Starting phenix.real_space_refine
on Thu Jun  5 22:13:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f7e_28904/06_2025/8f7e_28904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f7e_28904/06_2025/8f7e_28904.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.13
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f7e_28904/06_2025/8f7e_28904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f7e_28904/06_2025/8f7e_28904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f7e_28904/06_2025/8f7e_28904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f7e_28904/06_2025/8f7e_28904.cif"
  }
  resolution = 4.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.045
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 6.81, per 1000 atoms: 1.03
  Number of scatterers: 6642
  At special positions: 0
  Unit cell: (86.984, 101.656, 92.224, 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: 1.56
  Conformation dependent library (CDL) restraints added in 840.1 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: 0.90
  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: 3.843A  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: 4.279A  pdb=" N   SER B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 3.509A  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: 3.912A  pdb=" N   GLY B 539 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 4.149A  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: 3.638A  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: 3.776A  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: 3.635A  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: 3.525A  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: 3.745A  pdb=" N   GLN C 636 " --> pdb=" O   ILE C 633 " (cutoff:3.500A)
      removed outlier: 3.732A  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: 3.750A  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: 3.762A  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: 6.966A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.180A  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: 7.938A  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: 3.765A  pdb=" N   LYS B 552 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 3.581A  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: 3.615A  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: 6.126A  pdb=" N   LEU C 453 " --> pdb=" O   TYR C 477 " (cutoff:3.500A)
      removed outlier: 4.277A  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: 1.80

  Time building geometry restraints manager: 1.88 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2144
        1.34 -     1.46: 654
        1.46 -     1.57: 3936
        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 7.70e+00
  bond pdb=" N   THR B 412 "
       pdb=" CA  THR B 412 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.034 1.31e-02 5.83e+03 6.83e+00
  bond pdb=" N   THR C 412 "
       pdb=" CA  THR C 412 "
    ideal  model  delta    sigma   weight residual
    1.453  1.488 -0.035 1.37e-02 5.33e+03 6.51e+00
  bond pdb=" N   LEU B 407 "
       pdb=" CA  LEU B 407 "
    ideal  model  delta    sigma   weight residual
    1.459  1.489 -0.030 1.21e-02 6.83e+03 6.07e+00
  bond pdb=" C   ILE C 508 "
       pdb=" N   PRO C 509 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.030 1.20e-02 6.94e+03 6.07e+00
  ... (remaining 6751 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 8674
        1.93 -     3.87: 399
        3.87 -     5.80: 57
        5.80 -     7.73: 19
        7.73 -     9.66: 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  117.16   -7.15 1.80e+00 3.09e-01 1.58e+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  117.62   -6.79 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  121.88   -7.78 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 1.42e+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  119.82   -8.52 2.30e+00 1.89e-01 1.37e+01
  ... (remaining 9155 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.46: 3639
       16.46 -    32.92: 428
       32.92 -    49.38: 91
       49.38 -    65.85: 25
       65.85 -    82.31: 5
  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 -155.49  -24.51     0      5.00e+00 4.00e-02 2.40e+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 -156.86  -23.14     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 -157.41  -22.59     0      5.00e+00 4.00e-02 2.04e+01
  ... (remaining 4185 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 727
       0.043 -    0.085: 278
       0.085 -    0.128: 72
       0.128 -    0.170: 15
       0.170 -    0.213: 6
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" CA  LEU C 407 "
            pdb=" N   LEU C 407 "
            pdb=" C   LEU C 407 "
            pdb=" CB  LEU C 407 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.13e+00
  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 9.85e-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 8.88e-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   9.32e-02 1.39e+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   8.35e-02 1.12e+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   1.77e-02 5.47e+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: 1462
        2.79 -     3.32: 6280
        3.32 -     3.85: 11061
        3.85 -     4.37: 13743
        4.37 -     4.90: 21617
  Nonbonded interactions: 54163
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 560 "
            pdb=" OG1 THR C 563 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   ARG B 492 "
            pdb=" OG1 THR B 517 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   PRO B 777 "
            pdb=" NZ  LYS B 780 "
     model   vdw
     2.297 3.120
  nonbonded pdb=" O   GLN B 560 "
            pdb=" OG1 THR B 563 "
     model   vdw
     2.325 3.040
  nonbonded pdb=" N   HIS C 694 "
            pdb=" O   THR C 716 "
     model   vdw
     2.365 3.120
  ... (remaining 54158 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: 0.03
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:             4.820
  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:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.200
  Find NCS groups from input model:        0.210
  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:             0.010
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.620
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5806
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.098   6756  Z= 0.255
  Angle     :  0.982   9.664   9160  Z= 0.557
  Chirality :  0.049   0.213   1098
  Planarity :  0.007   0.093   1156
  Dihedral  : 15.172  82.307   2612
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  0.53 %
    Allowed  : 18.78 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.38 (0.27), residues: 810
  helix: -2.83 (0.29), residues: 221
  sheet: -2.57 (0.54), residues: 90
  loop : -1.92 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.003   TRP B 475 
 HIS   0.007   0.001   HIS B 522 
 PHE   0.039   0.002   PHE B 682 
 TYR   0.009   0.001   TYR C 668 
 ARG   0.008   0.001   ARG B 731 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.24194 (  163)
  hydrogen bonds       : angle       9.78414 (  351)
  covalent geometry    : bond        0.00465 ( 6756)
  covalent geometry    : angle       0.98212 ( 9160)

*********************** 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
  291 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 287
  time to evaluate  : 0.846 
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: symmetry clash
REVERT: B  410 GLU cc_start: 0.8190 (tt0) cc_final: 0.7821 (tm-30)
REVERT: B  412 THR cc_start: 0.9113 (p) cc_final: 0.8664 (p)
REVERT: B  419 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7560 (ttm110)
REVERT: B  452 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7982 (tttt)
REVERT: B  571 LYS cc_start: 0.8553 (tttt) cc_final: 0.8185 (tptt)
REVERT: B  590 MET cc_start: -0.1767 (tpt) cc_final: -0.4918 (mtm)
REVERT: B  599 ILE cc_start: 0.5698 (mm) cc_final: 0.5423 (mm)
REVERT: B  615 ASN cc_start: 0.7141 (m-40) cc_final: 0.6915 (t0)
REVERT: B  656 ILE cc_start: 0.8564 (pt) cc_final: 0.7839 (pt)
REVERT: B  682 PHE cc_start: 0.7736 (m-80) cc_final: 0.7506 (m-10)
REVERT: B  688 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7095 (mtm180)
REVERT: B  784 LEU cc_start: 0.5851 (pp) cc_final: 0.5445 (pt)
REVERT: C  413 LEU cc_start: 0.8044 (tt) cc_final: 0.7540 (tt)
REVERT: C  426 ASP cc_start: 0.7291 (m-30) cc_final: 0.7051 (t0)
REVERT: C  455 LEU cc_start: 0.8288 (mt) cc_final: 0.6806 (mt)
REVERT: C  474 LEU cc_start: 0.8426 (tp) cc_final: 0.8144 (tp)
REVERT: C  501 LYS cc_start: 0.8306 (tttt) cc_final: 0.6724 (tttt)
REVERT: C  522 HIS cc_start: 0.7856 (p-80) cc_final: 0.6182 (p-80)
REVERT: C  640 ARG cc_start: 0.6614 (mtm180) cc_final: 0.6201 (mmp80)
REVERT: C  728 PHE cc_start: 0.7698 (m-80) cc_final: 0.7291 (m-80)
REVERT: C  736 LEU cc_start: 0.7057 (mp) cc_final: 0.6802 (mt)
REVERT: C  785 VAL cc_start: 0.6470 (t) cc_final: 0.5887 (t)
REVERT: C  786 VAL cc_start: 0.7233 (p) cc_final: 0.6489 (m)
  outliers start: 4
  outliers final: 0
  residues processed: 290
  average time/residue: 0.2419
  time to fit residues: 86.9265
Evaluate side-chains
  158 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.774 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 72 optimal weight:    0.1980
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
B 617 GLN
C 478 HIS
C 650 HIS
C 696 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4537 r_free = 0.4537 target = 0.139945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4293 r_free = 0.4293 target = 0.123091 restraints weight = 30371.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.125740 restraints weight = 20668.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4360 r_free = 0.4360 target = 0.127592 restraints weight = 14988.876|
|-----------------------------------------------------------------------------|
r_work (final): 0.4352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6109
moved from start:          0.5013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6756  Z= 0.191
  Angle     :  0.824   9.382   9160  Z= 0.411
  Chirality :  0.047   0.206   1098
  Planarity :  0.007   0.079   1156
  Dihedral  :  6.037  26.987    878
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.23 %
    Favored  : 95.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.07 (0.28), residues: 810
  helix: -2.75 (0.31), residues: 210
  sheet: -2.42 (0.59), residues: 88
  loop : -1.66 (0.27), residues: 512

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP C 475 
 HIS   0.013   0.001   HIS C 608 
 PHE   0.020   0.003   PHE B 682 
 TYR   0.031   0.003   TYR C 477 
 ARG   0.011   0.001   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05081 (  163)
  hydrogen bonds       : angle       7.97778 (  351)
  covalent geometry    : bond        0.00433 ( 6756)
  covalent geometry    : angle       0.82427 ( 9160)

*********************** 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
  210 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.759 
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  411 TRP cc_start: 0.7044 (m100) cc_final: 0.6838 (m100)
REVERT: B  434 MET cc_start: 0.7118 (mmp) cc_final: 0.6665 (mmm)
REVERT: B  440 ASP cc_start: 0.7227 (t0) cc_final: 0.6823 (t0)
REVERT: B  511 TRP cc_start: 0.6788 (p-90) cc_final: 0.4749 (p-90)
REVERT: B  517 THR cc_start: 0.6504 (p) cc_final: 0.6303 (t)
REVERT: B  571 LYS cc_start: 0.8883 (tttt) cc_final: 0.8553 (tptt)
REVERT: B  572 LEU cc_start: 0.7818 (tp) cc_final: 0.7315 (tt)
REVERT: B  590 MET cc_start: -0.2194 (tpt) cc_final: -0.5294 (mtm)
REVERT: B  600 ARG cc_start: 0.6064 (ttt180) cc_final: 0.5384 (mmt90)
REVERT: B  611 PHE cc_start: 0.5921 (m-80) cc_final: 0.5552 (m-10)
REVERT: B  617 GLN cc_start: 0.7796 (mt0) cc_final: 0.7545 (mm110)
REVERT: B  682 PHE cc_start: 0.7668 (m-80) cc_final: 0.7391 (m-80)
REVERT: B  688 ARG cc_start: 0.7262 (mtm180) cc_final: 0.7029 (mtp180)
REVERT: C  455 LEU cc_start: 0.7437 (mt) cc_final: 0.6948 (mt)
REVERT: C  465 ILE cc_start: 0.7705 (tt) cc_final: 0.6937 (tt)
REVERT: C  501 LYS cc_start: 0.8325 (tttt) cc_final: 0.7002 (tttt)
REVERT: C  537 ILE cc_start: 0.8107 (tp) cc_final: 0.7443 (tp)
REVERT: C  603 LEU cc_start: 0.6216 (mp) cc_final: 0.5990 (mp)
REVERT: C  666 ARG cc_start: 0.8783 (mtp85) cc_final: 0.7946 (mtp85)
REVERT: C  689 TYR cc_start: 0.6483 (m-80) cc_final: 0.6273 (m-80)
REVERT: C  734 ARG cc_start: 0.7569 (mmt180) cc_final: 0.7201 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2293
  time to fit residues: 61.3326
Evaluate side-chains
  144 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 65 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 52 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    1.9784

-------------------------------------------------------------------------------
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 649 ASN
B 729 GLN
C 568 HIS
C 709 ASN
C 711 GLN
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4468 r_free = 0.4468 target = 0.135102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.120797 restraints weight = 30832.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.123042 restraints weight = 21337.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.124596 restraints weight = 15814.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.4309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6296
moved from start:          0.6597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6756  Z= 0.196
  Angle     :  0.811  10.317   9160  Z= 0.403
  Chirality :  0.048   0.167   1098
  Planarity :  0.007   0.074   1156
  Dihedral  :  5.975  25.748    878
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 19.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.90 %
    Favored  : 92.10 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.86 (0.29), residues: 810
  helix: -2.72 (0.33), residues: 192
  sheet: -2.45 (0.49), residues: 118
  loop : -1.39 (0.28), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B 647 
 HIS   0.013   0.002   HIS C 499 
 PHE   0.018   0.002   PHE B 682 
 TYR   0.027   0.003   TYR C 513 
 ARG   0.021   0.001   ARG C 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04639 (  163)
  hydrogen bonds       : angle       7.47226 (  351)
  covalent geometry    : bond        0.00443 ( 6756)
  covalent geometry    : angle       0.81078 ( 9160)

*********************** 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
  186 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 186
  time to evaluate  : 0.809 
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  434 MET cc_start: 0.7767 (mmp) cc_final: 0.7544 (mmp)
REVERT: B  567 VAL cc_start: 0.8192 (p) cc_final: 0.7798 (t)
REVERT: B  568 HIS cc_start: 0.4115 (p-80) cc_final: 0.3426 (p-80)
REVERT: B  571 LYS cc_start: 0.8923 (tttt) cc_final: 0.8545 (tptt)
REVERT: B  572 LEU cc_start: 0.7887 (tp) cc_final: 0.7351 (tt)
REVERT: B  590 MET cc_start: -0.2080 (tpt) cc_final: -0.5405 (mtm)
REVERT: B  611 PHE cc_start: 0.5840 (m-80) cc_final: 0.5633 (m-10)
REVERT: B  698 THR cc_start: 0.6996 (p) cc_final: 0.6552 (p)
REVERT: C  455 LEU cc_start: 0.7650 (mt) cc_final: 0.7140 (mt)
REVERT: C  458 ASP cc_start: 0.8043 (m-30) cc_final: 0.7590 (t70)
REVERT: C  465 ILE cc_start: 0.7767 (tt) cc_final: 0.7102 (tt)
REVERT: C  501 LYS cc_start: 0.8328 (tttt) cc_final: 0.7798 (tttt)
REVERT: C  548 VAL cc_start: 0.7956 (t) cc_final: 0.5672 (t)
REVERT: C  666 ARG cc_start: 0.8799 (mtp85) cc_final: 0.7843 (mtp85)
REVERT: C  734 ARG cc_start: 0.7644 (mmt180) cc_final: 0.7100 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 186
  average time/residue: 0.2251
  time to fit residues: 53.0953
Evaluate side-chains
  133 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.758 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 42 optimal weight:    0.0770
   chunk 55 optimal weight:    0.9980
   chunk 6 optimal weight:    0.0370
   chunk 18 optimal weight:    5.9990
   chunk 58 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 3 optimal weight:    6.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:   10.0000
   chunk 17 optimal weight:    8.9990
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 636 GLN
B 639 HIS
B 649 ASN
** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 478 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.137151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.123012 restraints weight = 31029.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.125868 restraints weight = 22074.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.127255 restraints weight = 14397.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.4353
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6162
moved from start:          0.6984

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= 0.127
  Angle     :  0.697   7.912   9160  Z= 0.347
  Chirality :  0.047   0.284   1098
  Planarity :  0.005   0.050   1156
  Dihedral  :  5.480  23.789    878
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.29), residues: 810
  helix: -2.56 (0.33), residues: 199
  sheet: -2.49 (0.44), residues: 141
  loop : -1.19 (0.30), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.002   TRP B 647 
 HIS   0.007   0.001   HIS C 608 
 PHE   0.019   0.002   PHE B 682 
 TYR   0.021   0.002   TYR C 513 
 ARG   0.004   0.000   ARG C 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03720 (  163)
  hydrogen bonds       : angle       6.83158 (  351)
  covalent geometry    : bond        0.00286 ( 6756)
  covalent geometry    : angle       0.69739 ( 9160)

*********************** 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
  192 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.785 
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  450 VAL cc_start: 0.8615 (t) cc_final: 0.7574 (t)
REVERT: B  463 PRO cc_start: 0.8808 (Cg_endo) cc_final: 0.7807 (Cg_exo)
REVERT: B  567 VAL cc_start: 0.8297 (p) cc_final: 0.7961 (t)
REVERT: B  568 HIS cc_start: 0.3920 (p-80) cc_final: 0.3308 (p-80)
REVERT: B  571 LYS cc_start: 0.8926 (tttt) cc_final: 0.8493 (tptt)
REVERT: B  572 LEU cc_start: 0.7890 (tp) cc_final: 0.7402 (tt)
REVERT: B  590 MET cc_start: -0.1806 (tpt) cc_final: -0.5339 (mtm)
REVERT: C  458 ASP cc_start: 0.7600 (m-30) cc_final: 0.7348 (t0)
REVERT: C  501 LYS cc_start: 0.8339 (tttt) cc_final: 0.7666 (tttt)
REVERT: C  524 THR cc_start: 0.7967 (m) cc_final: 0.7416 (m)
REVERT: C  610 ILE cc_start: 0.8415 (pt) cc_final: 0.8042 (mp)
REVERT: C  670 ASN cc_start: 0.6886 (p0) cc_final: 0.6600 (p0)
REVERT: C  734 ARG cc_start: 0.7684 (mmt180) cc_final: 0.7303 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.2028
  time to fit residues: 51.0677
Evaluate side-chains
  131 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.793 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.0670
   chunk 46 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 59 optimal weight:    9.9990
   chunk 73 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9980
   chunk 9 optimal weight:    4.9990
   chunk 28 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   overall best weight:    1.2122

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 639 HIS
B 649 ASN
B 737 HIS
** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN
C 711 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4481 r_free = 0.4481 target = 0.135644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.120324 restraints weight = 30047.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.122794 restraints weight = 20916.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.124521 restraints weight = 15209.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.4313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6282
moved from start:          0.7559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.065   6756  Z= 0.145
  Angle     :  0.696  11.160   9160  Z= 0.351
  Chirality :  0.046   0.240   1098
  Planarity :  0.005   0.049   1156
  Dihedral  :  5.469  30.617    878
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 17.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.72 (0.29), residues: 810
  helix: -2.50 (0.34), residues: 199
  sheet: -2.07 (0.46), residues: 133
  loop : -1.36 (0.29), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP B 475 
 HIS   0.005   0.001   HIS C 522 
 PHE   0.017   0.002   PHE B 682 
 TYR   0.043   0.002   TYR C 477 
 ARG   0.008   0.001   ARG C 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  163)
  hydrogen bonds       : angle       6.71536 (  351)
  covalent geometry    : bond        0.00334 ( 6756)
  covalent geometry    : angle       0.69627 ( 9160)

*********************** 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
  167 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.761 
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: B  450 VAL cc_start: 0.8223 (t) cc_final: 0.7694 (t)
REVERT: B  567 VAL cc_start: 0.8216 (p) cc_final: 0.7747 (t)
REVERT: B  568 HIS cc_start: 0.4099 (p-80) cc_final: 0.3474 (p-80)
REVERT: B  571 LYS cc_start: 0.8875 (tttt) cc_final: 0.8448 (tptt)
REVERT: B  572 LEU cc_start: 0.7884 (tp) cc_final: 0.7416 (tt)
REVERT: B  590 MET cc_start: -0.1638 (tpt) cc_final: -0.5333 (mtm)
REVERT: C  455 LEU cc_start: 0.7705 (mp) cc_final: 0.7431 (mp)
REVERT: C  465 ILE cc_start: 0.7655 (tt) cc_final: 0.7379 (tt)
REVERT: C  689 TYR cc_start: 0.6410 (m-10) cc_final: 0.6034 (m-10)
REVERT: C  734 ARG cc_start: 0.7651 (mmt180) cc_final: 0.7064 (mmt180)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1844
  time to fit residues: 40.6480
Evaluate side-chains
  125 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 24 optimal weight:    9.9990
   chunk 77 optimal weight:    8.9990
   chunk 61 optimal weight:    7.9990
   chunk 38 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 78 optimal weight:    0.0970
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 639 HIS
B 649 ASN
C 431 HIS
** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4483 r_free = 0.4483 target = 0.135855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.120769 restraints weight = 30586.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.123208 restraints weight = 20664.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.124819 restraints weight = 15093.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.4306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6277
moved from start:          0.8061

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6756  Z= 0.134
  Angle     :  0.676   8.352   9160  Z= 0.342
  Chirality :  0.045   0.212   1098
  Planarity :  0.005   0.047   1156
  Dihedral  :  5.330  31.392    878
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 16.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.72 %
    Favored  : 98.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.29), residues: 810
  helix: -2.55 (0.33), residues: 207
  sheet: -2.17 (0.46), residues: 132
  loop : -1.31 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP C 511 
 HIS   0.005   0.001   HIS C 431 
 PHE   0.028   0.002   PHE C 433 
 TYR   0.016   0.002   TYR C 513 
 ARG   0.005   0.001   ARG C 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03449 (  163)
  hydrogen bonds       : angle       6.40743 (  351)
  covalent geometry    : bond        0.00305 ( 6756)
  covalent geometry    : angle       0.67641 ( 9160)

*********************** 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
  167 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.780 
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: B  567 VAL cc_start: 0.8003 (p) cc_final: 0.7420 (t)
REVERT: B  568 HIS cc_start: 0.4187 (p-80) cc_final: 0.3698 (p-80)
REVERT: B  571 LYS cc_start: 0.8832 (tttt) cc_final: 0.8389 (tptt)
REVERT: B  572 LEU cc_start: 0.7949 (tp) cc_final: 0.7456 (tt)
REVERT: B  590 MET cc_start: -0.1437 (tpt) cc_final: -0.5257 (mtm)
REVERT: C  448 LEU cc_start: 0.7656 (tp) cc_final: 0.7333 (tp)
REVERT: C  465 ILE cc_start: 0.7628 (tt) cc_final: 0.7325 (tt)
REVERT: C  499 HIS cc_start: 0.5301 (m90) cc_final: 0.4087 (m-70)
REVERT: C  522 HIS cc_start: 0.7252 (p-80) cc_final: 0.5934 (p-80)
REVERT: C  734 ARG cc_start: 0.7500 (mmt180) cc_final: 0.6954 (mmt-90)
REVERT: C  801 ARG cc_start: 0.7331 (ptp-170) cc_final: 0.6929 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1904
  time to fit residues: 42.2267
Evaluate side-chains
  121 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 38 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0050
   chunk 13 optimal weight:    6.9990
   chunk 53 optimal weight:    8.9990
   chunk 73 optimal weight:   10.0000
   chunk 70 optimal weight:    0.8980
   chunk 63 optimal weight:    9.9990
   chunk 22 optimal weight:    9.9990
   chunk 29 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    2.7800

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

Flipped N/Q/H residues before XYZ refinement:
B 614 HIS
B 649 ASN
B 709 ASN
** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.128809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4161 r_free = 0.4161 target = 0.114784 restraints weight = 31056.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.117274 restraints weight = 20179.397|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.118933 restraints weight = 14315.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4220
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6539
moved from start:          0.9288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   6756  Z= 0.241
  Angle     :  0.913   9.674   9160  Z= 0.455
  Chirality :  0.052   0.200   1098
  Planarity :  0.006   0.058   1156
  Dihedral  :  6.214  32.105    878
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 27.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.26 %
    Favored  : 90.74 %
  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 : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.15 (0.28), residues: 810
  helix: -2.86 (0.31), residues: 213
  sheet: -2.34 (0.43), residues: 142
  loop : -1.54 (0.29), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.004   TRP C 411 
 HIS   0.013   0.002   HIS C 499 
 PHE   0.017   0.003   PHE B 443 
 TYR   0.019   0.002   TYR B 683 
 ARG   0.011   0.001   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04622 (  163)
  hydrogen bonds       : angle       7.32837 (  351)
  covalent geometry    : bond        0.00541 ( 6756)
  covalent geometry    : angle       0.91334 ( 9160)

*********************** 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
  148 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 148
  time to evaluate  : 0.781 
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: B  568 HIS cc_start: 0.4690 (p-80) cc_final: 0.4375 (p-80)
REVERT: B  571 LYS cc_start: 0.8822 (tttt) cc_final: 0.8374 (tptt)
REVERT: B  572 LEU cc_start: 0.7812 (tp) cc_final: 0.7237 (tt)
REVERT: B  590 MET cc_start: -0.1056 (tpt) cc_final: -0.5750 (mtm)
REVERT: C  448 LEU cc_start: 0.7909 (tp) cc_final: 0.7607 (tp)
REVERT: C  801 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7503 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 148
  average time/residue: 0.1925
  time to fit residues: 37.8838
Evaluate side-chains
  106 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:    0.0870
   chunk 76 optimal weight:    0.0070
   chunk 14 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:   10.0000
   chunk 29 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    0.7980
   chunk 70 optimal weight:    0.0570
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.3494

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 649 ASN
B 660 ASN
** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4446 r_free = 0.4446 target = 0.133857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.119252 restraints weight = 30466.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.121520 restraints weight = 20680.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.123078 restraints weight = 15110.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.4282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6343
moved from start:          0.9246

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6756  Z= 0.132
  Angle     :  0.720   7.400   9160  Z= 0.359
  Chirality :  0.047   0.270   1098
  Planarity :  0.005   0.050   1156
  Dihedral  :  5.591  31.007    878
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 17.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.92 (0.29), residues: 810
  helix: -2.57 (0.32), residues: 225
  sheet: -2.22 (0.43), residues: 147
  loop : -1.39 (0.30), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 411 
 HIS   0.009   0.001   HIS C 499 
 PHE   0.018   0.002   PHE C 433 
 TYR   0.017   0.002   TYR C 513 
 ARG   0.004   0.001   ARG C 781 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03574 (  163)
  hydrogen bonds       : angle       6.42119 (  351)
  covalent geometry    : bond        0.00299 ( 6756)
  covalent geometry    : angle       0.72012 ( 9160)

*********************** 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
  156 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.752 
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: B  410 GLU cc_start: 0.8268 (tp30) cc_final: 0.8058 (tp30)
REVERT: B  567 VAL cc_start: 0.8103 (p) cc_final: 0.7340 (t)
REVERT: B  568 HIS cc_start: 0.4079 (p-80) cc_final: 0.3642 (p-80)
REVERT: B  571 LYS cc_start: 0.8819 (tttt) cc_final: 0.8392 (tptt)
REVERT: B  572 LEU cc_start: 0.7862 (tp) cc_final: 0.7356 (tt)
REVERT: B  590 MET cc_start: -0.1326 (tpt) cc_final: -0.6041 (mpp)
REVERT: B  649 ASN cc_start: 0.6617 (m-40) cc_final: 0.6228 (m-40)
REVERT: B  758 GLN cc_start: 0.8117 (mm110) cc_final: 0.7634 (mt0)
REVERT: C  414 ASP cc_start: 0.7929 (m-30) cc_final: 0.7609 (m-30)
REVERT: C  448 LEU cc_start: 0.7471 (tp) cc_final: 0.6965 (tp)
REVERT: C  520 GLU cc_start: 0.7136 (mm-30) cc_final: 0.6920 (mm-30)
REVERT: C  801 ARG cc_start: 0.7559 (ptp-170) cc_final: 0.7336 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.1714
  time to fit residues: 35.9666
Evaluate side-chains
  117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    1.9990
   chunk 19 optimal weight:    8.9990
   chunk 13 optimal weight:    8.9990
   chunk 34 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 48 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 24 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    5.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4426 r_free = 0.4426 target = 0.132831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.118907 restraints weight = 31233.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.121269 restraints weight = 20668.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.122824 restraints weight = 14648.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.4275
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          0.9486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6756  Z= 0.146
  Angle     :  0.793  11.298   9160  Z= 0.391
  Chirality :  0.048   0.263   1098
  Planarity :  0.005   0.048   1156
  Dihedral  :  5.585  29.892    878
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 20.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.85 (0.29), residues: 810
  helix: -2.53 (0.33), residues: 219
  sheet: -2.19 (0.43), residues: 147
  loop : -1.34 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP B 647 
 HIS   0.013   0.001   HIS C 499 
 PHE   0.027   0.002   PHE C 433 
 TYR   0.015   0.002   TYR C 668 
 ARG   0.004   0.000   ARG C 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03856 (  163)
  hydrogen bonds       : angle       6.53148 (  351)
  covalent geometry    : bond        0.00339 ( 6756)
  covalent geometry    : angle       0.79265 ( 9160)

*********************** 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
  153 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.835 
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  410 GLU cc_start: 0.8358 (tp30) cc_final: 0.8125 (tp30)
REVERT: B  567 VAL cc_start: 0.8119 (p) cc_final: 0.7367 (t)
REVERT: B  568 HIS cc_start: 0.4259 (p-80) cc_final: 0.3821 (p-80)
REVERT: B  571 LYS cc_start: 0.8797 (tttt) cc_final: 0.8327 (tptt)
REVERT: B  572 LEU cc_start: 0.7861 (tp) cc_final: 0.7298 (tt)
REVERT: B  590 MET cc_start: -0.1247 (tpt) cc_final: -0.5922 (mtm)
REVERT: B  649 ASN cc_start: 0.6717 (m-40) cc_final: 0.6411 (m-40)
REVERT: B  758 GLN cc_start: 0.8066 (mm110) cc_final: 0.7535 (mt0)
REVERT: C  414 ASP cc_start: 0.8008 (m-30) cc_final: 0.7659 (m-30)
REVERT: C  448 LEU cc_start: 0.7426 (tp) cc_final: 0.7061 (tp)
REVERT: C  522 HIS cc_start: 0.7839 (p-80) cc_final: 0.7561 (p-80)
REVERT: C  728 PHE cc_start: 0.8111 (m-10) cc_final: 0.7690 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.1852
  time to fit residues: 38.4532
Evaluate side-chains
  111 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.866 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 16 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    0.7980
   chunk 12 optimal weight:    0.3980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4431 r_free = 0.4431 target = 0.133304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.119607 restraints weight = 32784.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.121861 restraints weight = 21962.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.123407 restraints weight = 15748.058|
|-----------------------------------------------------------------------------|
r_work (final): 0.4280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6379
moved from start:          0.9688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6756  Z= 0.133
  Angle     :  0.720   8.140   9160  Z= 0.361
  Chirality :  0.046   0.184   1098
  Planarity :  0.005   0.047   1156
  Dihedral  :  5.439  29.105    878
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.29), residues: 810
  helix: -2.30 (0.34), residues: 211
  sheet: -2.14 (0.44), residues: 147
  loop : -1.32 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 647 
 HIS   0.013   0.001   HIS C 499 
 PHE   0.029   0.002   PHE C 433 
 TYR   0.020   0.001   TYR C 689 
 ARG   0.006   0.001   ARG C 600 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03516 (  163)
  hydrogen bonds       : angle       6.22193 (  351)
  covalent geometry    : bond        0.00311 ( 6756)
  covalent geometry    : angle       0.71980 ( 9160)

********************** 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
  145 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 1.319 
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: B  568 HIS cc_start: 0.4180 (p-80) cc_final: 0.3791 (p-80)
REVERT: B  571 LYS cc_start: 0.8773 (tttt) cc_final: 0.8244 (tptt)
REVERT: B  572 LEU cc_start: 0.7840 (tp) cc_final: 0.7226 (tt)
REVERT: B  590 MET cc_start: -0.0719 (tpt) cc_final: -0.5550 (mtm)
REVERT: B  649 ASN cc_start: 0.6774 (m-40) cc_final: 0.6525 (m-40)
REVERT: B  758 GLN cc_start: 0.8220 (mm110) cc_final: 0.7629 (mt0)
REVERT: C  414 ASP cc_start: 0.7870 (m-30) cc_final: 0.7645 (m-30)
REVERT: C  520 GLU cc_start: 0.7166 (mm-30) cc_final: 0.6885 (mm-30)
REVERT: C  640 ARG cc_start: 0.7840 (mtt180) cc_final: 0.7638 (mtt180)
REVERT: C  671 ARG cc_start: 0.8749 (mmm-85) cc_final: 0.8495 (mmt-90)
REVERT: C  728 PHE cc_start: 0.8211 (m-10) cc_final: 0.7783 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.1727
  time to fit residues: 34.7355
Evaluate side-chains
  110 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 30 optimal weight:    3.9990
   chunk 3 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 70 optimal weight:    7.9990
   chunk 20 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    2.0786

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4380 r_free = 0.4380 target = 0.129766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4180 r_free = 0.4180 target = 0.116061 restraints weight = 31881.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.118234 restraints weight = 21416.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.119700 restraints weight = 15466.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          1.0146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6756  Z= 0.189
  Angle     :  0.822   9.262   9160  Z= 0.409
  Chirality :  0.049   0.211   1098
  Planarity :  0.005   0.049   1156
  Dihedral  :  5.701  29.321    878
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 23.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.99 (0.28), residues: 810
  helix: -2.49 (0.33), residues: 217
  sheet: -2.30 (0.44), residues: 146
  loop : -1.53 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 647 
 HIS   0.018   0.002   HIS C 499 
 PHE   0.018   0.002   PHE C 635 
 TYR   0.013   0.001   TYR B 683 
 ARG   0.004   0.001   ARG B 417 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04115 (  163)
  hydrogen bonds       : angle       6.75993 (  351)
  covalent geometry    : bond        0.00435 ( 6756)
  covalent geometry    : angle       0.82169 ( 9160)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3006.23 seconds
wall clock time: 52 minutes 29.69 seconds (3149.69 seconds total)