Starting phenix.real_space_refine
on Thu Jul 24 23:17:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dro_27679/07_2025/8dro_27679.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dro_27679/07_2025/8dro_27679.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dro_27679/07_2025/8dro_27679.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dro_27679/07_2025/8dro_27679.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dro_27679/07_2025/8dro_27679.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dro_27679/07_2025/8dro_27679.cif"
  }
  resolution = 4.06
  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=   0.001 sd=   0.049
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    4270      2.51       5
     N    1166      2.21       5
     O    1190      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 5.85, per 1000 atoms: 0.88
  Number of scatterers: 6642
  At special positions: 0
  Unit cell: (89.08, 100.608, 90.128, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O    1190      8.00
     N    1166      7.00
     C    4270      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.57
  Conformation dependent library (CDL) restraints added in 976.9 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: 0.82
  Creating SS restraints...
    Processing helix  chain 'B' and resid 402 through 411
    Processing helix  chain 'B' and resid 412 through 419
    Processing helix  chain 'B' and resid 439 through 445
      removed outlier: 3.844A  pdb=" N   PHE B 443 " --> pdb=" O   PRO B 439 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 462 through 467
    Processing helix  chain 'B' and resid 484 through 495
      removed outlier: 3.740A  pdb=" N   GLU B 493 " --> pdb=" O   ALA B 489 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 503 through 508
      removed outlier: 3.854A  pdb=" N   GLU B 507 " --> pdb=" O   ASP B 504 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 515
      removed outlier: 4.280A  pdb=" N   SER B 514 " --> pdb=" O   LEU B 510 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU B 515 " --> pdb=" O   TRP B 511 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 510 through 515'
    Processing helix  chain 'B' and resid 535 through 543
      removed outlier: 3.532A  pdb=" N   ASP B 538 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   GLY B 539 " --> pdb=" O   VAL B 536 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ARG B 541 " --> pdb=" O   ASP B 538 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   GLU B 542 " --> pdb=" O   GLY B 539 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 559 through 566
    Processing helix  chain 'B' and resid 567 through 569
      No H-bonds generated for 'chain 'B' and resid 567 through 569'
    Processing helix  chain 'B' and resid 634 through 638
    Processing helix  chain 'B' and resid 655 through 661
      removed outlier: 3.684A  pdb=" N   ILE B 658 " --> pdb=" O   PRO B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 679 through 684
      removed outlier: 3.508A  pdb=" N   TYR B 683 " --> pdb=" O   GLN B 680 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   CYS B 684 " --> pdb=" O   LEU B 681 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 701 through 707
    Processing helix  chain 'B' and resid 724 through 730
      removed outlier: 3.637A  pdb=" N   CYS B 730 " --> pdb=" O   GLU B 726 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 747 through 752
      removed outlier: 3.508A  pdb=" N   GLY B 751 " --> pdb=" O   PRO B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 770 through 774
      removed outlier: 3.775A  pdb=" N   LEU B 773 " --> pdb=" O   PRO B 770 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 787 through 792
      removed outlier: 3.557A  pdb=" N   SER B 792 " --> pdb=" O   GLU B 788 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 795 through 808
    Processing helix  chain 'C' and resid 403 through 411
    Processing helix  chain 'C' and resid 412 through 419
      removed outlier: 4.003A  pdb=" N   GLN C 418 " --> pdb=" O   ASP C 414 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ARG C 419 " --> pdb=" O   LYS C 415 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 439 through 444
      removed outlier: 3.634A  pdb=" N   PHE C 443 " --> pdb=" O   PRO C 439 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 462 through 468
    Processing helix  chain 'C' and resid 484 through 494
    Processing helix  chain 'C' and resid 535 through 541
      removed outlier: 3.755A  pdb=" N   ASP C 538 " --> pdb=" O   ILE C 535 " (cutoff:3.500A)
      removed outlier: 4.415A  pdb=" N   GLY C 539 " --> pdb=" O   VAL C 536 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ARG C 541 " --> pdb=" O   ASP C 538 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 559 through 566
    Processing helix  chain 'C' and resid 607 through 612
      removed outlier: 4.247A  pdb=" N   PHE C 611 " --> pdb=" O   PRO C 607 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 629 through 638
      removed outlier: 3.526A  pdb=" N   ILE C 632 " --> pdb=" O   ILE C 629 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   ILE C 633 " --> pdb=" O   GLU C 630 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN C 636 " --> pdb=" O   ILE C 633 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   HIS C 637 " --> pdb=" O   SER C 634 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 656 through 661
      removed outlier: 3.823A  pdb=" N   LEU C 661 " --> pdb=" O   ILE C 658 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 678 through 684
      removed outlier: 3.751A  pdb=" N   CYS C 684 " --> pdb=" O   LEU C 681 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 701 through 707
      removed outlier: 3.662A  pdb=" N   ILE C 704 " --> pdb=" O   PRO C 701 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 725 through 730
      removed outlier: 3.763A  pdb=" N   CYS C 730 " --> pdb=" O   LEU C 727 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 747 through 753
    Processing helix  chain 'C' and resid 770 through 775
    Processing helix  chain 'C' and resid 787 through 792
    Processing helix  chain 'C' and resid 795 through 807
    Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422
      removed outlier: 6.965A  pdb=" N   LEU B 451 " --> pdb=" O   TRP B 475 " (cutoff:3.500A)
      removed outlier: 7.181A  pdb=" N   TYR B 477 " --> pdb=" O   LEU B 451 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   LEU B 453 " --> pdb=" O   TYR B 477 " (cutoff:3.500A)
      removed outlier: 6.473A  pdb=" N   LEU B 474 " --> pdb=" O   HIS B 499 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   LYS B 501 " --> pdb=" O   LEU B 474 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   LEU B 476 " --> pdb=" O   LYS B 501 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   ARG B 550 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LEU B 523 " --> pdb=" O   ARG B 550 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   LYS B 552 " --> pdb=" O   LEU B 523 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   SER B 573 " --> pdb=" O   LEU B 549 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   ASP B 620 " --> pdb=" O   LEU B 596 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   ILE B 619 " --> pdb=" O   CYS B 643 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   LEU B 644 " --> pdb=" O   TYR B 668 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 736 through 737
      removed outlier: 6.611A  pdb=" N   LEU B 736 " --> pdb=" O   GLU B 760 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 421 through 422
      removed outlier: 5.953A  pdb=" N   LEU C 451 " --> pdb=" O   TRP C 475 " (cutoff:3.500A)
      removed outlier: 6.757A  pdb=" N   TYR C 477 " --> pdb=" O   LEU C 451 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   LEU C 453 " --> pdb=" O   TYR C 477 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   HIS C 522 " --> pdb=" O   LEU C 498 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   SER C 573 " --> pdb=" O   LEU C 549 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   LEU C 572 " --> pdb=" O   GLU C 595 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   LYS C 645 " --> pdb=" O   ILE C 619 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   LEU C 644 " --> pdb=" O   TYR C 668 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 459 through 461
      removed outlier: 6.032A  pdb=" N   VAL C 459 " --> pdb=" O   LYS C 482 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 735 through 736
      removed outlier: 8.155A  pdb=" N   LEU C 736 " --> pdb=" O   GLU C 760 " (cutoff:3.500A)
      removed outlier: 6.179A  pdb=" N   ILE C 759 " --> pdb=" O   VAL C 785 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5

    163 hydrogen bonds defined for protein.
    351 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.81

  Time building geometry restraints manager: 1.89 seconds

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

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

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

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

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

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

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1486
        2.79 -     3.32: 6256
        3.32 -     3.85: 11128
        3.85 -     4.37: 13749
        4.37 -     4.90: 21659
  Nonbonded interactions: 54278
  Sorted by model distance:
  nonbonded pdb=" O   GLN C 560 "
            pdb=" OG1 THR C 563 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ARG B 492 "
            pdb=" OG1 THR B 517 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" O   PRO B 777 "
            pdb=" NZ  LYS B 780 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" OE2 GLU B 493 "
            pdb=" NZ  LYS C 501 "
     model   vdw
     2.320 3.120
  nonbonded pdb=" O   GLN B 560 "
            pdb=" OG1 THR B 563 "
     model   vdw
     2.325 3.040
  ... (remaining 54273 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.470
  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:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     20.980
  Find NCS groups from input model:        0.230
  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:2.990
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5410
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.098   6756  Z= 0.206
  Angle     :  0.957   9.695   9160  Z= 0.519
  Chirality :  0.046   0.199   1098
  Planarity :  0.007   0.093   1156
  Dihedral  : 15.273  82.350   2612
  Min Nonbonded Distance : 2.265

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

Rama-Z (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: -3.39 (0.27), residues: 810
  helix: -2.86 (0.29), residues: 220
  sheet: -2.57 (0.54), residues: 90
  loop : -1.93 (0.27), residues: 500

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

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

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 233
  time to evaluate  : 0.833 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  453 LEU cc_start: 0.9064 (pp) cc_final: 0.8813 (pp)
REVERT: B  519 GLU cc_start: 0.6964 (tp30) cc_final: 0.5596 (tp30)
REVERT: B  551 LEU cc_start: 0.8119 (mt) cc_final: 0.6990 (pp)
REVERT: B  595 GLU cc_start: 0.7689 (mt-10) cc_final: 0.7358 (mp0)
REVERT: B  675 GLU cc_start: 0.6095 (mm-30) cc_final: 0.5844 (mp0)
REVERT: B  690 LEU cc_start: 0.8504 (mp) cc_final: 0.8216 (mp)
REVERT: B  710 LEU cc_start: 0.7860 (mt) cc_final: 0.7508 (mp)
REVERT: B  804 ARG cc_start: 0.3552 (tpt170) cc_final: 0.3153 (tpt-90)
REVERT: C  412 THR cc_start: 0.5060 (p) cc_final: 0.4828 (t)
REVERT: C  433 PHE cc_start: 0.6844 (t80) cc_final: 0.6068 (t80)
REVERT: C  443 PHE cc_start: 0.6891 (m-80) cc_final: 0.5619 (m-80)
REVERT: C  503 THR cc_start: 0.7434 (m) cc_final: 0.7172 (m)
REVERT: C  744 GLN cc_start: 0.5638 (OUTLIER) cc_final: 0.5210 (pm20)
  outliers start: 3
  outliers final: 1
  residues processed: 236
  average time/residue: 0.2361
  time to fit residues: 69.7277
Evaluate side-chains
  124 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 122
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 60 optimal weight:    9.9990
   chunk 33 optimal weight:    8.9990
   chunk 20 optimal weight:    8.9990
   chunk 40 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 24 optimal weight:    8.9990
   chunk 38 optimal weight:    1.9990
   chunk 46 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    2.5788

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

Flipped N/Q/H residues before XYZ refinement:
** B 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 478 HIS
** B 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 614 HIS
B 694 HIS
C 467 GLN
C 650 HIS
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 764 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4710 r_free = 0.4710 target = 0.168494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4511 r_free = 0.4511 target = 0.153740 restraints weight = 26429.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.156249 restraints weight = 18250.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.4569 r_free = 0.4569 target = 0.158103 restraints weight = 13387.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.4561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5553
moved from start:          0.4507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   6756  Z= 0.220
  Angle     :  0.875   9.229   9160  Z= 0.438
  Chirality :  0.048   0.226   1098
  Planarity :  0.007   0.076   1156
  Dihedral  :  6.201  23.661    878
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 23.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  6.35 %
    Favored  : 93.25 %
  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: -3.16 (0.28), residues: 810
  helix: -2.85 (0.29), residues: 219
  sheet: -2.45 (0.49), residues: 107
  loop : -1.62 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.003   TRP C 411 
 HIS   0.007   0.002   HIS C 499 
 PHE   0.020   0.003   PHE B 682 
 TYR   0.030   0.003   TYR C 513 
 ARG   0.007   0.001   ARG C 749 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04912 (  163)
  hydrogen bonds       : angle       7.61034 (  351)
  covalent geometry    : bond        0.00497 ( 6756)
  covalent geometry    : angle       0.87547 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 155
  time to evaluate  : 0.726 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  645 LYS cc_start: 0.6387 (mttt) cc_final: 0.5188 (mmmt)
REVERT: B  647 TRP cc_start: 0.5242 (p90) cc_final: 0.4825 (p90)
REVERT: B  804 ARG cc_start: 0.4847 (tpp-160) cc_final: 0.4297 (tpt-90)
REVERT: C  403 ARG cc_start: 0.4232 (OUTLIER) cc_final: 0.3541 (mtm180)
REVERT: C  443 PHE cc_start: 0.6575 (m-80) cc_final: 0.5991 (m-80)
REVERT: C  473 GLU cc_start: 0.6856 (mt-10) cc_final: 0.6635 (mt-10)
REVERT: C  590 MET cc_start: 0.5908 (mmm) cc_final: 0.5534 (mmm)
REVERT: C  613 LEU cc_start: 0.4734 (tp) cc_final: 0.4524 (tp)
REVERT: C  747 PRO cc_start: 0.3338 (Cg_endo) cc_final: 0.3107 (Cg_exo)
  outliers start: 3
  outliers final: 1
  residues processed: 157
  average time/residue: 0.1969
  time to fit residues: 40.4354
Evaluate side-chains
  105 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 3 optimal weight:    3.9990
   chunk 57 optimal weight:   10.0000
   chunk 38 optimal weight:    0.6980
   chunk 65 optimal weight:    0.5980
   chunk 66 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 42 optimal weight:    7.9990
   chunk 52 optimal weight:    0.4980
   chunk 76 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.1582

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 711 GLN
C 404 GLN
C 639 HIS
C 711 GLN
C 737 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4726 r_free = 0.4726 target = 0.170681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 95)----------------|
| r_work = 0.4571 r_free = 0.4571 target = 0.159368 restraints weight = 26717.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 57)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.161089 restraints weight = 19437.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4614 r_free = 0.4614 target = 0.162274 restraints weight = 14548.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.4594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5421
moved from start:          0.5140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6756  Z= 0.138
  Angle     :  0.702   8.062   9160  Z= 0.353
  Chirality :  0.044   0.147   1098
  Planarity :  0.005   0.064   1156
  Dihedral  :  5.750  20.835    878
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 17.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.67 %
    Favored  : 93.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    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 (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 (0.29), residues: 810
  helix: -2.51 (0.32), residues: 214
  sheet: -2.80 (0.43), residues: 130
  loop : -1.53 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP C 411 
 HIS   0.005   0.001   HIS C 522 
 PHE   0.021   0.002   PHE B 635 
 TYR   0.019   0.002   TYR C 513 
 ARG   0.005   0.001   ARG C 600 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  163)
  hydrogen bonds       : angle       6.89512 (  351)
  covalent geometry    : bond        0.00315 ( 6756)
  covalent geometry    : angle       0.70203 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.840 
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  551 LEU cc_start: 0.8034 (mt) cc_final: 0.6215 (pp)
REVERT: B  645 LYS cc_start: 0.6770 (mttt) cc_final: 0.5978 (mmtp)
REVERT: B  754 THR cc_start: 0.4945 (p) cc_final: 0.4352 (p)
REVERT: B  755 ASN cc_start: 0.4986 (t0) cc_final: 0.4631 (m-40)
REVERT: C  616 LEU cc_start: 0.7973 (mp) cc_final: 0.7739 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 156
  average time/residue: 0.2143
  time to fit residues: 43.3276
Evaluate side-chains
  102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 42 optimal weight:    8.9990
   chunk 55 optimal weight:    0.3980
   chunk 6 optimal weight:    0.1980
   chunk 18 optimal weight:    0.0170
   chunk 58 optimal weight:    0.9990
   chunk 57 optimal weight:    0.2980
   chunk 41 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   overall best weight:    0.3418

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 672 ASN
C 409 ASN
** C 418 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 737 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4729 r_free = 0.4729 target = 0.171729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4595 r_free = 0.4595 target = 0.161097 restraints weight = 29147.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4618 r_free = 0.4618 target = 0.162605 restraints weight = 21325.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 63)----------------|
| r_work = 0.4635 r_free = 0.4635 target = 0.163824 restraints weight = 16425.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5240
moved from start:          0.5575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6756  Z= 0.119
  Angle     :  0.674   8.262   9160  Z= 0.337
  Chirality :  0.044   0.195   1098
  Planarity :  0.005   0.058   1156
  Dihedral  :  5.402  21.352    878
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 14.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.65 %
    Favored  : 92.35 %
  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 : 0.00 %

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: -2.67 (0.29), residues: 810
  helix: -2.07 (0.35), residues: 205
  sheet: -2.31 (0.49), residues: 114
  loop : -1.49 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.003   0.001   HIS C 522 
 PHE   0.029   0.002   PHE C 433 
 TYR   0.022   0.002   TYR C 477 
 ARG   0.004   0.000   ARG B 496 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03376 (  163)
  hydrogen bonds       : angle       6.26889 (  351)
  covalent geometry    : bond        0.00265 ( 6756)
  covalent geometry    : angle       0.67386 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.756 
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  548 VAL cc_start: 0.7499 (t) cc_final: 0.7274 (t)
REVERT: B  645 LYS cc_start: 0.6776 (mttt) cc_final: 0.5876 (mmtp)
REVERT: B  695 ASN cc_start: 0.3697 (m-40) cc_final: 0.2762 (p0)
REVERT: B  754 THR cc_start: 0.4445 (p) cc_final: 0.4011 (t)
REVERT: B  804 ARG cc_start: 0.5062 (tpp-160) cc_final: 0.3353 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.2069
  time to fit residues: 39.1730
Evaluate side-chains
  102 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 52 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0060
   chunk 47 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 70 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 73 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 28 optimal weight:    9.9990
   chunk 19 optimal weight:    0.7980
   overall best weight:    1.1602

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

Flipped N/Q/H residues before XYZ refinement:
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 494 ASN
** C 737 HIS ** 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 = 0.4715 r_free = 0.4715 target = 0.170144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 85)----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.159693 restraints weight = 28909.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4600 r_free = 0.4600 target = 0.160983 restraints weight = 22057.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4617 r_free = 0.4617 target = 0.162116 restraints weight = 17388.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5356
moved from start:          0.6115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6756  Z= 0.133
  Angle     :  0.674   7.304   9160  Z= 0.338
  Chirality :  0.044   0.167   1098
  Planarity :  0.005   0.059   1156
  Dihedral  :  5.374  21.332    878
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.16 %
    Favored  : 92.84 %
  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 : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.69 (0.30), residues: 810
  helix: -2.23 (0.34), residues: 213
  sheet: -2.43 (0.47), residues: 120
  loop : -1.34 (0.30), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP C 411 
 HIS   0.003   0.001   HIS C 522 
 PHE   0.016   0.002   PHE B 443 
 TYR   0.044   0.002   TYR C 513 
 ARG   0.004   0.000   ARG B 765 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03242 (  163)
  hydrogen bonds       : angle       6.35125 (  351)
  covalent geometry    : bond        0.00306 ( 6756)
  covalent geometry    : angle       0.67439 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.712 
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  645 LYS cc_start: 0.5913 (mttt) cc_final: 0.5422 (mmtm)
REVERT: B  695 ASN cc_start: 0.3648 (m-40) cc_final: 0.2806 (p0)
REVERT: B  804 ARG cc_start: 0.5263 (tpp-160) cc_final: 0.3497 (tpt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.2024
  time to fit residues: 35.5793
Evaluate side-chains
  92 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.808 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 24 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 61 optimal weight:    9.9990
   chunk 38 optimal weight:    0.4980
   chunk 19 optimal weight:    0.9980
   chunk 64 optimal weight:    9.9990
   chunk 53 optimal weight:    0.9980
   chunk 20 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    1.6984

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4690 r_free = 0.4690 target = 0.167915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 79)----------------|
| r_work = 0.4546 r_free = 0.4546 target = 0.157275 restraints weight = 27798.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.4567 r_free = 0.4567 target = 0.158701 restraints weight = 20805.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4583 r_free = 0.4583 target = 0.159844 restraints weight = 16113.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.4569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5497
moved from start:          0.6613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6756  Z= 0.149
  Angle     :  0.713   8.689   9160  Z= 0.352
  Chirality :  0.044   0.150   1098
  Planarity :  0.005   0.059   1156
  Dihedral  :  5.545  21.778    878
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 19.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.75 (0.29), residues: 810
  helix: -2.41 (0.32), residues: 219
  sheet: -2.42 (0.43), residues: 130
  loop : -1.26 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP C 411 
 HIS   0.005   0.001   HIS B 499 
 PHE   0.018   0.002   PHE C 433 
 TYR   0.027   0.002   TYR C 513 
 ARG   0.006   0.001   ARG C 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03270 (  163)
  hydrogen bonds       : angle       6.32499 (  351)
  covalent geometry    : bond        0.00344 ( 6756)
  covalent geometry    : angle       0.71253 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 0.804 
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  695 ASN cc_start: 0.3970 (m-40) cc_final: 0.3259 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1969
  time to fit residues: 33.5201
Evaluate side-chains
  86 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0870
   chunk 69 optimal weight:    0.0970
   chunk 13 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 73 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 29 optimal weight:    0.8980
   chunk 50 optimal weight:    5.9990
   overall best weight:    1.2160

-------------------------------------------------------------------------------
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 494 ASN
B 755 ASN
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.168516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 100)---------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.157963 restraints weight = 27856.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4563 r_free = 0.4563 target = 0.159272 restraints weight = 22782.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4577 r_free = 0.4577 target = 0.160143 restraints weight = 17460.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.4565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5485
moved from start:          0.6908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6756  Z= 0.135
  Angle     :  0.703   7.007   9160  Z= 0.346
  Chirality :  0.044   0.142   1098
  Planarity :  0.005   0.084   1156
  Dihedral  :  5.499  28.587    878
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 19.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  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: -2.48 (0.32), residues: 219
  sheet: -2.51 (0.43), residues: 129
  loop : -1.35 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP C 411 
 HIS   0.004   0.001   HIS C 522 
 PHE   0.015   0.002   PHE B 443 
 TYR   0.026   0.002   TYR C 477 
 ARG   0.004   0.000   ARG B 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03446 (  163)
  hydrogen bonds       : angle       6.50272 (  351)
  covalent geometry    : bond        0.00309 ( 6756)
  covalent geometry    : angle       0.70350 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  695 ASN cc_start: 0.3928 (m-40) cc_final: 0.3395 (p0)
REVERT: B  760 GLU cc_start: 0.7078 (tt0) cc_final: 0.6739 (tt0)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.2169
  time to fit residues: 35.8045
Evaluate side-chains
  81 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 50 optimal weight:   10.0000
   chunk 76 optimal weight:    0.8980
   chunk 14 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 56 optimal weight:    5.9990
   chunk 29 optimal weight:   10.0000
   chunk 36 optimal weight:    0.0970
   chunk 45 optimal weight:    0.8980
   chunk 20 optimal weight:    7.9990
   chunk 70 optimal weight:    5.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    1.1780

-------------------------------------------------------------------------------
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
B 758 GLN
C 409 ASN
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4678 r_free = 0.4678 target = 0.167513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.158754 restraints weight = 28558.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.159522 restraints weight = 27340.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4588 r_free = 0.4588 target = 0.160931 restraints weight = 19121.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.4590
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5268
moved from start:          0.7259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6756  Z= 0.132
  Angle     :  0.728  12.334   9160  Z= 0.353
  Chirality :  0.044   0.140   1098
  Planarity :  0.006   0.073   1156
  Dihedral  :  5.506  27.526    878
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.52 %
    Favored  : 91.48 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  0.93 %
    Favored  : 98.81 %
  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: -2.89 (0.29), residues: 810
  helix: -2.44 (0.32), residues: 218
  sheet: -2.63 (0.41), residues: 131
  loop : -1.35 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP C 511 
 HIS   0.004   0.001   HIS C 522 
 PHE   0.020   0.002   PHE C 433 
 TYR   0.026   0.002   TYR C 513 
 ARG   0.008   0.001   ARG C 492 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03272 (  163)
  hydrogen bonds       : angle       6.44383 (  351)
  covalent geometry    : bond        0.00306 ( 6756)
  covalent geometry    : angle       0.72759 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 124
  time to evaluate  : 0.857 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  404 GLN cc_start: 0.8429 (tm130) cc_final: 0.7871 (tm-30)
REVERT: B  695 ASN cc_start: 0.4171 (m-40) cc_final: 0.3708 (p0)
  outliers start: 2
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1966
  time to fit residues: 33.1300
Evaluate side-chains
  86 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.823 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 55 optimal weight:    6.9990
   chunk 19 optimal weight:    0.9980
   chunk 13 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 56 optimal weight:    4.9990
   chunk 24 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9980
   chunk 46 optimal weight:    0.8980
   chunk 28 optimal weight:    9.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 406 ASN
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 649 ASN
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 737 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.166887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4551 r_free = 0.4551 target = 0.158095 restraints weight = 28304.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4566 r_free = 0.4566 target = 0.159334 restraints weight = 23051.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4576 r_free = 0.4576 target = 0.160085 restraints weight = 15323.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.4577
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5372
moved from start:          0.7690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6756  Z= 0.135
  Angle     :  0.707   7.181   9160  Z= 0.347
  Chirality :  0.045   0.161   1098
  Planarity :  0.005   0.065   1156
  Dihedral  :  5.489  25.119    878
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 20.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.01 %
    Favored  : 90.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.96 (0.29), residues: 810
  helix: -2.48 (0.32), residues: 224
  sheet: -2.35 (0.44), residues: 131
  loop : -1.51 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP C 411 
 HIS   0.006   0.001   HIS C 499 
 PHE   0.028   0.002   PHE C 635 
 TYR   0.031   0.002   TYR C 477 
 ARG   0.005   0.001   ARG B 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03254 (  163)
  hydrogen bonds       : angle       6.50266 (  351)
  covalent geometry    : bond        0.00310 ( 6756)
  covalent geometry    : angle       0.70748 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.900 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  404 GLN cc_start: 0.8294 (tm130) cc_final: 0.7756 (tm-30)
REVERT: B  434 MET cc_start: 0.4355 (mtp) cc_final: 0.4101 (mtp)
REVERT: B  695 ASN cc_start: 0.4281 (m-40) cc_final: 0.3842 (p0)
REVERT: C  503 THR cc_start: 0.6000 (m) cc_final: 0.5671 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.1965
  time to fit residues: 31.5787
Evaluate side-chains
  86 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    0.4980
   chunk 79 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0470
   chunk 52 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 7 optimal weight:    5.9990
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 72 optimal weight:    6.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.6478

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 406 ASN
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 649 ASN
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 431 HIS
C 737 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4683 r_free = 0.4683 target = 0.168627 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.4570 r_free = 0.4570 target = 0.159816 restraints weight = 29405.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4582 r_free = 0.4582 target = 0.160794 restraints weight = 21201.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4594 r_free = 0.4594 target = 0.161654 restraints weight = 15083.130|
|-----------------------------------------------------------------------------|
r_work (final): 0.4592
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5302
moved from start:          0.7806

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= 0.118
  Angle     :  0.705  11.636   9160  Z= 0.340
  Chirality :  0.044   0.152   1098
  Planarity :  0.005   0.061   1156
  Dihedral  :  5.380  26.204    878
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 18.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  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 : 0.00 %

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: -2.83 (0.29), residues: 810
  helix: -2.39 (0.33), residues: 217
  sheet: -2.49 (0.45), residues: 120
  loop : -1.41 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 411 
 HIS   0.008   0.001   HIS C 431 
 PHE   0.025   0.002   PHE C 433 
 TYR   0.028   0.002   TYR C 477 
 ARG   0.009   0.001   ARG B 666 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03211 (  163)
  hydrogen bonds       : angle       6.35675 (  351)
  covalent geometry    : bond        0.00265 ( 6756)
  covalent geometry    : angle       0.70524 ( 9160)

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

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

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

  1620 Ramachandran restraints generated.
    810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.775 
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  404 GLN cc_start: 0.8130 (tm130) cc_final: 0.7640 (tm-30)
REVERT: B  695 ASN cc_start: 0.4182 (m-40) cc_final: 0.3790 (p0)
REVERT: C  503 THR cc_start: 0.5973 (m) cc_final: 0.5636 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1954
  time to fit residues: 30.7746
Evaluate side-chains
  91 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 69 optimal weight:    8.9990
   chunk 7 optimal weight:    0.8980
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0670
   chunk 10 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0170
   chunk 47 optimal weight:   10.0000
   overall best weight:    0.5556

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

Flipped N/Q/H residues before XYZ refinement:
B 404 GLN
B 406 ASN
** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 758 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4691 r_free = 0.4691 target = 0.169356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4578 r_free = 0.4578 target = 0.160731 restraints weight = 29098.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4597 r_free = 0.4597 target = 0.162145 restraints weight = 22710.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.162743 restraints weight = 14685.516|
|-----------------------------------------------------------------------------|
r_work (final): 0.4603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5268
moved from start:          0.7916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6756  Z= 0.112
  Angle     :  0.669   8.763   9160  Z= 0.324
  Chirality :  0.044   0.172   1098
  Planarity :  0.005   0.058   1156
  Dihedral  :  5.182  25.789    878
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 17.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.02 %
    Favored  : 91.98 %
  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 (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: -2.46 (0.30), residues: 810
  helix: -2.22 (0.35), residues: 204
  sheet: -2.07 (0.49), residues: 118
  loop : -1.21 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP C 411 
 HIS   0.004   0.001   HIS C 522 
 PHE   0.020   0.002   PHE C 433 
 TYR   0.027   0.002   TYR C 477 
 ARG   0.006   0.000   ARG B 801 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03039 (  163)
  hydrogen bonds       : angle       6.13797 (  351)
  covalent geometry    : bond        0.00256 ( 6756)
  covalent geometry    : angle       0.66932 ( 9160)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2926.06 seconds
wall clock time: 51 minutes 12.18 seconds (3072.18 seconds total)