066 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.2343

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  10936  Z= 0.108
  Angle     :  0.492   9.140  14880  Z= 0.250
  Chirality :  0.038   0.293   1686
  Planarity :  0.004   0.048   1832
  Dihedral  :  3.442  19.367   1406
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 15.86 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.84 (0.24), residues: 1282
  helix:  2.44 (0.17), residues: 940
  sheet:  None (None), residues: 0
  loop :  0.37 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  69 
 TYR   0.018   0.001   TYR C 256 
 PHE   0.014   0.001   PHE A 164 
 TRP   0.011   0.001   TRP A 271 
 HIS   0.000   0.000   HIS C 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (10934)
  covalent geometry    : angle       0.49196 (14876)
  SS BOND              : bond        0.00198 (    2)
  SS BOND              : angle       0.41919 (    4)
  hydrogen bonds       : bond        0.03748 (  686)
  hydrogen bonds       : angle       3.55751 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 111
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  331 PHE cc_start: 0.7770 (t80) cc_final: 0.7478 (t80)
REVERT: A  390 ASP cc_start: 0.7890 (t70) cc_final: 0.7259 (t0)
REVERT: A  499 PHE cc_start: 0.7618 (t80) cc_final: 0.7299 (t80)
REVERT: A  602 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8077 (mt-10)
REVERT: A  637 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7562 (mp0)
REVERT: C  390 ASP cc_start: 0.7910 (t70) cc_final: 0.7251 (t0)
REVERT: C  511 GLU cc_start: 0.6755 (tp30) cc_final: 0.6302 (tm-30)
  outliers start: 8
  outliers final: 3
  residues processed: 119
  average time/residue: 0.4766
  time to fit residues: 62.2219
Evaluate side-chains
  110 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 106
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  637 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 85 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 111 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 497 ASN
A 585 GLN
C 497 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.169318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.112743 restraints weight = 13224.786|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 1.91
r_work: 0.3168 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3048 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8244
moved from start:          0.2392

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10936  Z= 0.125
  Angle     :  0.524   9.743  14880  Z= 0.265
  Chirality :  0.038   0.303   1686
  Planarity :  0.004   0.049   1832
  Dihedral  :  3.506  18.952   1406
  Min Nonbonded Distance : 2.261

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.25 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.80 (0.24), residues: 1282
  helix:  2.41 (0.16), residues: 940
  sheet:  None (None), residues: 0
  loop :  0.34 (0.37), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 379 
 TYR   0.020   0.001   TYR C 256 
 PHE   0.025   0.001   PHE C 331 
 TRP   0.012   0.001   TRP C 271 
 HIS   0.000   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (10934)
  covalent geometry    : angle       0.52439 (14876)
  SS BOND              : bond        0.00172 (    2)
  SS BOND              : angle       0.33492 (    4)
  hydrogen bonds       : bond        0.03983 (  686)
  hydrogen bonds       : angle       3.60123 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 107
  time to evaluate  : 0.372 
Fit side-chains
REVERT: A  331 PHE cc_start: 0.7775 (t80) cc_final: 0.7546 (t80)
REVERT: A  390 ASP cc_start: 0.7871 (t70) cc_final: 0.7245 (t0)
REVERT: A  499 PHE cc_start: 0.7644 (t80) cc_final: 0.7316 (t80)
REVERT: A  602 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8125 (mt-10)
REVERT: C  390 ASP cc_start: 0.7928 (t70) cc_final: 0.7266 (t0)
REVERT: C  511 GLU cc_start: 0.6769 (tp30) cc_final: 0.6314 (tm-30)
  outliers start: 12
  outliers final: 6
  residues processed: 116
  average time/residue: 0.5117
  time to fit residues: 64.4617
Evaluate side-chains
  108 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 102
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain A residue  483 ILE
Chi-restraints excluded: chain A residue  497 ASN
Chi-restraints excluded: chain C residue  497 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 120 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 71 optimal weight:    4.9990
   chunk 18 optimal weight:    0.8980
   chunk 60 optimal weight:    0.6980
   chunk 76 optimal weight:    0.8980
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 48 optimal weight:    0.0570
   chunk 12 optimal weight:    0.9990
   overall best weight:    0.6698

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

Flipped N/Q/H residues before XYZ refinement:
C 497 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.169920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.113295 restraints weight = 13164.998|
|-----------------------------------------------------------------------------|
r_work (start): 0.3307 rms_B_bonded: 1.91
r_work: 0.3180 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.09 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10936  Z= 0.115
  Angle     :  0.530   9.908  14880  Z= 0.265
  Chirality :  0.038   0.309   1686
  Planarity :  0.004   0.066   1832
  Dihedral  :  3.490  18.681   1406
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 15.86 %
    Favored  : 83.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.87 (0.24), residues: 1282
  helix:  2.46 (0.16), residues: 938
  sheet:  None (None), residues: 0
  loop :  0.40 (0.37), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG C 379 
 TYR   0.019   0.001   TYR C 256 
 PHE   0.017   0.001   PHE A 501 
 TRP   0.013   0.001   TRP A 492 
 HIS   0.000   0.000   HIS C 416 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10934)
  covalent geometry    : angle       0.53048 (14876)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.28281 (    4)
  hydrogen bonds       : bond        0.03857 (  686)
  hydrogen bonds       : angle       3.59282 ( 2025)

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

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

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2564 Ramachandran restraints generated.
    1282 Oldfield, 0 Emsley, 1282 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.399 
Fit side-chains
REVERT: A  331 PHE cc_start: 0.7832 (t80) cc_final: 0.7619 (t80)
REVERT: A  390 ASP cc_start: 0.7869 (t70) cc_final: 0.7243 (t0)
REVERT: A  499 PHE cc_start: 0.7589 (t80) cc_final: 0.7282 (t80)
REVERT: A  602 GLU cc_start: 0.8321 (mt-10) cc_final: 0.8075 (mt-10)
REVERT: C  390 ASP cc_start: 0.7928 (t70) cc_final: 0.7261 (t0)
REVERT: C  499 PHE cc_start: 0.7504 (t80) cc_final: 0.7165 (t80)
REVERT: C  511 GLU cc_start: 0.6773 (tp30) cc_final: 0.6364 (tm-30)
REVERT: C  602 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8141 (mt-10)
REVERT: C  637 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7749 (mp0)
  outliers start: 6
  outliers final: 3
  residues processed: 112
  average time/residue: 0.4744
  time to fit residues: 58.3018
Evaluate side-chains
  107 residues out of total 1156 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 103
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ARG
Chi-restraints excluded: chain A residue  324 ARG
Chi-restraints excluded: chain A residue  348 ILE
Chi-restraints excluded: chain C residue  637 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 128
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 63 optimal weight:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9990
   chunk 127 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   chunk 73 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 81 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 497 ASN
C 497 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.169012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.112270 restraints weight = 13229.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3288 rms_B_bonded: 1.91
r_work: 0.3164 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.06 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2487

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10936  Z= 0.125
  Angle     :  0.538   9.645  14880  Z= 0.269
  Chirality :  0.038   0.306   1686
  Planarity :  0.004   0.055   1832
  Dihedral  :  3.534  18.984   1406
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 15.34 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.83 (0.24), residues: 1282
  helix:  2.43 (0.16), residues: 938
  sheet:  None (None), residues: 0
  loop :  0.38 (0.37), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 379 
 TYR   0.020   0.001   TYR C 256 
 PHE   0.025   0.001   PHE C 331 
 TRP   0.016   0.001   TRP C 492 
 HIS   0.000   0.000   HIS A 134 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10934)
  covalent geometry    : angle       0.53845 (14876)
  SS BOND              : bond        0.00125 (    2)
  SS BOND              : angle       0.37697 (    4)
  hydrogen bonds       : bond        0.04009 (  686)
  hydrogen bonds       : angle       3.60499 ( 2025)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4121.50 seconds
wall clock time: 70 minutes 36.74 seconds (4236.74 seconds total)