Starting phenix.real_space_refine
on Fri Dec 27 21:51:51 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8f7e_28904/12_2024/8f7e_28904.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8f7e_28904/12_2024/8f7e_28904.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8f7e_28904/12_2024/8f7e_28904.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8f7e_28904/12_2024/8f7e_28904.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8f7e_28904/12_2024/8f7e_28904.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8f7e_28904/12_2024/8f7e_28904.cif"
  }
  resolution = 4.13
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.045
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    4270      2.51       5
     N    1166      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 6642
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
    Chain: "C"
      Number of atoms: 3321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3321
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 18, 'TRANS': 388}
  Time building chain proxies: 5.66, per 1000 atoms: 0.85
  Number of scatterers: 6642
  At special positions: 0
  Unit cell: (86.984, 101.656, 92.224, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O    1190      8.00
     N    1166      7.00
     C    4270      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 980.3 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 5 sheets defined
      32.9% alpha, 11.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.78
  Creating SS restraints...
    Processing helix  chain 'B' and resid 402 through 411
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 439 through 445
      removed outlier: 3.843A  pdb=" N   PHE B 443 " --> pdb=" O   PRO B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 467
    Processing helix  chain 'B' and resid 484 through 495
      removed outlier: 3.740A  pdb=" N   GLU B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.854A  pdb=" N   GLU B 507 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 515
      removed outlier: 4.279A  pdb=" N   SER B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LEU B 515 " --> pdb=" O   TRP B 511 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 510 through 515'
    Processing helix  chain 'B' and resid 535 through 543
      removed outlier: 3.532A  pdb=" N   ASP B 538 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   GLY B 539 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   ARG B 541 " --> pdb=" O   ASP B 538 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   GLU B 542 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 566
    Processing helix  chain 'B' and resid 567 through 569
      No H-bonds generated for 'chain 'B' and resid 567 through 569'
    Processing helix  chain 'B' and resid 634 through 638
    Processing helix  chain 'B' and resid 655 through 661
      removed outlier: 3.684A  pdb=" N   ILE B 658 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 684
      removed outlier: 3.508A  pdb=" N   TYR B 683 " --> pdb=" O   GLN B 680 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   CYS B 684 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 707
    Processing helix  chain 'B' and resid 724 through 730
      removed outlier: 3.638A  pdb=" N   CYS B 730 " --> pdb=" O   GLU B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.508A  pdb=" N   GLY B 751 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 774
      removed outlier: 3.776A  pdb=" N   LEU B 773 " --> pdb=" O   PRO B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 792
      removed outlier: 3.557A  pdb=" N   SER B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 795 through 808
    Processing helix  chain 'C' and resid 403 through 411
    Processing helix  chain 'C' and resid 412 through 419
      removed outlier: 4.003A  pdb=" N   GLN C 418 " --> pdb=" O   ASP C 414 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ARG C 419 " --> pdb=" O   LYS C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 444
      removed outlier: 3.635A  pdb=" N   PHE C 443 " --> pdb=" O   PRO C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 468
    Processing helix  chain 'C' and resid 484 through 494
    Processing helix  chain 'C' and resid 535 through 541
      removed outlier: 3.755A  pdb=" N   ASP C 538 " --> pdb=" O   ILE C 535 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY C 539 " --> pdb=" O   VAL C 536 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG C 541 " --> pdb=" O   ASP C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 566
    Processing helix  chain 'C' and resid 607 through 612
      removed outlier: 4.247A  pdb=" N   PHE C 611 " --> pdb=" O   PRO C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 629 through 638
      removed outlier: 3.525A  pdb=" N   ILE C 632 " --> pdb=" O   ILE C 629 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE C 633 " --> pdb=" O   GLU C 630 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   GLN C 636 " --> pdb=" O   ILE C 633 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   HIS C 637 " --> pdb=" O   SER C 634 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 656 through 661
      removed outlier: 3.823A  pdb=" N   LEU C 661 " --> pdb=" O   ILE C 658 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 678 through 684
      removed outlier: 3.750A  pdb=" N   CYS C 684 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 701 through 707
      removed outlier: 3.662A  pdb=" N   ILE C 704 " --> pdb=" O   PRO C 701 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 725 through 730
      removed outlier: 3.762A  pdb=" N   CYS C 730 " --> pdb=" O   LEU C 727 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 747 through 753
    Processing helix  chain 'C' and resid 770 through 775
    Processing helix  chain 'C' and resid 787 through 792
    Processing helix  chain 'C' and resid 795 through 807
    Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422
      removed outlier: 6.966A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.180A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 453 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU B 474 " --> pdb=" O   HIS B 499 " (cutoff:3.500A)
      removed outlier: 7.938A  pdb=" N   LYS B 501 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU B 476 " --> pdb=" O   LYS B 501 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG B 550 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 523 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS B 552 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   SER B 573 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP B 620 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE B 619 " --> pdb=" O   CYS B 643 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   LEU B 644 " --> pdb=" O   TYR B 668 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 736 through 737
      removed outlier: 6.611A  pdb=" N   LEU B 736 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 421 through 422
      removed outlier: 5.953A  pdb=" N   LEU C 451 " --> pdb=" O   TRP C 475 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   TYR C 477 " --> pdb=" O   LEU C 451 " (cutoff:3.500A)
      removed outlier: 6.126A  pdb=" N   LEU C 453 " --> pdb=" O   TYR C 477 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   HIS C 522 " --> pdb=" O   LEU C 498 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER C 573 " --> pdb=" O   LEU C 549 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU C 572 " --> pdb=" O   GLU C 595 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS C 645 " --> pdb=" O   ILE C 619 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU C 644 " --> pdb=" O   TYR C 668 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 459 through 461
      removed outlier: 6.032A  pdb=" N   VAL C 459 " --> pdb=" O   LYS C 482 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 735 through 736
      removed outlier: 8.155A  pdb=" N   LEU C 736 " --> pdb=" O   GLU C 760 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ILE C 759 " --> pdb=" O   VAL C 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    163 hydrogen bonds defined for protein.
    351 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.90

  Time building geometry restraints manager: 1.84 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.050
  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:             0.000
  Extract box with map and model:          0.280
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.370
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.880
-------------------------------------------------------------------------------
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= 0.297
  Angle     :  0.982   9.664   9160  Z= 0.557
  Chirality :  0.049   0.213   1098
  Planarity :  0.007   0.093   1156
  Dihedral  : 15.172  82.307   2612
  Min Nonbonded Distance : 2.266

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

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

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

*********************** 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  : 0.819 
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: 0.2425
  time to fit residues: 87.2771
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  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 60 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    8.9990
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    9.9990
   chunk 38 optimal weight:    3.9990
   chunk 46 optimal weight:    0.2980
   chunk 72 optimal weight:    0.1980
   overall best weight:    1.6584

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

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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6179
moved from start:          0.5013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6756  Z= 0.280
  Angle     :  0.824   9.382   9160  Z= 0.411
  Chirality :  0.047   0.206   1098
  Planarity :  0.007   0.079   1156
  Dihedral  :  6.037  26.987    878
  Min Nonbonded Distance : 2.519

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

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

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

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 209
  time to evaluate  : 0.930 
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: 0.8345 (tt0) cc_final: 0.7799 (tm-30)
REVERT: B  411 TRP cc_start: 0.7909 (m100) cc_final: 0.7335 (m100)
REVERT: B  434 MET cc_start: 0.8181 (mmp) cc_final: 0.7765 (mmm)
REVERT: B  440 ASP cc_start: 0.7916 (t0) cc_final: 0.7626 (t0)
REVERT: B  483 ILE cc_start: 0.7707 (tt) cc_final: 0.7397 (tt)
REVERT: B  511 TRP cc_start: 0.7323 (p-90) cc_final: 0.5199 (p-90)
REVERT: B  571 LYS cc_start: 0.8770 (tttt) cc_final: 0.8417 (tptt)
REVERT: B  572 LEU cc_start: 0.7829 (tp) cc_final: 0.7358 (tt)
REVERT: B  590 MET cc_start: -0.1951 (tpt) cc_final: -0.5249 (mtm)
REVERT: B  600 ARG cc_start: 0.6602 (ttt180) cc_final: 0.5384 (mmt90)
REVERT: B  611 PHE cc_start: 0.5783 (m-80) cc_final: 0.5398 (m-10)
REVERT: B  617 GLN cc_start: 0.8259 (mt0) cc_final: 0.7866 (mm110)
REVERT: B  635 PHE cc_start: 0.7780 (m-80) cc_final: 0.7458 (m-80)
REVERT: B  682 PHE cc_start: 0.7729 (m-80) cc_final: 0.7395 (m-80)
REVERT: B  688 ARG cc_start: 0.7299 (mtm180) cc_final: 0.6923 (mtp180)
REVERT: B  689 TYR cc_start: 0.8513 (m-80) cc_final: 0.8288 (m-80)
REVERT: C  455 LEU cc_start: 0.7861 (mt) cc_final: 0.7414 (mt)
REVERT: C  465 ILE cc_start: 0.7963 (tt) cc_final: 0.7074 (tt)
REVERT: C  501 LYS cc_start: 0.8367 (tttt) cc_final: 0.7030 (tttt)
REVERT: C  524 THR cc_start: 0.8229 (m) cc_final: 0.8027 (m)
REVERT: C  537 ILE cc_start: 0.8108 (tp) cc_final: 0.7483 (tp)
REVERT: C  603 LEU cc_start: 0.6327 (mp) cc_final: 0.6058 (mp)
REVERT: C  666 ARG cc_start: 0.8842 (mtp85) cc_final: 0.8026 (mtp85)
REVERT: C  689 TYR cc_start: 0.6598 (m-80) cc_final: 0.6388 (m-80)
REVERT: C  728 PHE cc_start: 0.7951 (m-80) cc_final: 0.7713 (m-80)
REVERT: C  734 ARG cc_start: 0.7806 (mmt180) cc_final: 0.7375 (mmm160)
  outliers start: 1
  outliers final: 0
  residues processed: 210
  average time/residue: 0.2312
  time to fit residues: 61.9903
Evaluate side-chains
  145 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    1.9990
   chunk 60 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 20 optimal weight:    4.9990
   chunk 72 optimal weight:    5.9990
   chunk 78 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 24 optimal weight:    6.9990
   chunk 58 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
B 614 HIS
B 649 ASN
B 729 GLN
C 568 HIS
C 657 GLN
** C 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 711 GLN
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6523
moved from start:          0.7484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.047   6756  Z= 0.420
  Angle     :  1.018  11.565   9160  Z= 0.504
  Chirality :  0.054   0.271   1098
  Planarity :  0.008   0.083   1156
  Dihedral  :  6.781  30.785    878
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 28.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.77 %
    Favored  : 91.23 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  6.61 %
    Favored  : 93.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.08 (0.28), residues: 810
  helix: -2.89 (0.33), residues: 190
  sheet: -2.50 (0.46), residues: 120
  loop : -1.57 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.004   TRP B 647 
 HIS   0.020   0.003   HIS C 499 
 PHE   0.018   0.003   PHE B 682 
 TYR   0.024   0.003   TYR C 513 
 ARG   0.030   0.001   ARG C 801 

*********************** 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
  168 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 167
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  410 GLU cc_start: 0.8452 (tt0) cc_final: 0.7872 (tm-30)
REVERT: B  411 TRP cc_start: 0.8142 (m100) cc_final: 0.7756 (m100)
REVERT: B  412 THR cc_start: 0.9085 (p) cc_final: 0.8626 (p)
REVERT: B  567 VAL cc_start: 0.8320 (p) cc_final: 0.7950 (t)
REVERT: B  568 HIS cc_start: 0.4490 (p-80) cc_final: 0.3783 (p-80)
REVERT: B  571 LYS cc_start: 0.8694 (tttt) cc_final: 0.8281 (tptt)
REVERT: B  572 LEU cc_start: 0.7798 (tp) cc_final: 0.7281 (tt)
REVERT: B  590 MET cc_start: -0.1928 (tpt) cc_final: -0.5395 (mtm)
REVERT: B  635 PHE cc_start: 0.8082 (m-80) cc_final: 0.7584 (m-80)
REVERT: C  411 TRP cc_start: 0.6896 (m-90) cc_final: 0.6618 (m-90)
REVERT: C  443 PHE cc_start: 0.8708 (m-80) cc_final: 0.8407 (m-80)
REVERT: C  455 LEU cc_start: 0.8094 (mt) cc_final: 0.7741 (mt)
REVERT: C  458 ASP cc_start: 0.8364 (m-30) cc_final: 0.8009 (t70)
REVERT: C  501 LYS cc_start: 0.8520 (tttt) cc_final: 0.7967 (tttt)
REVERT: C  522 HIS cc_start: 0.7520 (p-80) cc_final: 0.6992 (p-80)
REVERT: C  537 ILE cc_start: 0.7801 (tp) cc_final: 0.7573 (tp)
REVERT: C  666 ARG cc_start: 0.8926 (mtp85) cc_final: 0.7924 (mtp85)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2232
  time to fit residues: 47.7486
Evaluate side-chains
  120 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.801 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 54 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 8 optimal weight:    0.5980
   chunk 34 optimal weight:    5.9990
   chunk 48 optimal weight:    0.0370
   chunk 73 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    4.9990
   chunk 20 optimal weight:    6.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    1.3262

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

Flipped N/Q/H residues before XYZ refinement:
B 636 GLN
B 649 ASN
** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN
C 709 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6449
moved from start:          0.7854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   6756  Z= 0.237
  Angle     :  0.745   7.112   9160  Z= 0.379
  Chirality :  0.047   0.267   1098
  Planarity :  0.006   0.055   1156
  Dihedral  :  6.001  25.930    878
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 18.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.79 %
    Favored  : 93.21 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.28), residues: 810
  helix: -2.80 (0.32), residues: 205
  sheet: -2.48 (0.44), residues: 133
  loop : -1.47 (0.28), residues: 472

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.003   TRP B 647 
 HIS   0.014   0.002   HIS B 637 
 PHE   0.023   0.003   PHE B 682 
 TYR   0.034   0.002   TYR C 477 
 ARG   0.005   0.000   ARG B 492 

*********************** 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
  168 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.725 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  414 ASP cc_start: 0.8787 (p0) cc_final: 0.8344 (t70)
REVERT: B  567 VAL cc_start: 0.8222 (p) cc_final: 0.7667 (t)
REVERT: B  571 LYS cc_start: 0.8723 (tttt) cc_final: 0.8278 (tptt)
REVERT: B  572 LEU cc_start: 0.7866 (tp) cc_final: 0.7374 (tt)
REVERT: B  590 MET cc_start: -0.1430 (tpt) cc_final: -0.5322 (mtm)
REVERT: B  635 PHE cc_start: 0.8145 (m-80) cc_final: 0.7602 (m-80)
REVERT: B  688 ARG cc_start: 0.7174 (mtm180) cc_final: 0.6901 (mtm180)
REVERT: C  452 LYS cc_start: 0.8279 (tptt) cc_final: 0.8059 (tppt)
REVERT: C  455 LEU cc_start: 0.8089 (mt) cc_final: 0.7592 (mt)
REVERT: C  458 ASP cc_start: 0.8146 (m-30) cc_final: 0.7912 (t0)
REVERT: C  537 ILE cc_start: 0.7710 (tp) cc_final: 0.7496 (tp)
REVERT: C  548 VAL cc_start: 0.7663 (t) cc_final: 0.5916 (t)
REVERT: C  590 MET cc_start: 0.4717 (mmm) cc_final: 0.4299 (mpp)
REVERT: C  610 ILE cc_start: 0.8465 (pt) cc_final: 0.8155 (mt)
REVERT: C  623 ASP cc_start: 0.7660 (p0) cc_final: 0.7349 (p0)
REVERT: C  666 ARG cc_start: 0.8846 (mtp85) cc_final: 0.7990 (mtp85)
REVERT: C  734 ARG cc_start: 0.7701 (mmt180) cc_final: 0.6911 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.2110
  time to fit residues: 45.6330
Evaluate side-chains
  134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 43 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 31 optimal weight:    7.9990
   chunk 65 optimal weight:    0.0020
   chunk 53 optimal weight:    6.9990
   chunk 0 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 69 optimal weight:    5.9990
   chunk 19 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    2.1794

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

Flipped N/Q/H residues before XYZ refinement:
B 709 ASN
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6551
moved from start:          0.8754

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6756  Z= 0.281
  Angle     :  0.797  12.475   9160  Z= 0.398
  Chirality :  0.048   0.189   1098
  Planarity :  0.006   0.054   1156
  Dihedral  :  6.007  26.507    878
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 22.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.14 (0.28), residues: 810
  helix: -2.73 (0.32), residues: 211
  sheet: -2.39 (0.44), residues: 133
  loop : -1.63 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.003   TRP B 647 
 HIS   0.007   0.001   HIS C 608 
 PHE   0.021   0.002   PHE B 682 
 TYR   0.037   0.003   TYR C 477 
 ARG   0.006   0.001   ARG B 492 

*********************** 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
  158 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.820 
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  568 HIS cc_start: 0.4403 (p-80) cc_final: 0.3862 (p-80)
REVERT: B  571 LYS cc_start: 0.8688 (tttt) cc_final: 0.8186 (tptt)
REVERT: B  572 LEU cc_start: 0.7929 (tp) cc_final: 0.7333 (tt)
REVERT: B  590 MET cc_start: -0.1182 (tpt) cc_final: -0.5403 (mtm)
REVERT: B  635 PHE cc_start: 0.8320 (m-80) cc_final: 0.7852 (m-80)
REVERT: B  688 ARG cc_start: 0.7120 (mtm180) cc_final: 0.6700 (mtm180)
REVERT: B  689 TYR cc_start: 0.7977 (m-10) cc_final: 0.7672 (m-10)
REVERT: B  760 GLU cc_start: 0.6916 (mm-30) cc_final: 0.6628 (mp0)
REVERT: C  452 LYS cc_start: 0.8232 (tptt) cc_final: 0.8012 (tppt)
REVERT: C  455 LEU cc_start: 0.8061 (mt) cc_final: 0.7562 (mp)
REVERT: C  537 ILE cc_start: 0.7618 (tp) cc_final: 0.7409 (tp)
REVERT: C  572 LEU cc_start: 0.7573 (mt) cc_final: 0.7262 (mt)
REVERT: C  650 HIS cc_start: 0.7256 (m90) cc_final: 0.7002 (m90)
REVERT: C  801 ARG cc_start: 0.7850 (ptp-170) cc_final: 0.7468 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 158
  average time/residue: 0.2075
  time to fit residues: 42.6644
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  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 19 optimal weight:   10.0000
   chunk 77 optimal weight:    0.4980
   chunk 64 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0170
   chunk 25 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.6420

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

Flipped N/Q/H residues before XYZ refinement:
C 478 HIS
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6461
moved from start:          0.8844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6756  Z= 0.181
  Angle     :  0.702   7.060   9160  Z= 0.356
  Chirality :  0.046   0.194   1098
  Planarity :  0.005   0.050   1156
  Dihedral  :  5.531  25.107    878
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.05 (0.28), residues: 810
  helix: -2.64 (0.31), residues: 221
  sheet: -2.10 (0.47), residues: 127
  loop : -1.65 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 647 
 HIS   0.005   0.001   HIS C 608 
 PHE   0.025   0.002   PHE C 433 
 TYR   0.027   0.002   TYR C 477 
 ARG   0.008   0.001   ARG C 666 

*********************** 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
  161 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.740 
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  414 ASP cc_start: 0.8934 (p0) cc_final: 0.8062 (t70)
REVERT: B  415 LYS cc_start: 0.9178 (mtmt) cc_final: 0.8529 (mmmt)
REVERT: B  418 GLN cc_start: 0.8912 (mp10) cc_final: 0.8596 (mp10)
REVERT: B  568 HIS cc_start: 0.4145 (p-80) cc_final: 0.3502 (p-80)
REVERT: B  571 LYS cc_start: 0.8661 (tttt) cc_final: 0.8188 (tptt)
REVERT: B  572 LEU cc_start: 0.7961 (tp) cc_final: 0.7440 (tt)
REVERT: B  590 MET cc_start: -0.1004 (tpt) cc_final: -0.5938 (mtm)
REVERT: B  635 PHE cc_start: 0.8333 (m-80) cc_final: 0.7850 (m-80)
REVERT: B  758 GLN cc_start: 0.8333 (mm110) cc_final: 0.7532 (mt0)
REVERT: B  760 GLU cc_start: 0.6769 (mm-30) cc_final: 0.6492 (mp0)
REVERT: B  799 LYS cc_start: 0.5509 (mttt) cc_final: 0.4639 (mmtp)
REVERT: C  454 GLU cc_start: 0.8524 (pp20) cc_final: 0.8166 (pp20)
REVERT: C  455 LEU cc_start: 0.8060 (mt) cc_final: 0.7353 (mt)
REVERT: C  520 GLU cc_start: 0.7268 (mm-30) cc_final: 0.6941 (mm-30)
REVERT: C  572 LEU cc_start: 0.7512 (mt) cc_final: 0.7293 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 161
  average time/residue: 0.2012
  time to fit residues: 42.3730
Evaluate side-chains
  129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 56 optimal weight:    8.9990
   chunk 43 optimal weight:    0.7980
   chunk 65 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   chunk 35 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0770
   chunk 46 optimal weight:    0.9990
   overall best weight:    0.6138

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6448
moved from start:          0.9053

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= 0.185
  Angle     :  0.702  11.888   9160  Z= 0.353
  Chirality :  0.045   0.190   1098
  Planarity :  0.005   0.048   1156
  Dihedral  :  5.422  29.848    878
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.87 (0.29), residues: 810
  helix: -2.44 (0.33), residues: 214
  sheet: -2.17 (0.44), residues: 139
  loop : -1.48 (0.29), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 475 
 HIS   0.005   0.001   HIS C 522 
 PHE   0.014   0.002   PHE B 611 
 TYR   0.014   0.002   TYR C 668 
 ARG   0.006   0.001   ARG C 550 

*********************** 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
  155 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.825 
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  414 ASP cc_start: 0.8885 (p0) cc_final: 0.8032 (t70)
REVERT: B  415 LYS cc_start: 0.9150 (mtmt) cc_final: 0.8855 (mtmt)
REVERT: B  450 VAL cc_start: 0.8995 (t) cc_final: 0.8448 (t)
REVERT: B  546 LEU cc_start: 0.8359 (tp) cc_final: 0.8105 (tp)
REVERT: B  568 HIS cc_start: 0.4256 (p-80) cc_final: 0.3575 (p-80)
REVERT: B  571 LYS cc_start: 0.8671 (tttt) cc_final: 0.8166 (tptt)
REVERT: B  572 LEU cc_start: 0.7948 (tp) cc_final: 0.7391 (tt)
REVERT: B  590 MET cc_start: -0.1028 (tpt) cc_final: -0.6022 (mtm)
REVERT: B  635 PHE cc_start: 0.8320 (m-80) cc_final: 0.7840 (m-80)
REVERT: B  758 GLN cc_start: 0.8405 (mm110) cc_final: 0.7496 (mt0)
REVERT: B  760 GLU cc_start: 0.6839 (mm-30) cc_final: 0.6592 (mp0)
REVERT: B  799 LYS cc_start: 0.5433 (mttt) cc_final: 0.4589 (mmtp)
REVERT: C  452 LYS cc_start: 0.8684 (tptp) cc_final: 0.8310 (tptt)
REVERT: C  501 LYS cc_start: 0.8675 (tptp) cc_final: 0.7916 (tptm)
REVERT: C  520 GLU cc_start: 0.7163 (mm-30) cc_final: 0.6809 (mm-30)
REVERT: C  689 TYR cc_start: 0.7265 (m-80) cc_final: 0.6942 (m-80)
REVERT: C  797 GLU cc_start: 0.6989 (tm-30) cc_final: 0.6787 (tp30)
REVERT: C  801 ARG cc_start: 0.7900 (ptp-170) cc_final: 0.7547 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 155
  average time/residue: 0.1809
  time to fit residues: 37.9811
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  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 52 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 60 optimal weight:    0.9990
   chunk 70 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   chunk 67 optimal weight:    0.0870
   overall best weight:    0.9764

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

Flipped N/Q/H residues before XYZ refinement:
B 660 ASN
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.9381

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= 0.208
  Angle     :  0.710   6.998   9160  Z= 0.360
  Chirality :  0.047   0.254   1098
  Planarity :  0.005   0.048   1156
  Dihedral  :  5.389  30.475    878
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 17.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.89 (0.29), residues: 810
  helix: -2.46 (0.32), residues: 220
  sheet: -2.04 (0.47), residues: 132
  loop : -1.54 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP B 647 
 HIS   0.005   0.001   HIS C 478 
 PHE   0.025   0.002   PHE C 433 
 TYR   0.013   0.002   TYR C 668 
 ARG   0.005   0.001   ARG C 666 

*********************** 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
  146 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 146
  time to evaluate  : 0.739 
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  414 ASP cc_start: 0.8936 (p0) cc_final: 0.8520 (p0)
REVERT: B  415 LYS cc_start: 0.9103 (mtmt) cc_final: 0.8524 (mmmt)
REVERT: B  546 LEU cc_start: 0.8262 (tp) cc_final: 0.8049 (tp)
REVERT: B  568 HIS cc_start: 0.4233 (p-80) cc_final: 0.3704 (p-80)
REVERT: B  571 LYS cc_start: 0.8623 (tttt) cc_final: 0.8125 (tptt)
REVERT: B  572 LEU cc_start: 0.7880 (tp) cc_final: 0.7313 (tt)
REVERT: B  590 MET cc_start: -0.0937 (tpt) cc_final: -0.6017 (mtm)
REVERT: B  635 PHE cc_start: 0.8336 (m-80) cc_final: 0.7885 (m-80)
REVERT: B  649 ASN cc_start: 0.7224 (m-40) cc_final: 0.6817 (m110)
REVERT: B  758 GLN cc_start: 0.8460 (mm110) cc_final: 0.7593 (mt0)
REVERT: B  760 GLU cc_start: 0.6976 (mm-30) cc_final: 0.6666 (mp0)
REVERT: C  452 LYS cc_start: 0.8609 (tptp) cc_final: 0.8205 (tptt)
REVERT: C  501 LYS cc_start: 0.8729 (tptp) cc_final: 0.8395 (tptm)
REVERT: C  801 ARG cc_start: 0.7939 (ptp-170) cc_final: 0.7612 (ptm160)
  outliers start: 0
  outliers final: 0
  residues processed: 146
  average time/residue: 0.1921
  time to fit residues: 37.2451
Evaluate side-chains
  107 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 73 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    7.9990
   chunk 56 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 64 optimal weight:    8.9990
   chunk 67 optimal weight:    0.0170
   chunk 47 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.7618

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

Flipped N/Q/H residues before XYZ refinement:
B 625 ASN
** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6477
moved from start:          0.9590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6756  Z= 0.188
  Angle     :  0.725  12.032   9160  Z= 0.362
  Chirality :  0.047   0.231   1098
  Planarity :  0.005   0.047   1156
  Dihedral  :  5.295  30.431    878
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 16.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  1.46 %
    Favored  : 98.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.67 (0.29), residues: 810
  helix: -2.24 (0.34), residues: 213
  sheet: -1.89 (0.47), residues: 130
  loop : -1.46 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP B 475 
 HIS   0.005   0.001   HIS B 499 
 PHE   0.016   0.002   PHE B 490 
 TYR   0.022   0.002   TYR C 648 
 ARG   0.006   0.001   ARG B 731 

*********************** 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
  141 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.790 
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  414 ASP cc_start: 0.8736 (p0) cc_final: 0.7919 (t70)
REVERT: B  546 LEU cc_start: 0.8262 (tp) cc_final: 0.8023 (tp)
REVERT: B  568 HIS cc_start: 0.4450 (p-80) cc_final: 0.3714 (p-80)
REVERT: B  571 LYS cc_start: 0.8672 (tttt) cc_final: 0.8163 (tptt)
REVERT: B  572 LEU cc_start: 0.7941 (tp) cc_final: 0.7370 (tt)
REVERT: B  590 MET cc_start: -0.0937 (tpt) cc_final: -0.6061 (mtm)
REVERT: B  625 ASN cc_start: 0.6177 (OUTLIER) cc_final: 0.5317 (t0)
REVERT: B  635 PHE cc_start: 0.8358 (m-80) cc_final: 0.7905 (m-80)
REVERT: B  758 GLN cc_start: 0.8404 (mm110) cc_final: 0.7522 (mt0)
REVERT: B  760 GLU cc_start: 0.6963 (mm-30) cc_final: 0.6672 (mp0)
REVERT: C  501 LYS cc_start: 0.8732 (tptp) cc_final: 0.8446 (tptm)
REVERT: C  520 GLU cc_start: 0.7247 (mm-30) cc_final: 0.6951 (mm-30)
REVERT: C  688 ARG cc_start: 0.6999 (ptt-90) cc_final: 0.6357 (ptt-90)
REVERT: C  689 TYR cc_start: 0.7161 (m-80) cc_final: 0.6629 (m-80)
REVERT: C  801 ARG cc_start: 0.7609 (ptp-170) cc_final: 0.7335 (ptm160)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.2087
  time to fit residues: 38.2623
Evaluate side-chains
  117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 52 optimal weight:    0.2980
   chunk 79 optimal weight:    0.0570
   chunk 73 optimal weight:    0.0670
   chunk 63 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0020
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 50 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0060
   chunk 19 optimal weight:    9.9990
   overall best weight:    0.0860

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

Flipped N/Q/H residues before XYZ refinement:
C 431 HIS
C 657 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6406
moved from start:          0.9657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6756  Z= 0.183
  Angle     :  0.714   9.786   9160  Z= 0.356
  Chirality :  0.047   0.333   1098
  Planarity :  0.005   0.046   1156
  Dihedral  :  5.254  30.098    878
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.13 %
    Favored  : 99.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.29), residues: 810
  helix: -2.27 (0.32), residues: 219
  sheet: -1.86 (0.49), residues: 129
  loop : -1.32 (0.29), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 475 
 HIS   0.006   0.001   HIS B 499 
 PHE   0.027   0.002   PHE C 433 
 TYR   0.013   0.002   TYR C 513 
 ARG   0.012   0.001   ARG C 781 

********************** 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
  157 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.743 
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  410 GLU cc_start: 0.9067 (tp30) cc_final: 0.8825 (tp30)
REVERT: B  414 ASP cc_start: 0.8693 (p0) cc_final: 0.8152 (t70)
REVERT: B  568 HIS cc_start: 0.4321 (p-80) cc_final: 0.3600 (p-80)
REVERT: B  571 LYS cc_start: 0.8654 (tttt) cc_final: 0.8089 (tptt)
REVERT: B  572 LEU cc_start: 0.7939 (tp) cc_final: 0.7255 (tt)
REVERT: B  590 MET cc_start: -0.0163 (tpt) cc_final: -0.5426 (mtm)
REVERT: B  635 PHE cc_start: 0.8336 (m-80) cc_final: 0.8007 (m-80)
REVERT: B  649 ASN cc_start: 0.7461 (m-40) cc_final: 0.6941 (m110)
REVERT: B  758 GLN cc_start: 0.8408 (mm110) cc_final: 0.7556 (mt0)
REVERT: B  760 GLU cc_start: 0.7051 (mm-30) cc_final: 0.6709 (mp0)
REVERT: B  799 LYS cc_start: 0.5621 (mttt) cc_final: 0.5247 (mmtp)
REVERT: C  465 ILE cc_start: 0.8247 (tt) cc_final: 0.7848 (tt)
REVERT: C  520 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6955 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1904
  time to fit residues: 39.9869
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  : 0.765 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 9 optimal weight:    6.9990
   chunk 17 optimal weight:    0.9990
   chunk 63 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 8 optimal weight:    0.9980
   chunk 11 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
C 657 GLN
** C 711 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.132641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4229 r_free = 0.4229 target = 0.119506 restraints weight = 30593.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4261 r_free = 0.4261 target = 0.121679 restraints weight = 20276.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.123139 restraints weight = 14581.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6326
moved from start:          0.9963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6756  Z= 0.219
  Angle     :  0.770  12.958   9160  Z= 0.379
  Chirality :  0.048   0.320   1098
  Planarity :  0.005   0.066   1156
  Dihedral  :  5.377  29.844    878
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 19.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.28 %
    Favored  : 92.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.29), residues: 810
  helix: -2.17 (0.34), residues: 219
  sheet: -1.75 (0.47), residues: 140
  loop : -1.36 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 475 
 HIS   0.009   0.001   HIS C 499 
 PHE   0.014   0.002   PHE B 490 
 TYR   0.014   0.002   TYR C 668 
 ARG   0.010   0.001   ARG B 417 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2052.69 seconds
wall clock time: 37 minutes 58.15 seconds (2278.15 seconds total)