Starting phenix.real_space_refine
on Wed Sep 17 17:30:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9dbq_46724/09_2025/9dbq_46724.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9dbq_46724/09_2025/9dbq_46724.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9dbq_46724/09_2025/9dbq_46724.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9dbq_46724/09_2025/9dbq_46724.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9dbq_46724/09_2025/9dbq_46724.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9dbq_46724/09_2025/9dbq_46724.map"
  }
  resolution = 2.9
  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=   0.002 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      34      5.16       5
     C    6636      2.51       5
     N    1622      2.21       5
     O    1770      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10062
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4681
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4681
          Classifications: {'peptide': 591}
          Link IDs: {'PTRANS': 13, 'TRANS': 577}
    Chain: "B"
      Number of atoms: 4681
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 591, 4681
          Classifications: {'peptide': 591}
          Link IDs: {'PTRANS': 13, 'TRANS': 577}
    Chain: "A"
      Number of atoms: 350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 350
          Unusual residues: {'Y01': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
    Chain: "B"
      Number of atoms: 350
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 10, 350
          Unusual residues: {'Y01': 10}
          Classifications: {'undetermined': 10}
          Link IDs: {None: 9}
  Time building chain proxies: 2.18, per 1000 atoms: 0.22
  Number of scatterers: 10062
  At special positions: 0
  Unit cell: (116.33, 83.7144, 136.987, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      34     16.00
     O    1770      8.00
     N    1622      7.00
     C    6636      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.02
  Conformation dependent library (CDL) restraints added in 368.8 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2172

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 8 sheets defined
      71.8% alpha, 5.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 237 through 254
    Processing helix  chain 'A' and resid 258 through 295
      removed outlier: 3.974A  pdb=" N   GLN A 262 " --> pdb=" O   SER A 258 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A 263 " --> pdb=" O   PRO A 259 " (cutoff:3.500A)
      Proline residue:  A 283  - end of helix
      removed outlier: 3.589A  pdb=" N   GLU A 295 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 317
      removed outlier: 3.893A  pdb=" N   TRP A 304 " --> pdb=" O   ASN A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 356
      removed outlier: 3.691A  pdb=" N   ILE A 335 " --> pdb=" O   THR A 331 " (cutoff:3.500A)
      removed outlier: 4.921A  pdb=" N   ARG A 336 " --> pdb=" O   PHE A 332 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   VAL A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 364
    Processing helix  chain 'A' and resid 365 through 390
      removed outlier: 3.856A  pdb=" N   VAL A 369 " --> pdb=" O   ARG A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 390 through 409
      removed outlier: 3.761A  pdb=" N   THR A 394 " --> pdb=" O   ASN A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 459
      removed outlier: 4.056A  pdb=" N   GLY A 414 " --> pdb=" O   ASN A 410 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   GLU A 433 " --> pdb=" O   ILE A 429 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   TRP A 434 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   ALA A 441 " --> pdb=" O   LYS A 437 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   MET A 442 " --> pdb=" O   PHE A 438 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ASN A 443 " --> pdb=" O   ARG A 439 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   THR A 444 " --> pdb=" O   ARG A 440 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ASN A 459 " --> pdb=" O   ASP A 455 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 467
    Processing helix  chain 'A' and resid 468 through 522
    Processing helix  chain 'A' and resid 526 through 542
      removed outlier: 3.884A  pdb=" N   TYR A 530 " --> pdb=" O   GLN A 526 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   VAL A 531 " --> pdb=" O   VAL A 527 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ILE A 538 " --> pdb=" O   GLY A 534 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 543 through 545
      No H-bonds generated for 'chain 'A' and resid 543 through 545'
    Processing helix  chain 'A' and resid 546 through 570
      removed outlier: 3.879A  pdb=" N   GLN A 555 " --> pdb=" O   TYR A 551 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   THR A 556 " --> pdb=" O   ARG A 552 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   GLU A 570 " --> pdb=" O   ASP A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 627 through 637
      removed outlier: 3.595A  pdb=" N   ILE A 632 " --> pdb=" O   GLY A 628 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LEU A 633 " --> pdb=" O   LYS A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 665
      removed outlier: 3.577A  pdb=" N   LEU A 662 " --> pdb=" O   THR A 658 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   HIS A 665 " --> pdb=" O   SER A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 680 through 685
    Processing helix  chain 'A' and resid 686 through 688
      No H-bonds generated for 'chain 'A' and resid 686 through 688'
    Processing helix  chain 'A' and resid 692 through 704
    Processing helix  chain 'A' and resid 705 through 712
    Processing helix  chain 'A' and resid 728 through 744
      removed outlier: 3.622A  pdb=" N   ALA A 744 " --> pdb=" O   THR A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 758 through 773
    Processing helix  chain 'A' and resid 807 through 815
    Processing helix  chain 'A' and resid 816 through 827
      removed outlier: 3.926A  pdb=" N   ASP A 820 " --> pdb=" O   GLY A 816 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 254
    Processing helix  chain 'B' and resid 258 through 295
      removed outlier: 3.946A  pdb=" N   GLN B 262 " --> pdb=" O   SER B 258 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU B 263 " --> pdb=" O   PRO B 259 " (cutoff:3.500A)
      Proline residue:  B 283  - end of helix
      removed outlier: 3.604A  pdb=" N   GLU B 295 " --> pdb=" O   ASN B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 317
      removed outlier: 3.878A  pdb=" N   TRP B 304 " --> pdb=" O   ASN B 300 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 324 through 356
      removed outlier: 3.689A  pdb=" N   ILE B 335 " --> pdb=" O   THR B 331 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   ARG B 336 " --> pdb=" O   PHE B 332 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL B 337 " --> pdb=" O   LEU B 333 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 357 through 364
    Processing helix  chain 'B' and resid 365 through 390
      removed outlier: 3.866A  pdb=" N   VAL B 369 " --> pdb=" O   ARG B 365 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 390 through 409
      removed outlier: 3.872A  pdb=" N   THR B 394 " --> pdb=" O   ASN B 390 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 410 through 459
      removed outlier: 4.050A  pdb=" N   GLY B 414 " --> pdb=" O   ASN B 410 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   GLU B 433 " --> pdb=" O   ILE B 429 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   TRP B 434 " --> pdb=" O   VAL B 430 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ALA B 441 " --> pdb=" O   LYS B 437 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   MET B 442 " --> pdb=" O   PHE B 438 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   ASN B 443 " --> pdb=" O   ARG B 439 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   THR B 444 " --> pdb=" O   ARG B 440 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ARG B 450 " --> pdb=" O   GLU B 446 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ASN B 459 " --> pdb=" O   ASP B 455 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 467
    Processing helix  chain 'B' and resid 468 through 522
    Processing helix  chain 'B' and resid 526 through 542
      removed outlier: 3.885A  pdb=" N   TYR B 530 " --> pdb=" O   GLN B 526 " (cutoff:3.500A)
      removed outlier: 3.962A  pdb=" N   VAL B 531 " --> pdb=" O   VAL B 527 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   ILE B 538 " --> pdb=" O   GLY B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 543 through 545
      No H-bonds generated for 'chain 'B' and resid 543 through 545'
    Processing helix  chain 'B' and resid 546 through 570
      removed outlier: 3.872A  pdb=" N   GLN B 555 " --> pdb=" O   TYR B 551 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   THR B 556 " --> pdb=" O   ARG B 552 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   GLU B 570 " --> pdb=" O   ASP B 566 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 637
      removed outlier: 3.575A  pdb=" N   ILE B 632 " --> pdb=" O   GLY B 628 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU B 633 " --> pdb=" O   LYS B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 658 through 665
      removed outlier: 3.585A  pdb=" N   LEU B 662 " --> pdb=" O   THR B 658 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   HIS B 665 " --> pdb=" O   SER B 661 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 680 through 685
    Processing helix  chain 'B' and resid 686 through 688
      No H-bonds generated for 'chain 'B' and resid 686 through 688'
    Processing helix  chain 'B' and resid 692 through 704
    Processing helix  chain 'B' and resid 705 through 712
    Processing helix  chain 'B' and resid 728 through 744
      removed outlier: 3.643A  pdb=" N   ALA B 744 " --> pdb=" O   THR B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 773
    Processing helix  chain 'B' and resid 807 through 815
    Processing helix  chain 'B' and resid 816 through 827
      removed outlier: 3.917A  pdb=" N   ASP B 820 " --> pdb=" O   GLY B 816 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 611 through 613
      removed outlier: 3.828A  pdb=" N   GLU A 593 " --> pdb=" O   CYS A 646 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   CYS A 646 " --> pdb=" O   GLU A 593 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 619 through 622
      removed outlier: 3.510A  pdb=" N   VAL A 622 " --> pdb=" O   LEU A 795 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE A 797 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   GLU A 804 " --> pdb=" O   VAL A 796 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 666 through 669
      removed outlier: 6.879A  pdb=" N   GLY A 667 " --> pdb=" O   LEU A 749 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 678 through 679
      removed outlier: 3.913A  pdb=" N   ASP A 678 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 611 through 613
      removed outlier: 3.864A  pdb=" N   GLU B 593 " --> pdb=" O   CYS B 646 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   CYS B 646 " --> pdb=" O   GLU B 593 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 619 through 622
      removed outlier: 6.192A  pdb=" N   ALA B 620 " --> pdb=" O   LEU B 795 " (cutoff:3.500A)
      removed outlier: 7.277A  pdb=" N   ILE B 797 " --> pdb=" O   ALA B 620 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   VAL B 622 " --> pdb=" O   ILE B 797 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   ILE B 794 " --> pdb=" O   ARG B 805 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ARG B 805 " --> pdb=" O   ILE B 794 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   VAL B 796 " --> pdb=" O   VAL B 803 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   CYS B 801 " --> pdb=" O   LYS B 798 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 666 through 669
      removed outlier: 6.781A  pdb=" N   GLY B 667 " --> pdb=" O   LEU B 749 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 678 through 679
      removed outlier: 3.861A  pdb=" N   ASP B 678 " --> pdb=" O   VAL B 720 " (cutoff:3.500A)

    631 hydrogen bonds defined for protein.
    1875 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: 1.62

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1667
        1.32 -     1.45: 2597
        1.45 -     1.57: 5988
        1.57 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 10308
  Sorted by residual:
  bond pdb=" N   SER B 237 "
       pdb=" CA  SER B 237 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.71e+00
  bond pdb=" N   SER A 237 "
       pdb=" CA  SER A 237 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 1.90e-02 2.77e+03 2.54e+00
  bond pdb=" CAT Y01 B 906 "
       pdb=" CBH Y01 B 906 "
    ideal  model  delta    sigma   weight residual
    1.545  1.528  0.017 2.00e-02 2.50e+03 7.00e-01
  bond pdb=" CBE Y01 B 901 "
       pdb=" CBI Y01 B 901 "
    ideal  model  delta    sigma   weight residual
    1.550  1.567 -0.017 2.00e-02 2.50e+03 6.84e-01
  bond pdb=" CA  VAL B 282 "
       pdb=" CB  VAL B 282 "
    ideal  model  delta    sigma   weight residual
    1.539  1.543 -0.004 5.40e-03 3.43e+04 6.26e-01
  ... (remaining 10303 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.26: 13536
        1.26 -     2.52: 435
        2.52 -     3.78: 102
        3.78 -     5.05: 9
        5.05 -     6.31: 6
  Bond angle restraints: 14088
  Sorted by residual:
  angle pdb=" N   VAL A 803 "
        pdb=" CA  VAL A 803 "
        pdb=" C   VAL A 803 "
      ideal   model   delta    sigma   weight residual
     111.81  109.81    2.00 8.60e-01 1.35e+00 5.39e+00
  angle pdb=" CAO Y01 B 907 "
        pdb=" CBB Y01 B 907 "
        pdb=" CBE Y01 B 907 "
      ideal   model   delta    sigma   weight residual
     109.88  116.19   -6.31 3.00e+00 1.11e-01 4.42e+00
  angle pdb=" CAO Y01 A 905 "
        pdb=" CBB Y01 A 905 "
        pdb=" CBE Y01 A 905 "
      ideal   model   delta    sigma   weight residual
     109.88  116.14   -6.26 3.00e+00 1.11e-01 4.36e+00
  angle pdb=" CAO Y01 A 910 "
        pdb=" CBB Y01 A 910 "
        pdb=" CBE Y01 A 910 "
      ideal   model   delta    sigma   weight residual
     109.88  115.91   -6.03 3.00e+00 1.11e-01 4.04e+00
  angle pdb=" CAO Y01 B 902 "
        pdb=" CBB Y01 B 902 "
        pdb=" CBE Y01 B 902 "
      ideal   model   delta    sigma   weight residual
     109.88  115.90   -6.02 3.00e+00 1.11e-01 4.03e+00
  ... (remaining 14083 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.11: 6294
       15.11 -    30.23: 544
       30.23 -    45.34: 138
       45.34 -    60.46: 60
       60.46 -    75.57: 6
  Dihedral angle restraints: 7042
    sinusoidal: 3646
      harmonic: 3396
  Sorted by residual:
  dihedral pdb=" CB  MET B 407 "
           pdb=" CG  MET B 407 "
           pdb=" SD  MET B 407 "
           pdb=" CE  MET B 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.23  -59.23     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET A 407 "
           pdb=" CG  MET A 407 "
           pdb=" SD  MET A 407 "
           pdb=" CE  MET A 407 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00  119.16  -59.16     3      1.50e+01 4.44e-03 9.48e+00
  dihedral pdb=" CB  MET A 614 "
           pdb=" CG  MET A 614 "
           pdb=" SD  MET A 614 "
           pdb=" CE  MET A 614 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  121.40   58.60     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 7039 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 1172
       0.031 -    0.062: 328
       0.062 -    0.092: 105
       0.092 -    0.123: 33
       0.123 -    0.154: 12
  Chirality restraints: 1650
  Sorted by residual:
  chirality pdb=" CBE Y01 A 910 "
            pdb=" CAP Y01 A 910 "
            pdb=" CBB Y01 A 910 "
            pdb=" CBI Y01 A 910 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.41    0.15 2.00e-01 2.50e+01 5.93e-01
  chirality pdb=" CBE Y01 B 902 "
            pdb=" CAP Y01 B 902 "
            pdb=" CBB Y01 B 902 "
            pdb=" CBI Y01 B 902 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.57    2.42    0.15 2.00e-01 2.50e+01 5.74e-01
  chirality pdb=" CA  VAL A 669 "
            pdb=" N   VAL A 669 "
            pdb=" C   VAL A 669 "
            pdb=" CB  VAL A 669 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.58   -0.14 2.00e-01 2.50e+01 4.87e-01
  ... (remaining 1647 not shown)

  Planarity restraints: 1676
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 297 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO B 298 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO B 298 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO B 298 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 297 "    0.019 5.00e-02 4.00e+02   2.82e-02 1.27e+00
        pdb=" N   PRO A 298 "   -0.049 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP B 254 "    0.017 5.00e-02 4.00e+02   2.57e-02 1.06e+00
        pdb=" N   PRO B 255 "   -0.044 5.00e-02 4.00e+02
        pdb=" CA  PRO B 255 "    0.013 5.00e-02 4.00e+02
        pdb=" CD  PRO B 255 "    0.014 5.00e-02 4.00e+02
  ... (remaining 1673 not shown)

  Histogram of nonbonded interaction distances:
        2.06 -     2.63: 79
        2.63 -     3.19: 9224
        3.19 -     3.76: 14894
        3.76 -     4.33: 20025
        4.33 -     4.90: 33424
  Nonbonded interactions: 77646
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 379 "
            pdb=" OD1 ASN A 557 "
     model   vdw
     2.057 3.040
  nonbonded pdb=" OG  SER B 456 "
            pdb=" OE1 GLU B 472 "
     model   vdw
     2.078 3.040
  nonbonded pdb=" OG  SER A 456 "
            pdb=" OE1 GLU A 472 "
     model   vdw
     2.095 3.040
  nonbonded pdb=" O   ALA A 627 "
            pdb=" OG1 THR A 631 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" OG  SER B 379 "
            pdb=" OD1 ASN B 557 "
     model   vdw
     2.223 3.040
  ... (remaining 77641 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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     10.060
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.970
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
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      :  0.003   0.039  10310  Z= 0.140
  Angle     :  0.559   6.307  14088  Z= 0.263
  Chirality :  0.035   0.154   1650
  Planarity :  0.003   0.030   1676
  Dihedral  : 12.628  75.574   4870
  Min Nonbonded Distance : 2.057

Molprobity Statistics.
  All-atom Clashscore : 2.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.21 %
    Favored  : 97.79 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.80 %
    Favored  : 99.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.15 (0.25), residues: 1178
  helix:  1.88 (0.19), residues: 792
  sheet: -0.52 (0.80), residues: 48
  loop : -1.83 (0.30), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.009   0.001   TYR B 286 
 PHE   0.010   0.001   PHE B 637 
 TRP   0.011   0.001   TRP A 434 
 HIS   0.004   0.001   HIS A 596 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 (10308)
  covalent geometry    : angle       0.55897 (14088)
  hydrogen bonds       : bond        0.16494 (  631)
  hydrogen bonds       : angle       5.44529 ( 1875)
  Misc. bond           : bond        0.00212 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 213
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8134 (mm-30) cc_final: 0.7751 (mt-10)
REVERT: A  546 TRP cc_start: 0.8596 (m100) cc_final: 0.8233 (m100)
REVERT: A  553 MET cc_start: 0.7514 (ttm) cc_final: 0.7119 (ttp)
REVERT: A  569 LYS cc_start: 0.7495 (mttt) cc_final: 0.7085 (mttp)
REVERT: A  621 LEU cc_start: 0.7179 (tp) cc_final: 0.6869 (mp)
REVERT: A  635 LEU cc_start: 0.7050 (tp) cc_final: 0.6801 (mt)
REVERT: A  710 MET cc_start: 0.6766 (tpt) cc_final: 0.6036 (mtm)
REVERT: A  772 VAL cc_start: 0.7516 (p) cc_final: 0.7311 (m)
REVERT: A  779 ILE cc_start: 0.7854 (mt) cc_final: 0.7625 (mm)
REVERT: B  346 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7704 (mt-10)
REVERT: B  546 TRP cc_start: 0.8604 (m100) cc_final: 0.8240 (m100)
REVERT: B  553 MET cc_start: 0.7501 (ttm) cc_final: 0.7219 (ttm)
REVERT: B  635 LEU cc_start: 0.7043 (tp) cc_final: 0.6696 (mt)
REVERT: B  710 MET cc_start: 0.6653 (tpt) cc_final: 0.5877 (mtm)
REVERT: B  772 VAL cc_start: 0.7730 (p) cc_final: 0.7504 (m)
REVERT: B  779 ILE cc_start: 0.7735 (mt) cc_final: 0.7524 (mm)
REVERT: B  785 LEU cc_start: 0.7905 (mt) cc_final: 0.7533 (mm)
  outliers start: 1
  outliers final: 1
  residues processed: 214
  average time/residue: 0.7040
  time to fit residues: 159.4280
Evaluate side-chains
  112 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  566 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 97 optimal weight:   10.0000
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    9.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    1.2388

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 484 GLN
A 539 GLN
A 557 ASN
A 563 ASN
B 279 ASN
B 484 GLN
B 539 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.171643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.130915 restraints weight = 14932.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 2.57
r_work: 0.3761 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.3761
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3750
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3750 r_free = 0.3750    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3745 r_free = 0.3745    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
r_final: 0.3745
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7236
moved from start:          0.2479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  10310  Z= 0.173
  Angle     :  0.604   6.583  14088  Z= 0.312
  Chirality :  0.039   0.149   1650
  Planarity :  0.004   0.046   1676
  Dihedral  :  8.797  57.967   2730
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  :  9.80 %
    Favored  : 86.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.25), residues: 1178
  helix:  2.17 (0.19), residues: 798
  sheet: -2.31 (0.62), residues: 56
  loop : -1.64 (0.31), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 256 
 TYR   0.018   0.002   TYR A 550 
 PHE   0.021   0.002   PHE B 547 
 TRP   0.014   0.001   TRP A 434 
 HIS   0.004   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 (10308)
  covalent geometry    : angle       0.60449 (14088)
  hydrogen bonds       : bond        0.06823 (  631)
  hydrogen bonds       : angle       4.09453 ( 1875)
  Misc. bond           : bond        0.00023 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 118
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8197 (mm-30) cc_final: 0.7848 (mt-10)
REVERT: A  456 SER cc_start: 0.8193 (t) cc_final: 0.7879 (p)
REVERT: A  546 TRP cc_start: 0.8485 (m100) cc_final: 0.8136 (m100)
REVERT: A  614 MET cc_start: 0.5125 (mpp) cc_final: 0.4562 (mpp)
REVERT: A  621 LEU cc_start: 0.7469 (tp) cc_final: 0.7115 (mp)
REVERT: A  635 LEU cc_start: 0.7150 (tp) cc_final: 0.6801 (mt)
REVERT: A  654 ILE cc_start: 0.5839 (OUTLIER) cc_final: 0.5350 (pt)
REVERT: A  701 GLN cc_start: 0.5937 (mm-40) cc_final: 0.5682 (mm-40)
REVERT: A  765 ILE cc_start: 0.6650 (OUTLIER) cc_final: 0.6425 (tp)
REVERT: A  779 ILE cc_start: 0.8041 (mt) cc_final: 0.7550 (mm)
REVERT: B  346 GLU cc_start: 0.8089 (mm-30) cc_final: 0.7787 (mt-10)
REVERT: B  371 ARG cc_start: 0.8232 (tpp-160) cc_final: 0.8025 (mmp80)
REVERT: B  456 SER cc_start: 0.8291 (t) cc_final: 0.7946 (p)
REVERT: B  546 TRP cc_start: 0.8518 (m100) cc_final: 0.8160 (m100)
REVERT: B  558 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6306 (m-80)
REVERT: B  569 LYS cc_start: 0.7391 (mttt) cc_final: 0.7157 (mttp)
REVERT: B  614 MET cc_start: 0.4918 (mpp) cc_final: 0.4398 (mpp)
REVERT: B  635 LEU cc_start: 0.7304 (tp) cc_final: 0.6955 (mt)
REVERT: B  654 ILE cc_start: 0.6006 (OUTLIER) cc_final: 0.5529 (pt)
REVERT: B  765 ILE cc_start: 0.6637 (OUTLIER) cc_final: 0.6408 (tp)
REVERT: B  779 ILE cc_start: 0.8016 (mt) cc_final: 0.7605 (mm)
REVERT: B  822 TRP cc_start: 0.5065 (OUTLIER) cc_final: 0.4785 (t60)
  outliers start: 38
  outliers final: 10
  residues processed: 141
  average time/residue: 0.6281
  time to fit residues: 94.1426
Evaluate side-chains
  101 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 85
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain B residue  558 PHE
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  643 SER
Chi-restraints excluded: chain B residue  654 ILE
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  659 GLN
Chi-restraints excluded: chain B residue  706 HIS
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  822 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 65 optimal weight:    0.7980
   chunk 98 optimal weight:    4.9990
   chunk 112 optimal weight:    0.3980
   chunk 113 optimal weight:    0.0970
   chunk 74 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 2 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 101 optimal weight:    0.8980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
A 316 GLN
A 706 HIS
B 316 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.176739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.134078 restraints weight = 15014.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3893 rms_B_bonded: 2.68
r_work: 0.3763 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3791
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3791 r_free = 0.3791    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3791
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7175
moved from start:          0.2975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10310  Z= 0.131
  Angle     :  0.546   5.673  14088  Z= 0.282
  Chirality :  0.037   0.142   1650
  Planarity :  0.004   0.034   1676
  Dihedral  :  8.366  58.443   2730
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 13.90 %
    Favored  : 82.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.25), residues: 1178
  helix:  2.47 (0.19), residues: 788
  sheet: -1.95 (0.62), residues: 56
  loop : -1.55 (0.31), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 375 
 TYR   0.009   0.001   TYR A 471 
 PHE   0.025   0.001   PHE A 547 
 TRP   0.015   0.001   TRP A 434 
 HIS   0.004   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10308)
  covalent geometry    : angle       0.54578 (14088)
  hydrogen bonds       : bond        0.05838 (  631)
  hydrogen bonds       : angle       3.91301 ( 1875)
  Misc. bond           : bond        0.00012 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 101
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8153 (mm-30) cc_final: 0.7824 (mt-10)
REVERT: A  558 PHE cc_start: 0.6701 (OUTLIER) cc_final: 0.6218 (m-80)
REVERT: A  569 LYS cc_start: 0.7488 (mttt) cc_final: 0.7144 (mttp)
REVERT: A  614 MET cc_start: 0.4817 (mpp) cc_final: 0.4390 (mpp)
REVERT: A  635 LEU cc_start: 0.6882 (tp) cc_final: 0.6543 (mt)
REVERT: A  656 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6904 (pm20)
REVERT: A  710 MET cc_start: 0.6614 (tpp) cc_final: 0.5849 (mtm)
REVERT: A  779 ILE cc_start: 0.7881 (mt) cc_final: 0.7351 (mm)
REVERT: A  822 TRP cc_start: 0.5191 (t60) cc_final: 0.4945 (t60)
REVERT: B  346 GLU cc_start: 0.8127 (mm-30) cc_final: 0.7812 (mt-10)
REVERT: B  456 SER cc_start: 0.8214 (t) cc_final: 0.7891 (p)
REVERT: B  552 ARG cc_start: 0.8422 (ttp80) cc_final: 0.8087 (ttp80)
REVERT: B  553 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7258 (ptp)
REVERT: B  558 PHE cc_start: 0.6650 (OUTLIER) cc_final: 0.6216 (m-80)
REVERT: B  614 MET cc_start: 0.4664 (mpp) cc_final: 0.4320 (mpp)
REVERT: B  635 LEU cc_start: 0.7135 (tp) cc_final: 0.6761 (mt)
REVERT: B  710 MET cc_start: 0.6563 (tpp) cc_final: 0.5762 (mtm)
REVERT: B  779 ILE cc_start: 0.7813 (mt) cc_final: 0.7376 (mm)
REVERT: B  822 TRP cc_start: 0.5052 (OUTLIER) cc_final: 0.4610 (t60)
  outliers start: 34
  outliers final: 8
  residues processed: 125
  average time/residue: 0.5805
  time to fit residues: 77.8194
Evaluate side-chains
  95 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.297 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  656 GLN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  558 PHE
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  659 GLN
Chi-restraints excluded: chain B residue  706 HIS
Chi-restraints excluded: chain B residue  822 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 89 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 15 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0770
   chunk 113 optimal weight:    4.9990
   chunk 52 optimal weight:    4.9990
   chunk 8 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9990
   overall best weight:    1.0144

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

Flipped N/Q/H residues before XYZ refinement:
A 523 GLN
B 523 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.174139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.131487 restraints weight = 14995.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3860 rms_B_bonded: 2.65
r_work: 0.3729 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3729
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3757
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3757 r_free = 0.3757    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3757
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10310  Z= 0.151
  Angle     :  0.566   6.878  14088  Z= 0.291
  Chirality :  0.038   0.145   1650
  Planarity :  0.004   0.031   1676
  Dihedral  :  8.313  58.628   2728
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 14.70 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.25), residues: 1178
  helix:  2.43 (0.19), residues: 800
  sheet: -1.87 (0.62), residues: 56
  loop : -1.58 (0.32), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 375 
 TYR   0.015   0.002   TYR A 550 
 PHE   0.025   0.001   PHE A 547 
 TRP   0.014   0.001   TRP A 434 
 HIS   0.003   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 (10308)
  covalent geometry    : angle       0.56580 (14088)
  hydrogen bonds       : bond        0.06099 (  631)
  hydrogen bonds       : angle       3.89672 ( 1875)
  Misc. bond           : bond        0.00002 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 89
  time to evaluate  : 0.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7824 (mt-10)
REVERT: A  456 SER cc_start: 0.8193 (t) cc_final: 0.7854 (p)
REVERT: A  552 ARG cc_start: 0.8305 (ttp80) cc_final: 0.7894 (ttp80)
REVERT: A  569 LYS cc_start: 0.7455 (mttt) cc_final: 0.7114 (mttp)
REVERT: A  614 MET cc_start: 0.4811 (mpp) cc_final: 0.4413 (mpp)
REVERT: A  635 LEU cc_start: 0.6925 (tp) cc_final: 0.6558 (mt)
REVERT: A  654 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5372 (pt)
REVERT: A  710 MET cc_start: 0.6607 (tpp) cc_final: 0.5749 (mtm)
REVERT: A  776 ARG cc_start: 0.5885 (OUTLIER) cc_final: 0.5651 (ttm170)
REVERT: A  779 ILE cc_start: 0.7857 (mt) cc_final: 0.7369 (mm)
REVERT: B  346 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7764 (mt-10)
REVERT: B  456 SER cc_start: 0.8235 (t) cc_final: 0.7903 (p)
REVERT: B  553 MET cc_start: 0.7577 (ttp) cc_final: 0.7293 (ptp)
REVERT: B  569 LYS cc_start: 0.7453 (mttt) cc_final: 0.7172 (mttp)
REVERT: B  614 MET cc_start: 0.4655 (mpp) cc_final: 0.4381 (mpp)
REVERT: B  635 LEU cc_start: 0.7092 (tp) cc_final: 0.6652 (mt)
REVERT: B  654 ILE cc_start: 0.5996 (OUTLIER) cc_final: 0.5540 (pt)
REVERT: B  710 MET cc_start: 0.6547 (tpp) cc_final: 0.5779 (mpp)
REVERT: B  779 ILE cc_start: 0.7924 (mt) cc_final: 0.7504 (mm)
REVERT: B  822 TRP cc_start: 0.4907 (t60) cc_final: 0.4531 (t60)
  outliers start: 44
  outliers final: 19
  residues processed: 123
  average time/residue: 0.5372
  time to fit residues: 71.4481
Evaluate side-chains
  108 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  654 ILE
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  776 ARG
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain B residue  654 ILE
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  659 GLN
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  706 HIS
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain B residue  718 THR
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  781 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   chunk 53 optimal weight:    5.9990
   chunk 52 optimal weight:    1.9990
   chunk 110 optimal weight:   10.0000
   chunk 85 optimal weight:    0.9980
   chunk 59 optimal weight:   20.0000
   chunk 95 optimal weight:    9.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
B 671 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.171861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.128741 restraints weight = 14957.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3824 rms_B_bonded: 2.65
r_work: 0.3694 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3729 r_free = 0.3729    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
r_final: 0.3729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7226
moved from start:          0.3354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10310  Z= 0.173
  Angle     :  0.590   7.407  14088  Z= 0.302
  Chirality :  0.039   0.153   1650
  Planarity :  0.004   0.031   1676
  Dihedral  :  8.337  59.331   2728
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  4.90 %
    Allowed  : 16.20 %
    Favored  : 78.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.25), residues: 1178
  helix:  2.41 (0.18), residues: 796
  sheet: -1.81 (0.64), residues: 56
  loop : -1.61 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 552 
 TYR   0.013   0.002   TYR A 424 
 PHE   0.026   0.002   PHE B 547 
 TRP   0.017   0.001   TRP A 434 
 HIS   0.002   0.001   HIS B 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (10308)
  covalent geometry    : angle       0.59020 (14088)
  hydrogen bonds       : bond        0.06515 (  631)
  hydrogen bonds       : angle       3.94988 ( 1875)
  Misc. bond           : bond        0.00021 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 89
  time to evaluate  : 0.445 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8135 (mm-30) cc_final: 0.7775 (mt-10)
REVERT: A  355 GLU cc_start: 0.8008 (tp30) cc_final: 0.7801 (tp30)
REVERT: A  552 ARG cc_start: 0.8404 (ttp80) cc_final: 0.8171 (ttp80)
REVERT: A  569 LYS cc_start: 0.7475 (mttt) cc_final: 0.7143 (mttp)
REVERT: A  614 MET cc_start: 0.4829 (mpp) cc_final: 0.4501 (mpp)
REVERT: A  635 LEU cc_start: 0.7052 (tp) cc_final: 0.6628 (mt)
REVERT: A  656 GLN cc_start: 0.7297 (OUTLIER) cc_final: 0.6269 (pm20)
REVERT: A  779 ILE cc_start: 0.7896 (mt) cc_final: 0.7442 (mm)
REVERT: B  346 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7782 (mt-10)
REVERT: B  553 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.7280 (ptp)
REVERT: B  558 PHE cc_start: 0.6702 (OUTLIER) cc_final: 0.6199 (m-80)
REVERT: B  569 LYS cc_start: 0.7416 (mttt) cc_final: 0.7145 (mttp)
REVERT: B  614 MET cc_start: 0.4652 (mpp) cc_final: 0.4374 (mpp)
REVERT: B  654 ILE cc_start: 0.5977 (OUTLIER) cc_final: 0.5515 (pt)
REVERT: B  779 ILE cc_start: 0.8032 (mt) cc_final: 0.7554 (mm)
REVERT: B  822 TRP cc_start: 0.4860 (t60) cc_final: 0.4478 (t60)
  outliers start: 49
  outliers final: 25
  residues processed: 122
  average time/residue: 0.5367
  time to fit residues: 70.7438
Evaluate side-chains
  107 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 78
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  655 SER
Chi-restraints excluded: chain A residue  656 GLN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  679 THR
Chi-restraints excluded: chain A residue  680 ILE
Chi-restraints excluded: chain A residue  706 HIS
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  553 MET
Chi-restraints excluded: chain B residue  558 PHE
Chi-restraints excluded: chain B residue  566 ASP
Chi-restraints excluded: chain B residue  643 SER
Chi-restraints excluded: chain B residue  654 ILE
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  659 GLN
Chi-restraints excluded: chain B residue  679 THR
Chi-restraints excluded: chain B residue  709 ILE
Chi-restraints excluded: chain B residue  718 THR
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  781 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   chunk 57 optimal weight:    5.9990
   chunk 82 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 1 optimal weight:    1.9990
   chunk 91 optimal weight:    4.9990
   chunk 43 optimal weight:    7.9990
   chunk 37 optimal weight:    6.9990
   chunk 95 optimal weight:    8.9990
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 328 ASN
A 706 HIS
B 328 ASN
B 671 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.174126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.131478 restraints weight = 14936.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3858 rms_B_bonded: 2.65
r_work: 0.3730 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3759 r_free = 0.3759    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3759 r_free = 0.3759    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7195
moved from start:          0.3526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10310  Z= 0.136
  Angle     :  0.548   6.372  14088  Z= 0.282
  Chirality :  0.037   0.149   1650
  Planarity :  0.004   0.055   1676
  Dihedral  :  8.061  59.848   2728
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 18.30 %
    Favored  : 77.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.25), residues: 1178
  helix:  2.57 (0.18), residues: 796
  sheet: -1.77 (0.65), residues: 56
  loop : -1.53 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 552 
 TYR   0.010   0.001   TYR A 424 
 PHE   0.028   0.001   PHE A 547 
 TRP   0.020   0.001   TRP B 434 
 HIS   0.002   0.001   HIS A 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (10308)
  covalent geometry    : angle       0.54838 (14088)
  hydrogen bonds       : bond        0.05860 (  631)
  hydrogen bonds       : angle       3.82578 ( 1875)
  Misc. bond           : bond        0.00005 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 93
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7723 (mt-10)
REVERT: A  355 GLU cc_start: 0.7887 (tp30) cc_final: 0.7634 (tp30)
REVERT: A  456 SER cc_start: 0.8185 (t) cc_final: 0.7803 (p)
REVERT: A  569 LYS cc_start: 0.7402 (mttt) cc_final: 0.6879 (mmtt)
REVERT: A  614 MET cc_start: 0.4741 (mpp) cc_final: 0.4397 (mpp)
REVERT: A  635 LEU cc_start: 0.6907 (tp) cc_final: 0.6519 (mt)
REVERT: A  656 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6286 (pm20)
REVERT: A  709 ILE cc_start: 0.3297 (OUTLIER) cc_final: 0.3069 (pt)
REVERT: A  710 MET cc_start: 0.6578 (tpp) cc_final: 0.5712 (mpp)
REVERT: A  779 ILE cc_start: 0.7879 (mt) cc_final: 0.7418 (mm)
REVERT: B  346 GLU cc_start: 0.8087 (mm-30) cc_final: 0.7734 (mt-10)
REVERT: B  558 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6320 (m-80)
REVERT: B  569 LYS cc_start: 0.7394 (mttt) cc_final: 0.7132 (mttp)
REVERT: B  614 MET cc_start: 0.4571 (mpp) cc_final: 0.4308 (mpp)
REVERT: B  635 LEU cc_start: 0.6961 (tp) cc_final: 0.6560 (mt)
REVERT: B  779 ILE cc_start: 0.7959 (mt) cc_final: 0.7532 (mm)
REVERT: B  822 TRP cc_start: 0.4981 (t60) cc_final: 0.4616 (t60)
  outliers start: 43
  outliers final: 17
  residues processed: 118
  average time/residue: 0.5021
  time to fit residues: 64.4556
Evaluate side-chains
  100 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  656 GLN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  706 HIS
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain B residue  558 PHE
Chi-restraints excluded: chain B residue  643 SER
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  718 THR
Chi-restraints excluded: chain B residue  765 ILE
Chi-restraints excluded: chain B residue  781 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 5 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 110 optimal weight:    0.0370
   chunk 68 optimal weight:    0.9980
   chunk 37 optimal weight:    6.9990
   chunk 46 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 18 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
B 701 GLN
B 706 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.174491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.131591 restraints weight = 14963.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 2.66
r_work: 0.3731 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3759
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3759 r_free = 0.3759    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3759 r_free = 0.3759    target_work(ls_wunit_k1) = 0.123         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3759
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3625

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10310  Z= 0.134
  Angle     :  0.553   8.032  14088  Z= 0.284
  Chirality :  0.038   0.155   1650
  Planarity :  0.004   0.056   1676
  Dihedral  :  8.017  59.040   2728
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.70 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.25), residues: 1178
  helix:  2.60 (0.18), residues: 796
  sheet: -1.79 (0.65), residues: 56
  loop : -1.51 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG B 552 
 TYR   0.010   0.001   TYR A 424 
 PHE   0.028   0.001   PHE B 547 
 TRP   0.023   0.001   TRP B 434 
 HIS   0.004   0.001   HIS B 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (10308)
  covalent geometry    : angle       0.55264 (14088)
  hydrogen bonds       : bond        0.05732 (  631)
  hydrogen bonds       : angle       3.79796 ( 1875)
  Misc. bond           : bond        0.00009 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7734 (mt-10)
REVERT: A  355 GLU cc_start: 0.7892 (tp30) cc_final: 0.7689 (tp30)
REVERT: A  558 PHE cc_start: 0.6705 (OUTLIER) cc_final: 0.6205 (m-80)
REVERT: A  569 LYS cc_start: 0.7404 (mttt) cc_final: 0.7087 (mttp)
REVERT: A  614 MET cc_start: 0.4706 (mpp) cc_final: 0.4267 (mpp)
REVERT: A  635 LEU cc_start: 0.6901 (tp) cc_final: 0.6528 (mt)
REVERT: A  656 GLN cc_start: 0.7247 (OUTLIER) cc_final: 0.6242 (pm20)
REVERT: A  779 ILE cc_start: 0.7865 (mt) cc_final: 0.7401 (mm)
REVERT: B  346 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7741 (mt-10)
REVERT: B  558 PHE cc_start: 0.6812 (OUTLIER) cc_final: 0.6299 (m-80)
REVERT: B  569 LYS cc_start: 0.7341 (mttt) cc_final: 0.7108 (mttp)
REVERT: B  614 MET cc_start: 0.4530 (mpp) cc_final: 0.4324 (mpp)
REVERT: B  618 THR cc_start: 0.4282 (OUTLIER) cc_final: 0.3920 (t)
REVERT: B  635 LEU cc_start: 0.6976 (tp) cc_final: 0.6572 (mt)
REVERT: B  779 ILE cc_start: 0.7914 (mt) cc_final: 0.7483 (mm)
REVERT: B  822 TRP cc_start: 0.5084 (t60) cc_final: 0.4739 (t60)
  outliers start: 34
  outliers final: 16
  residues processed: 106
  average time/residue: 0.4852
  time to fit residues: 56.0529
Evaluate side-chains
  97 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  656 GLN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  558 PHE
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain B residue  643 SER
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  718 THR
Chi-restraints excluded: chain B residue  781 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 68 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.2980
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    0.9990
   chunk 30 optimal weight:    0.4980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 706 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 706 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.175126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.131597 restraints weight = 14948.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3867 rms_B_bonded: 2.70
r_work: 0.3737 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3766 r_free = 0.3766    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3766 r_free = 0.3766    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7203
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10310  Z= 0.132
  Angle     :  0.548   7.760  14088  Z= 0.282
  Chirality :  0.037   0.146   1650
  Planarity :  0.003   0.036   1676
  Dihedral  :  7.902  58.301   2728
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.80 %
    Favored  : 76.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.06 (0.25), residues: 1178
  helix:  2.65 (0.18), residues: 796
  sheet: -1.78 (0.65), residues: 56
  loop : -1.45 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG B 552 
 TYR   0.013   0.001   TYR A 471 
 PHE   0.029   0.001   PHE A 547 
 TRP   0.025   0.001   TRP A 434 
 HIS   0.012   0.001   HIS B 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10308)
  covalent geometry    : angle       0.54770 (14088)
  hydrogen bonds       : bond        0.05600 (  631)
  hydrogen bonds       : angle       3.74885 ( 1875)
  Misc. bond           : bond        0.00012 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 84
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7747 (mt-10)
REVERT: A  355 GLU cc_start: 0.7879 (tp30) cc_final: 0.7669 (tp30)
REVERT: A  558 PHE cc_start: 0.6716 (OUTLIER) cc_final: 0.6257 (m-80)
REVERT: A  569 LYS cc_start: 0.7415 (mttt) cc_final: 0.7101 (mttp)
REVERT: A  614 MET cc_start: 0.4684 (mpp) cc_final: 0.4378 (mpp)
REVERT: A  619 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5424 (mp)
REVERT: A  635 LEU cc_start: 0.6970 (tp) cc_final: 0.6598 (mt)
REVERT: A  656 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6277 (pm20)
REVERT: A  709 ILE cc_start: 0.3353 (OUTLIER) cc_final: 0.3107 (pt)
REVERT: A  710 MET cc_start: 0.6621 (tpp) cc_final: 0.6272 (mmm)
REVERT: A  779 ILE cc_start: 0.7878 (mt) cc_final: 0.7421 (mm)
REVERT: B  346 GLU cc_start: 0.8105 (mm-30) cc_final: 0.7759 (mt-10)
REVERT: B  355 GLU cc_start: 0.7566 (tp30) cc_final: 0.6790 (tt0)
REVERT: B  558 PHE cc_start: 0.6820 (OUTLIER) cc_final: 0.6312 (m-80)
REVERT: B  569 LYS cc_start: 0.7324 (mttt) cc_final: 0.7093 (mttp)
REVERT: B  614 MET cc_start: 0.4534 (mpp) cc_final: 0.4170 (mpp)
REVERT: B  618 THR cc_start: 0.4401 (OUTLIER) cc_final: 0.3805 (t)
REVERT: B  619 LEU cc_start: 0.5575 (OUTLIER) cc_final: 0.5061 (mp)
REVERT: B  635 LEU cc_start: 0.7023 (tp) cc_final: 0.6618 (mt)
REVERT: B  779 ILE cc_start: 0.7862 (mt) cc_final: 0.7415 (mm)
REVERT: B  822 TRP cc_start: 0.5105 (t60) cc_final: 0.4753 (t60)
  outliers start: 34
  outliers final: 17
  residues processed: 110
  average time/residue: 0.4664
  time to fit residues: 56.0351
Evaluate side-chains
  99 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 75
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  312 LEU
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  656 GLN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  709 ILE
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  558 PHE
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  643 SER
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  718 THR
Chi-restraints excluded: chain B residue  781 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 58 optimal weight:    5.9990
   chunk 22 optimal weight:    0.6980
   chunk 72 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 98 optimal weight:    0.6980
   chunk 39 optimal weight:    0.7980
   chunk 105 optimal weight:    0.7980
   chunk 108 optimal weight:    3.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 701 GLN
A 706 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.174935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.131490 restraints weight = 14840.769|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 2.68
r_work: 0.3733 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3766
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3766 r_free = 0.3766    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3766 r_free = 0.3766    target_work(ls_wunit_k1) = 0.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3766
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.3808

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10310  Z= 0.133
  Angle     :  0.553   6.844  14088  Z= 0.284
  Chirality :  0.037   0.147   1650
  Planarity :  0.003   0.031   1676
  Dihedral  :  7.866  59.193   2728
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  3.10 %
    Allowed  : 20.30 %
    Favored  : 76.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.09 (0.25), residues: 1178
  helix:  2.67 (0.18), residues: 796
  sheet: -1.81 (0.65), residues: 56
  loop : -1.41 (0.33), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 552 
 TYR   0.010   0.001   TYR A 471 
 PHE   0.028   0.001   PHE B 547 
 TRP   0.027   0.001   TRP B 434 
 HIS   0.010   0.001   HIS A 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 (10308)
  covalent geometry    : angle       0.55291 (14088)
  hydrogen bonds       : bond        0.05596 (  631)
  hydrogen bonds       : angle       3.74503 ( 1875)
  Misc. bond           : bond        0.00015 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 81
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7749 (mt-10)
REVERT: A  355 GLU cc_start: 0.7847 (tp30) cc_final: 0.7645 (tp30)
REVERT: A  558 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6240 (m-80)
REVERT: A  569 LYS cc_start: 0.7415 (mttt) cc_final: 0.7096 (mttp)
REVERT: A  614 MET cc_start: 0.4683 (mpp) cc_final: 0.4366 (mpp)
REVERT: A  619 LEU cc_start: 0.6047 (OUTLIER) cc_final: 0.5446 (mp)
REVERT: A  635 LEU cc_start: 0.7072 (tp) cc_final: 0.6695 (mt)
REVERT: A  656 GLN cc_start: 0.7326 (OUTLIER) cc_final: 0.6345 (pm20)
REVERT: A  706 HIS cc_start: 0.6507 (t-170) cc_final: 0.5912 (t70)
REVERT: A  710 MET cc_start: 0.6504 (tpp) cc_final: 0.5558 (mtt)
REVERT: A  779 ILE cc_start: 0.7887 (mt) cc_final: 0.7468 (mm)
REVERT: B  346 GLU cc_start: 0.8098 (mm-30) cc_final: 0.7762 (mt-10)
REVERT: B  558 PHE cc_start: 0.6826 (OUTLIER) cc_final: 0.6314 (m-80)
REVERT: B  569 LYS cc_start: 0.7437 (mttt) cc_final: 0.7189 (mttp)
REVERT: B  614 MET cc_start: 0.4529 (mpp) cc_final: 0.4179 (mpp)
REVERT: B  618 THR cc_start: 0.4382 (OUTLIER) cc_final: 0.3774 (t)
REVERT: B  619 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5105 (mp)
REVERT: B  635 LEU cc_start: 0.7035 (tp) cc_final: 0.6653 (mt)
REVERT: B  779 ILE cc_start: 0.7876 (mt) cc_final: 0.7433 (mm)
REVERT: B  822 TRP cc_start: 0.5216 (t60) cc_final: 0.4888 (t60)
  outliers start: 31
  outliers final: 17
  residues processed: 105
  average time/residue: 0.4647
  time to fit residues: 53.1604
Evaluate side-chains
  101 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.304 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  656 GLN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  765 ILE
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  558 PHE
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  643 SER
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  662 LEU
Chi-restraints excluded: chain B residue  718 THR
Chi-restraints excluded: chain B residue  781 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 51 optimal weight:    8.9990
   chunk 74 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 62 optimal weight:    3.9990
   chunk 50 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 110 optimal weight:    0.5980
   chunk 67 optimal weight:    5.9990
   chunk 54 optimal weight:    0.0170
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.6420

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

Flipped N/Q/H residues before XYZ refinement:
A 701 GLN
B 706 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4334 r_free = 0.4334 target = 0.175718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.132198 restraints weight = 14794.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.3875 rms_B_bonded: 2.67
r_work: 0.3748 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3748
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3748 r_free = 0.3748    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3748
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.3893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10310  Z= 0.130
  Angle     :  0.550   8.013  14088  Z= 0.283
  Chirality :  0.037   0.148   1650
  Planarity :  0.003   0.030   1676
  Dihedral  :  7.798  59.772   2728
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.20 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.25), residues: 1178
  helix:  2.70 (0.18), residues: 796
  sheet: -1.82 (0.64), residues: 56
  loop : -1.38 (0.32), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 552 
 TYR   0.010   0.001   TYR A 471 
 PHE   0.029   0.001   PHE A 547 
 TRP   0.030   0.001   TRP A 434 
 HIS   0.008   0.001   HIS B 706 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (10308)
  covalent geometry    : angle       0.54973 (14088)
  hydrogen bonds       : bond        0.05453 (  631)
  hydrogen bonds       : angle       3.71907 ( 1875)
  Misc. bond           : bond        0.00018 (    2)

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

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

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2356 Ramachandran restraints generated.
    1178 Oldfield, 0 Emsley, 1178 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 GLU cc_start: 0.8070 (mm-30) cc_final: 0.7748 (mt-10)
REVERT: A  558 PHE cc_start: 0.6747 (OUTLIER) cc_final: 0.6267 (m-80)
REVERT: A  569 LYS cc_start: 0.7407 (mttt) cc_final: 0.7101 (mttp)
REVERT: A  614 MET cc_start: 0.4670 (mpp) cc_final: 0.4406 (mpp)
REVERT: A  619 LEU cc_start: 0.6128 (OUTLIER) cc_final: 0.5481 (mp)
REVERT: A  635 LEU cc_start: 0.7080 (tp) cc_final: 0.6723 (mt)
REVERT: A  656 GLN cc_start: 0.7268 (OUTLIER) cc_final: 0.6281 (pm20)
REVERT: A  779 ILE cc_start: 0.7900 (mt) cc_final: 0.7426 (mm)
REVERT: B  346 GLU cc_start: 0.8101 (mm-30) cc_final: 0.7771 (mt-10)
REVERT: B  542 MET cc_start: 0.8540 (ttp) cc_final: 0.8246 (ttm)
REVERT: B  569 LYS cc_start: 0.7410 (mttt) cc_final: 0.7109 (mttp)
REVERT: B  614 MET cc_start: 0.4582 (mpp) cc_final: 0.4315 (mpp)
REVERT: B  618 THR cc_start: 0.4317 (OUTLIER) cc_final: 0.3731 (t)
REVERT: B  619 LEU cc_start: 0.5644 (OUTLIER) cc_final: 0.5100 (mp)
REVERT: B  635 LEU cc_start: 0.7009 (tp) cc_final: 0.6621 (mt)
REVERT: B  779 ILE cc_start: 0.7885 (mt) cc_final: 0.7438 (mm)
REVERT: B  822 TRP cc_start: 0.5220 (t60) cc_final: 0.4905 (t60)
  outliers start: 25
  outliers final: 15
  residues processed: 100
  average time/residue: 0.5038
  time to fit residues: 54.8081
Evaluate side-chains
  96 residues out of total 1000 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  370 LEU
Chi-restraints excluded: chain A residue  457 LEU
Chi-restraints excluded: chain A residue  487 GLU
Chi-restraints excluded: chain A residue  558 PHE
Chi-restraints excluded: chain A residue  613 VAL
Chi-restraints excluded: chain A residue  619 LEU
Chi-restraints excluded: chain A residue  643 SER
Chi-restraints excluded: chain A residue  656 GLN
Chi-restraints excluded: chain A residue  662 LEU
Chi-restraints excluded: chain A residue  718 THR
Chi-restraints excluded: chain A residue  781 VAL
Chi-restraints excluded: chain B residue  312 LEU
Chi-restraints excluded: chain B residue  457 LEU
Chi-restraints excluded: chain B residue  613 VAL
Chi-restraints excluded: chain B residue  618 THR
Chi-restraints excluded: chain B residue  619 LEU
Chi-restraints excluded: chain B residue  643 SER
Chi-restraints excluded: chain B residue  655 SER
Chi-restraints excluded: chain B residue  718 THR
Chi-restraints excluded: chain B residue  781 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 108 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    0.0270
   chunk 87 optimal weight:    0.5980
   chunk 94 optimal weight:    0.0370
   chunk 6 optimal weight:    0.8980
   chunk 56 optimal weight:    0.1980
   chunk 104 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   overall best weight:    0.3116

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

Flipped N/Q/H residues before XYZ refinement:
A 659 GLN
B 659 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.178037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.134745 restraints weight = 14869.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3906 rms_B_bonded: 2.67
r_work: 0.3777 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3800
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3800 r_free = 0.3800    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3800 r_free = 0.3800    target_work(ls_wunit_k1) = 0.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
r_final: 0.3800
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037  10310  Z= 0.122
  Angle     :  0.556   9.175  14088  Z= 0.286
  Chirality :  0.037   0.143   1650
  Planarity :  0.003   0.030   1676
  Dihedral  :  7.653  59.872   2728
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.55 %
    Favored  : 97.45 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 22.20 %
    Favored  : 75.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.25 (0.26), residues: 1178
  helix:  2.75 (0.18), residues: 800
  sheet: -0.43 (0.61), residues: 82
  loop : -1.64 (0.34), residues: 296

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 552 
 TYR   0.019   0.001   TYR B 550 
 PHE   0.011   0.001   PHE A 639 
 TRP   0.033   0.001   TRP B 434 
 HIS   0.002   0.000   HIS B 354 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10308)
  covalent geometry    : angle       0.55584 (14088)
  hydrogen bonds       : bond        0.04956 (  631)
  hydrogen bonds       : angle       3.63597 ( 1875)
  Misc. bond           : bond        0.00033 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3207.54 seconds
wall clock time: 55 minutes 24.34 seconds (3324.34 seconds total)