Starting phenix.real_space_refine
on Wed Jul 30 20:33:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ioa_35613/07_2025/8ioa_35613.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ioa_35613/07_2025/8ioa_35613.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ioa_35613/07_2025/8ioa_35613.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ioa_35613/07_2025/8ioa_35613.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ioa_35613/07_2025/8ioa_35613.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ioa_35613/07_2025/8ioa_35613.cif"
  }
  resolution = 2.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.048
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     Mg      2      5.21       5
     S      32      5.16       5
     C    7972      2.51       5
     N    2252      2.21       5
     O    2308      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12570
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6258
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 788, 6240
          Classifications: {'peptide': 788}
          Link IDs: {'PTRANS': 49, 'TRANS': 738}
      Conformer: "B"
        Number of residues, atoms: 788, 6240
          Classifications: {'peptide': 788}
          Link IDs: {'PTRANS': 49, 'TRANS': 738}
          bond proxies already assigned to first conformer: 6393
    Chain: "B"
      Number of atoms: 6258
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 788, 6240
          Classifications: {'peptide': 788}
          Link IDs: {'PTRANS': 49, 'TRANS': 738}
      Conformer: "B"
        Number of residues, atoms: 788, 6240
          Classifications: {'peptide': 788}
          Link IDs: {'PTRANS': 49, 'TRANS': 738}
          bond proxies already assigned to first conformer: 6393
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 27
          Unusual residues: {' MG': 1, 'TPP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 27
          Unusual residues: {' MG': 1, 'TPP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 14.16, per 1000 atoms: 1.13
  Number of scatterers: 12570
  At special positions: 0
  Unit cell: (98.4, 107.42, 99.22, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      32     16.00
     P       4     15.00
     Mg      2     11.99
     O    2308      8.00
     N    2252      7.00
     C    7972      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 3.38
  Conformation dependent library (CDL) restraints added in 3.3 seconds
  

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2932

  Finding SS restraints...
    Secondary structure from input PDB file:
      76 helices and 10 sheets defined
      51.0% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 14 through 38
    Processing helix  chain 'A' and resid 49 through 53
    Processing helix  chain 'A' and resid 63 through 82
      removed outlier: 3.566A  pdb=" N   HIS A  73 " --> pdb=" O   PHE A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 106
      removed outlier: 3.589A  pdb=" N   LEU A  98 " --> pdb=" O   GLY A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 112
    Processing helix  chain 'A' and resid 118 through 129
      removed outlier: 4.018A  pdb=" N   PHE A 129 " --> pdb=" O   PHE A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 164
    Processing helix  chain 'A' and resid 179 through 182
    Processing helix  chain 'A' and resid 183 through 190
      removed outlier: 3.599A  pdb=" N   TRP A 190 " --> pdb=" O   LEU A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 191 through 195
    Processing helix  chain 'A' and resid 225 through 236
    Processing helix  chain 'A' and resid 247 through 275
      removed outlier: 4.230A  pdb=" N   GLY A 253 " --> pdb=" O   ALA A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 313
    Processing helix  chain 'A' and resid 323 through 336
    Processing helix  chain 'A' and resid 337 through 342
      removed outlier: 5.990A  pdb=" N   GLU A 340 " --> pdb=" O   TYR A 337 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 356
      removed outlier: 3.939A  pdb=" N   ILE A 356 " --> pdb=" O   GLU A 352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 367
      removed outlier: 3.741A  pdb=" N   ARG A 363 " --> pdb=" O   GLY A 360 " (cutoff:3.500A)
      removed outlier: 5.662A  pdb=" N   MET A 364 " --> pdb=" O   ASP A 361 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   SER A 365 " --> pdb=" O   ARG A 362 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   ASN A 367 " --> pdb=" O   MET A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 376
    Processing helix  chain 'A' and resid 383 through 387
    Processing helix  chain 'A' and resid 401 through 416
      removed outlier: 4.236A  pdb=" N   LEU A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 433 through 439
    Processing helix  chain 'A' and resid 449 through 455
      removed outlier: 4.007A  pdb=" N   GLU A 453 " --> pdb=" O   ILE A 449 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASP A 454 " --> pdb=" O   PRO A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 483
      removed outlier: 3.614A  pdb=" N   LEU A 473 " --> pdb=" O   SER A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 494 through 496
      No H-bonds generated for 'chain 'A' and resid 494 through 496'
    Processing helix  chain 'A' and resid 499 through 516
    Processing helix  chain 'A' and resid 547 through 556
      removed outlier: 3.957A  pdb=" N   ASP A 551 " --> pdb=" O   PRO A 547 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   LYS A 556 " --> pdb=" O   LEU A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 580
    Processing helix  chain 'A' and resid 601 through 612
    Processing helix  chain 'A' and resid 636 through 653
    Processing helix  chain 'A' and resid 665 through 669
    Processing helix  chain 'A' and resid 680 through 688
    Processing helix  chain 'A' and resid 702 through 709
      removed outlier: 4.083A  pdb=" N   HIS A 706 " --> pdb=" O   PRO A 702 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 716
      removed outlier: 3.545A  pdb=" N   HIS A 715 " --> pdb=" O   ARG A 712 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ASN A 716 " --> pdb=" O   HIS A 713 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 712 through 716'
    Processing helix  chain 'A' and resid 731 through 739
    Processing helix  chain 'A' and resid 742 through 754
    Processing helix  chain 'A' and resid 755 through 758
      removed outlier: 3.739A  pdb=" N   ARG A 758 " --> pdb=" O   PRO A 755 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 755 through 758'
    Processing helix  chain 'A' and resid 761 through 783
    Processing helix  chain 'A' and resid 786 through 791
    Processing helix  chain 'B' and resid 14 through 38
    Processing helix  chain 'B' and resid 49 through 53
      removed outlier: 3.509A  pdb=" N   ILE B  53 " --> pdb=" O   PRO B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 63 through 82
      removed outlier: 3.600A  pdb=" N   HIS B  73 " --> pdb=" O   PHE B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 94 through 106
      removed outlier: 3.561A  pdb=" N   LEU B  98 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 112
    Processing helix  chain 'B' and resid 118 through 129
      removed outlier: 4.006A  pdb=" N   PHE B 129 " --> pdb=" O   PHE B 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 164
    Processing helix  chain 'B' and resid 178 through 182
    Processing helix  chain 'B' and resid 183 through 190
      removed outlier: 3.633A  pdb=" N   TRP B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 196
      removed outlier: 3.570A  pdb=" N   LEU B 196 " --> pdb=" O   ASN B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 225 through 236
    Processing helix  chain 'B' and resid 247 through 275
      removed outlier: 4.231A  pdb=" N   GLY B 253 " --> pdb=" O   ALA B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 309 through 313
    Processing helix  chain 'B' and resid 323 through 336
    Processing helix  chain 'B' and resid 337 through 342
      removed outlier: 5.988A  pdb=" N   GLU B 340 " --> pdb=" O   TYR B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 355
    Processing helix  chain 'B' and resid 359 through 363
      removed outlier: 3.721A  pdb=" N   ARG B 363 " --> pdb=" O   GLY B 360 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 376
    Processing helix  chain 'B' and resid 383 through 387
    Processing helix  chain 'B' and resid 401 through 416
      removed outlier: 4.297A  pdb=" N   LEU B 405 " --> pdb=" O   SER B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 439
      removed outlier: 3.528A  pdb=" N   VAL B 439 " --> pdb=" O   VAL B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 456
      removed outlier: 3.978A  pdb=" N   GLU B 453 " --> pdb=" O   ILE B 449 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   ASP B 454 " --> pdb=" O   PRO B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 483
    Processing helix  chain 'B' and resid 494 through 496
      No H-bonds generated for 'chain 'B' and resid 494 through 496'
    Processing helix  chain 'B' and resid 499 through 516
    Processing helix  chain 'B' and resid 547 through 556
      removed outlier: 3.973A  pdb=" N   ASP B 551 " --> pdb=" O   PRO B 547 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   LYS B 556 " --> pdb=" O   LEU B 552 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 568 through 580
    Processing helix  chain 'B' and resid 601 through 612
    Processing helix  chain 'B' and resid 636 through 653
    Processing helix  chain 'B' and resid 665 through 669
    Processing helix  chain 'B' and resid 680 through 688
    Processing helix  chain 'B' and resid 702 through 709
      removed outlier: 4.069A  pdb=" N   HIS B 706 " --> pdb=" O   PRO B 702 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 712 through 716
      removed outlier: 3.542A  pdb=" N   HIS B 715 " --> pdb=" O   ARG B 712 " (cutoff:3.500A)
      removed outlier: 4.442A  pdb=" N   ASN B 716 " --> pdb=" O   HIS B 713 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 712 through 716'
    Processing helix  chain 'B' and resid 731 through 739
    Processing helix  chain 'B' and resid 742 through 754
    Processing helix  chain 'B' and resid 755 through 758
      removed outlier: 3.509A  pdb=" N   ARG B 758 " --> pdb=" O   PRO B 755 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 755 through 758'
    Processing helix  chain 'B' and resid 761 through 783
    Processing helix  chain 'B' and resid 786 through 791
    Processing sheet with id=AA1, first strand: chain 'A' and resid 171 through 177
      removed outlier: 6.492A  pdb=" N   VAL A 172 " --> pdb=" O   LEU A 205 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   ILE A 207 " --> pdb=" O   VAL A 172 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   CYS A 174 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 6.804A  pdb=" N   HIS A 209 " --> pdb=" O   CYS A 174 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   ILE A 176 " --> pdb=" O   HIS A 209 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 398 through 399
    Processing sheet with id=AA3, first strand: chain 'A' and resid 464 through 465
      removed outlier: 8.381A  pdb=" N   MET A 465 " --> pdb=" O   PHE A 420 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU A 422 " --> pdb=" O   MET A 465 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   GLY A 487 " --> pdb=" O   ASN A 527 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   LEU A 529 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   PHE A 489 " --> pdb=" O   LEU A 529 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   SER A 531 " --> pdb=" O   PHE A 489 " (cutoff:3.500A)
      removed outlier: 6.734A  pdb=" N   THR A 491 " --> pdb=" O   SER A 531 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 442 through 443
      removed outlier: 5.472A  pdb=" N   LYS A 442 " --> pdb=" O   SER A 459 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 613 through 615
      removed outlier: 6.514A  pdb=" N   VAL A 630 " --> pdb=" O   ILE A 695 " (cutoff:3.500A)
      removed outlier: 7.613A  pdb=" N   ASN A 697 " --> pdb=" O   VAL A 630 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   ALA A 632 " --> pdb=" O   ASN A 697 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 171 through 177
      removed outlier: 6.498A  pdb=" N   VAL B 172 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   ILE B 207 " --> pdb=" O   VAL B 172 " (cutoff:3.500A)
      removed outlier: 6.185A  pdb=" N   CYS B 174 " --> pdb=" O   ILE B 207 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   HIS B 209 " --> pdb=" O   CYS B 174 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   ILE B 176 " --> pdb=" O   HIS B 209 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 397 through 400
      removed outlier: 4.708A  pdb=" N   SER B 397 " --> pdb=" O   GLN B 598 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 464 through 465
      removed outlier: 8.414A  pdb=" N   MET B 465 " --> pdb=" O   PHE B 420 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   LEU B 422 " --> pdb=" O   MET B 465 " (cutoff:3.500A)
      removed outlier: 7.171A  pdb=" N   GLY B 487 " --> pdb=" O   ASN B 527 " (cutoff:3.500A)
      removed outlier: 8.469A  pdb=" N   LEU B 529 " --> pdb=" O   GLY B 487 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   PHE B 489 " --> pdb=" O   LEU B 529 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   SER B 531 " --> pdb=" O   PHE B 489 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   THR B 491 " --> pdb=" O   SER B 531 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443
      removed outlier: 5.545A  pdb=" N   LYS B 442 " --> pdb=" O   SER B 459 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'B' and resid 613 through 615
      removed outlier: 6.551A  pdb=" N   VAL B 629 " --> pdb=" O   ARG B 659 " (cutoff:3.500A)
      removed outlier: 7.694A  pdb=" N   VAL B 661 " --> pdb=" O   VAL B 629 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   ILE B 631 " --> pdb=" O   VAL B 661 " (cutoff:3.500A)
      removed outlier: 7.798A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 631 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   SER B 633 " --> pdb=" O   VAL B 663 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   VAL B 630 " --> pdb=" O   ILE B 695 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   ASN B 697 " --> pdb=" O   VAL B 630 " (cutoff:3.500A)
      removed outlier: 6.385A  pdb=" N   ALA B 632 " --> pdb=" O   ASN B 697 " (cutoff:3.500A)

    547 hydrogen bonds defined for protein.
    1516 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: 4.32

  Time building geometry restraints manager: 3.89 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2091
        1.30 -     1.43: 3541
        1.43 -     1.55: 7246
        1.55 -     1.68: 8
        1.68 -     1.81: 46
  Bond restraints: 12932
  Sorted by residual:
  bond pdb=" C   ASN A 697 "
       pdb=" O   ASN A 697 "
    ideal  model  delta    sigma   weight residual
    1.235  1.172  0.064 1.22e-02 6.72e+03 2.72e+01
  bond pdb=" O1A TPP A 802 "
       pdb=" PA  TPP A 802 "
    ideal  model  delta    sigma   weight residual
    1.479  1.524 -0.045 1.00e-02 1.00e+04 2.01e+01
  bond pdb=" O1A TPP B 801 "
       pdb=" PA  TPP B 801 "
    ideal  model  delta    sigma   weight residual
    1.479  1.523 -0.044 1.00e-02 1.00e+04 1.90e+01
  bond pdb=" CA  ASN A 697 "
       pdb=" CB  ASN A 697 "
    ideal  model  delta    sigma   weight residual
    1.529  1.489  0.040 1.43e-02 4.89e+03 7.76e+00
  bond pdb=" CG  ASN A 697 "
       pdb=" OD1 ASN A 697 "
    ideal  model  delta    sigma   weight residual
    1.231  1.181  0.050 1.90e-02 2.77e+03 6.93e+00
  ... (remaining 12927 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 17291
        1.42 -     2.85: 250
        2.85 -     4.27: 89
        4.27 -     5.70: 18
        5.70 -     7.12: 8
  Bond angle restraints: 17656
  Sorted by residual:
  angle pdb=" N   ASN B 621 "
        pdb=" CA  ASN B 621 "
        pdb=" C   ASN B 621 "
      ideal   model   delta    sigma   weight residual
     111.14  116.88   -5.74 1.08e+00 8.57e-01 2.83e+01
  angle pdb=" O3A TPP A 802 "
        pdb=" PB  TPP A 802 "
        pdb=" O3B TPP A 802 "
      ideal   model   delta    sigma   weight residual
     104.26  111.21   -6.95 1.33e+00 5.64e-01 2.72e+01
  angle pdb=" O2B TPP B 801 "
        pdb=" PB  TPP B 801 "
        pdb=" O3A TPP B 801 "
      ideal   model   delta    sigma   weight residual
     104.26  111.04   -6.78 1.33e+00 5.64e-01 2.59e+01
  angle pdb=" N   LEU B 666 "
        pdb=" CA  LEU B 666 "
        pdb=" C   LEU B 666 "
      ideal   model   delta    sigma   weight residual
     111.28  116.13   -4.85 1.09e+00 8.42e-01 1.98e+01
  angle pdb=" N   ARG B  39 "
        pdb=" CA  ARG B  39 "
        pdb=" C   ARG B  39 "
      ideal   model   delta    sigma   weight residual
     114.56  108.93    5.63 1.27e+00 6.20e-01 1.96e+01
  ... (remaining 17651 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.89: 7167
       17.89 -    35.79: 365
       35.79 -    53.68: 55
       53.68 -    71.58: 10
       71.58 -    89.47: 1
  Dihedral angle restraints: 7598
    sinusoidal: 3040
      harmonic: 4558
  Sorted by residual:
  dihedral pdb=" CA  TRP B 295 "
           pdb=" C   TRP B 295 "
           pdb=" N   THR B 296 "
           pdb=" CA  THR B 296 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.58   15.42     0      5.00e+00 4.00e-02 9.52e+00
  dihedral pdb=" CA  GLU B 466 "
           pdb=" CB  GLU B 466 "
           pdb=" CG  GLU B 466 "
           pdb=" CD  GLU B 466 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -120.11  -59.89     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CA  LEU B 733 "
           pdb=" CB  LEU B 733 "
           pdb=" CG  LEU B 733 "
           pdb=" CD1 LEU B 733 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.03   58.97     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 7595 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1356
       0.041 -    0.082: 367
       0.082 -    0.123: 154
       0.123 -    0.164: 9
       0.164 -    0.204: 2
  Chirality restraints: 1888
  Sorted by residual:
  chirality pdb=" CA  LYS A 214 "
            pdb=" N   LYS A 214 "
            pdb=" C   LYS A 214 "
            pdb=" CB  LYS A 214 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CA  ASN B 621 "
            pdb=" N   ASN B 621 "
            pdb=" C   ASN B 621 "
            pdb=" CB  ASN B 621 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.27e-01
  chirality pdb=" CA  LEU B 666 "
            pdb=" N   LEU B 666 "
            pdb=" C   LEU B 666 "
            pdb=" CB  LEU B 666 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.16 2.00e-01 2.50e+01 6.03e-01
  ... (remaining 1885 not shown)

  Planarity restraints: 2324
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 453 "   -0.012 2.00e-02 2.50e+03   2.53e-02 6.38e+00
        pdb=" C   GLU A 453 "    0.044 2.00e-02 2.50e+03
        pdb=" O   GLU A 453 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   ASP A 454 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 696 "    0.011 2.00e-02 2.50e+03   2.26e-02 5.10e+00
        pdb=" C   PHE A 696 "   -0.039 2.00e-02 2.50e+03
        pdb=" O   PHE A 696 "    0.015 2.00e-02 2.50e+03
        pdb=" N   ASN A 697 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 213 "    0.011 2.00e-02 2.50e+03   2.12e-02 4.51e+00
        pdb=" C   TYR A 213 "   -0.037 2.00e-02 2.50e+03
        pdb=" O   TYR A 213 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LYS A 214 "    0.012 2.00e-02 2.50e+03
  ... (remaining 2321 not shown)

  Histogram of nonbonded interaction distances:
        1.87 -     2.47: 63
        2.47 -     3.08: 9046
        3.08 -     3.69: 19389
        3.69 -     4.29: 30610
        4.29 -     4.90: 51276
  Nonbonded interactions: 110384
  Sorted by model distance:
  nonbonded pdb="MG    MG A 801 "
            pdb=" O3B TPP A 802 "
     model   vdw
     1.866 2.170
  nonbonded pdb=" O1A TPP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.068 2.170
  nonbonded pdb=" O1B TPP B 801 "
            pdb="MG    MG B 802 "
     model   vdw
     2.097 2.170
  nonbonded pdb=" OD1 ASN A 211 "
            pdb="MG    MG A 801 "
     model   vdw
     2.102 2.170
  nonbonded pdb=" OD1 ASP A 178 "
            pdb="MG    MG A 801 "
     model   vdw
     2.123 2.170
  ... (remaining 110379 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: 0.06
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 9 through 702 or resid 704 through 718 or resid 720 throug \ 
h 796))
  selection = (chain 'B' and (resid 9 through 702 or resid 704 through 718 or resid 720 throug \ 
h 796))
}

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=0.50 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:             7.060
  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:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.110
  Process input model:                     40.200
  Find NCS groups from input model:        0.650
  Set up NCS constraints:                  0.090
  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:13.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   62.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8594
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      :  0.005   0.064  12932  Z= 0.230
  Angle     :  0.517   7.119  17656  Z= 0.278
  Chirality :  0.044   0.204   1888
  Planarity :  0.004   0.038   2324
  Dihedral  : 10.790  89.473   4666
  Min Nonbonded Distance : 1.866

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  :  4.06 %
    Favored  : 95.41 %
  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:  0.69 (0.22), residues: 1576
  helix:  1.53 (0.20), residues: 674
  sheet:  0.31 (0.41), residues: 188
  loop : -0.51 (0.23), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 295 
 HIS   0.003   0.001   HIS A 756 
 PHE   0.010   0.001   PHE B 233 
 TYR   0.008   0.001   TYR B 480 
 ARG   0.002   0.000   ARG A 338 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.22216 (  547)
  hydrogen bonds       : angle       6.09283 ( 1516)
  covalent geometry    : bond        0.00499 (12932)
  covalent geometry    : angle       0.51699 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 1.468 
Fit side-chains
REVERT: A  474 GLU cc_start: 0.8793 (tp30) cc_final: 0.8538 (tp30)
REVERT: A  681 ASP cc_start: 0.8040 (m-30) cc_final: 0.7823 (m-30)
REVERT: A  734 GLU cc_start: 0.7949 (tt0) cc_final: 0.7593 (tt0)
REVERT: B  474 GLU cc_start: 0.8763 (tp30) cc_final: 0.8321 (tp30)
REVERT: B  478 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7692 (mt-10)
REVERT: B  500 ASP cc_start: 0.8420 (t0) cc_final: 0.8191 (t0)
REVERT: B  681 ASP cc_start: 0.7970 (m-30) cc_final: 0.7739 (m-30)
  outliers start: 7
  outliers final: 2
  residues processed: 104
  average time/residue: 1.5259
  time to fit residues: 171.6928
Evaluate side-chains
  62 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 60
  time to evaluate  : 1.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  460 ASP
Chi-restraints excluded: chain A residue  613 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 131 optimal weight:    0.8980
   chunk 118 optimal weight:    0.8980
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    0.6980
   chunk 79 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 122 optimal weight:   10.0000
   chunk 47 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    4.9990
   chunk 141 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 128 GLN
A 217 ASN
A 544 HIS
A 677 HIS
A 719 HIS    B
B 128 GLN
B 313 HIS
B 537 GLN
B 544 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.092534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.067065 restraints weight = 39678.727|
|-----------------------------------------------------------------------------|
r_work (start): 0.2877 rms_B_bonded: 3.87
r_work: 0.2704 rms_B_bonded: 4.34 restraints_weight: 0.5000
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2715
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2715 r_free = 0.2715    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2715
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.1136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12932  Z= 0.128
  Angle     :  0.545   6.811  17656  Z= 0.280
  Chirality :  0.044   0.137   1888
  Planarity :  0.005   0.044   2324
  Dihedral  :  5.592  82.567   1750
  Min Nonbonded Distance : 1.957

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.93 %
    Favored  : 97.07 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  6.69 %
    Favored  : 92.11 %
  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:  0.92 (0.22), residues: 1576
  helix:  1.67 (0.20), residues: 700
  sheet:  0.18 (0.41), residues: 172
  loop : -0.30 (0.24), residues: 704

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 295 
 HIS   0.003   0.001   HIS B 326 
 PHE   0.011   0.001   PHE B 495 
 TYR   0.013   0.001   TYR A 108 
 ARG   0.007   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04507 (  547)
  hydrogen bonds       : angle       4.44137 ( 1516)
  covalent geometry    : bond        0.00289 (12932)
  covalent geometry    : angle       0.54465 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 77
  time to evaluate  : 1.501 
Fit side-chains
REVERT: A  286 MET cc_start: 0.9083 (ttp) cc_final: 0.8871 (ppp)
REVERT: A  674 GLU cc_start: 0.8202 (mp0) cc_final: 0.7962 (mp0)
REVERT: A  721 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7987 (mmp-170)
REVERT: A  749 ASP cc_start: 0.8029 (m-30) cc_final: 0.7803 (m-30)
REVERT: A  791 GLN cc_start: 0.8934 (mm110) cc_final: 0.8709 (mt0)
REVERT: B  474 GLU cc_start: 0.8870 (tp30) cc_final: 0.8311 (tp30)
REVERT: B  681 ASP cc_start: 0.8160 (m-30) cc_final: 0.7936 (m-30)
REVERT: B  721 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8272 (mmp-170)
REVERT: B  734 GLU cc_start: 0.8335 (tt0) cc_final: 0.8069 (tt0)
REVERT: B  749 ASP cc_start: 0.8124 (m-30) cc_final: 0.7868 (m-30)
  outliers start: 16
  outliers final: 3
  residues processed: 89
  average time/residue: 1.5795
  time to fit residues: 154.9144
Evaluate side-chains
  68 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 63
  time to evaluate  : 1.682 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain B residue  502 MET
Chi-restraints excluded: chain B residue  721 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 92 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 120 optimal weight:    2.9990
   chunk 42 optimal weight:   10.0000
   chunk 40 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 71 optimal weight:    7.9990
   chunk 14 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    2.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 677 HIS
B 677 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.089919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.064414 restraints weight = 41726.892|
|-----------------------------------------------------------------------------|
r_work (start): 0.2824 rms_B_bonded: 3.90
r_work: 0.2655 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.2655
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2675
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2675 r_free = 0.2675    target_work(ls_wunit_k1) = 0.057         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2675
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8519
moved from start:          0.1226

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.056  12932  Z= 0.266
  Angle     :  0.583   6.856  17656  Z= 0.297
  Chirality :  0.046   0.138   1888
  Planarity :  0.005   0.040   2324
  Dihedral  :  5.640  86.039   1746
  Min Nonbonded Distance : 1.858

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.69 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  7.22 %
    Favored  : 91.43 %
  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:  0.91 (0.22), residues: 1576
  helix:  1.73 (0.20), residues: 688
  sheet:  0.00 (0.40), residues: 174
  loop : -0.31 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 295 
 HIS   0.008   0.001   HIS B 313 
 PHE   0.018   0.002   PHE A 495 
 TYR   0.011   0.001   TYR B 492 
 ARG   0.012   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04500 (  547)
  hydrogen bonds       : angle       4.21969 ( 1516)
  covalent geometry    : bond        0.00630 (12932)
  covalent geometry    : angle       0.58279 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 1.396 
Fit side-chains
REVERT: A  474 GLU cc_start: 0.9032 (tp30) cc_final: 0.8575 (tp30)
REVERT: A  721 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7914 (mmp-170)
REVERT: A  749 ASP cc_start: 0.8051 (m-30) cc_final: 0.7792 (m-30)
REVERT: B  681 ASP cc_start: 0.8193 (m-30) cc_final: 0.7959 (m-30)
REVERT: B  721 ARG cc_start: 0.8527 (OUTLIER) cc_final: 0.8292 (mmp-170)
REVERT: B  734 GLU cc_start: 0.8444 (tt0) cc_final: 0.8168 (tt0)
REVERT: B  738 ARG cc_start: 0.8645 (mmp80) cc_final: 0.8285 (ttm-80)
REVERT: B  749 ASP cc_start: 0.8116 (m-30) cc_final: 0.7866 (m-30)
REVERT: B  791 GLN cc_start: 0.8669 (mm-40) cc_final: 0.8462 (mt0)
  outliers start: 18
  outliers final: 5
  residues processed: 83
  average time/residue: 1.1772
  time to fit residues: 108.9192
Evaluate side-chains
  65 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 2.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain B residue  721 ARG
Chi-restraints excluded: chain B residue  746 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 41 optimal weight:    3.9990
   chunk 110 optimal weight:    0.9980
   chunk 32 optimal weight:    0.7980
   chunk 79 optimal weight:    0.9990
   chunk 97 optimal weight:    0.5980
   chunk 143 optimal weight:    0.6980
   chunk 25 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 13 optimal weight:    6.9990
   chunk 16 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN
A 677 HIS
A 730 ASN
B 677 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.093915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.068477 restraints weight = 36703.584|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 3.78
r_work: 0.2735 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2757 r_free = 0.2757    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12932  Z= 0.105
  Angle     :  0.500   5.470  17656  Z= 0.254
  Chirality :  0.042   0.143   1888
  Planarity :  0.004   0.043   2324
  Dihedral  :  5.455  88.734   1746
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  7.37 %
    Favored  : 91.28 %
  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:  1.03 (0.22), residues: 1576
  helix:  1.86 (0.20), residues: 688
  sheet:  0.03 (0.40), residues: 170
  loop : -0.26 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 295 
 HIS   0.009   0.001   HIS B 313 
 PHE   0.011   0.001   PHE B 495 
 TYR   0.010   0.001   TYR B 480 
 ARG   0.012   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03108 (  547)
  hydrogen bonds       : angle       3.96156 ( 1516)
  covalent geometry    : bond        0.00241 (12932)
  covalent geometry    : angle       0.50001 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 1.665 
Fit side-chains
REVERT: A  537 GLN cc_start: 0.8654 (OUTLIER) cc_final: 0.8238 (pt0)
REVERT: A  674 GLU cc_start: 0.8171 (mp0) cc_final: 0.7868 (mp0)
REVERT: A  721 ARG cc_start: 0.8576 (OUTLIER) cc_final: 0.7822 (mmp-170)
REVERT: A  749 ASP cc_start: 0.7955 (m-30) cc_final: 0.7603 (m-30)
REVERT: B  277 GLU cc_start: 0.8267 (pp20) cc_final: 0.8016 (pp20)
REVERT: B  674 GLU cc_start: 0.8083 (mp0) cc_final: 0.7860 (mp0)
REVERT: B  734 GLU cc_start: 0.8448 (tt0) cc_final: 0.8213 (tt0)
REVERT: B  738 ARG cc_start: 0.8619 (mmp80) cc_final: 0.8280 (ttm-80)
  outliers start: 18
  outliers final: 6
  residues processed: 93
  average time/residue: 1.1383
  time to fit residues: 117.9185
Evaluate side-chains
  71 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 1.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  445 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 10 optimal weight:    0.9990
   chunk 1 optimal weight:    5.9990
   chunk 43 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 47 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 150 optimal weight:    9.9990
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN
A 677 HIS
B 677 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.093065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.068204 restraints weight = 32801.085|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.55
r_work: 0.2743 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2743
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2755
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2755 r_free = 0.2755    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2755
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8511
moved from start:          0.1628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12932  Z= 0.138
  Angle     :  0.507   6.379  17656  Z= 0.257
  Chirality :  0.043   0.183   1888
  Planarity :  0.005   0.053   2324
  Dihedral  :  5.428  88.555   1746
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  :  7.82 %
    Favored  : 90.53 %
  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:  1.07 (0.22), residues: 1576
  helix:  1.92 (0.20), residues: 688
  sheet: -0.01 (0.40), residues: 174
  loop : -0.25 (0.24), residues: 714

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 295 
 HIS   0.007   0.001   HIS B 313 
 PHE   0.012   0.001   PHE A 495 
 TYR   0.009   0.001   TYR B 492 
 ARG   0.013   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03240 (  547)
  hydrogen bonds       : angle       3.89927 ( 1516)
  covalent geometry    : bond        0.00326 (12932)
  covalent geometry    : angle       0.50699 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 65
  time to evaluate  : 1.552 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.8235 (mp0) cc_final: 0.8023 (mp0)
REVERT: A  537 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8275 (pt0)
REVERT: A  674 GLU cc_start: 0.8151 (mp0) cc_final: 0.7919 (mp0)
REVERT: A  721 ARG cc_start: 0.8607 (OUTLIER) cc_final: 0.7813 (mmp-170)
REVERT: A  749 ASP cc_start: 0.8020 (m-30) cc_final: 0.7692 (m-30)
REVERT: B  465 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8894 (mmm)
REVERT: B  474 GLU cc_start: 0.9004 (tp30) cc_final: 0.8645 (tp30)
REVERT: B  674 GLU cc_start: 0.8059 (mp0) cc_final: 0.7763 (mp0)
REVERT: B  711 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8367 (mtp85)
REVERT: B  721 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8275 (mmp-170)
REVERT: B  734 GLU cc_start: 0.8437 (tt0) cc_final: 0.8178 (tt0)
REVERT: B  738 ARG cc_start: 0.8681 (mmp80) cc_final: 0.8330 (ttm-80)
  outliers start: 22
  outliers final: 8
  residues processed: 80
  average time/residue: 1.5038
  time to fit residues: 134.4112
Evaluate side-chains
  75 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 2.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  537 GLN
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  721 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 30 optimal weight:   20.0000
   chunk 116 optimal weight:    0.1980
   chunk 137 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 17 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0050
   chunk 141 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   overall best weight:    0.4994

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

Flipped N/Q/H residues before XYZ refinement:
A 537 GLN
A 677 HIS
B 677 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.094615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.069199 restraints weight = 40019.036|
|-----------------------------------------------------------------------------|
r_work (start): 0.2923 rms_B_bonded: 3.88
r_work: 0.2754 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2754
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2765
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2765 r_free = 0.2765    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2765
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  12932  Z= 0.095
  Angle     :  0.490   6.086  17656  Z= 0.248
  Chirality :  0.042   0.248   1888
  Planarity :  0.004   0.055   2324
  Dihedral  :  5.325  86.531   1746
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  :  8.20 %
    Favored  : 90.38 %
  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:  1.16 (0.22), residues: 1576
  helix:  1.96 (0.20), residues: 688
  sheet:  0.11 (0.40), residues: 170
  loop : -0.19 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 295 
 HIS   0.007   0.001   HIS B 313 
 PHE   0.010   0.001   PHE A 495 
 TYR   0.009   0.001   TYR B 480 
 ARG   0.013   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02879 (  547)
  hydrogen bonds       : angle       3.80622 ( 1516)
  covalent geometry    : bond        0.00219 (12932)
  covalent geometry    : angle       0.48979 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 3.420 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.8239 (mp0) cc_final: 0.8018 (mp0)
REVERT: A  537 GLN cc_start: 0.8635 (tt0) cc_final: 0.8012 (pp30)
REVERT: A  674 GLU cc_start: 0.8108 (mp0) cc_final: 0.7848 (mp0)
REVERT: A  721 ARG cc_start: 0.8596 (OUTLIER) cc_final: 0.7793 (mmp-170)
REVERT: A  749 ASP cc_start: 0.8022 (m-30) cc_final: 0.7692 (m-30)
REVERT: B  277 GLU cc_start: 0.8250 (pp20) cc_final: 0.8040 (pp20)
REVERT: B  465 MET cc_start: 0.9397 (OUTLIER) cc_final: 0.8911 (mmm)
REVERT: B  552 LEU cc_start: 0.8426 (tt) cc_final: 0.8199 (tp)
REVERT: B  674 GLU cc_start: 0.8051 (mp0) cc_final: 0.7659 (mp0)
REVERT: B  711 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8383 (mtp85)
REVERT: B  721 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8280 (mmp-170)
REVERT: B  734 GLU cc_start: 0.8448 (tt0) cc_final: 0.8197 (tt0)
REVERT: B  738 ARG cc_start: 0.8711 (mmp80) cc_final: 0.8361 (ttm-80)
  outliers start: 19
  outliers final: 8
  residues processed: 85
  average time/residue: 1.8947
  time to fit residues: 178.7810
Evaluate side-chains
  79 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 67
  time to evaluate  : 2.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  721 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 139 optimal weight:    0.0670
   chunk 137 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   chunk 135 optimal weight:    6.9990
   chunk 104 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 98 optimal weight:    0.9980
   chunk 146 optimal weight:    3.9990
   chunk 136 optimal weight:    1.9990
   overall best weight:    0.7318

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

Flipped N/Q/H residues before XYZ refinement:
A 677 HIS
B 540 ASN
B 677 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.094083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2947 r_free = 0.2947 target = 0.070087 restraints weight = 31109.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 3.38
r_work: 0.2762 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2789
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2789 r_free = 0.2789    target_work(ls_wunit_k1) = 0.063         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2789
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  12932  Z= 0.102
  Angle     :  0.481   5.349  17656  Z= 0.244
  Chirality :  0.043   0.207   1888
  Planarity :  0.004   0.049   2324
  Dihedral  :  5.212  83.132   1746
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  1.35 %
    Allowed  :  8.27 %
    Favored  : 90.38 %
  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:  1.21 (0.22), residues: 1576
  helix:  1.97 (0.20), residues: 690
  sheet:  0.21 (0.40), residues: 170
  loop : -0.16 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 295 
 HIS   0.006   0.001   HIS B 313 
 PHE   0.008   0.001   PHE B 495 
 TYR   0.010   0.001   TYR A  71 
 ARG   0.015   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02867 (  547)
  hydrogen bonds       : angle       3.73723 ( 1516)
  covalent geometry    : bond        0.00240 (12932)
  covalent geometry    : angle       0.48076 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 1.793 
Fit side-chains
REVERT: A  537 GLN cc_start: 0.8601 (tt0) cc_final: 0.8305 (pt0)
REVERT: A  674 GLU cc_start: 0.8095 (mp0) cc_final: 0.7824 (mp0)
REVERT: A  721 ARG cc_start: 0.8565 (OUTLIER) cc_final: 0.7714 (mmp-170)
REVERT: A  749 ASP cc_start: 0.7957 (m-30) cc_final: 0.7631 (m-30)
REVERT: B  277 GLU cc_start: 0.8245 (pp20) cc_final: 0.8042 (pp20)
REVERT: B  465 MET cc_start: 0.9388 (OUTLIER) cc_final: 0.8952 (mmm)
REVERT: B  711 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8374 (mtp85)
REVERT: B  721 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8187 (mtp180)
REVERT: B  734 GLU cc_start: 0.8400 (tt0) cc_final: 0.8127 (tt0)
REVERT: B  738 ARG cc_start: 0.8741 (mmp80) cc_final: 0.8406 (ttm-80)
  outliers start: 18
  outliers final: 9
  residues processed: 91
  average time/residue: 1.6978
  time to fit residues: 170.3351
Evaluate side-chains
  80 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  721 ARG
Chi-restraints excluded: chain B residue  746 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 50 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 151 optimal weight:    4.9990
   chunk 123 optimal weight:    0.9980
   chunk 69 optimal weight:    0.9980
   chunk 134 optimal weight:    4.9990
   chunk 60 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 148 optimal weight:    7.9990
   chunk 136 optimal weight:    0.9990
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
A 540 ASN
A 677 HIS
B 677 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.093974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.069058 restraints weight = 43035.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.2901 rms_B_bonded: 3.90
r_work: 0.2730 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2748 r_free = 0.2748    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8467
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12932  Z= 0.114
  Angle     :  0.503   6.250  17656  Z= 0.255
  Chirality :  0.043   0.196   1888
  Planarity :  0.004   0.059   2324
  Dihedral  :  5.194  81.597   1746
  Min Nonbonded Distance : 1.972

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  :  9.25 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.22), residues: 1576
  helix:  1.98 (0.20), residues: 690
  sheet:  0.25 (0.40), residues: 170
  loop : -0.13 (0.24), residues: 716

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 295 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.009   0.001   PHE B 495 
 TYR   0.009   0.001   TYR B 492 
 ARG   0.014   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02894 (  547)
  hydrogen bonds       : angle       3.71866 ( 1516)
  covalent geometry    : bond        0.00273 (12932)
  covalent geometry    : angle       0.50277 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 70
  time to evaluate  : 1.443 
Fit side-chains
REVERT: A  516 GLU cc_start: 0.8540 (mm-30) cc_final: 0.8185 (mp0)
REVERT: A  537 GLN cc_start: 0.8600 (tt0) cc_final: 0.8316 (pt0)
REVERT: A  674 GLU cc_start: 0.8102 (mp0) cc_final: 0.7810 (mp0)
REVERT: A  721 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.7700 (mmp-170)
REVERT: A  749 ASP cc_start: 0.7978 (m-30) cc_final: 0.7647 (m-30)
REVERT: A  791 GLN cc_start: 0.8974 (mt0) cc_final: 0.8769 (mm110)
REVERT: B  277 GLU cc_start: 0.8257 (pp20) cc_final: 0.7975 (pp20)
REVERT: B  465 MET cc_start: 0.9379 (OUTLIER) cc_final: 0.8949 (mmm)
REVERT: B  516 GLU cc_start: 0.8285 (mp0) cc_final: 0.8085 (mp0)
REVERT: B  711 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8432 (mtp85)
REVERT: B  721 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8219 (mtp180)
REVERT: B  734 GLU cc_start: 0.8445 (tt0) cc_final: 0.8167 (tt0)
REVERT: B  738 ARG cc_start: 0.8791 (mmp80) cc_final: 0.8438 (ttm-80)
  outliers start: 15
  outliers final: 9
  residues processed: 82
  average time/residue: 1.2492
  time to fit residues: 113.1569
Evaluate side-chains
  78 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  721 ARG
Chi-restraints excluded: chain B residue  746 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 113 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 131 optimal weight:    2.9990
   chunk 150 optimal weight:    4.9990
   chunk 109 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 116 optimal weight:    3.9990
   chunk 155 optimal weight:    5.9990
   chunk 77 optimal weight:    0.0970
   chunk 78 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 677 HIS
B 540 ASN
B 677 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.094348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.068988 restraints weight = 50252.945|
|-----------------------------------------------------------------------------|
r_work (start): 0.2892 rms_B_bonded: 4.19
r_work: 0.2714 rms_B_bonded: 4.55 restraints_weight: 0.5000
r_work (final): 0.2714
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2730
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2730 r_free = 0.2730    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2730
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  12932  Z= 0.103
  Angle     :  0.489   6.222  17656  Z= 0.248
  Chirality :  0.042   0.182   1888
  Planarity :  0.004   0.059   2324
  Dihedral  :  5.131  79.863   1746
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  :  9.25 %
    Favored  : 89.47 %
  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:  1.29 (0.22), residues: 1576
  helix:  2.04 (0.20), residues: 688
  sheet:  0.28 (0.40), residues: 170
  loop : -0.11 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 295 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.008   0.001   PHE B 125 
 TYR   0.009   0.001   TYR B 492 
 ARG   0.015   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02768 (  547)
  hydrogen bonds       : angle       3.67301 ( 1516)
  covalent geometry    : bond        0.00245 (12932)
  covalent geometry    : angle       0.48948 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 1.480 
Fit side-chains
REVERT: A  474 GLU cc_start: 0.9033 (tp30) cc_final: 0.8426 (tp30)
REVERT: A  516 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8209 (mp0)
REVERT: A  536 ARG cc_start: 0.8742 (tpp80) cc_final: 0.8534 (mmt180)
REVERT: A  537 GLN cc_start: 0.8568 (tt0) cc_final: 0.8242 (pt0)
REVERT: A  540 ASN cc_start: 0.6941 (m-40) cc_final: 0.5873 (t0)
REVERT: A  674 GLU cc_start: 0.8105 (mp0) cc_final: 0.7805 (mp0)
REVERT: A  721 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.7729 (mmp-170)
REVERT: A  749 ASP cc_start: 0.7983 (m-30) cc_final: 0.7658 (m-30)
REVERT: A  791 GLN cc_start: 0.8986 (mt0) cc_final: 0.8762 (mm-40)
REVERT: B  277 GLU cc_start: 0.8258 (pp20) cc_final: 0.8040 (pp20)
REVERT: B  465 MET cc_start: 0.9375 (OUTLIER) cc_final: 0.8950 (mmm)
REVERT: B  516 GLU cc_start: 0.8261 (mp0) cc_final: 0.7781 (mp0)
REVERT: B  674 GLU cc_start: 0.7966 (mp0) cc_final: 0.7717 (mp0)
REVERT: B  711 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8423 (mtp85)
REVERT: B  721 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.8244 (mtp180)
REVERT: B  734 GLU cc_start: 0.8462 (tt0) cc_final: 0.8195 (tt0)
REVERT: B  738 ARG cc_start: 0.8814 (mmp80) cc_final: 0.8467 (ttm-80)
REVERT: B  791 GLN cc_start: 0.9021 (mt0) cc_final: 0.8767 (mt0)
  outliers start: 17
  outliers final: 10
  residues processed: 90
  average time/residue: 1.2226
  time to fit residues: 121.4613
Evaluate side-chains
  81 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 1.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  445 LEU
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  465 MET
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  721 ARG
Chi-restraints excluded: chain B residue  746 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 68 optimal weight:    0.9990
   chunk 78 optimal weight:   10.9990
   chunk 0 optimal weight:   10.0000
   chunk 134 optimal weight:    3.9990
   chunk 127 optimal weight:    1.9990
   chunk 138 optimal weight:    5.9990
   chunk 121 optimal weight:   20.0000
   chunk 30 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   overall best weight:    1.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
A 677 HIS
B 540 ASN
B 677 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.092635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.068349 restraints weight = 35318.008|
|-----------------------------------------------------------------------------|
r_work (start): 0.2899 rms_B_bonded: 3.57
r_work: 0.2738 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2750 r_free = 0.2750    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2750
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  12932  Z= 0.158
  Angle     :  0.519   6.399  17656  Z= 0.264
  Chirality :  0.044   0.191   1888
  Planarity :  0.005   0.062   2324
  Dihedral  :  5.255  79.993   1746
  Min Nonbonded Distance : 1.923

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  9.40 %
    Favored  : 89.40 %
  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 (0.22), residues: 1576
  helix:  2.03 (0.20), residues: 688
  sheet:  0.10 (0.39), residues: 182
  loop : -0.12 (0.24), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 295 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.022   0.001   PHE A 495 
 TYR   0.011   0.001   TYR B 492 
 ARG   0.015   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03180 (  547)
  hydrogen bonds       : angle       3.73683 ( 1516)
  covalent geometry    : bond        0.00379 (12932)
  covalent geometry    : angle       0.51916 (17656)

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

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

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3152 Ramachandran restraints generated.
    1576 Oldfield, 0 Emsley, 1576 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 1.434 
Fit side-chains
REVERT: A  474 GLU cc_start: 0.9015 (tp30) cc_final: 0.8359 (tp30)
REVERT: A  516 GLU cc_start: 0.8467 (mm-30) cc_final: 0.8179 (mp0)
REVERT: A  536 ARG cc_start: 0.8768 (tpp80) cc_final: 0.8510 (mmt180)
REVERT: A  537 GLN cc_start: 0.8596 (tt0) cc_final: 0.8261 (pt0)
REVERT: A  674 GLU cc_start: 0.8108 (mp0) cc_final: 0.7804 (mp0)
REVERT: A  721 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.7729 (mmp-170)
REVERT: A  749 ASP cc_start: 0.7978 (m-30) cc_final: 0.7658 (m-30)
REVERT: A  791 GLN cc_start: 0.9009 (mt0) cc_final: 0.8752 (mm-40)
REVERT: B  277 GLU cc_start: 0.8235 (pp20) cc_final: 0.8021 (pp20)
REVERT: B  516 GLU cc_start: 0.8223 (mp0) cc_final: 0.8006 (mp0)
REVERT: B  711 ARG cc_start: 0.8872 (OUTLIER) cc_final: 0.8405 (mtp85)
REVERT: B  721 ARG cc_start: 0.8567 (OUTLIER) cc_final: 0.8256 (mtp180)
REVERT: B  734 GLU cc_start: 0.8434 (tt0) cc_final: 0.8141 (tt0)
REVERT: B  738 ARG cc_start: 0.8800 (mmp80) cc_final: 0.8466 (ttm-80)
  outliers start: 16
  outliers final: 9
  residues processed: 81
  average time/residue: 1.3024
  time to fit residues: 116.7644
Evaluate side-chains
  77 residues out of total 1322 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 1.536 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   13 LEU
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  468 LEU
Chi-restraints excluded: chain A residue  721 ARG
Chi-restraints excluded: chain A residue  746 LEU
Chi-restraints excluded: chain A residue  759 ASP
Chi-restraints excluded: chain B residue   13 LEU
Chi-restraints excluded: chain B residue  445 LEU
Chi-restraints excluded: chain B residue  468 LEU
Chi-restraints excluded: chain B residue  711 ARG
Chi-restraints excluded: chain B residue  721 ARG
Chi-restraints excluded: chain B residue  746 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 156
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 120 optimal weight:    9.9990
   chunk 127 optimal weight:    0.9990
   chunk 55 optimal weight:    1.9990
   chunk 117 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 63 optimal weight:    0.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 217 ASN
A 540 ASN
A 677 HIS
B 540 ASN
B 677 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.093901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2923 r_free = 0.2923 target = 0.068577 restraints weight = 48963.224|
|-----------------------------------------------------------------------------|
r_work (start): 0.2911 rms_B_bonded: 4.13
r_work: 0.2738 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2738
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2724
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2724 r_free = 0.2724    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2724
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1960

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  12932  Z= 0.112
  Angle     :  0.498   6.416  17656  Z= 0.253
  Chirality :  0.043   0.184   1888
  Planarity :  0.005   0.062   2324
  Dihedral  :  5.219  79.564   1746
  Min Nonbonded Distance : 1.986

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.61 %
    Favored  : 97.39 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  9.77 %
    Favored  : 89.25 %
  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:  1.27 (0.22), residues: 1576
  helix:  2.03 (0.20), residues: 688
  sheet:  0.26 (0.40), residues: 170
  loop : -0.12 (0.24), residues: 718

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 295 
 HIS   0.005   0.001   HIS B 313 
 PHE   0.022   0.001   PHE A 495 
 TYR   0.010   0.001   TYR B 492 
 ARG   0.016   0.000   ARG A 758 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02859 (  547)
  hydrogen bonds       : angle       3.68174 ( 1516)
  covalent geometry    : bond        0.00268 (12932)
  covalent geometry    : angle       0.49752 (17656)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 9189.01 seconds
wall clock time: 166 minutes 50.27 seconds (10010.27 seconds total)