Starting phenix.real_space_refine
on Fri Aug 22 18:19:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f7e_28904/08_2025/8f7e_28904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f7e_28904/08_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f7e_28904/08_2025/8f7e_28904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f7e_28904/08_2025/8f7e_28904.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f7e_28904/08_2025/8f7e_28904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f7e_28904/08_2025/8f7e_28904.map"
  }
  resolution = 4.13
  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=   0.003 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 1.35, per 1000 atoms: 0.20
  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: 0.32
  Conformation dependent library (CDL) restraints added in 240.6 milliseconds
  
  Enol-peptide restraints added in 1.4 microseconds
  

  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: 0.24
  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: 0.96

  Time building geometry restraints manager: 0.45 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: 0.01
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:             5.490
  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:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.690
  Find NCS groups from input model:        0.100
  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:1.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.450
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.008   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 B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 6756)
  covalent geometry    : angle       0.98212 ( 9160)
  hydrogen bonds       : bond        0.24194 (  163)
  hydrogen bonds       : angle       9.78414 (  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
  291 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 287
  time to evaluate  : 0.203 
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: 0.0985
  time to fit residues: 35.4025
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  : 0.266 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.9586

-------------------------------------------------------------------------------
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 = 0.4522 r_free = 0.4522 target = 0.138941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.122400 restraints weight = 31040.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.125002 restraints weight = 21054.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.126925 restraints weight = 15241.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.128193 restraints weight = 11637.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.128945 restraints weight = 9378.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6113
moved from start:          0.5185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6756  Z= 0.202
  Angle     :  0.847   8.524   9160  Z= 0.421
  Chirality :  0.047   0.188   1098
  Planarity :  0.007   0.075   1156
  Dihedral  :  6.110  28.139    878
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 21.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  4.50 %
    Favored  : 95.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.10 (0.28), residues: 810
  helix: -2.81 (0.31), residues: 210
  sheet: -2.49 (0.56), residues: 98
  loop : -1.63 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 417 
 TYR   0.031   0.003   TYR C 477 
 PHE   0.020   0.003   PHE B 682 
 TRP   0.017   0.002   TRP C 411 
 HIS   0.013   0.002   HIS C 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 6756)
  covalent geometry    : angle       0.84658 ( 9160)
  hydrogen bonds       : bond        0.05212 (  163)
  hydrogen bonds       : angle       8.03177 (  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
  206 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 205
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  411 TRP cc_start: 0.7146 (m100) cc_final: 0.6943 (m100)
REVERT: B  434 MET cc_start: 0.7118 (mmp) cc_final: 0.6648 (mmm)
REVERT: B  440 ASP cc_start: 0.7192 (t0) cc_final: 0.6859 (t0)
REVERT: B  511 TRP cc_start: 0.6875 (p-90) cc_final: 0.4708 (p-90)
REVERT: B  517 THR cc_start: 0.6510 (p) cc_final: 0.6287 (t)
REVERT: B  571 LYS cc_start: 0.8905 (tttt) cc_final: 0.8571 (tptt)
REVERT: B  572 LEU cc_start: 0.7779 (tp) cc_final: 0.7246 (tt)
REVERT: B  590 MET cc_start: -0.2084 (tpt) cc_final: -0.5225 (mtm)
REVERT: B  600 ARG cc_start: 0.6327 (ttt180) cc_final: 0.5584 (mmt90)
REVERT: B  611 PHE cc_start: 0.5866 (m-80) cc_final: 0.5496 (m-10)
REVERT: B  617 GLN cc_start: 0.7808 (mt0) cc_final: 0.7570 (mm110)
REVERT: B  648 TYR cc_start: 0.4637 (m-10) cc_final: 0.4038 (m-80)
REVERT: B  682 PHE cc_start: 0.7642 (m-80) cc_final: 0.7367 (m-10)
REVERT: C  411 TRP cc_start: 0.6563 (m-90) cc_final: 0.6344 (m-90)
REVERT: C  455 LEU cc_start: 0.7533 (mt) cc_final: 0.7024 (mt)
REVERT: C  465 ILE cc_start: 0.7608 (tt) cc_final: 0.6773 (tt)
REVERT: C  501 LYS cc_start: 0.8236 (tttt) cc_final: 0.7056 (tttt)
REVERT: C  537 ILE cc_start: 0.8046 (tp) cc_final: 0.7433 (tp)
REVERT: C  666 ARG cc_start: 0.8760 (mtp85) cc_final: 0.7916 (mtp85)
REVERT: C  689 TYR cc_start: 0.6493 (m-80) cc_final: 0.6280 (m-80)
REVERT: C  734 ARG cc_start: 0.7601 (mmt180) cc_final: 0.7228 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0979
  time to fit residues: 25.7633
Evaluate side-chains
  138 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 138
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 25 optimal weight:    0.6980
   chunk 36 optimal weight:    0.3980
   chunk 71 optimal weight:    7.9990
   chunk 26 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 49 optimal weight:    8.9990
   chunk 16 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 639 HIS
B 649 ASN
B 694 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4534 r_free = 0.4534 target = 0.139640 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.123995 restraints weight = 29824.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4347 r_free = 0.4347 target = 0.126620 restraints weight = 20259.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.128422 restraints weight = 14589.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.129692 restraints weight = 11108.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.130595 restraints weight = 8932.907|
|-----------------------------------------------------------------------------|
r_work (final): 0.4403
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6016
moved from start:          0.5968

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6756  Z= 0.136
  Angle     :  0.718  10.466   9160  Z= 0.359
  Chirality :  0.045   0.173   1098
  Planarity :  0.006   0.070   1156
  Dihedral  :  5.658  23.329    878
  Min Nonbonded Distance : 2.450

Molprobity Statistics.
  All-atom Clashscore : 17.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  3.31 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.87 (0.29), residues: 810
  helix: -2.66 (0.32), residues: 205
  sheet: -2.22 (0.54), residues: 108
  loop : -1.48 (0.28), residues: 497

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG C 801 
 TYR   0.029   0.002   TYR C 513 
 PHE   0.019   0.002   PHE C 635 
 TRP   0.029   0.002   TRP B 647 
 HIS   0.008   0.001   HIS C 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6756)
  covalent geometry    : angle       0.71829 ( 9160)
  hydrogen bonds       : bond        0.04259 (  163)
  hydrogen bonds       : angle       7.15109 (  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
  201 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  434 MET cc_start: 0.6986 (mmp) cc_final: 0.6486 (mmm)
REVERT: B  450 VAL cc_start: 0.8592 (t) cc_final: 0.8361 (t)
REVERT: B  571 LYS cc_start: 0.8845 (tttt) cc_final: 0.8545 (tptt)
REVERT: B  572 LEU cc_start: 0.7859 (tp) cc_final: 0.7426 (tt)
REVERT: B  590 MET cc_start: -0.2272 (tpt) cc_final: -0.5431 (mtm)
REVERT: B  600 ARG cc_start: 0.6333 (ttt180) cc_final: 0.6001 (mmt90)
REVERT: B  611 PHE cc_start: 0.5610 (m-80) cc_final: 0.5371 (m-10)
REVERT: C  501 LYS cc_start: 0.8142 (tttt) cc_final: 0.7602 (tttt)
REVERT: C  524 THR cc_start: 0.7744 (m) cc_final: 0.7472 (m)
REVERT: C  668 TYR cc_start: 0.7230 (m-10) cc_final: 0.6980 (m-80)
REVERT: C  693 SER cc_start: 0.7823 (t) cc_final: 0.7613 (p)
REVERT: C  716 THR cc_start: 0.5899 (p) cc_final: 0.5680 (p)
REVERT: C  734 ARG cc_start: 0.7667 (mmt180) cc_final: 0.7342 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0951
  time to fit residues: 24.2804
Evaluate side-chains
  140 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 140
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 79 optimal weight:    0.3980
   chunk 74 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   chunk 32 optimal weight:    7.9990
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    1.0586

-------------------------------------------------------------------------------
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 649 ASN
B 737 HIS
C 431 HIS
C 709 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4515 r_free = 0.4515 target = 0.138873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.123778 restraints weight = 30858.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.126251 restraints weight = 20942.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.127890 restraints weight = 15110.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.129083 restraints weight = 11619.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.129812 restraints weight = 9429.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.4385
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6102
moved from start:          0.6692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6756  Z= 0.148
  Angle     :  0.716   8.713   9160  Z= 0.361
  Chirality :  0.046   0.352   1098
  Planarity :  0.005   0.050   1156
  Dihedral  :  5.463  23.687    878
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 17.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  2.91 %
    Favored  : 96.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.85 (0.29), residues: 810
  helix: -2.68 (0.33), residues: 207
  sheet: -2.36 (0.46), residues: 131
  loop : -1.31 (0.29), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 419 
 TYR   0.020   0.002   TYR C 513 
 PHE   0.022   0.002   PHE B 682 
 TRP   0.026   0.002   TRP B 647 
 HIS   0.007   0.001   HIS C 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6756)
  covalent geometry    : angle       0.71613 ( 9160)
  hydrogen bonds       : bond        0.04140 (  163)
  hydrogen bonds       : angle       6.83913 (  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
  185 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 184
  time to evaluate  : 0.327 
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  414 ASP cc_start: 0.6996 (t70) cc_final: 0.6770 (t70)
REVERT: B  419 ARG cc_start: 0.8591 (ttm-80) cc_final: 0.8297 (tpp80)
REVERT: B  567 VAL cc_start: 0.8254 (t) cc_final: 0.7661 (t)
REVERT: B  568 HIS cc_start: 0.3993 (p-80) cc_final: 0.3375 (p-80)
REVERT: B  571 LYS cc_start: 0.8932 (tttt) cc_final: 0.8557 (tptt)
REVERT: B  572 LEU cc_start: 0.7918 (tp) cc_final: 0.7357 (tt)
REVERT: B  590 MET cc_start: -0.2013 (tpt) cc_final: -0.5365 (mtm)
REVERT: B  611 PHE cc_start: 0.5632 (m-80) cc_final: 0.5419 (m-10)
REVERT: B  698 THR cc_start: 0.6972 (p) cc_final: 0.6619 (p)
REVERT: C  501 LYS cc_start: 0.8367 (tttt) cc_final: 0.7825 (tttt)
REVERT: C  524 THR cc_start: 0.7751 (m) cc_final: 0.7354 (m)
REVERT: C  610 ILE cc_start: 0.8144 (pt) cc_final: 0.7913 (mp)
REVERT: C  666 ARG cc_start: 0.8526 (mtp85) cc_final: 0.7718 (mtp85)
REVERT: C  734 ARG cc_start: 0.7634 (mmt180) cc_final: 0.7169 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1019
  time to fit residues: 24.1200
Evaluate side-chains
  135 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 135
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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:    8.9990
   chunk 44 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0040
   chunk 12 optimal weight:    9.9990
   chunk 14 optimal weight:    7.9990
   chunk 74 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   overall best weight:    1.7996

-------------------------------------------------------------------------------
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 729 GLN
** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 568 HIS
C 657 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.134193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.119800 restraints weight = 31577.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.122221 restraints weight = 21052.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.123852 restraints weight = 15136.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.124977 restraints weight = 11590.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.125770 restraints weight = 9405.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.4323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6271
moved from start:          0.7816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6756  Z= 0.184
  Angle     :  0.780   7.587   9160  Z= 0.393
  Chirality :  0.049   0.329   1098
  Planarity :  0.006   0.073   1156
  Dihedral  :  5.682  24.046    878
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 21.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  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 aren not related in a simple way.
  whole: -3.08 (0.28), residues: 810
  helix: -2.87 (0.31), residues: 215
  sheet: -1.97 (0.46), residues: 130
  loop : -1.61 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 600 
 TYR   0.018   0.002   TYR C 513 
 PHE   0.016   0.002   PHE B 682 
 TRP   0.022   0.003   TRP B 647 
 HIS   0.009   0.002   HIS B 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 6756)
  covalent geometry    : angle       0.78042 ( 9160)
  hydrogen bonds       : bond        0.04058 (  163)
  hydrogen bonds       : angle       6.97004 (  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
  159 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.267 
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  567 VAL cc_start: 0.8125 (t) cc_final: 0.7473 (t)
REVERT: B  568 HIS cc_start: 0.4328 (p-80) cc_final: 0.3879 (p-80)
REVERT: B  571 LYS cc_start: 0.8917 (tttt) cc_final: 0.8537 (tptt)
REVERT: B  572 LEU cc_start: 0.7977 (tp) cc_final: 0.7450 (tt)
REVERT: B  590 MET cc_start: -0.1540 (tpt) cc_final: -0.5183 (mtm)
REVERT: C  499 HIS cc_start: 0.5062 (m-70) cc_final: 0.4189 (m-70)
REVERT: C  522 HIS cc_start: 0.7200 (p-80) cc_final: 0.5762 (p-80)
REVERT: C  797 GLU cc_start: 0.7289 (tt0) cc_final: 0.7054 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0977
  time to fit residues: 19.8657
Evaluate side-chains
  114 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 24 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   chunk 56 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0370
   chunk 43 optimal weight:    0.0980
   chunk 62 optimal weight:    6.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.5662

-------------------------------------------------------------------------------
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 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN
C 711 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4476 r_free = 0.4476 target = 0.136415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.121693 restraints weight = 31131.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.124281 restraints weight = 20581.219|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.125953 restraints weight = 14607.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4343 r_free = 0.4343 target = 0.127116 restraints weight = 11153.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.127932 restraints weight = 8999.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.4348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6191
moved from start:          0.7943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.072   6756  Z= 0.127
  Angle     :  0.700  11.016   9160  Z= 0.345
  Chirality :  0.047   0.306   1098
  Planarity :  0.005   0.046   1156
  Dihedral  :  5.338  28.533    878
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.83 (0.29), residues: 810
  helix: -2.64 (0.32), residues: 209
  sheet: -2.10 (0.44), residues: 141
  loop : -1.36 (0.29), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 801 
 TYR   0.017   0.001   TYR C 513 
 PHE   0.026   0.002   PHE C 433 
 TRP   0.024   0.002   TRP B 475 
 HIS   0.005   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6756)
  covalent geometry    : angle       0.69989 ( 9160)
  hydrogen bonds       : bond        0.03593 (  163)
  hydrogen bonds       : angle       6.46087 (  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
  159 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.307 
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  450 VAL cc_start: 0.8832 (t) cc_final: 0.8220 (t)
REVERT: B  567 VAL cc_start: 0.8059 (t) cc_final: 0.7420 (t)
REVERT: B  571 LYS cc_start: 0.8937 (tttt) cc_final: 0.8490 (tptt)
REVERT: B  572 LEU cc_start: 0.7939 (tp) cc_final: 0.7396 (tt)
REVERT: B  590 MET cc_start: -0.1506 (tpt) cc_final: -0.5159 (mtm)
REVERT: C  499 HIS cc_start: 0.4945 (m-70) cc_final: 0.4354 (m-70)
REVERT: C  522 HIS cc_start: 0.7332 (p-80) cc_final: 0.5765 (p-80)
REVERT: C  670 ASN cc_start: 0.7253 (p0) cc_final: 0.6739 (p0)
REVERT: C  734 ARG cc_start: 0.7561 (mmt180) cc_final: 0.7051 (mmt-90)
REVERT: C  797 GLU cc_start: 0.7244 (tt0) cc_final: 0.7027 (tp30)
REVERT: C  801 ARG cc_start: 0.7300 (ptp-170) cc_final: 0.7000 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0832
  time to fit residues: 17.2318
Evaluate side-chains
  115 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.213 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 10 optimal weight:    0.0030
   chunk 21 optimal weight:   10.0000
   chunk 69 optimal weight:    0.3980
   chunk 9 optimal weight:    4.9990
   chunk 35 optimal weight:   10.0000
   chunk 54 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9990
   chunk 68 optimal weight:    5.9990
   chunk 32 optimal weight:    0.4980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
** B 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 709 ASN
C 657 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4509 r_free = 0.4509 target = 0.139145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.127564 restraints weight = 33241.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.129447 restraints weight = 22805.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.130665 restraints weight = 16561.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 56)----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.131612 restraints weight = 12897.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4403 r_free = 0.4403 target = 0.132257 restraints weight = 10492.633|
|-----------------------------------------------------------------------------|
r_work (final): 0.4371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6197
moved from start:          0.8207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6756  Z= 0.124
  Angle     :  0.697   7.413   9160  Z= 0.347
  Chirality :  0.046   0.247   1098
  Planarity :  0.005   0.051   1156
  Dihedral  :  5.168  30.059    878
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 16.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.80 (0.29), residues: 810
  helix: -2.49 (0.33), residues: 214
  sheet: -2.09 (0.46), residues: 129
  loop : -1.43 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 666 
 TYR   0.018   0.002   TYR C 513 
 PHE   0.018   0.002   PHE B 682 
 TRP   0.022   0.002   TRP B 475 
 HIS   0.011   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6756)
  covalent geometry    : angle       0.69708 ( 9160)
  hydrogen bonds       : bond        0.03540 (  163)
  hydrogen bonds       : angle       6.42086 (  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
  164 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.270 
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  492 ARG cc_start: 0.8381 (mtt-85) cc_final: 0.7980 (ttm-80)
REVERT: B  567 VAL cc_start: 0.8037 (t) cc_final: 0.7383 (t)
REVERT: B  571 LYS cc_start: 0.8922 (tttt) cc_final: 0.8422 (tptt)
REVERT: B  572 LEU cc_start: 0.7989 (tp) cc_final: 0.7433 (tt)
REVERT: B  590 MET cc_start: -0.1751 (tpt) cc_final: -0.5241 (mtm)
REVERT: B  799 LYS cc_start: 0.6004 (mttt) cc_final: 0.5755 (mttt)
REVERT: C  465 ILE cc_start: 0.7745 (tt) cc_final: 0.7403 (tt)
REVERT: C  499 HIS cc_start: 0.4684 (m-70) cc_final: 0.3920 (m-70)
REVERT: C  511 TRP cc_start: 0.6505 (p-90) cc_final: 0.6294 (p-90)
REVERT: C  522 HIS cc_start: 0.7397 (p-80) cc_final: 0.5787 (p-80)
REVERT: C  650 HIS cc_start: 0.7216 (m90) cc_final: 0.7010 (m90)
REVERT: C  689 TYR cc_start: 0.6992 (m-80) cc_final: 0.6669 (m-80)
REVERT: C  734 ARG cc_start: 0.7505 (mmt180) cc_final: 0.6953 (mmt-90)
REVERT: C  801 ARG cc_start: 0.7320 (ptp-170) cc_final: 0.7058 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 164
  average time/residue: 0.0741
  time to fit residues: 15.8873
Evaluate side-chains
  122 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
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:    4.9990
   chunk 0 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 76 optimal weight:    5.9990
   chunk 35 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 28 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    1.9990
   chunk 34 optimal weight:    6.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
B 614 HIS
B 615 ASN
** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.128185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4155 r_free = 0.4155 target = 0.114783 restraints weight = 31850.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.117170 restraints weight = 21168.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.118672 restraints weight = 15077.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.119712 restraints weight = 11503.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.120431 restraints weight = 9337.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.4233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6507
moved from start:          0.9640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.066   6756  Z= 0.296
  Angle     :  1.027  12.256   9160  Z= 0.511
  Chirality :  0.055   0.271   1098
  Planarity :  0.007   0.056   1156
  Dihedral  :  6.615  31.965    878
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 31.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.26 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.34 (0.28), residues: 810
  helix: -3.10 (0.29), residues: 213
  sheet: -2.38 (0.42), residues: 143
  loop : -1.64 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG C 671 
 TYR   0.026   0.003   TYR C 668 
 PHE   0.021   0.003   PHE C 490 
 TRP   0.025   0.004   TRP B 411 
 HIS   0.011   0.003   HIS C 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00678 ( 6756)
  covalent geometry    : angle       1.02671 ( 9160)
  hydrogen bonds       : bond        0.05148 (  163)
  hydrogen bonds       : angle       7.56400 (  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
  151 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.211 
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  412 THR cc_start: 0.8716 (p) cc_final: 0.8313 (p)
REVERT: B  571 LYS cc_start: 0.8826 (tttt) cc_final: 0.8471 (tptt)
REVERT: B  590 MET cc_start: -0.1419 (tpt) cc_final: -0.5228 (mtm)
REVERT: C  448 LEU cc_start: 0.8003 (tp) cc_final: 0.7719 (tp)
REVERT: C  501 LYS cc_start: 0.8487 (tptm) cc_final: 0.8162 (tptp)
REVERT: C  522 HIS cc_start: 0.7765 (p-80) cc_final: 0.7165 (p-80)
REVERT: C  650 HIS cc_start: 0.6948 (m90) cc_final: 0.6743 (m90)
REVERT: C  666 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8233 (mtp85)
REVERT: C  801 ARG cc_start: 0.7450 (ptp-170) cc_final: 0.7115 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 151
  average time/residue: 0.0692
  time to fit residues: 13.8581
Evaluate side-chains
  101 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
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:    0.0570
   chunk 31 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 63 optimal weight:    6.9990
   chunk 22 optimal weight:    5.9990
   chunk 76 optimal weight:    0.0770
   chunk 77 optimal weight:    0.0270
   chunk 45 optimal weight:    0.9980
   chunk 64 optimal weight:    0.1980
   chunk 54 optimal weight:    4.9990
   chunk 30 optimal weight:    8.9990
   overall best weight:    0.2714

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 660 ASN
** B 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN
C 709 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4457 r_free = 0.4457 target = 0.134799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4247 r_free = 0.4247 target = 0.120404 restraints weight = 30401.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.122707 restraints weight = 20728.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.124281 restraints weight = 15124.044|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.125390 restraints weight = 11731.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4333 r_free = 0.4333 target = 0.126231 restraints weight = 9568.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.4330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6260
moved from start:          0.9529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6756  Z= 0.137
  Angle     :  0.793   8.528   9160  Z= 0.386
  Chirality :  0.048   0.252   1098
  Planarity :  0.005   0.047   1156
  Dihedral  :  5.695  30.596    878
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 18.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.66 %
    Favored  : 99.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.78 (0.28), residues: 810
  helix: -2.46 (0.33), residues: 205
  sheet: -1.91 (0.47), residues: 126
  loop : -1.52 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 671 
 TYR   0.018   0.002   TYR C 513 
 PHE   0.035   0.003   PHE C 635 
 TRP   0.030   0.003   TRP C 511 
 HIS   0.005   0.001   HIS B 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6756)
  covalent geometry    : angle       0.79343 ( 9160)
  hydrogen bonds       : bond        0.03532 (  163)
  hydrogen bonds       : angle       6.53320 (  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
  160 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 160
  time to evaluate  : 0.257 
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  410 GLU cc_start: 0.8169 (tp30) cc_final: 0.7789 (tp30)
REVERT: B  571 LYS cc_start: 0.8847 (tttt) cc_final: 0.8391 (tptt)
REVERT: B  572 LEU cc_start: 0.7393 (tt) cc_final: 0.6600 (tt)
REVERT: B  590 MET cc_start: -0.1364 (tpt) cc_final: -0.5932 (mpp)
REVERT: B  691 ASP cc_start: 0.6098 (t0) cc_final: 0.5778 (t0)
REVERT: B  799 LYS cc_start: 0.6124 (mttt) cc_final: 0.5052 (mmtp)
REVERT: C  414 ASP cc_start: 0.7928 (m-30) cc_final: 0.7681 (m-30)
REVERT: C  501 LYS cc_start: 0.8351 (tptm) cc_final: 0.8084 (tptp)
  outliers start: 0
  outliers final: 0
  residues processed: 160
  average time/residue: 0.0726
  time to fit residues: 15.4056
Evaluate side-chains
  115 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
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:    0.0050
   chunk 64 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 6 optimal weight:    0.4980
   chunk 61 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 20 optimal weight:    0.0170
   chunk 1 optimal weight:    0.6980
   chunk 10 optimal weight:    7.9990
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.4432

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
C 418 GLN
C 657 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.134712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.121187 restraints weight = 31192.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.123560 restraints weight = 20698.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.125121 restraints weight = 14704.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.126239 restraints weight = 11175.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4341 r_free = 0.4341 target = 0.127027 restraints weight = 8963.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.4336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6255
moved from start:          0.9706

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= 0.134
  Angle     :  0.792  11.063   9160  Z= 0.385
  Chirality :  0.047   0.217   1098
  Planarity :  0.006   0.087   1156
  Dihedral  :  5.513  29.185    878
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.40 %
    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 aren not related in a simple way.
  whole: -2.97 (0.28), residues: 810
  helix: -2.56 (0.32), residues: 225
  sheet: -2.11 (0.47), residues: 128
  loop : -1.56 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 688 
 TYR   0.014   0.001   TYR C 513 
 PHE   0.019   0.002   PHE C 635 
 TRP   0.030   0.003   TRP B 647 
 HIS   0.017   0.002   HIS B 499 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6756)
  covalent geometry    : angle       0.79229 ( 9160)
  hydrogen bonds       : bond        0.03437 (  163)
  hydrogen bonds       : angle       6.42213 (  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
  150 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 149
  time to evaluate  : 0.194 
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  410 GLU cc_start: 0.8232 (tp30) cc_final: 0.7990 (tp30)
REVERT: B  514 SER cc_start: 0.7964 (m) cc_final: 0.7647 (p)
REVERT: B  571 LYS cc_start: 0.8798 (tttt) cc_final: 0.8451 (tptt)
REVERT: B  590 MET cc_start: -0.0771 (tpt) cc_final: -0.5623 (mpp)
REVERT: C  414 ASP cc_start: 0.7813 (m-30) cc_final: 0.7589 (m-30)
REVERT: C  501 LYS cc_start: 0.8426 (tptm) cc_final: 0.8126 (tptp)
REVERT: C  522 HIS cc_start: 0.7516 (p-80) cc_final: 0.7017 (p-80)
REVERT: C  688 ARG cc_start: 0.7179 (ttp-110) cc_final: 0.6843 (ttp80)
REVERT: C  728 PHE cc_start: 0.8406 (m-80) cc_final: 0.7905 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 150
  average time/residue: 0.0784
  time to fit residues: 15.7535
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  : 0.181 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 66 optimal weight:    0.7980
   chunk 55 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0770
   chunk 29 optimal weight:    0.3980
   chunk 0 optimal weight:    3.9990
   chunk 63 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 431 HIS
** B 522 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4471 r_free = 0.4471 target = 0.136569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4307 r_free = 0.4307 target = 0.125506 restraints weight = 33014.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.127073 restraints weight = 24537.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.128314 restraints weight = 17842.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.128401 restraints weight = 15082.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.128595 restraints weight = 13951.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.4327
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6318
moved from start:          0.9877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6756  Z= 0.128
  Angle     :  0.741  14.506   9160  Z= 0.362
  Chirality :  0.046   0.201   1098
  Planarity :  0.005   0.044   1156
  Dihedral  :  5.350  28.524    878
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 17.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.29), residues: 810
  helix: -2.31 (0.34), residues: 211
  sheet: -1.88 (0.49), residues: 118
  loop : -1.46 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG C 688 
 TYR   0.014   0.001   TYR C 683 
 PHE   0.019   0.002   PHE C 635 
 TRP   0.024   0.002   TRP C 511 
 HIS   0.008   0.001   HIS C 522 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6756)
  covalent geometry    : angle       0.74073 ( 9160)
  hydrogen bonds       : bond        0.03399 (  163)
  hydrogen bonds       : angle       6.16663 (  351)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1515.44 seconds
wall clock time: 26 minutes 48.59 seconds (1608.59 seconds total)