Starting phenix.real_space_refine
on Tue Mar  3 15:51:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dro_27679/03_2026/8dro_27679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dro_27679/03_2026/8dro_27679.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dro_27679/03_2026/8dro_27679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dro_27679/03_2026/8dro_27679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dro_27679/03_2026/8dro_27679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dro_27679/03_2026/8dro_27679.cif"
  }
  resolution = 4.06
  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=   0.001 sd=   0.049
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      16      5.16       5
     C    4270      2.51       5
     N    1166      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6642
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "C"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
  Time building chain proxies: 1.44, per 1000 atoms: 0.22
  Number of scatterers: 6642
  At special positions: 0
  Unit cell: (89.08, 100.608, 90.128, 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      16     16.00
     O    1190      8.00
     N    1166      7.00
     C    4270      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 235.2 milliseconds
  

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1576

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 5 sheets defined
      32.9% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'B' and resid 402 through 411
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 439 through 445
      removed outlier: 3.844A  pdb=" N   PHE B 443 " --> pdb=" O   PRO B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 467
    Processing helix  chain 'B' and resid 484 through 495
      removed outlier: 3.740A  pdb=" N   GLU B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.854A  pdb=" N   GLU B 507 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 515
      removed outlier: 4.280A  pdb=" N   SER B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 515 " --> pdb=" O   TRP B 511 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 510 through 515'
    Processing helix  chain 'B' and resid 535 through 543
      removed outlier: 3.532A  pdb=" N   ASP B 538 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY B 539 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ARG B 541 " --> pdb=" O   ASP B 538 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   GLU B 542 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 566
    Processing helix  chain 'B' and resid 567 through 569
      No H-bonds generated for 'chain 'B' and resid 567 through 569'
    Processing helix  chain 'B' and resid 634 through 638
    Processing helix  chain 'B' and resid 655 through 661
      removed outlier: 3.684A  pdb=" N   ILE B 658 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 684
      removed outlier: 3.508A  pdb=" N   TYR B 683 " --> pdb=" O   GLN B 680 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   CYS B 684 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 707
    Processing helix  chain 'B' and resid 724 through 730
      removed outlier: 3.637A  pdb=" N   CYS B 730 " --> pdb=" O   GLU B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.508A  pdb=" N   GLY B 751 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 774
      removed outlier: 3.775A  pdb=" N   LEU B 773 " --> pdb=" O   PRO B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 792
      removed outlier: 3.557A  pdb=" N   SER B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 795 through 808
    Processing helix  chain 'C' and resid 403 through 411
    Processing helix  chain 'C' and resid 412 through 419
      removed outlier: 4.003A  pdb=" N   GLN C 418 " --> pdb=" O   ASP C 414 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ARG C 419 " --> pdb=" O   LYS C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 444
      removed outlier: 3.634A  pdb=" N   PHE C 443 " --> pdb=" O   PRO C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 468
    Processing helix  chain 'C' and resid 484 through 494
    Processing helix  chain 'C' and resid 535 through 541
      removed outlier: 3.755A  pdb=" N   ASP C 538 " --> pdb=" O   ILE C 535 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY C 539 " --> pdb=" O   VAL C 536 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG C 541 " --> pdb=" O   ASP C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 566
    Processing helix  chain 'C' and resid 607 through 612
      removed outlier: 4.247A  pdb=" N   PHE C 611 " --> pdb=" O   PRO C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 629 through 638
      removed outlier: 3.526A  pdb=" N   ILE C 632 " --> pdb=" O   ILE C 629 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE C 633 " --> pdb=" O   GLU C 630 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN C 636 " --> pdb=" O   ILE C 633 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   HIS C 637 " --> pdb=" O   SER C 634 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 656 through 661
      removed outlier: 3.823A  pdb=" N   LEU C 661 " --> pdb=" O   ILE C 658 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 678 through 684
      removed outlier: 3.751A  pdb=" N   CYS C 684 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 701 through 707
      removed outlier: 3.662A  pdb=" N   ILE C 704 " --> pdb=" O   PRO C 701 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 725 through 730
      removed outlier: 3.763A  pdb=" N   CYS C 730 " --> pdb=" O   LEU C 727 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 747 through 753
    Processing helix  chain 'C' and resid 770 through 775
    Processing helix  chain 'C' and resid 787 through 792
    Processing helix  chain 'C' and resid 795 through 807
    Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422
      removed outlier: 6.965A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 453 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU B 474 " --> pdb=" O   HIS B 499 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   LYS B 501 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU B 476 " --> pdb=" O   LYS B 501 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG B 550 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 523 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS B 552 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER B 573 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP B 620 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 619 " --> pdb=" O   CYS B 643 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   LEU B 644 " --> pdb=" O   TYR B 668 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 736 through 737
      removed outlier: 6.611A  pdb=" N   LEU B 736 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 421 through 422
      removed outlier: 5.953A  pdb=" N   LEU C 451 " --> pdb=" O   TRP C 475 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   TYR C 477 " --> pdb=" O   LEU C 451 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU C 453 " --> pdb=" O   TYR C 477 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   HIS C 522 " --> pdb=" O   LEU C 498 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER C 573 " --> pdb=" O   LEU C 549 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU C 572 " --> pdb=" O   GLU C 595 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS C 645 " --> pdb=" O   ILE C 619 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU C 644 " --> pdb=" O   TYR C 668 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 459 through 461
      removed outlier: 6.032A  pdb=" N   VAL C 459 " --> pdb=" O   LYS C 482 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 735 through 736
      removed outlier: 8.155A  pdb=" N   LEU C 736 " --> pdb=" O   GLU C 760 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ILE C 759 " --> pdb=" O   VAL C 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    163 hydrogen bonds defined for protein.
    351 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: 0.89

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1247
        1.33 -     1.45: 1433
        1.45 -     1.57: 4054
        1.57 -     1.69: 2
        1.69 -     1.81: 20
  Bond restraints: 6756
  Sorted by residual:
  bond pdb=" CA  HIS C 522 "
       pdb=" CB  HIS C 522 "
    ideal  model  delta    sigma   weight residual
    1.533  1.597 -0.064 2.29e-02 1.91e+03 7.69e+00
  bond pdb=" C   ILE C 508 "
       pdb=" N   PRO C 509 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.029 1.20e-02 6.94e+03 5.90e+00
  bond pdb=" CB  PRO B 509 "
       pdb=" CG  PRO B 509 "
    ideal  model  delta    sigma   weight residual
    1.492  1.590 -0.098 5.00e-02 4.00e+02 3.83e+00
  bond pdb=" CG  LEU B 681 "
       pdb=" CD1 LEU B 681 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.51e+00
  bond pdb=" N   GLY C 437 "
       pdb=" CA  GLY C 437 "
    ideal  model  delta    sigma   weight residual
    1.445  1.459 -0.014 9.90e-03 1.02e+04 2.04e+00
  ... (remaining 6751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 8743
        1.94 -     3.88: 327
        3.88 -     5.82: 61
        5.82 -     7.76: 18
        7.76 -     9.70: 11
  Bond angle restraints: 9160
  Sorted by residual:
  angle pdb=" C   ASP B 703 "
        pdb=" CA  ASP B 703 "
        pdb=" CB  ASP B 703 "
      ideal   model   delta    sigma   weight residual
     110.01  117.18   -7.17 1.80e+00 3.09e-01 1.59e+01
  angle pdb=" N   HIS C 522 "
        pdb=" CA  HIS C 522 "
        pdb=" CB  HIS C 522 "
      ideal   model   delta    sigma   weight residual
     110.83  117.61   -6.78 1.74e+00 3.30e-01 1.52e+01
  angle pdb=" CA  LYS B 472 "
        pdb=" CB  LYS B 472 "
        pdb=" CG  LYS B 472 "
      ideal   model   delta    sigma   weight residual
     114.10  121.86   -7.76 2.00e+00 2.50e-01 1.51e+01
  angle pdb=" CB  LYS B 472 "
        pdb=" CG  LYS B 472 "
        pdb=" CD  LYS B 472 "
      ideal   model   delta    sigma   weight residual
     111.30  119.95   -8.65 2.30e+00 1.89e-01 1.41e+01
  angle pdb=" CB  ARG B 781 "
        pdb=" CG  ARG B 781 "
        pdb=" CD  ARG B 781 "
      ideal   model   delta    sigma   weight residual
     111.30  119.83   -8.53 2.30e+00 1.89e-01 1.37e+01
  ... (remaining 9155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.47: 3633
       16.47 -    32.94: 429
       32.94 -    49.41: 97
       49.41 -    65.88: 25
       65.88 -    82.35: 4
  Dihedral angle restraints: 4188
    sinusoidal: 1784
      harmonic: 2404
  Sorted by residual:
  dihedral pdb=" CA  LYS B 589 "
           pdb=" C   LYS B 589 "
           pdb=" N   MET B 590 "
           pdb=" CA  MET B 590 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.55  -24.45     0      5.00e+00 4.00e-02 2.39e+01
  dihedral pdb=" CA  GLY B 774 "
           pdb=" C   GLY B 774 "
           pdb=" N   GLU B 775 "
           pdb=" CA  GLU B 775 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.85  -23.15     0      5.00e+00 4.00e-02 2.14e+01
  dihedral pdb=" CA  THR B 679 "
           pdb=" C   THR B 679 "
           pdb=" N   GLN B 680 "
           pdb=" CA  GLN B 680 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.42  -22.58     0      5.00e+00 4.00e-02 2.04e+01
  ... (remaining 4185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 708
       0.040 -    0.080: 298
       0.080 -    0.120: 76
       0.120 -    0.159: 10
       0.159 -    0.199: 6
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" CB  ILE B 677 "
            pdb=" CA  ILE B 677 "
            pdb=" CG1 ILE B 677 "
            pdb=" CG2 ILE B 677 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.92e-01
  chirality pdb=" CG  LEU C 416 "
            pdb=" CB  LEU C 416 "
            pdb=" CD1 LEU C 416 "
            pdb=" CD2 LEU C 416 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.86e-01
  chirality pdb=" CG  LEU B 491 "
            pdb=" CB  LEU B 491 "
            pdb=" CD1 LEU B 491 "
            pdb=" CD2 LEU B 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.18 2.00e-01 2.50e+01 8.55e-01
  ... (remaining 1095 not shown)

  Planarity restraints: 1156
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO C 462 "    0.062 5.00e-02 4.00e+02   9.29e-02 1.38e+01
        pdb=" N   PRO C 463 "   -0.161 5.00e-02 4.00e+02
        pdb=" CA  PRO C 463 "    0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO C 463 "    0.050 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO B 724 "   -0.055 5.00e-02 4.00e+02   8.34e-02 1.11e+01
        pdb=" N   PRO B 725 "    0.144 5.00e-02 4.00e+02
        pdb=" CA  PRO B 725 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO B 725 "   -0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 682 "    0.014 2.00e-02 2.50e+03   1.78e-02 5.53e+00
        pdb=" CG  PHE B 682 "   -0.039 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 682 "    0.019 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 682 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 682 "   -0.007 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 682 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 682 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1153 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1486
        2.79 -     3.32: 6256
        3.32 -     3.85: 11128
        3.85 -     4.37: 13749
        4.37 -     4.90: 21659
  Nonbonded interactions: 54278
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 560 "
            pdb=" OG1 THR C 563 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ARG B 492 "
            pdb=" OG1 THR B 517 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   PRO B 777 "
            pdb=" NZ  LYS B 780 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OE2 GLU B 493 "
            pdb=" NZ  LYS C 501 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" O   GLN B 560 "
            pdb=" OG1 THR B 563 "
     model   vdw
     2.325 3.040
  ... (remaining 54273 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.760
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.910
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.010
  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:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5410
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      :  0.004   0.098   6756  Z= 0.206
  Angle     :  0.957   9.695   9160  Z= 0.519
  Chirality :  0.046   0.199   1098
  Planarity :  0.007   0.093   1156
  Dihedral  : 15.273  82.350   2612
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  : 19.44 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.27), residues: 810
  helix: -2.86 (0.29), residues: 220
  sheet: -2.57 (0.54), residues: 90
  loop : -1.93 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 731 
 TYR   0.009   0.001   TYR C 668 
 PHE   0.039   0.002   PHE B 682 
 TRP   0.028   0.003   TRP B 475 
 HIS   0.007   0.001   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 6756)
  covalent geometry    : angle       0.95652 ( 9160)
  hydrogen bonds       : bond        0.23715 (  163)
  hydrogen bonds       : angle       9.99528 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 233
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  453 LEU cc_start: 0.9064 (pp) cc_final: 0.8813 (pp)
REVERT: B  519 GLU cc_start: 0.6964 (tp30) cc_final: 0.5596 (tp30)
REVERT: B  551 LEU cc_start: 0.8119 (mt) cc_final: 0.6991 (pp)
REVERT: B  595 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7358 (mp0)
REVERT: B  675 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5844 (mp0)
REVERT: B  690 LEU cc_start: 0.8505 (mp) cc_final: 0.8216 (mp)
REVERT: B  710 LEU cc_start: 0.7860 (mt) cc_final: 0.7508 (mp)
REVERT: B  804 ARG cc_start: 0.3552 (tpt170) cc_final: 0.3153 (tpt-90)
REVERT: C  412 THR cc_start: 0.5060 (p) cc_final: 0.4828 (t)
REVERT: C  433 PHE cc_start: 0.6844 (t80) cc_final: 0.6068 (t80)
REVERT: C  443 PHE cc_start: 0.6891 (m-80) cc_final: 0.5619 (m-80)
REVERT: C  503 THR cc_start: 0.7434 (m) cc_final: 0.7172 (m)
REVERT: C  744 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.5210 (pm20)
  outliers start: 3
  outliers final: 1
  residues processed: 236
  average time/residue: 0.1033
  time to fit residues: 30.6704
Evaluate side-chains
  124 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 406 ASN
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 737 HIS
C 467 GLN
C 639 HIS
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 764 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4771 r_free = 0.4771 target = 0.174291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.160270 restraints weight = 25546.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.162651 restraints weight = 17868.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.164325 restraints weight = 13232.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.4664 r_free = 0.4664 target = 0.165583 restraints weight = 10389.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 55)----------------|
| r_work = 0.4675 r_free = 0.4675 target = 0.166567 restraints weight = 8467.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.4666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5233
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.075   6756  Z= 0.157
  Angle     :  0.755  11.075   9160  Z= 0.381
  Chirality :  0.045   0.191   1098
  Planarity :  0.006   0.067   1156
  Dihedral  :  5.740  23.072    878
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 18.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.13 (0.28), residues: 810
  helix: -2.70 (0.30), residues: 227
  sheet: -2.71 (0.47), residues: 117
  loop : -1.52 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 734 
 TYR   0.028   0.002   TYR C 513 
 PHE   0.023   0.003   PHE C 635 
 TRP   0.020   0.002   TRP C 411 
 HIS   0.004   0.001   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6756)
  covalent geometry    : angle       0.75524 ( 9160)
  hydrogen bonds       : bond        0.04728 (  163)
  hydrogen bonds       : angle       7.68839 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  500 ILE cc_start: 0.7562 (mm) cc_final: 0.7330 (mp)
REVERT: B  551 LEU cc_start: 0.7666 (mt) cc_final: 0.6506 (pp)
REVERT: B  647 TRP cc_start: 0.5124 (p90) cc_final: 0.4920 (p90)
REVERT: B  804 ARG cc_start: 0.4889 (tpp-160) cc_final: 0.4570 (tpt-90)
REVERT: C  443 PHE cc_start: 0.6246 (m-80) cc_final: 0.5721 (m-10)
REVERT: C  590 MET cc_start: 0.5818 (mmm) cc_final: 0.5364 (mmm)
REVERT: C  613 LEU cc_start: 0.5201 (tp) cc_final: 0.4823 (tp)
REVERT: C  747 PRO cc_start: 0.3911 (Cg_endo) cc_final: 0.3570 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0784
  time to fit residues: 17.4162
Evaluate side-chains
  108 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 25 optimal weight:    0.0970
   chunk 36 optimal weight:    2.9990
   chunk 71 optimal weight:    0.1980
   chunk 26 optimal weight:    1.9990
   chunk 33 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0060
   chunk 65 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 16 optimal weight:    5.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
B 406 ASN
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 711 GLN
C 409 ASN
C 712 ASN
C 737 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.173562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.4599 r_free = 0.4599 target = 0.160284 restraints weight = 26767.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 63)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.162466 restraints weight = 19057.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.163887 restraints weight = 14312.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4658 r_free = 0.4658 target = 0.164700 restraints weight = 11406.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 53)----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.165613 restraints weight = 9732.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.4657
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5269
moved from start:          0.4578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6756  Z= 0.130
  Angle     :  0.691   9.382   9160  Z= 0.347
  Chirality :  0.044   0.180   1098
  Planarity :  0.005   0.057   1156
  Dihedral  :  5.563  24.279    878
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 19.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.30 %
    Favored  : 93.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.85 (0.29), residues: 810
  helix: -2.46 (0.31), residues: 214
  sheet: -2.27 (0.54), residues: 101
  loop : -1.53 (0.28), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG C 600 
 TYR   0.018   0.002   TYR C 513 
 PHE   0.022   0.002   PHE B 635 
 TRP   0.022   0.002   TRP C 411 
 HIS   0.016   0.002   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 6756)
  covalent geometry    : angle       0.69063 ( 9160)
  hydrogen bonds       : bond        0.04085 (  163)
  hydrogen bonds       : angle       7.13657 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  456 ILE cc_start: 0.7483 (tt) cc_final: 0.7273 (tt)
REVERT: B  517 THR cc_start: 0.5526 (p) cc_final: 0.5202 (p)
REVERT: B  647 TRP cc_start: 0.5033 (p90) cc_final: 0.4803 (p90)
REVERT: B  804 ARG cc_start: 0.4911 (tpp-160) cc_final: 0.4488 (tpt-90)
REVERT: C  443 PHE cc_start: 0.5868 (m-80) cc_final: 0.5517 (m-80)
REVERT: C  747 PRO cc_start: 0.3383 (Cg_endo) cc_final: 0.3043 (Cg_exo)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0839
  time to fit residues: 16.7739
Evaluate side-chains
  102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 5 optimal weight:    0.0970
   chunk 22 optimal weight:    0.0050
   chunk 66 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 3 optimal weight:    6.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    0.7796

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4756 r_free = 0.4756 target = 0.173421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.162429 restraints weight = 28300.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4636 r_free = 0.4636 target = 0.163996 restraints weight = 20618.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4654 r_free = 0.4654 target = 0.165219 restraints weight = 15832.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4667 r_free = 0.4667 target = 0.166159 restraints weight = 12671.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4674 r_free = 0.4674 target = 0.166682 restraints weight = 10469.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.4660
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5066
moved from start:          0.5119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6756  Z= 0.124
  Angle     :  0.673   8.435   9160  Z= 0.333
  Chirality :  0.044   0.214   1098
  Planarity :  0.005   0.055   1156
  Dihedral  :  5.420  19.994    878
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.30), residues: 810
  helix: -2.25 (0.33), residues: 208
  sheet: -2.73 (0.44), residues: 136
  loop : -1.16 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 496 
 TYR   0.015   0.001   TYR C 513 
 PHE   0.021   0.002   PHE C 433 
 TRP   0.021   0.002   TRP C 411 
 HIS   0.018   0.001   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 6756)
  covalent geometry    : angle       0.67282 ( 9160)
  hydrogen bonds       : bond        0.03594 (  163)
  hydrogen bonds       : angle       6.88218 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  519 GLU cc_start: 0.5806 (tp30) cc_final: 0.5523 (tp30)
REVERT: B  754 THR cc_start: 0.4213 (p) cc_final: 0.3562 (p)
REVERT: B  804 ARG cc_start: 0.5640 (tpp-160) cc_final: 0.4859 (tpt-90)
REVERT: C  477 TYR cc_start: 0.4971 (m-10) cc_final: 0.4315 (m-10)
REVERT: C  503 THR cc_start: 0.7070 (m) cc_final: 0.6818 (m)
REVERT: C  581 LEU cc_start: 0.5574 (tp) cc_final: 0.5094 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.0769
  time to fit residues: 15.1203
Evaluate side-chains
  105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 21 optimal weight:    0.0870
   chunk 44 optimal weight:    5.9990
   chunk 30 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 72 optimal weight:    0.4980
   chunk 51 optimal weight:    7.9990
   chunk 48 optimal weight:    3.9990
   chunk 12 optimal weight:   10.0000
   chunk 14 optimal weight:    4.9990
   chunk 74 optimal weight:    9.9990
   chunk 67 optimal weight:    9.9990
   overall best weight:    1.4762

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 404 GLN
C 711 GLN
C 737 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.171083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 87)----------------|
| r_work = 0.4598 r_free = 0.4598 target = 0.160610 restraints weight = 29076.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.161620 restraints weight = 23575.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.4629 r_free = 0.4629 target = 0.162574 restraints weight = 19538.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4639 r_free = 0.4639 target = 0.163302 restraints weight = 14710.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.164281 restraints weight = 12270.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.4633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5357
moved from start:          0.5753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6756  Z= 0.143
  Angle     :  0.687   8.839   9160  Z= 0.342
  Chirality :  0.044   0.208   1098
  Planarity :  0.005   0.059   1156
  Dihedral  :  5.413  19.925    878
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 19.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.29), residues: 810
  helix: -2.48 (0.32), residues: 212
  sheet: -2.29 (0.45), residues: 132
  loop : -1.18 (0.30), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 801 
 TYR   0.014   0.001   TYR C 513 
 PHE   0.011   0.002   PHE B 682 
 TRP   0.025   0.002   TRP C 411 
 HIS   0.013   0.001   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6756)
  covalent geometry    : angle       0.68746 ( 9160)
  hydrogen bonds       : bond        0.03358 (  163)
  hydrogen bonds       : angle       6.44904 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.209 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  695 ASN cc_start: 0.3998 (m-40) cc_final: 0.2778 (p0)
REVERT: B  804 ARG cc_start: 0.5419 (tpp-160) cc_final: 0.4696 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.0773
  time to fit residues: 14.9933
Evaluate side-chains
  93 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 46 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 17 optimal weight:    8.9990
   chunk 56 optimal weight:    1.9990
   chunk 52 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 58 optimal weight:    0.7980
   chunk 43 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 758 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4730 r_free = 0.4730 target = 0.171136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4602 r_free = 0.4602 target = 0.160621 restraints weight = 28850.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4625 r_free = 0.4625 target = 0.162229 restraints weight = 20880.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.4643 r_free = 0.4643 target = 0.163463 restraints weight = 15875.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.164120 restraints weight = 12469.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.4660 r_free = 0.4660 target = 0.164708 restraints weight = 10351.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.4655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5233
moved from start:          0.6135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6756  Z= 0.125
  Angle     :  0.667   8.841   9160  Z= 0.332
  Chirality :  0.043   0.178   1098
  Planarity :  0.005   0.057   1156
  Dihedral  :  5.349  21.615    878
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 18.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.59 (0.30), residues: 810
  helix: -2.38 (0.32), residues: 212
  sheet: -2.42 (0.45), residues: 137
  loop : -1.06 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 801 
 TYR   0.021   0.002   TYR B 668 
 PHE   0.013   0.002   PHE C 433 
 TRP   0.021   0.002   TRP B 803 
 HIS   0.012   0.001   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6756)
  covalent geometry    : angle       0.66725 ( 9160)
  hydrogen bonds       : bond        0.03202 (  163)
  hydrogen bonds       : angle       6.25447 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  695 ASN cc_start: 0.3689 (m-40) cc_final: 0.2729 (p0)
REVERT: B  804 ARG cc_start: 0.5389 (tpp-160) cc_final: 0.4664 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.0839
  time to fit residues: 14.4733
Evaluate side-chains
  100 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 10 optimal weight:    0.8980
   chunk 21 optimal weight:   10.0000
   chunk 69 optimal weight:    8.9990
   chunk 9 optimal weight:    0.0670
   chunk 35 optimal weight:    0.7980
   chunk 54 optimal weight:   10.0000
   chunk 50 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 ASN
B 755 ASN
** B 764 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4732 r_free = 0.4732 target = 0.171539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.160602 restraints weight = 28294.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.162153 restraints weight = 21029.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.163404 restraints weight = 16214.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.4648 r_free = 0.4648 target = 0.164215 restraints weight = 12721.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4657 r_free = 0.4657 target = 0.164868 restraints weight = 10676.438|
|-----------------------------------------------------------------------------|
r_work (final): 0.4642
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5304
moved from start:          0.6419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6756  Z= 0.115
  Angle     :  0.663   7.631   9160  Z= 0.328
  Chirality :  0.044   0.163   1098
  Planarity :  0.005   0.086   1156
  Dihedral  :  5.203  23.904    878
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 16.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.04 %
    Favored  : 92.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.30), residues: 810
  helix: -2.23 (0.33), residues: 212
  sheet: -2.29 (0.45), residues: 135
  loop : -1.08 (0.30), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 545 
 TYR   0.041   0.002   TYR C 513 
 PHE   0.012   0.002   PHE C 443 
 TRP   0.019   0.002   TRP B 647 
 HIS   0.012   0.001   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6756)
  covalent geometry    : angle       0.66329 ( 9160)
  hydrogen bonds       : bond        0.03182 (  163)
  hydrogen bonds       : angle       6.10181 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  695 ASN cc_start: 0.3433 (m-40) cc_final: 0.2572 (p0)
REVERT: B  760 GLU cc_start: 0.7243 (tt0) cc_final: 0.6792 (tt0)
REVERT: B  804 ARG cc_start: 0.5336 (tpp-160) cc_final: 0.4751 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.0848
  time to fit residues: 14.5951
Evaluate side-chains
  94 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 0 optimal weight:    5.9990
   chunk 2 optimal weight:    0.8980
   chunk 76 optimal weight:    8.9990
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 28 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 34 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
B 467 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4727 r_free = 0.4727 target = 0.170511 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 86)----------------|
| r_work = 0.4592 r_free = 0.4592 target = 0.159487 restraints weight = 28968.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.161084 restraints weight = 21477.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.4623 r_free = 0.4623 target = 0.161760 restraints weight = 16847.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.4640 r_free = 0.4640 target = 0.162928 restraints weight = 14095.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4647 r_free = 0.4647 target = 0.163456 restraints weight = 11689.995|
|-----------------------------------------------------------------------------|
r_work (final): 0.4632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5351
moved from start:          0.6685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6756  Z= 0.115
  Angle     :  0.659   6.555   9160  Z= 0.324
  Chirality :  0.043   0.155   1098
  Planarity :  0.005   0.073   1156
  Dihedral  :  5.137  20.788    878
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.79 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.19 (0.30), residues: 810
  helix: -2.16 (0.34), residues: 200
  sheet: -2.00 (0.47), residues: 132
  loop : -0.88 (0.30), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 801 
 TYR   0.027   0.002   TYR C 477 
 PHE   0.015   0.002   PHE C 490 
 TRP   0.018   0.002   TRP B 511 
 HIS   0.009   0.001   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6756)
  covalent geometry    : angle       0.65933 ( 9160)
  hydrogen bonds       : bond        0.03107 (  163)
  hydrogen bonds       : angle       6.16547 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 131
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  695 ASN cc_start: 0.3569 (m-40) cc_final: 0.2760 (p0)
REVERT: B  760 GLU cc_start: 0.7367 (tt0) cc_final: 0.6935 (tt0)
  outliers start: 1
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0793
  time to fit residues: 13.9460
Evaluate side-chains
  91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 51 optimal weight:    7.9990
   chunk 31 optimal weight:    0.0980
   chunk 71 optimal weight:    0.2980
   chunk 63 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   chunk 45 optimal weight:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 54 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.6384

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4721 r_free = 0.4721 target = 0.170998 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 103)---------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.160523 restraints weight = 28474.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 71)----------------|
| r_work = 0.4621 r_free = 0.4621 target = 0.162063 restraints weight = 21197.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4632 r_free = 0.4632 target = 0.162877 restraints weight = 16634.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.163746 restraints weight = 13927.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4652 r_free = 0.4652 target = 0.164427 restraints weight = 11501.462|
|-----------------------------------------------------------------------------|
r_work (final): 0.4648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5231
moved from start:          0.6968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6756  Z= 0.114
  Angle     :  0.669   7.505   9160  Z= 0.331
  Chirality :  0.043   0.150   1098
  Planarity :  0.005   0.065   1156
  Dihedral  :  5.108  20.763    878
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 16.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.22 (0.30), residues: 810
  helix: -2.21 (0.34), residues: 206
  sheet: -1.94 (0.48), residues: 137
  loop : -0.87 (0.31), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 550 
 TYR   0.022   0.002   TYR C 513 
 PHE   0.022   0.002   PHE C 490 
 TRP   0.022   0.002   TRP B 511 
 HIS   0.009   0.001   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 6756)
  covalent geometry    : angle       0.66882 ( 9160)
  hydrogen bonds       : bond        0.03143 (  163)
  hydrogen bonds       : angle       6.28842 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  668 TYR cc_start: 0.2741 (m-80) cc_final: 0.2279 (m-80)
REVERT: B  695 ASN cc_start: 0.3596 (m-40) cc_final: 0.2890 (p0)
REVERT: B  760 GLU cc_start: 0.7183 (tt0) cc_final: 0.6819 (tt0)
REVERT: C  477 TYR cc_start: 0.4727 (m-10) cc_final: 0.4344 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0836
  time to fit residues: 14.1971
Evaluate side-chains
  95 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 64 optimal weight:   10.0000
   chunk 66 optimal weight:    5.9990
   chunk 6 optimal weight:    0.5980
   chunk 61 optimal weight:    5.9990
   chunk 57 optimal weight:    0.6980
   chunk 33 optimal weight:    8.9990
   chunk 20 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   overall best weight:    2.6586

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

Flipped N/Q/H residues before XYZ refinement:
B 467 GLN
** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 494 ASN
C 650 HIS
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4627 r_free = 0.4627 target = 0.163220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.154386 restraints weight = 27849.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.155157 restraints weight = 24593.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4518 r_free = 0.4518 target = 0.155359 restraints weight = 16278.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.155870 restraints weight = 14398.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.156696 restraints weight = 11030.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.4529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5501
moved from start:          0.7762

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   6756  Z= 0.210
  Angle     :  0.881  12.267   9160  Z= 0.433
  Chirality :  0.049   0.170   1098
  Planarity :  0.007   0.092   1156
  Dihedral  :  6.034  20.413    878
  Min Nonbonded Distance : 2.386

Molprobity Statistics.
  All-atom Clashscore : 25.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.64 %
    Favored  : 91.36 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.79 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.78 (0.29), residues: 810
  helix: -2.94 (0.29), residues: 206
  sheet: -1.94 (0.47), residues: 134
  loop : -1.22 (0.29), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG C 545 
 TYR   0.029   0.003   TYR C 513 
 PHE   0.019   0.002   PHE C 490 
 TRP   0.022   0.003   TRP C 411 
 HIS   0.010   0.002   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 6756)
  covalent geometry    : angle       0.88054 ( 9160)
  hydrogen bonds       : bond        0.03964 (  163)
  hydrogen bonds       : angle       6.91964 (  351)

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 126
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  695 ASN cc_start: 0.4306 (m-40) cc_final: 0.3614 (p0)
  outliers start: 1
  outliers final: 0
  residues processed: 127
  average time/residue: 0.0827
  time to fit residues: 14.0860
Evaluate side-chains
  91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 1 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 66 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 72 optimal weight:    0.4980
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:    4.9990
   chunk 63 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 25 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   overall best weight:    2.8186

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 522 HIS
** B 649 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.162445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4491 r_free = 0.4491 target = 0.153157 restraints weight = 28243.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.154180 restraints weight = 23966.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4522 r_free = 0.4522 target = 0.155492 restraints weight = 18527.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4531 r_free = 0.4531 target = 0.156065 restraints weight = 13510.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4536 r_free = 0.4536 target = 0.156421 restraints weight = 12413.693|
|-----------------------------------------------------------------------------|
r_work (final): 0.4528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5523
moved from start:          0.8357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   6756  Z= 0.208
  Angle     :  0.879  15.989   9160  Z= 0.431
  Chirality :  0.049   0.215   1098
  Planarity :  0.007   0.094   1156
  Dihedral  :  6.380  23.272    878
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 25.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.00 %
    Favored  : 90.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.02 (0.28), residues: 810
  helix: -3.03 (0.28), residues: 204
  sheet: -1.96 (0.46), residues: 148
  loop : -1.45 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG C 545 
 TYR   0.030   0.003   TYR C 683 
 PHE   0.023   0.003   PHE B 443 
 TRP   0.021   0.003   TRP C 411 
 HIS   0.010   0.002   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 6756)
  covalent geometry    : angle       0.87908 ( 9160)
  hydrogen bonds       : bond        0.03906 (  163)
  hydrogen bonds       : angle       7.09817 (  351)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1457.91 seconds
wall clock time: 25 minutes 43.82 seconds (1543.82 seconds total)