Starting phenix.real_space_refine
on Sun Apr  5 09:34:49 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9yjz_73040/04_2026/9yjz_73040_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9yjz_73040/04_2026/9yjz_73040.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9yjz_73040/04_2026/9yjz_73040.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9yjz_73040/04_2026/9yjz_73040.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9yjz_73040/04_2026/9yjz_73040_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9yjz_73040/04_2026/9yjz_73040_trim.cif"
  }
  resolution = 2.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.068
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       8      5.49       5
     Mg      2      5.21       5
     S      54      5.16       5
     C    5776      2.51       5
     N    1592      2.21       5
     O    1690      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9122
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4481
          Classifications: {'peptide': 582}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 543}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 4481
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 582, 4481
          Classifications: {'peptide': 582}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 37, 'TRANS': 543}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 80
          Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 80
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 80
          Unusual residues: {' MG': 1, 'FAD': 1, 'TPP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.58, per 1000 atoms: 0.28
  Number of scatterers: 9122
  At special positions: 0
  Unit cell: (125.567, 89.903, 77.272, 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      54     16.00
     P       8     15.00
     Mg      2     11.99
     O    1690      8.00
     N    1592      7.00
     C    5776      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: 0.84
  Conformation dependent library (CDL) restraints added in 345.8 milliseconds
  

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 6 sheets defined
      50.4% alpha, 10.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 152 through 164
    Processing helix  chain 'A' and resid 177 through 184
    Processing helix  chain 'A' and resid 197 through 213
    Processing helix  chain 'A' and resid 223 through 228
    Processing helix  chain 'A' and resid 229 through 240
    Processing helix  chain 'A' and resid 264 through 270
    Processing helix  chain 'A' and resid 271 through 273
      No H-bonds generated for 'chain 'A' and resid 271 through 273'
    Processing helix  chain 'A' and resid 284 through 298
    Processing helix  chain 'A' and resid 310 through 315
    Processing helix  chain 'A' and resid 346 through 359
      removed outlier: 3.613A  pdb=" N   ILE A 359 " --> pdb=" O   ARG A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 374
      removed outlier: 4.070A  pdb=" N   ARG A 374 " --> pdb=" O   LEU A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 389
      removed outlier: 4.101A  pdb=" N   LYS A 379 " --> pdb=" O   PRO A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 428
    Processing helix  chain 'A' and resid 439 through 444
    Processing helix  chain 'A' and resid 445 through 449
    Processing helix  chain 'A' and resid 450 through 459
      removed outlier: 3.688A  pdb=" N   SER A 458 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   GLU A 459 " --> pdb=" O   LEU A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 496
    Processing helix  chain 'A' and resid 497 through 499
      No H-bonds generated for 'chain 'A' and resid 497 through 499'
    Processing helix  chain 'A' and resid 505 through 519
    Processing helix  chain 'A' and resid 534 through 546
    Processing helix  chain 'A' and resid 547 through 553
      removed outlier: 5.034A  pdb=" N   ASP A 551 " --> pdb=" O   PRO A 548 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   THR A 553 " --> pdb=" O   LYS A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 570
      removed outlier: 3.724A  pdb=" N   MET A 564 " --> pdb=" O   GLY A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 601
    Processing helix  chain 'A' and resid 612 through 618
      removed outlier: 3.670A  pdb=" N   MET A 617 " --> pdb=" O   ALA A 613 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   THR A 618 " --> pdb=" O   SER A 614 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 629
    Processing helix  chain 'A' and resid 642 through 653
    Processing helix  chain 'A' and resid 666 through 675
    Processing helix  chain 'A' and resid 683 through 685
      No H-bonds generated for 'chain 'A' and resid 683 through 685'
    Processing helix  chain 'A' and resid 686 through 697
      removed outlier: 3.580A  pdb=" N   TRP A 693 " --> pdb=" O   GLU A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 730 through 744
      removed outlier: 3.713A  pdb=" N   SER A 743 " --> pdb=" O   ALA A 739 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A 744 " --> pdb=" O   LEU A 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 164
    Processing helix  chain 'B' and resid 177 through 184
      removed outlier: 3.522A  pdb=" N   ALA B 183 " --> pdb=" O   PRO B 179 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 197 through 213
    Processing helix  chain 'B' and resid 223 through 228
    Processing helix  chain 'B' and resid 229 through 240
    Processing helix  chain 'B' and resid 264 through 270
    Processing helix  chain 'B' and resid 271 through 273
      No H-bonds generated for 'chain 'B' and resid 271 through 273'
    Processing helix  chain 'B' and resid 284 through 297
    Processing helix  chain 'B' and resid 310 through 315
    Processing helix  chain 'B' and resid 346 through 359
      removed outlier: 3.613A  pdb=" N   ILE B 359 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 374
      removed outlier: 4.294A  pdb=" N   ARG B 374 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 389
      removed outlier: 4.140A  pdb=" N   LYS B 379 " --> pdb=" O   PRO B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 428
    Processing helix  chain 'B' and resid 439 through 444
    Processing helix  chain 'B' and resid 445 through 449
    Processing helix  chain 'B' and resid 450 through 459
      removed outlier: 3.675A  pdb=" N   SER B 458 " --> pdb=" O   LYS B 454 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   GLU B 459 " --> pdb=" O   LEU B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 487 through 496
    Processing helix  chain 'B' and resid 497 through 499
      No H-bonds generated for 'chain 'B' and resid 497 through 499'
    Processing helix  chain 'B' and resid 505 through 519
    Processing helix  chain 'B' and resid 534 through 546
    Processing helix  chain 'B' and resid 547 through 553
      removed outlier: 5.049A  pdb=" N   ASP B 551 " --> pdb=" O   PRO B 548 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   THR B 553 " --> pdb=" O   LYS B 550 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 560 through 570
      removed outlier: 3.711A  pdb=" N   MET B 564 " --> pdb=" O   GLY B 560 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 589 through 601
    Processing helix  chain 'B' and resid 612 through 618
      removed outlier: 3.603A  pdb=" N   MET B 617 " --> pdb=" O   ALA B 613 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   THR B 618 " --> pdb=" O   SER B 614 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 621 through 629
    Processing helix  chain 'B' and resid 642 through 653
      removed outlier: 3.762A  pdb=" N   LEU B 651 " --> pdb=" O   GLN B 647 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   PHE B 652 " --> pdb=" O   TRP B 648 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 666 through 675
    Processing helix  chain 'B' and resid 683 through 685
      No H-bonds generated for 'chain 'B' and resid 683 through 685'
    Processing helix  chain 'B' and resid 686 through 697
      removed outlier: 3.616A  pdb=" N   LYS B 692 " --> pdb=" O   GLU B 688 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TRP B 693 " --> pdb=" O   GLU B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 730 through 744
      removed outlier: 3.694A  pdb=" N   SER B 743 " --> pdb=" O   ALA B 739 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   ARG B 744 " --> pdb=" O   LEU B 740 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 193
      removed outlier: 3.555A  pdb=" N   GLY A 171 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   HIS A 168 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 8.537A  pdb=" N   LEU A 219 " --> pdb=" O   HIS A 168 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   PHE A 170 " --> pdb=" O   LEU A 219 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   TRP A 275 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 8.311A  pdb=" N   ASP A 307 " --> pdb=" O   TRP A 275 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   VAL A 277 " --> pdb=" O   ASP A 307 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 392 through 394
      removed outlier: 6.367A  pdb=" N   ILE A 464 " --> pdb=" O   GLU A 482 " (cutoff:3.500A)
      removed outlier: 8.098A  pdb=" N   VAL A 484 " --> pdb=" O   ILE A 464 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   HIS A 466 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 578 through 579
      removed outlier: 6.470A  pdb=" N   ILE A 555 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
      removed outlier: 6.518A  pdb=" N   THR A 556 " --> pdb=" O   ILE A 609 " (cutoff:3.500A)
      removed outlier: 8.259A  pdb=" N   GLY A 611 " --> pdb=" O   THR A 556 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   VAL A 634 " --> pdb=" O   LEU A 703 " (cutoff:3.500A)
      removed outlier: 7.253A  pdb=" N   VAL A 705 " --> pdb=" O   VAL A 634 " (cutoff:3.500A)
      removed outlier: 6.209A  pdb=" N   LEU A 636 " --> pdb=" O   VAL A 705 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   GLU A 679 " --> pdb=" O   GLU A 704 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   PHE A 706 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   CYS A 681 " --> pdb=" O   PHE A 706 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 191 through 193
      removed outlier: 3.563A  pdb=" N   GLY B 171 " --> pdb=" O   VAL B 193 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   HIS B 168 " --> pdb=" O   VAL B 217 " (cutoff:3.500A)
      removed outlier: 8.499A  pdb=" N   LEU B 219 " --> pdb=" O   HIS B 168 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   PHE B 170 " --> pdb=" O   LEU B 219 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   TRP B 275 " --> pdb=" O   LEU B 305 " (cutoff:3.500A)
      removed outlier: 8.272A  pdb=" N   ASP B 307 " --> pdb=" O   TRP B 275 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   VAL B 277 " --> pdb=" O   ASP B 307 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 392 through 393
      removed outlier: 6.453A  pdb=" N   ILE B 464 " --> pdb=" O   GLU B 482 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   VAL B 484 " --> pdb=" O   ILE B 464 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   HIS B 466 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 578 through 579
      removed outlier: 6.490A  pdb=" N   ILE B 555 " --> pdb=" O   ILE B 579 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   THR B 556 " --> pdb=" O   ILE B 609 " (cutoff:3.500A)
      removed outlier: 8.200A  pdb=" N   GLY B 611 " --> pdb=" O   THR B 556 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   VAL B 634 " --> pdb=" O   LEU B 703 " (cutoff:3.500A)
      removed outlier: 7.254A  pdb=" N   VAL B 705 " --> pdb=" O   VAL B 634 " (cutoff:3.500A)
      removed outlier: 6.198A  pdb=" N   LEU B 636 " --> pdb=" O   VAL B 705 " (cutoff:3.500A)
      removed outlier: 6.389A  pdb=" N   GLU B 679 " --> pdb=" O   GLU B 704 " (cutoff:3.500A)
      removed outlier: 7.998A  pdb=" N   PHE B 706 " --> pdb=" O   GLU B 679 " (cutoff:3.500A)
      removed outlier: 7.295A  pdb=" N   CYS B 681 " --> pdb=" O   PHE B 706 " (cutoff:3.500A)

    383 hydrogen bonds defined for protein.
    1113 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.58

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        0.91 -     1.09: 2
        1.09 -     1.27: 1512
        1.27 -     1.45: 2400
        1.45 -     1.63: 5314
        1.63 -     1.81: 104
  Bond restraints: 9332
  Sorted by residual:
  bond pdb=" C2  TPP A 802 "
       pdb=" S1  TPP A 802 "
    ideal  model  delta    sigma   weight residual
    1.675  1.492  0.183 1.00e-02 1.00e+04 3.35e+02
  bond pdb=" C2  TPP B 802 "
       pdb=" S1  TPP B 802 "
    ideal  model  delta    sigma   weight residual
    1.675  1.492  0.183 1.00e-02 1.00e+04 3.34e+02
  bond pdb=" C4  TPP A 802 "
       pdb=" N3  TPP A 802 "
    ideal  model  delta    sigma   weight residual
    1.394  1.523 -0.129 1.00e-02 1.00e+04 1.65e+02
  bond pdb=" C4  TPP B 802 "
       pdb=" N3  TPP B 802 "
    ideal  model  delta    sigma   weight residual
    1.394  1.522 -0.128 1.00e-02 1.00e+04 1.63e+02
  bond pdb=" CB  PRO B 497 "
       pdb=" CG  PRO B 497 "
    ideal  model  delta    sigma   weight residual
    1.492  0.915  0.577 5.00e-02 4.00e+02 1.33e+02
  ... (remaining 9327 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    13.32: 12664
       13.32 -    26.64: 8
       26.64 -    39.96: 2
       39.96 -    53.28: 0
       53.28 -    66.60: 2
  Bond angle restraints: 12676
  Sorted by residual:
  angle pdb=" CB  PRO B 497 "
        pdb=" CG  PRO B 497 "
        pdb=" CD  PRO B 497 "
      ideal   model   delta    sigma   weight residual
     106.10  172.70  -66.60 3.20e+00 9.77e-02 4.33e+02
  angle pdb=" CB  PRO A 497 "
        pdb=" CG  PRO A 497 "
        pdb=" CD  PRO A 497 "
      ideal   model   delta    sigma   weight residual
     106.10  167.17  -61.07 3.20e+00 9.77e-02 3.64e+02
  angle pdb=" N   PRO A 497 "
        pdb=" CD  PRO A 497 "
        pdb=" CG  PRO A 497 "
      ideal   model   delta    sigma   weight residual
     103.20   77.67   25.53 1.50e+00 4.44e-01 2.90e+02
  angle pdb=" PA  TPP B 802 "
        pdb=" O3A TPP B 802 "
        pdb=" PB  TPP B 802 "
      ideal   model   delta    sigma   weight residual
     139.87  122.99   16.88 1.00e+00 1.00e+00 2.85e+02
  angle pdb=" N   PRO B 497 "
        pdb=" CD  PRO B 497 "
        pdb=" CG  PRO B 497 "
      ideal   model   delta    sigma   weight residual
     103.20   77.93   25.27 1.50e+00 4.44e-01 2.84e+02
  ... (remaining 12671 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.58: 5290
       33.58 -    67.17: 352
       67.17 -   100.75: 20
      100.75 -   134.33: 4
      134.33 -   167.92: 2
  Dihedral angle restraints: 5668
    sinusoidal: 2354
      harmonic: 3314
  Sorted by residual:
  dihedral pdb=" N   PRO B 497 "
           pdb=" CG  PRO B 497 "
           pdb=" CD  PRO B 497 "
           pdb=" CB  PRO B 497 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00 -101.00   71.00     1      1.50e+01 4.44e-03 2.88e+01
  dihedral pdb=" N   PRO A 497 "
           pdb=" CG  PRO A 497 "
           pdb=" CD  PRO A 497 "
           pdb=" CB  PRO A 497 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -96.54   66.54     1      1.50e+01 4.44e-03 2.57e+01
  dihedral pdb=" O5' FAD B 803 "
           pdb=" O3P FAD B 803 "
           pdb=" P   FAD B 803 "
           pdb=" PA  FAD B 803 "
      ideal   model   delta sinusoidal    sigma   weight residual
     298.23  130.31  167.92     1      3.00e+01 1.11e-03 2.11e+01
  ... (remaining 5665 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.025: 1392
       1.025 -    2.051: 0
       2.051 -    3.076: 2
       3.076 -    4.102: 0
       4.102 -    5.127: 4
  Chirality restraints: 1398
  Sorted by residual:
  chirality pdb=" C4' FAD A 803 "
            pdb=" C3' FAD A 803 "
            pdb=" C5' FAD A 803 "
            pdb=" O4' FAD A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48    2.65   -5.13 2.00e-01 2.50e+01 6.57e+02
  chirality pdb=" C4' FAD B 803 "
            pdb=" C3' FAD B 803 "
            pdb=" C5' FAD B 803 "
            pdb=" O4' FAD B 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48    2.63   -5.11 2.00e-01 2.50e+01 6.53e+02
  chirality pdb=" C4B FAD A 803 "
            pdb=" C3B FAD A 803 "
            pdb=" C5B FAD A 803 "
            pdb=" O4B FAD A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53    2.47   -5.00 2.00e-01 2.50e+01 6.24e+02
  ... (remaining 1395 not shown)

  Planarity restraints: 1630
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FAD A 803 "   -0.452 2.00e-02 2.50e+03   2.21e-01 2.32e+03
        pdb=" C10 FAD A 803 "   -0.102 2.00e-02 2.50e+03
        pdb=" C2  FAD A 803 "    0.227 2.00e-02 2.50e+03
        pdb=" C4  FAD A 803 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4X FAD A 803 "   -0.153 2.00e-02 2.50e+03
        pdb=" C5X FAD A 803 "   -0.186 2.00e-02 2.50e+03
        pdb=" C6  FAD A 803 "   -0.072 2.00e-02 2.50e+03
        pdb=" C7  FAD A 803 "    0.093 2.00e-02 2.50e+03
        pdb=" C7M FAD A 803 "    0.208 2.00e-02 2.50e+03
        pdb=" C8  FAD A 803 "    0.154 2.00e-02 2.50e+03
        pdb=" C8M FAD A 803 "    0.331 2.00e-02 2.50e+03
        pdb=" C9  FAD A 803 "    0.038 2.00e-02 2.50e+03
        pdb=" C9A FAD A 803 "   -0.130 2.00e-02 2.50e+03
        pdb=" N1  FAD A 803 "    0.089 2.00e-02 2.50e+03
        pdb=" N10 FAD A 803 "   -0.246 2.00e-02 2.50e+03
        pdb=" N3  FAD A 803 "    0.191 2.00e-02 2.50e+03
        pdb=" N5  FAD A 803 "   -0.352 2.00e-02 2.50e+03
        pdb=" O2  FAD A 803 "    0.406 2.00e-02 2.50e+03
        pdb=" O4  FAD A 803 "   -0.040 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1' FAD B 803 "   -0.480 2.00e-02 2.50e+03   2.15e-01 2.20e+03
        pdb=" C10 FAD B 803 "   -0.087 2.00e-02 2.50e+03
        pdb=" C2  FAD B 803 "    0.219 2.00e-02 2.50e+03
        pdb=" C4  FAD B 803 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4X FAD B 803 "   -0.144 2.00e-02 2.50e+03
        pdb=" C5X FAD B 803 "   -0.174 2.00e-02 2.50e+03
        pdb=" C6  FAD B 803 "   -0.071 2.00e-02 2.50e+03
        pdb=" C7  FAD B 803 "    0.088 2.00e-02 2.50e+03
        pdb=" C7M FAD B 803 "    0.190 2.00e-02 2.50e+03
        pdb=" C8  FAD B 803 "    0.151 2.00e-02 2.50e+03
        pdb=" C8M FAD B 803 "    0.320 2.00e-02 2.50e+03
        pdb=" C9  FAD B 803 "    0.046 2.00e-02 2.50e+03
        pdb=" C9A FAD B 803 "   -0.114 2.00e-02 2.50e+03
        pdb=" N1  FAD B 803 "    0.095 2.00e-02 2.50e+03
        pdb=" N10 FAD B 803 "   -0.218 2.00e-02 2.50e+03
        pdb=" N3  FAD B 803 "    0.178 2.00e-02 2.50e+03
        pdb=" N5  FAD B 803 "   -0.333 2.00e-02 2.50e+03
        pdb=" O2  FAD B 803 "    0.391 2.00e-02 2.50e+03
        pdb=" O4  FAD B 803 "   -0.050 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 496 "   -0.035 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO A 497 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 497 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 497 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1627 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 44
        2.45 -     3.07: 6185
        3.07 -     3.68: 13667
        3.68 -     4.29: 21580
        4.29 -     4.90: 36426
  Nonbonded interactions: 77902
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP B 612 "
            pdb="MG    MG B 801 "
     model   vdw
     1.842 2.170
  nonbonded pdb=" OD1 ASP A 612 "
            pdb="MG    MG A 801 "
     model   vdw
     1.850 2.170
  nonbonded pdb="MG    MG B 801 "
            pdb=" O1A TPP B 802 "
     model   vdw
     1.945 2.170
  nonbonded pdb="MG    MG A 801 "
            pdb=" O1A TPP A 802 "
     model   vdw
     1.977 2.170
  nonbonded pdb=" OD1 ASN A 650 "
            pdb=" OH  TYR A 657 "
     model   vdw
     2.035 3.040
  ... (remaining 77897 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             5.680
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.010
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.050
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:8.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
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      :  0.013   0.577   9332  Z= 0.593
  Angle     :  1.300  66.596  12676  Z= 0.642
  Chirality :  0.290   5.127   1398
  Planarity :  0.008   0.221   1630
  Dihedral  : 20.072 167.915   3536
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 20.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.89 %
    Favored  : 96.11 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 32.53 %
    Favored  : 63.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.25), residues: 1156
  helix:  0.86 (0.24), residues: 512
  sheet:  0.53 (0.38), residues: 192
  loop : -0.12 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 163 
 TYR   0.012   0.001   TYR A 589 
 PHE   0.013   0.001   PHE B 521 
 TRP   0.008   0.001   TRP A 275 
 HIS   0.004   0.001   HIS A 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.01272 ( 9332)
  covalent geometry    : angle       1.29992 (12676)
  hydrogen bonds       : bond        0.13128 (  383)
  hydrogen bonds       : angle       6.52618 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 97
  time to evaluate  : 0.405 
Fit side-chains
REVERT: B  348 SER cc_start: 0.6288 (OUTLIER) cc_final: 0.6006 (p)
REVERT: B  742 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.6030 (ttp-170)
  outliers start: 42
  outliers final: 32
  residues processed: 137
  average time/residue: 0.4885
  time to fit residues: 72.3430
Evaluate side-chains
  129 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  231 THR
Chi-restraints excluded: chain A residue  252 THR
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  254 SER
Chi-restraints excluded: chain A residue  259 SER
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  304 VAL
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  430 LEU
Chi-restraints excluded: chain A residue  447 SER
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  253 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  295 ILE
Chi-restraints excluded: chain B residue  348 SER
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  413 LEU
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  742 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.4980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 100 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 527 GLN
A 724 HIS
B 189 HIS
B 290 GLN
B 397 GLN
B 724 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.184522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.161065 restraints weight = 10825.241|
|-----------------------------------------------------------------------------|
r_work (start): 0.3979 rms_B_bonded: 1.98
r_work: 0.3884 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3762 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9332  Z= 0.129
  Angle     :  0.575   6.986  12676  Z= 0.285
  Chirality :  0.047   0.147   1398
  Planarity :  0.004   0.035   1630
  Dihedral  : 12.359 177.643   1407
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 26.99 %
    Favored  : 67.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.25), residues: 1156
  helix:  1.15 (0.23), residues: 506
  sheet:  0.36 (0.38), residues: 198
  loop :  0.26 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 352 
 TYR   0.012   0.001   TYR B 420 
 PHE   0.010   0.001   PHE B 509 
 TRP   0.011   0.001   TRP A 275 
 HIS   0.004   0.001   HIS A 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 9332)
  covalent geometry    : angle       0.57454 (12676)
  hydrogen bonds       : bond        0.03347 (  383)
  hydrogen bonds       : angle       5.08796 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 108
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  348 SER cc_start: 0.6478 (OUTLIER) cc_final: 0.6168 (p)
REVERT: A  423 MET cc_start: 0.7847 (OUTLIER) cc_final: 0.6723 (mpp)
REVERT: B  415 MET cc_start: 0.8023 (ptm) cc_final: 0.7811 (ptp)
REVERT: B  423 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.6675 (mpp)
REVERT: B  485 GLU cc_start: 0.5945 (OUTLIER) cc_final: 0.5215 (mp0)
  outliers start: 52
  outliers final: 18
  residues processed: 147
  average time/residue: 0.5651
  time to fit residues: 88.8771
Evaluate side-chains
  116 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.378 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  478 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  721 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 102 optimal weight:    2.9990
   chunk 61 optimal weight:    7.9990
   chunk 55 optimal weight:    9.9990
   chunk 30 optimal weight:    0.8980
   chunk 90 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0870
   chunk 22 optimal weight:    0.7980
   chunk 85 optimal weight:    0.6980
   chunk 58 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0870
   overall best weight:    0.5136

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A 563 GLN
A 724 HIS
B 290 GLN
B 397 GLN
B 724 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.186186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.162569 restraints weight = 10795.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 1.99
r_work: 0.3908 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3786 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1319

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   9332  Z= 0.103
  Angle     :  0.519   7.300  12676  Z= 0.256
  Chirality :  0.045   0.125   1398
  Planarity :  0.004   0.031   1630
  Dihedral  : 10.175 173.323   1367
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 26.05 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.25), residues: 1156
  helix:  1.34 (0.23), residues: 506
  sheet:  0.49 (0.39), residues: 196
  loop :  0.36 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 352 
 TYR   0.010   0.001   TYR B 420 
 PHE   0.009   0.001   PHE A 521 
 TRP   0.008   0.001   TRP A 275 
 HIS   0.004   0.001   HIS A 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 9332)
  covalent geometry    : angle       0.51865 (12676)
  hydrogen bonds       : bond        0.02773 (  383)
  hydrogen bonds       : angle       4.71984 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 106
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7214 (tt) cc_final: 0.6688 (mt)
REVERT: A  348 SER cc_start: 0.6384 (OUTLIER) cc_final: 0.6137 (p)
REVERT: A  415 MET cc_start: 0.7999 (ptm) cc_final: 0.7752 (ptp)
REVERT: A  423 MET cc_start: 0.7755 (OUTLIER) cc_final: 0.6706 (mpp)
REVERT: A  541 LYS cc_start: 0.8118 (OUTLIER) cc_final: 0.7848 (tppt)
REVERT: A  552 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7213 (ptt180)
REVERT: B  147 ARG cc_start: 0.6171 (OUTLIER) cc_final: 0.4214 (ttt-90)
REVERT: B  160 MET cc_start: 0.8471 (mmm) cc_final: 0.8168 (mmp)
REVERT: B  397 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8382 (mm-40)
REVERT: B  423 MET cc_start: 0.7779 (OUTLIER) cc_final: 0.6578 (mpp)
REVERT: B  652 PHE cc_start: 0.7098 (m-80) cc_final: 0.6856 (m-80)
  outliers start: 57
  outliers final: 20
  residues processed: 149
  average time/residue: 0.6280
  time to fit residues: 99.5121
Evaluate side-chains
  121 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  230 ILE
Chi-restraints excluded: chain A residue  243 MET
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  458 SER
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  397 GLN
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  663 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 69 optimal weight:    8.9990
   chunk 88 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 168 HIS
A 290 GLN
A 724 HIS
B 290 GLN
B 724 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.182924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.159088 restraints weight = 10961.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3971 rms_B_bonded: 1.99
r_work: 0.3875 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3756 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   9332  Z= 0.152
  Angle     :  0.543   7.354  12676  Z= 0.272
  Chirality :  0.046   0.133   1398
  Planarity :  0.004   0.035   1630
  Dihedral  :  9.610 169.911   1362
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  5.44 %
    Allowed  : 26.57 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.98 (0.25), residues: 1156
  helix:  1.24 (0.23), residues: 508
  sheet:  0.35 (0.38), residues: 196
  loop :  0.29 (0.30), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.012   0.001   TYR A 589 
 PHE   0.014   0.001   PHE B 509 
 TRP   0.010   0.001   TRP A 275 
 HIS   0.004   0.001   HIS A 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 9332)
  covalent geometry    : angle       0.54345 (12676)
  hydrogen bonds       : bond        0.03249 (  383)
  hydrogen bonds       : angle       4.77154 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 97
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  348 SER cc_start: 0.6505 (OUTLIER) cc_final: 0.6196 (p)
REVERT: A  415 MET cc_start: 0.8017 (ptm) cc_final: 0.7789 (ptp)
REVERT: A  423 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.6798 (mpp)
REVERT: A  541 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7868 (tppt)
REVERT: A  552 ARG cc_start: 0.7814 (OUTLIER) cc_final: 0.7317 (ptt180)
REVERT: B  147 ARG cc_start: 0.6155 (OUTLIER) cc_final: 0.4271 (ttt-90)
REVERT: B  160 MET cc_start: 0.8492 (mmm) cc_final: 0.8066 (mmm)
REVERT: B  423 MET cc_start: 0.7888 (OUTLIER) cc_final: 0.6733 (mpp)
REVERT: B  485 GLU cc_start: 0.5974 (OUTLIER) cc_final: 0.5237 (mp0)
  outliers start: 52
  outliers final: 20
  residues processed: 138
  average time/residue: 0.5785
  time to fit residues: 85.2062
Evaluate side-chains
  119 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 92
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  295 ILE
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  663 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    0.0030
   chunk 57 optimal weight:    0.3980
   chunk 108 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 12 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 73 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A 563 GLN
A 724 HIS
B 290 GLN
B 724 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4240 r_free = 0.4240 target = 0.184954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.161122 restraints weight = 10877.926|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.00
r_work: 0.3894 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3773 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   9332  Z= 0.104
  Angle     :  0.506   7.853  12676  Z= 0.252
  Chirality :  0.045   0.134   1398
  Planarity :  0.004   0.034   1630
  Dihedral  :  9.351 172.959   1360
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 27.09 %
    Favored  : 67.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.13 (0.25), residues: 1156
  helix:  1.37 (0.23), residues: 508
  sheet:  0.35 (0.38), residues: 196
  loop :  0.38 (0.31), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.010   0.001   TYR B 589 
 PHE   0.010   0.001   PHE B 509 
 TRP   0.009   0.001   TRP A 275 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00241 ( 9332)
  covalent geometry    : angle       0.50640 (12676)
  hydrogen bonds       : bond        0.02726 (  383)
  hydrogen bonds       : angle       4.61150 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 105
  time to evaluate  : 0.459 
Fit side-chains
REVERT: A  155 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7890 (mm-40)
REVERT: A  162 LEU cc_start: 0.7247 (tt) cc_final: 0.6651 (mt)
REVERT: A  163 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7401 (ttt-90)
REVERT: A  348 SER cc_start: 0.6360 (OUTLIER) cc_final: 0.6152 (p)
REVERT: A  415 MET cc_start: 0.7974 (ptm) cc_final: 0.7748 (ptp)
REVERT: A  423 MET cc_start: 0.7781 (OUTLIER) cc_final: 0.6705 (mpp)
REVERT: A  541 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7844 (tppt)
REVERT: A  552 ARG cc_start: 0.7778 (OUTLIER) cc_final: 0.7182 (ptt180)
REVERT: A  752 LYS cc_start: 0.3376 (OUTLIER) cc_final: 0.1789 (ptmt)
REVERT: B  147 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.4191 (ttt-90)
REVERT: B  160 MET cc_start: 0.8506 (mmm) cc_final: 0.8050 (mmp)
REVERT: B  415 MET cc_start: 0.8019 (ptm) cc_final: 0.7752 (ptp)
REVERT: B  423 MET cc_start: 0.7801 (OUTLIER) cc_final: 0.6606 (mpp)
REVERT: B  485 GLU cc_start: 0.5979 (OUTLIER) cc_final: 0.5221 (mp0)
  outliers start: 47
  outliers final: 23
  residues processed: 141
  average time/residue: 0.6390
  time to fit residues: 95.7085
Evaluate side-chains
  129 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 0.344 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  155 GLN
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  663 LYS
Chi-restraints excluded: chain B residue  721 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 106 optimal weight:    6.9990
   chunk 11 optimal weight:    8.9990
   chunk 58 optimal weight:   10.0000
   chunk 110 optimal weight:    3.9990
   chunk 81 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 100 optimal weight:    0.6980
   chunk 96 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    1.7184

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A 724 HIS
B 290 GLN
B 724 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.181458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.157721 restraints weight = 10994.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3952 rms_B_bonded: 1.99
r_work: 0.3857 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3736 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9332  Z= 0.181
  Angle     :  0.565   7.804  12676  Z= 0.285
  Chirality :  0.047   0.130   1398
  Planarity :  0.004   0.038   1630
  Dihedral  :  9.506 172.504   1360
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 4.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  6.59 %
    Allowed  : 25.10 %
    Favored  : 68.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.25), residues: 1156
  helix:  1.13 (0.22), residues: 508
  sheet:  0.20 (0.38), residues: 194
  loop :  0.21 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 147 
 TYR   0.015   0.002   TYR A 589 
 PHE   0.014   0.002   PHE B 509 
 TRP   0.011   0.002   TRP A 275 
 HIS   0.004   0.001   HIS A 197 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 ( 9332)
  covalent geometry    : angle       0.56512 (12676)
  hydrogen bonds       : bond        0.03514 (  383)
  hydrogen bonds       : angle       4.78068 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 95
  time to evaluate  : 0.351 
Fit side-chains
REVERT: A  163 ARG cc_start: 0.8135 (OUTLIER) cc_final: 0.7386 (ttt-90)
REVERT: A  348 SER cc_start: 0.6446 (OUTLIER) cc_final: 0.6127 (p)
REVERT: A  415 MET cc_start: 0.7997 (ptm) cc_final: 0.7776 (ptp)
REVERT: A  423 MET cc_start: 0.7912 (OUTLIER) cc_final: 0.6849 (mpp)
REVERT: A  521 PHE cc_start: 0.7488 (OUTLIER) cc_final: 0.6060 (m-10)
REVERT: A  541 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7858 (tppt)
REVERT: A  552 ARG cc_start: 0.7817 (OUTLIER) cc_final: 0.7343 (ptt180)
REVERT: A  752 LYS cc_start: 0.3541 (OUTLIER) cc_final: 0.1920 (ptmt)
REVERT: B  147 ARG cc_start: 0.6157 (OUTLIER) cc_final: 0.4289 (ttt-90)
REVERT: B  415 MET cc_start: 0.8024 (ptm) cc_final: 0.7777 (ptp)
REVERT: B  423 MET cc_start: 0.7915 (OUTLIER) cc_final: 0.6792 (mpp)
REVERT: B  485 GLU cc_start: 0.6080 (OUTLIER) cc_final: 0.5248 (mp0)
REVERT: B  521 PHE cc_start: 0.7528 (OUTLIER) cc_final: 0.6098 (m-10)
  outliers start: 63
  outliers final: 28
  residues processed: 149
  average time/residue: 0.5919
  time to fit residues: 94.1155
Evaluate side-chains
  131 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 92
  time to evaluate  : 0.233 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  350 ILE
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  555 ILE
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  663 LYS
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  750 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 1 optimal weight:    0.5980
   chunk 75 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 42 optimal weight:    0.8980
   chunk 57 optimal weight:    7.9990
   chunk 22 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 17 optimal weight:    8.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A 616 ASN
A 724 HIS
B 290 GLN
B 724 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.182881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.159182 restraints weight = 10953.324|
|-----------------------------------------------------------------------------|
r_work (start): 0.3974 rms_B_bonded: 1.98
r_work: 0.3879 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3760 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9332  Z= 0.128
  Angle     :  0.533   8.484  12676  Z= 0.266
  Chirality :  0.045   0.127   1398
  Planarity :  0.004   0.036   1630
  Dihedral  :  9.542 176.807   1360
  Min Nonbonded Distance : 2.019

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 25.73 %
    Favored  : 68.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.90 (0.25), residues: 1156
  helix:  1.23 (0.23), residues: 508
  sheet:  0.19 (0.38), residues: 194
  loop :  0.23 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 461 
 TYR   0.012   0.001   TYR A 589 
 PHE   0.013   0.001   PHE B 509 
 TRP   0.010   0.001   TRP B 275 
 HIS   0.004   0.001   HIS A 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9332)
  covalent geometry    : angle       0.53296 (12676)
  hydrogen bonds       : bond        0.03024 (  383)
  hydrogen bonds       : angle       4.67931 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 98
  time to evaluate  : 0.286 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7305 (tt) cc_final: 0.6729 (mt)
REVERT: A  163 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7521 (ttt-90)
REVERT: A  348 SER cc_start: 0.6418 (OUTLIER) cc_final: 0.6146 (p)
REVERT: A  415 MET cc_start: 0.7990 (ptm) cc_final: 0.7778 (ptp)
REVERT: A  423 MET cc_start: 0.7857 (OUTLIER) cc_final: 0.6763 (mpp)
REVERT: A  521 PHE cc_start: 0.7493 (OUTLIER) cc_final: 0.6105 (m-10)
REVERT: A  541 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7864 (tppt)
REVERT: A  552 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7251 (ptt180)
REVERT: A  616 ASN cc_start: 0.7967 (OUTLIER) cc_final: 0.7762 (m110)
REVERT: A  651 LEU cc_start: 0.7556 (mp) cc_final: 0.7324 (mt)
REVERT: A  750 LEU cc_start: 0.6618 (mp) cc_final: 0.6322 (pp)
REVERT: A  752 LYS cc_start: 0.3484 (OUTLIER) cc_final: 0.1895 (ptmt)
REVERT: B  147 ARG cc_start: 0.6164 (OUTLIER) cc_final: 0.4356 (ttt-90)
REVERT: B  162 LEU cc_start: 0.7284 (tt) cc_final: 0.6750 (mt)
REVERT: B  415 MET cc_start: 0.8008 (ptm) cc_final: 0.7778 (ptp)
REVERT: B  423 MET cc_start: 0.7881 (OUTLIER) cc_final: 0.6757 (mpp)
REVERT: B  485 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5105 (mp0)
REVERT: B  521 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6088 (m-10)
  outliers start: 55
  outliers final: 25
  residues processed: 142
  average time/residue: 0.5797
  time to fit residues: 87.9109
Evaluate side-chains
  133 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 96
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain A residue  616 ASN
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  663 LYS
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  750 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 95 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    0.7980
   chunk 12 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 290 GLN
A 724 HIS
B 290 GLN
B 616 ASN
B 724 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.183060 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3981 r_free = 0.3981 target = 0.159415 restraints weight = 10847.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 1.97
r_work: 0.3877 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3756 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
moved from start:          0.1542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9332  Z= 0.128
  Angle     :  0.529   8.202  12676  Z= 0.264
  Chirality :  0.045   0.127   1398
  Planarity :  0.004   0.037   1630
  Dihedral  :  9.556 178.313   1360
  Min Nonbonded Distance : 2.018

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 26.57 %
    Favored  : 68.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.25), residues: 1156
  helix:  1.25 (0.23), residues: 508
  sheet:  0.19 (0.38), residues: 194
  loop :  0.25 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 147 
 TYR   0.012   0.001   TYR B 589 
 PHE   0.013   0.001   PHE B 509 
 TRP   0.010   0.001   TRP B 275 
 HIS   0.004   0.001   HIS A 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9332)
  covalent geometry    : angle       0.52916 (12676)
  hydrogen bonds       : bond        0.02997 (  383)
  hydrogen bonds       : angle       4.65958 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 98
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7280 (tt) cc_final: 0.6709 (mt)
REVERT: A  163 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7429 (ttt-90)
REVERT: A  348 SER cc_start: 0.6370 (OUTLIER) cc_final: 0.6127 (p)
REVERT: A  415 MET cc_start: 0.7987 (ptm) cc_final: 0.7775 (ptp)
REVERT: A  423 MET cc_start: 0.7807 (OUTLIER) cc_final: 0.6722 (mpp)
REVERT: A  521 PHE cc_start: 0.7523 (OUTLIER) cc_final: 0.6030 (m-10)
REVERT: A  526 LYS cc_start: 0.7689 (mmtt) cc_final: 0.7472 (mmmt)
REVERT: A  541 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7847 (tppt)
REVERT: A  552 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7278 (ptt180)
REVERT: A  651 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7230 (mt)
REVERT: A  750 LEU cc_start: 0.6618 (mp) cc_final: 0.6313 (pp)
REVERT: A  752 LYS cc_start: 0.3474 (OUTLIER) cc_final: 0.1909 (ptmt)
REVERT: B  147 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.4272 (ttt-90)
REVERT: B  162 LEU cc_start: 0.7254 (tt) cc_final: 0.6719 (mt)
REVERT: B  415 MET cc_start: 0.8001 (ptm) cc_final: 0.7771 (ptp)
REVERT: B  423 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.6734 (mpp)
REVERT: B  485 GLU cc_start: 0.5951 (OUTLIER) cc_final: 0.5111 (mp0)
REVERT: B  521 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6087 (m-10)
  outliers start: 49
  outliers final: 29
  residues processed: 140
  average time/residue: 0.5871
  time to fit residues: 87.8147
Evaluate side-chains
  136 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 95
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  266 VAL
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  364 VAL
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  307 ASP
Chi-restraints excluded: chain B residue  350 ILE
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  458 SER
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  545 LEU
Chi-restraints excluded: chain B residue  552 ARG
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  663 LYS
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  750 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 62 optimal weight:    0.3980
   chunk 112 optimal weight:    1.9990
   chunk 80 optimal weight:    0.3980
   chunk 29 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 37 optimal weight:    0.5980
   chunk 109 optimal weight:    0.5980
   chunk 24 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 616 ASN
A 724 HIS
B 290 GLN
B 563 GLN
B 724 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.185376 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.161708 restraints weight = 10885.288|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 1.98
r_work: 0.3909 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3792 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9332  Z= 0.101
  Angle     :  0.503   8.032  12676  Z= 0.250
  Chirality :  0.044   0.124   1398
  Planarity :  0.004   0.036   1630
  Dihedral  :  9.420 178.905   1360
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  4.60 %
    Allowed  : 27.09 %
    Favored  : 68.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.17 (0.25), residues: 1156
  helix:  1.46 (0.23), residues: 508
  sheet:  0.30 (0.38), residues: 194
  loop :  0.37 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 147 
 TYR   0.012   0.001   TYR B 420 
 PHE   0.010   0.001   PHE B 509 
 TRP   0.009   0.001   TRP B 275 
 HIS   0.004   0.001   HIS A 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9332)
  covalent geometry    : angle       0.50319 (12676)
  hydrogen bonds       : bond        0.02575 (  383)
  hydrogen bonds       : angle       4.53382 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 97
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7247 (tt) cc_final: 0.6714 (mt)
REVERT: A  163 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7505 (ttt-90)
REVERT: A  348 SER cc_start: 0.6378 (OUTLIER) cc_final: 0.6061 (p)
REVERT: A  415 MET cc_start: 0.7991 (ptm) cc_final: 0.7784 (ptp)
REVERT: A  423 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6667 (mpp)
REVERT: A  521 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.6009 (m-10)
REVERT: A  541 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7866 (tppt)
REVERT: A  552 ARG cc_start: 0.7804 (OUTLIER) cc_final: 0.7179 (ptt180)
REVERT: A  651 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7295 (mt)
REVERT: A  750 LEU cc_start: 0.6608 (mp) cc_final: 0.6365 (pp)
REVERT: A  752 LYS cc_start: 0.3361 (OUTLIER) cc_final: 0.1801 (ptmt)
REVERT: B  147 ARG cc_start: 0.6115 (OUTLIER) cc_final: 0.4906 (ttt180)
REVERT: B  162 LEU cc_start: 0.7240 (tt) cc_final: 0.6733 (mt)
REVERT: B  415 MET cc_start: 0.8008 (ptm) cc_final: 0.7787 (ptp)
REVERT: B  423 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.6647 (mpp)
REVERT: B  485 GLU cc_start: 0.5966 (OUTLIER) cc_final: 0.5147 (mp0)
REVERT: B  521 PHE cc_start: 0.7503 (OUTLIER) cc_final: 0.6123 (m-10)
  outliers start: 44
  outliers final: 21
  residues processed: 134
  average time/residue: 0.6184
  time to fit residues: 88.1586
Evaluate side-chains
  125 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 92
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  651 LEU
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  750 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 79 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 96 optimal weight:    2.9990
   chunk 101 optimal weight:    0.9980
   chunk 109 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 724 HIS
B 290 GLN
B 724 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.184699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.160854 restraints weight = 10965.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.3990 rms_B_bonded: 2.00
r_work: 0.3895 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3775 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7925
moved from start:          0.1676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9332  Z= 0.114
  Angle     :  0.515   7.976  12676  Z= 0.257
  Chirality :  0.045   0.126   1398
  Planarity :  0.004   0.036   1630
  Dihedral  :  9.394 177.897   1360
  Min Nonbonded Distance : 2.025

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 27.72 %
    Favored  : 68.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.18 (0.25), residues: 1156
  helix:  1.48 (0.23), residues: 508
  sheet:  0.30 (0.38), residues: 194
  loop :  0.37 (0.31), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 352 
 TYR   0.011   0.001   TYR B 420 
 PHE   0.011   0.001   PHE B 509 
 TRP   0.009   0.001   TRP A 275 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 9332)
  covalent geometry    : angle       0.51545 (12676)
  hydrogen bonds       : bond        0.02738 (  383)
  hydrogen bonds       : angle       4.55773 ( 1113)

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

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

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2312 Ramachandran restraints generated.
    1156 Oldfield, 0 Emsley, 1156 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 97
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  162 LEU cc_start: 0.7224 (tt) cc_final: 0.6678 (mt)
REVERT: A  163 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7539 (ttt-90)
REVERT: A  348 SER cc_start: 0.6306 (OUTLIER) cc_final: 0.6049 (p)
REVERT: A  415 MET cc_start: 0.7987 (ptm) cc_final: 0.7777 (ptp)
REVERT: A  423 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.6675 (mpp)
REVERT: A  521 PHE cc_start: 0.7534 (OUTLIER) cc_final: 0.6056 (m-10)
REVERT: A  541 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7844 (tppt)
REVERT: A  552 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7245 (ptt180)
REVERT: A  651 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.7238 (mt)
REVERT: A  750 LEU cc_start: 0.6563 (mp) cc_final: 0.6316 (pp)
REVERT: A  752 LYS cc_start: 0.3357 (OUTLIER) cc_final: 0.1793 (ptmt)
REVERT: B  147 ARG cc_start: 0.6130 (OUTLIER) cc_final: 0.4911 (ttt180)
REVERT: B  162 LEU cc_start: 0.7228 (tt) cc_final: 0.6717 (mt)
REVERT: B  415 MET cc_start: 0.8004 (ptm) cc_final: 0.7774 (ptp)
REVERT: B  423 MET cc_start: 0.7784 (OUTLIER) cc_final: 0.6621 (mpp)
REVERT: B  485 GLU cc_start: 0.5972 (OUTLIER) cc_final: 0.5148 (mp0)
REVERT: B  521 PHE cc_start: 0.7494 (OUTLIER) cc_final: 0.6083 (m-10)
REVERT: B  688 GLU cc_start: 0.7711 (pp20) cc_final: 0.7330 (mp0)
  outliers start: 39
  outliers final: 23
  residues processed: 131
  average time/residue: 0.6091
  time to fit residues: 84.8263
Evaluate side-chains
  132 residues out of total 956 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 97
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  163 ARG
Chi-restraints excluded: chain A residue  233 MET
Chi-restraints excluded: chain A residue  287 ARG
Chi-restraints excluded: chain A residue  348 SER
Chi-restraints excluded: chain A residue  406 ASP
Chi-restraints excluded: chain A residue  423 MET
Chi-restraints excluded: chain A residue  477 VAL
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  504 GLU
Chi-restraints excluded: chain A residue  521 PHE
Chi-restraints excluded: chain A residue  540 GLU
Chi-restraints excluded: chain A residue  541 LYS
Chi-restraints excluded: chain A residue  545 LEU
Chi-restraints excluded: chain A residue  552 ARG
Chi-restraints excluded: chain A residue  556 THR
Chi-restraints excluded: chain A residue  612 ASP
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  752 LYS
Chi-restraints excluded: chain B residue  147 ARG
Chi-restraints excluded: chain B residue  231 THR
Chi-restraints excluded: chain B residue  259 SER
Chi-restraints excluded: chain B residue  266 VAL
Chi-restraints excluded: chain B residue  364 VAL
Chi-restraints excluded: chain B residue  406 ASP
Chi-restraints excluded: chain B residue  423 MET
Chi-restraints excluded: chain B residue  477 VAL
Chi-restraints excluded: chain B residue  485 GLU
Chi-restraints excluded: chain B residue  504 GLU
Chi-restraints excluded: chain B residue  521 PHE
Chi-restraints excluded: chain B residue  612 ASP
Chi-restraints excluded: chain B residue  663 LYS
Chi-restraints excluded: chain B residue  721 SER
Chi-restraints excluded: chain B residue  750 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 60 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    0.6980
   chunk 95 optimal weight:    0.6980
   chunk 102 optimal weight:    0.0770
   chunk 25 optimal weight:    2.9990
   chunk 104 optimal weight:    0.7980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 724 HIS
B 290 GLN
B 724 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.185826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.162099 restraints weight = 10653.701|
|-----------------------------------------------------------------------------|
r_work (start): 0.4006 rms_B_bonded: 1.97
r_work: 0.3912 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3793 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7919
moved from start:          0.1779

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   9332  Z= 0.101
  Angle     :  0.508   7.843  12676  Z= 0.252
  Chirality :  0.044   0.124   1398
  Planarity :  0.004   0.036   1630
  Dihedral  :  9.295 176.495   1360
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 4.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.16 %
    Favored  : 97.84 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 28.14 %
    Favored  : 68.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.24 (0.25), residues: 1156
  helix:  1.53 (0.23), residues: 510
  sheet:  0.42 (0.37), residues: 198
  loop :  0.34 (0.31), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 147 
 TYR   0.011   0.001   TYR B 420 
 PHE   0.010   0.001   PHE B 509 
 TRP   0.010   0.001   TRP B 275 
 HIS   0.004   0.001   HIS B 724 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 ( 9332)
  covalent geometry    : angle       0.50774 (12676)
  hydrogen bonds       : bond        0.02543 (  383)
  hydrogen bonds       : angle       4.50305 ( 1113)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3288.42 seconds
wall clock time: 56 minutes 42.19 seconds (3402.19 seconds total)