Starting phenix.real_space_refine
on Thu Jul  2 05:25:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8cd0_16565/07_2026/8cd0_16565.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8cd0_16565/07_2026/8cd0_16565.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.42
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8cd0_16565/07_2026/8cd0_16565.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8cd0_16565/07_2026/8cd0_16565.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8cd0_16565/07_2026/8cd0_16565.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8cd0_16565/07_2026/8cd0_16565.cif"
  }
  resolution = 2.42
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.015 sd=   0.025
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: 6
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       2      5.49       5
     S      26      5.16       5
     C    4426      2.51       5
     N    1162      2.21       5
     O    1243      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 6860
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5883
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 716, 5883
          Classifications: {'peptide': 716}
          Link IDs: {'PCIS': 4, 'PTRANS': 32, 'TRANS': 679}
          Chain breaks: 6
    Chain: "C"
      Number of atoms: 945
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 121, 937
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 121, 937
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 2, 'TRANS': 118}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 946
    Chain: "A"
      Number of atoms: 27
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 27
          Unusual residues: {'A3P': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 3
          Ad-hoc single atom residues: {' CA': 1}
          Classifications: {'water': 3}
          Link IDs: {None: 2}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Classifications: {'water': 1}
  Time building chain proxies: 1.32, per 1000 atoms: 0.19
  Number of scatterers: 6860
  At special positions: 0
  Unit cell: (78.11, 97.82, 102.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Ca      1     19.99
     S      26     16.00
     P       2     15.00
     O    1243      8.00
     N    1162      7.00
     C    4426      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 586 " - pdb=" SG  CYS A 601 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 818 " - pdb=" SG  CYS A 828 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 103 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.77
  Conformation dependent library (CDL) restraints added in 335.3 milliseconds
  

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1566

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      42.7% alpha, 15.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 94 through 107
    Processing helix  chain 'A' and resid 141 through 146
    Processing helix  chain 'A' and resid 148 through 163
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 3.849A  pdb=" N   THR A 302 " --> pdb=" O   VAL A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 349
    Processing helix  chain 'A' and resid 367 through 374
    Processing helix  chain 'A' and resid 375 through 379
    Processing helix  chain 'A' and resid 401 through 420
      removed outlier: 3.732A  pdb=" N   LEU A 405 " --> pdb=" O   ASN A 401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 440 through 451
      removed outlier: 3.544A  pdb=" N   TYR A 444 " --> pdb=" O   HIS A 440 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A 448 " --> pdb=" O   TYR A 444 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   VAL A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 470
    Processing helix  chain 'A' and resid 501 through 510
      removed outlier: 4.025A  pdb=" N   LEU A 505 " --> pdb=" O   GLY A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 521
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 537 through 554
      removed outlier: 3.886A  pdb=" N   ARG A 548 " --> pdb=" O   LYS A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 574
    Processing helix  chain 'A' and resid 575 through 579
      removed outlier: 3.649A  pdb=" N   LYS A 578 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   ASP A 579 " --> pdb=" O   GLU A 576 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 575 through 579'
    Processing helix  chain 'A' and resid 588 through 595
    Processing helix  chain 'A' and resid 616 through 626
    Processing helix  chain 'A' and resid 636 through 640
      removed outlier: 3.517A  pdb=" N   PHE A 640 " --> pdb=" O   SER A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 648 through 653
      removed outlier: 3.905A  pdb=" N   TYR A 651 " --> pdb=" O   GLY A 648 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   HIS A 652 " --> pdb=" O   HIS A 649 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 678 through 681
      removed outlier: 3.758A  pdb=" N   PHE A 681 " --> pdb=" O   ALA A 678 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 678 through 681'
    Processing helix  chain 'A' and resid 685 through 694
      removed outlier: 3.572A  pdb=" N   ARG A 689 " --> pdb=" O   VAL A 685 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 720
    Processing helix  chain 'A' and resid 722 through 728
    Processing helix  chain 'A' and resid 729 through 734
    Processing helix  chain 'A' and resid 742 through 753
    Processing helix  chain 'A' and resid 756 through 768
      removed outlier: 3.842A  pdb=" N   HIS A 760 " --> pdb=" O   TRP A 756 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   ARG A 763 " --> pdb=" O   THR A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 779 through 784
    Processing helix  chain 'A' and resid 784 through 796
      removed outlier: 4.291A  pdb=" N   VAL A 788 " --> pdb=" O   GLU A 784 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 808
      removed outlier: 3.928A  pdb=" N   THR A 807 " --> pdb=" O   ASP A 803 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LEU A 808 " --> pdb=" O   TYR A 804 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 803 through 808'
    Processing helix  chain 'A' and resid 841 through 852
    Processing helix  chain 'A' and resid 853 through 866
    Processing helix  chain 'A' and resid 871 through 880
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.906A  pdb=" N   THR C  90 " --> pdb=" O   PRO C  87 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 110 through 114
    Processing sheet with id=AA1, first strand: chain 'A' and resid 111 through 114
      removed outlier: 6.602A  pdb=" N   ILE A 166 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ARG A 278 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 199 through 200
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388
      removed outlier: 5.415A  pdb=" N   LEU A 356 " --> pdb=" O   PHE A 387 " (cutoff:3.500A)
      removed outlier: 8.693A  pdb=" N   ASN A 355 " --> pdb=" O   ILE A 314 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   VAL A 316 " --> pdb=" O   ASN A 355 " (cutoff:3.500A)
      removed outlier: 7.540A  pdb=" N   GLY A 357 " --> pdb=" O   VAL A 316 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ILE A 318 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 10.967A  pdb=" N   ILE A 523 " --> pdb=" O   VAL A 480 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ILE A 525 " --> pdb=" O   PRO A 482 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 455 through 458
      removed outlier: 6.666A  pdb=" N   THR A 456 " --> pdb=" O   LEU A 481 " (cutoff:3.500A)
      removed outlier: 7.036A  pdb=" N   ARG A 483 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   THR A 458 " --> pdb=" O   ARG A 483 " (cutoff:3.500A)
      removed outlier: 10.967A  pdb=" N   ILE A 523 " --> pdb=" O   VAL A 480 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   ILE A 525 " --> pdb=" O   PRO A 482 " (cutoff:3.500A)
      removed outlier: 6.013A  pdb=" N   ARG A 312 " --> pdb=" O   GLN A 559 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 630 through 632
      removed outlier: 6.893A  pdb=" N   LEU A 607 " --> pdb=" O   GLU A 675 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   SER A 677 " --> pdb=" O   LEU A 607 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   ILE A 609 " --> pdb=" O   SER A 677 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   ILE A 702 " --> pdb=" O   ILE A 610 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 809 through 811
      removed outlier: 3.565A  pdb=" N   ALA A 809 " --> pdb=" O   CYS A 818 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ASP A 811 " --> pdb=" O   PHE A 816 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE A 816 " --> pdb=" O   ASP A 811 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 3 through 6
      removed outlier: 3.584A  pdb=" N   LEU C  18 " --> pdb=" O   MET C  82 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 57 through 59
      removed outlier: 6.885A  pdb=" N   TRP C  36 " --> pdb=" O   VAL C  48 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ALA C  91 " --> pdb=" O   VAL C 123 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR C 121 " --> pdb=" O   TYR C  93 " (cutoff:3.500A)

    273 hydrogen bonds defined for protein.
    759 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: 1.12

  Time building geometry restraints manager: 0.59 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: 2039
        1.34 -     1.46: 1607
        1.46 -     1.58: 3357
        1.58 -     1.70: 8
        1.70 -     1.82: 40
  Bond restraints: 7051
  Sorted by residual:
  bond pdb=" C   ALA A 430 "
       pdb=" N   PRO A 431 "
    ideal  model  delta    sigma   weight residual
    1.335  1.385 -0.050 1.30e-02 5.92e+03 1.48e+01
  bond pdb=" CB  PHE A 362 "
       pdb=" CG  PHE A 362 "
    ideal  model  delta    sigma   weight residual
    1.502  1.573 -0.071 2.30e-02 1.89e+03 9.64e+00
  bond pdb=" C   VAL A 429 "
       pdb=" N   ALA A 430 "
    ideal  model  delta    sigma   weight residual
    1.330  1.370 -0.040 1.37e-02 5.33e+03 8.51e+00
  bond pdb=" CB  PHE A 847 "
       pdb=" CG  PHE A 847 "
    ideal  model  delta    sigma   weight residual
    1.502  1.561 -0.059 2.30e-02 1.89e+03 6.53e+00
  bond pdb=" C   ALA A 686 "
       pdb=" N   PRO A 687 "
    ideal  model  delta    sigma   weight residual
    1.336  1.366 -0.031 1.23e-02 6.61e+03 6.16e+00
  ... (remaining 7046 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.42: 9322
        3.42 -     6.84: 189
        6.84 -    10.26: 43
       10.26 -    13.68: 9
       13.68 -    17.11: 2
  Bond angle restraints: 9565
  Sorted by residual:
  angle pdb=" C   THR A 485 "
        pdb=" N   CYS A 486 "
        pdb=" CA  CYS A 486 "
      ideal   model   delta    sigma   weight residual
     121.54  132.61  -11.07 1.91e+00 2.74e-01 3.36e+01
  angle pdb=" C   PHE A 399 "
        pdb=" N   HIS A 400 "
        pdb=" CA  HIS A 400 "
      ideal   model   delta    sigma   weight residual
     121.54  132.56  -11.02 1.91e+00 2.74e-01 3.33e+01
  angle pdb=" CB  GLU A 858 "
        pdb=" CG  GLU A 858 "
        pdb=" CD  GLU A 858 "
      ideal   model   delta    sigma   weight residual
     112.60  121.92   -9.32 1.70e+00 3.46e-01 3.01e+01
  angle pdb=" C   SER A 213 "
        pdb=" N   GLU A 214 "
        pdb=" CA  GLU A 214 "
      ideal   model   delta    sigma   weight residual
     121.70  131.18   -9.48 1.80e+00 3.09e-01 2.77e+01
  angle pdb=" CG  ARG C  74 "
        pdb=" CD  ARG C  74 "
        pdb=" NE  ARG C  74 "
      ideal   model   delta    sigma   weight residual
     112.00  123.50  -11.50 2.20e+00 2.07e-01 2.73e+01
  ... (remaining 9560 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.31: 3539
       17.31 -    34.62: 433
       34.62 -    51.93: 119
       51.93 -    69.24: 41
       69.24 -    86.55: 10
  Dihedral angle restraints: 4142
    sinusoidal: 1701
      harmonic: 2441
  Sorted by residual:
  dihedral pdb=" CB  CYS A 586 "
           pdb=" SG  CYS A 586 "
           pdb=" SG  CYS A 601 "
           pdb=" CB  CYS A 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.46  -72.46     1      1.00e+01 1.00e-02 6.71e+01
  dihedral pdb=" CA  ASN C  84 "
           pdb=" C   ASN C  84 "
           pdb=" N   LEU C  85 "
           pdb=" CA  LEU C  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.96  -26.04     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  SER C  11 "
           pdb=" C   SER C  11 "
           pdb=" N   VAL C  12 "
           pdb=" CA  VAL C  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.00   21.00     0      5.00e+00 4.00e-02 1.76e+01
  ... (remaining 4139 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.080: 858
       0.080 -    0.161: 126
       0.161 -    0.241: 24
       0.241 -    0.322: 6
       0.322 -    0.402: 2
  Chirality restraints: 1016
  Sorted by residual:
  chirality pdb=" CB  ILE C  51 "
            pdb=" CA  ILE C  51 "
            pdb=" CG1 ILE C  51 "
            pdb=" CG2 ILE C  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.04e+00
  chirality pdb=" CB  THR C  90 "
            pdb=" CA  THR C  90 "
            pdb=" OG1 THR C  90 "
            pdb=" CG2 THR C  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.20    0.35 2.00e-01 2.50e+01 3.06e+00
  chirality pdb=" CB  ILE A 421 "
            pdb=" CA  ILE A 421 "
            pdb=" CG1 ILE A 421 "
            pdb=" CG2 ILE A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.76e+00
  ... (remaining 1013 not shown)

  Planarity restraints: 1212
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 643 "   -0.017 2.00e-02 2.50e+03   3.39e-02 1.15e+01
        pdb=" C   ILE A 643 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ILE A 643 "   -0.022 2.00e-02 2.50e+03
        pdb=" N   GLN A 644 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 339 "    0.024 2.00e-02 2.50e+03   2.52e-02 1.11e+01
        pdb=" CG  PHE A 339 "   -0.058 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 339 "    0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 339 "    0.016 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 339 "    0.010 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 339 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 339 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 627 "   -0.053 5.00e-02 4.00e+02   8.02e-02 1.03e+01
        pdb=" N   PRO A 628 "    0.139 5.00e-02 4.00e+02
        pdb=" CA  PRO A 628 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 628 "   -0.044 5.00e-02 4.00e+02
  ... (remaining 1209 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 133
        2.68 -     3.23: 5773
        3.23 -     3.79: 11421
        3.79 -     4.34: 15664
        4.34 -     4.90: 25121
  Nonbonded interactions: 58112
  Sorted by model distance:
  nonbonded pdb="CA    CA A 902 "
            pdb=" O   HOH A1003 "
     model   vdw
     2.122 3.250
  nonbonded pdb=" OD1 ASP A 320 "
            pdb="CA    CA A 902 "
     model   vdw
     2.162 3.250
  nonbonded pdb=" NE2 HIS A 393 "
            pdb="CA    CA A 902 "
     model   vdw
     2.198 3.330
  nonbonded pdb=" O   GLU A 513 "
            pdb=" OG1 THR A 517 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" OG  SER C  17 "
            pdb=" OD1 ASN C  83 "
     model   vdw
     2.335 3.040
  ... (remaining 58107 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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=0.25 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.750
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.340
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7024
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      :  0.007   0.071   7055  Z= 0.319
  Angle     :  1.253  17.105   9573  Z= 0.679
  Chirality :  0.065   0.402   1016
  Planarity :  0.010   0.080   1212
  Dihedral  : 17.387  86.546   2564
  Min Nonbonded Distance : 2.122

Molprobity Statistics.
  All-atom Clashscore : 3.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 22.09 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.15 (0.25), residues: 820
  helix: -3.33 (0.17), residues: 300
  sheet: -1.35 (0.45), residues: 133
  loop : -1.10 (0.29), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 557 
 TYR   0.038   0.003   TYR A 680 
 PHE   0.058   0.004   PHE A 339 
 TRP   0.026   0.003   TRP A 595 
 HIS   0.027   0.003   HIS A 400 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00659 /  0.32 ( 7051)
  covalent geometry    : angle       1.25305 /  0.68 ( 9565)
  SS BOND              : bond        0.00285 /  0.17 (    4)
  SS BOND              : angle       0.96908 /  0.61 (    8)
  hydrogen bonds       : bond        0.19466 / 13.19 (  265)
  hydrogen bonds       : angle       8.09041 /  5.45 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 121
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7859 (tp30) cc_final: 0.7576 (mm-30)
REVERT: A  137 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5649 (mt)
REVERT: A  143 LYS cc_start: 0.6523 (mttp) cc_final: 0.6191 (mttm)
REVERT: A  203 LYS cc_start: 0.7110 (mptt) cc_final: 0.6848 (mttm)
REVERT: A  206 LEU cc_start: 0.7174 (OUTLIER) cc_final: 0.6795 (mp)
REVERT: A  208 TYR cc_start: 0.7867 (t80) cc_final: 0.7408 (t80)
REVERT: A  308 LEU cc_start: 0.7927 (mt) cc_final: 0.7636 (tp)
REVERT: A  400 HIS cc_start: 0.5718 (p-80) cc_final: 0.5413 (p90)
REVERT: A  413 LYS cc_start: 0.4280 (ttmt) cc_final: 0.3836 (ttmm)
REVERT: A  452 SER cc_start: 0.8106 (m) cc_final: 0.7894 (m)
REVERT: A  536 ASP cc_start: 0.6909 (m-30) cc_final: 0.6348 (t0)
REVERT: A  676 LYS cc_start: 0.7685 (tttt) cc_final: 0.7482 (tmtp)
REVERT: A  688 ARG cc_start: 0.6999 (ttp-110) cc_final: 0.6556 (ptm160)
REVERT: A  708 ASP cc_start: 0.6210 (t70) cc_final: 0.5944 (t70)
REVERT: A  743 LYS cc_start: 0.7804 (mttt) cc_final: 0.7075 (mptt)
REVERT: A  864 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.5160 (t80)
REVERT: C  106 LYS cc_start: 0.7626 (pttt) cc_final: 0.7251 (tttm)
  outliers start: 15
  outliers final: 7
  residues processed: 132
  average time/residue: 0.3833
  time to fit residues: 53.7935
Evaluate side-chains
  103 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 93
  time to evaluate  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  137 ILE
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  339 PHE
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   78 VAL
Chi-restraints excluded: chain C residue   98 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    0.0770
   chunk 62 optimal weight:    0.0980
   chunk 51 optimal weight:    0.0010
   chunk 38 optimal weight:    0.2980
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.1944

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
A 400 HIS
A 408 GLN
A 583 GLN
A 731 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.184455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.159297 restraints weight = 27203.557|
|-----------------------------------------------------------------------------|
r_work (start): 0.4184 rms_B_bonded: 3.45
r_work: 0.4067 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4073
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4073 r_free = 0.4073    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4073 r_free = 0.4073    target_work(ls_wunit_k1) = 0.148         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4073
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7055  Z= 0.110
  Angle     :  0.569   9.233   9573  Z= 0.298
  Chirality :  0.042   0.158   1016
  Planarity :  0.005   0.048   1212
  Dihedral  :  7.347  66.699    963
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 22.22 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.66 (0.27), residues: 820
  helix: -1.35 (0.25), residues: 319
  sheet: -0.84 (0.48), residues: 124
  loop : -0.77 (0.31), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 557 
 TYR   0.011   0.001   TYR C  59 
 PHE   0.014   0.001   PHE A 494 
 TRP   0.010   0.001   TRP A 595 
 HIS   0.014   0.001   HIS A 400 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 7051)
  covalent geometry    : angle       0.56906 /  0.30 ( 9565)
  SS BOND              : bond        0.00084 /  0.04 (    4)
  SS BOND              : angle       0.57311 /  0.37 (    8)
  hydrogen bonds       : bond        0.03826 /  2.49 (  265)
  hydrogen bonds       : angle       5.52166 /  3.76 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 GLN cc_start: 0.6012 (OUTLIER) cc_final: 0.5804 (pp30)
REVERT: A  114 GLU cc_start: 0.7741 (tp30) cc_final: 0.7484 (mm-30)
REVERT: A  143 LYS cc_start: 0.6410 (mttp) cc_final: 0.6159 (mtpm)
REVERT: A  308 LEU cc_start: 0.8147 (mt) cc_final: 0.7924 (tp)
REVERT: A  413 LYS cc_start: 0.4762 (ttmt) cc_final: 0.4449 (ttmm)
REVERT: A  452 SER cc_start: 0.7983 (OUTLIER) cc_final: 0.7780 (m)
REVERT: A  583 GLN cc_start: 0.6944 (OUTLIER) cc_final: 0.6372 (mp10)
REVERT: A  688 ARG cc_start: 0.7278 (ttp-110) cc_final: 0.7010 (ptt-90)
REVERT: A  708 ASP cc_start: 0.6463 (t70) cc_final: 0.6198 (t70)
REVERT: A  743 LYS cc_start: 0.7881 (mttt) cc_final: 0.7277 (mptt)
REVERT: A  784 GLU cc_start: 0.6263 (pp20) cc_final: 0.6008 (pp20)
REVERT: A  853 ARG cc_start: 0.5469 (OUTLIER) cc_final: 0.5074 (ttm170)
REVERT: A  858 GLU cc_start: 0.6521 (OUTLIER) cc_final: 0.6088 (mp0)
REVERT: A  864 TYR cc_start: 0.5775 (OUTLIER) cc_final: 0.5460 (m-80)
  outliers start: 25
  outliers final: 7
  residues processed: 121
  average time/residue: 0.3561
  time to fit residues: 45.9507
Evaluate side-chains
  111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue   95 GLN
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  583 GLN
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  858 GLU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   85 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 31 optimal weight:    0.8980
   chunk 54 optimal weight:    0.1980
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:   10.0000
   chunk 60 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   chunk 26 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 343 ASN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.178161 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.152037 restraints weight = 26241.887|
|-----------------------------------------------------------------------------|
r_work (start): 0.4100 rms_B_bonded: 3.44
r_work: 0.3981 rms_B_bonded: 3.94 restraints_weight: 0.5000
r_work (final): 0.3981
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3989
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3989 r_free = 0.3989    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3989 r_free = 0.3989    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3989
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2146

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7055  Z= 0.138
  Angle     :  0.574   8.918   9573  Z= 0.300
  Chirality :  0.043   0.161   1016
  Planarity :  0.005   0.040   1212
  Dihedral  :  6.789  64.097    952
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 22.49 %
    Favored  : 73.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.29), residues: 820
  helix: -0.39 (0.28), residues: 316
  sheet: -0.71 (0.50), residues: 126
  loop : -0.39 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.013   0.001   TYR C  32 
 PHE   0.019   0.002   PHE C 108 
 TRP   0.022   0.002   TRP A 391 
 HIS   0.008   0.001   HIS A 716 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00317 /  0.14 ( 7051)
  covalent geometry    : angle       0.57414 /  0.30 ( 9565)
  SS BOND              : bond        0.00244 /  0.14 (    4)
  SS BOND              : angle       0.87678 /  0.60 (    8)
  hydrogen bonds       : bond        0.03856 /  2.49 (  265)
  hydrogen bonds       : angle       5.14718 /  3.52 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 100
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  114 GLU cc_start: 0.7706 (OUTLIER) cc_final: 0.7426 (mm-30)
REVERT: A  143 LYS cc_start: 0.6379 (mttp) cc_final: 0.6104 (mtpm)
REVERT: A  413 LYS cc_start: 0.4803 (ttmt) cc_final: 0.4527 (ttmm)
REVERT: A  447 TRP cc_start: 0.7995 (OUTLIER) cc_final: 0.7748 (m-10)
REVERT: A  452 SER cc_start: 0.8174 (OUTLIER) cc_final: 0.7932 (m)
REVERT: A  634 TYR cc_start: 0.7042 (m-80) cc_final: 0.6840 (m-80)
REVERT: A  688 ARG cc_start: 0.7262 (ttp-110) cc_final: 0.6910 (ptt-90)
REVERT: A  708 ASP cc_start: 0.6457 (t70) cc_final: 0.6206 (t70)
REVERT: A  743 LYS cc_start: 0.7909 (mttt) cc_final: 0.7285 (mptt)
REVERT: A  784 GLU cc_start: 0.6337 (pp20) cc_final: 0.5820 (pp20)
REVERT: A  853 ARG cc_start: 0.5555 (OUTLIER) cc_final: 0.5110 (ttm170)
REVERT: A  864 TYR cc_start: 0.6017 (OUTLIER) cc_final: 0.5667 (m-80)
  outliers start: 33
  outliers final: 10
  residues processed: 118
  average time/residue: 0.3468
  time to fit residues: 43.9231
Evaluate side-chains
  106 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   82 MET
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 79 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 21 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 67 optimal weight:    8.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
A 475 HIS
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.176263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.150888 restraints weight = 20588.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.4088 rms_B_bonded: 2.99
r_work: 0.3979 rms_B_bonded: 3.54 restraints_weight: 0.5000
r_work (final): 0.3979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.41   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7280
moved from start:          0.2566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7055  Z= 0.133
  Angle     :  0.563   8.153   9573  Z= 0.292
  Chirality :  0.042   0.160   1016
  Planarity :  0.004   0.038   1212
  Dihedral  :  6.602  58.983    952
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 22.90 %
    Favored  : 72.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.47 (0.29), residues: 820
  helix:  0.09 (0.28), residues: 316
  sheet: -0.88 (0.51), residues: 118
  loop : -0.30 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.016   0.001   TYR C  32 
 PHE   0.026   0.002   PHE A 339 
 TRP   0.022   0.002   TRP A 391 
 HIS   0.006   0.001   HIS A 716 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 ( 7051)
  covalent geometry    : angle       0.56306 /  0.29 ( 9565)
  SS BOND              : bond        0.00217 /  0.12 (    4)
  SS BOND              : angle       0.66885 /  0.45 (    8)
  hydrogen bonds       : bond        0.03711 /  2.38 (  265)
  hydrogen bonds       : angle       4.98416 /  3.41 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 102
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 VAL cc_start: 0.6406 (m) cc_final: 0.6127 (t)
REVERT: A  114 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7363 (mm-30)
REVERT: A  143 LYS cc_start: 0.6406 (mttp) cc_final: 0.6086 (mttm)
REVERT: A  308 LEU cc_start: 0.8186 (mt) cc_final: 0.7892 (tp)
REVERT: A  413 LYS cc_start: 0.4710 (ttmt) cc_final: 0.4437 (ttmm)
REVERT: A  447 TRP cc_start: 0.7977 (OUTLIER) cc_final: 0.7407 (m-10)
REVERT: A  452 SER cc_start: 0.8183 (OUTLIER) cc_final: 0.7929 (m)
REVERT: A  634 TYR cc_start: 0.7259 (m-80) cc_final: 0.7036 (m-80)
REVERT: A  688 ARG cc_start: 0.7297 (ttp-110) cc_final: 0.6982 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7873 (mttt) cc_final: 0.7264 (mptt)
REVERT: A  784 GLU cc_start: 0.6433 (pp20) cc_final: 0.5887 (pp20)
REVERT: A  853 ARG cc_start: 0.5591 (OUTLIER) cc_final: 0.5097 (ttm170)
REVERT: A  864 TYR cc_start: 0.5986 (OUTLIER) cc_final: 0.5635 (m-80)
REVERT: C   64 LYS cc_start: 0.6364 (OUTLIER) cc_final: 0.6134 (tppt)
  outliers start: 34
  outliers final: 15
  residues processed: 125
  average time/residue: 0.3570
  time to fit residues: 47.9205
Evaluate side-chains
  114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   64 LYS
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 42 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 70 optimal weight:    0.4980
   chunk 32 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 73 optimal weight:    2.9990
   chunk 72 optimal weight:    0.0170
   chunk 4 optimal weight:    0.5980
   chunk 17 optimal weight:    8.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.8222

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.175685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.150352 restraints weight = 24093.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 3.34
r_work: 0.3957 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7294
moved from start:          0.2792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7055  Z= 0.129
  Angle     :  0.564   7.864   9573  Z= 0.292
  Chirality :  0.042   0.157   1016
  Planarity :  0.004   0.035   1212
  Dihedral  :  6.439  55.647    952
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 23.17 %
    Favored  : 72.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.30), residues: 820
  helix:  0.35 (0.29), residues: 316
  sheet: -1.01 (0.53), residues: 108
  loop : -0.24 (0.32), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 557 
 TYR   0.017   0.001   TYR C  32 
 PHE   0.029   0.002   PHE A 339 
 TRP   0.020   0.002   TRP A 391 
 HIS   0.005   0.001   HIS A 716 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00293 /  0.13 ( 7051)
  covalent geometry    : angle       0.56366 /  0.29 ( 9565)
  SS BOND              : bond        0.00211 /  0.11 (    4)
  SS BOND              : angle       0.62822 /  0.41 (    8)
  hydrogen bonds       : bond        0.03597 /  2.29 (  265)
  hydrogen bonds       : angle       4.90327 /  3.36 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 99
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
REVERT: A   89 VAL cc_start: 0.6406 (m) cc_final: 0.6121 (t)
REVERT: A  114 GLU cc_start: 0.7618 (OUTLIER) cc_final: 0.7359 (mm-30)
REVERT: A  143 LYS cc_start: 0.6348 (mttp) cc_final: 0.6018 (mttm)
REVERT: A  208 TYR cc_start: 0.8227 (t80) cc_final: 0.8023 (t80)
REVERT: A  308 LEU cc_start: 0.8139 (mt) cc_final: 0.7883 (tp)
REVERT: A  413 LYS cc_start: 0.4697 (ttmt) cc_final: 0.4441 (ttmm)
REVERT: A  447 TRP cc_start: 0.7990 (OUTLIER) cc_final: 0.7413 (m-10)
REVERT: A  452 SER cc_start: 0.8171 (OUTLIER) cc_final: 0.7916 (m)
REVERT: A  634 TYR cc_start: 0.7306 (m-80) cc_final: 0.7103 (m-80)
REVERT: A  688 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6997 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7854 (mttt) cc_final: 0.7243 (mptt)
REVERT: A  784 GLU cc_start: 0.6470 (pp20) cc_final: 0.5904 (pp20)
REVERT: A  853 ARG cc_start: 0.5479 (OUTLIER) cc_final: 0.5076 (ttm170)
REVERT: A  864 TYR cc_start: 0.6020 (OUTLIER) cc_final: 0.5666 (m-80)
  outliers start: 33
  outliers final: 15
  residues processed: 123
  average time/residue: 0.3585
  time to fit residues: 47.1759
Evaluate side-chains
  111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 91
  time to evaluate  : 0.182 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 47 optimal weight:    0.4980
   chunk 75 optimal weight:    9.9990
   chunk 1 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    4.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.173920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.148406 restraints weight = 35413.229|
|-----------------------------------------------------------------------------|
r_work (start): 0.4054 rms_B_bonded: 4.33
r_work: 0.3914 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3919
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3919 r_free = 0.3919    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3919 r_free = 0.3919    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3919
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
moved from start:          0.3017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7055  Z= 0.145
  Angle     :  0.590   7.331   9573  Z= 0.308
  Chirality :  0.043   0.163   1016
  Planarity :  0.004   0.034   1212
  Dihedral  :  6.505  55.103    952
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 22.76 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.30), residues: 820
  helix:  0.47 (0.29), residues: 315
  sheet: -1.04 (0.53), residues: 108
  loop : -0.22 (0.32), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 557 
 TYR   0.019   0.002   TYR C  32 
 PHE   0.034   0.002   PHE A 339 
 TRP   0.034   0.002   TRP A 391 
 HIS   0.006   0.001   HIS A 419 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.14 ( 7051)
  covalent geometry    : angle       0.58969 /  0.31 ( 9565)
  SS BOND              : bond        0.00232 /  0.13 (    4)
  SS BOND              : angle       0.70808 /  0.46 (    8)
  hydrogen bonds       : bond        0.03837 /  2.44 (  265)
  hydrogen bonds       : angle       4.95144 /  3.40 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 98
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7283 (mm-40) cc_final: 0.6871 (mm-40)
REVERT: A  114 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7314 (mm-30)
REVERT: A  143 LYS cc_start: 0.6348 (mttp) cc_final: 0.5998 (mttm)
REVERT: A  208 TYR cc_start: 0.8260 (t80) cc_final: 0.8008 (t80)
REVERT: A  413 LYS cc_start: 0.4820 (ttmt) cc_final: 0.4561 (ttmm)
REVERT: A  447 TRP cc_start: 0.8038 (OUTLIER) cc_final: 0.7475 (m-10)
REVERT: A  452 SER cc_start: 0.8271 (OUTLIER) cc_final: 0.8016 (m)
REVERT: A  688 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.7044 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7846 (mttt) cc_final: 0.7236 (mptt)
REVERT: A  782 ARG cc_start: 0.5174 (OUTLIER) cc_final: 0.4458 (mtp85)
REVERT: A  784 GLU cc_start: 0.6565 (pp20) cc_final: 0.5810 (pp20)
REVERT: A  853 ARG cc_start: 0.5593 (OUTLIER) cc_final: 0.5182 (ttm170)
REVERT: A  864 TYR cc_start: 0.6167 (OUTLIER) cc_final: 0.5790 (m-80)
  outliers start: 37
  outliers final: 17
  residues processed: 122
  average time/residue: 0.3735
  time to fit residues: 48.8094
Evaluate side-chains
  115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  782 ARG
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 58 optimal weight:    0.3980
   chunk 22 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 8 optimal weight:    0.3980
   chunk 70 optimal weight:    0.0000
   chunk 66 optimal weight:    2.9990
   chunk 44 optimal weight:    1.9990
   chunk 12 optimal weight:    4.9990
   overall best weight:    0.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4354 r_free = 0.4354 target = 0.175518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.152831 restraints weight = 15791.173|
|-----------------------------------------------------------------------------|
r_work (start): 0.4108 rms_B_bonded: 2.36
r_work: 0.3999 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4005 r_free = 0.4005    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.43   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4005 r_free = 0.4005    target_work(ls_wunit_k1) = 0.143         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.4005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7259
moved from start:          0.3077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7055  Z= 0.125
  Angle     :  0.572   7.290   9573  Z= 0.298
  Chirality :  0.042   0.157   1016
  Planarity :  0.004   0.034   1212
  Dihedral  :  6.367  53.830    952
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 9.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 23.31 %
    Favored  : 72.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.07 (0.30), residues: 820
  helix:  0.59 (0.29), residues: 316
  sheet: -1.06 (0.53), residues: 108
  loop : -0.12 (0.33), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  38 
 TYR   0.018   0.001   TYR C  32 
 PHE   0.036   0.001   PHE A 339 
 TRP   0.027   0.002   TRP A 391 
 HIS   0.005   0.001   HIS A 716 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.12 ( 7051)
  covalent geometry    : angle       0.57171 /  0.30 ( 9565)
  SS BOND              : bond        0.00173 /  0.10 (    4)
  SS BOND              : angle       0.46840 /  0.31 (    8)
  hydrogen bonds       : bond        0.03531 /  2.25 (  265)
  hydrogen bonds       : angle       4.83501 /  3.31 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 95
  time to evaluate  : 0.188 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7254 (mm-40) cc_final: 0.6876 (mm-40)
REVERT: A  110 LYS cc_start: 0.6829 (mmmt) cc_final: 0.6172 (mptt)
REVERT: A  114 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7312 (mm-30)
REVERT: A  143 LYS cc_start: 0.6387 (mttp) cc_final: 0.6030 (mttm)
REVERT: A  208 TYR cc_start: 0.8166 (t80) cc_final: 0.7948 (t80)
REVERT: A  413 LYS cc_start: 0.4767 (ttmt) cc_final: 0.4529 (ttmm)
REVERT: A  447 TRP cc_start: 0.7920 (OUTLIER) cc_final: 0.7485 (m-10)
REVERT: A  452 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7987 (m)
REVERT: A  504 GLU cc_start: 0.7290 (tp30) cc_final: 0.7056 (mm-30)
REVERT: A  688 ARG cc_start: 0.7233 (ttp-110) cc_final: 0.6981 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7841 (mttt) cc_final: 0.7262 (mptt)
REVERT: A  782 ARG cc_start: 0.5200 (OUTLIER) cc_final: 0.4447 (mtp85)
REVERT: A  784 GLU cc_start: 0.6514 (pp20) cc_final: 0.6123 (pp20)
REVERT: A  853 ARG cc_start: 0.5607 (OUTLIER) cc_final: 0.5241 (ttm170)
REVERT: A  864 TYR cc_start: 0.6096 (OUTLIER) cc_final: 0.5769 (m-80)
  outliers start: 34
  outliers final: 19
  residues processed: 118
  average time/residue: 0.3635
  time to fit residues: 45.7038
Evaluate side-chains
  116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 91
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  128 LYS
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  203 LYS
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  452 SER
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  782 ARG
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9980
   chunk 51 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 40 optimal weight:    0.9980
   chunk 45 optimal weight:    0.0980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
** A 389 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4359 r_free = 0.4359 target = 0.175942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.149697 restraints weight = 25913.877|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 3.42
r_work: 0.3957 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3964
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.44   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3964 r_free = 0.3964    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3964
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7293
moved from start:          0.3122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7055  Z= 0.122
  Angle     :  0.563   7.086   9573  Z= 0.295
  Chirality :  0.042   0.157   1016
  Planarity :  0.004   0.033   1212
  Dihedral  :  6.277  53.067    952
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 23.85 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.30), residues: 820
  helix:  0.61 (0.29), residues: 317
  sheet: -1.02 (0.53), residues: 108
  loop : -0.07 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C  38 
 TYR   0.018   0.001   TYR C  32 
 PHE   0.041   0.001   PHE A 339 
 TRP   0.035   0.002   TRP A 391 
 HIS   0.005   0.001   HIS A 716 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 ( 7051)
  covalent geometry    : angle       0.56340 /  0.29 ( 9565)
  SS BOND              : bond        0.00145 /  0.08 (    4)
  SS BOND              : angle       0.43078 /  0.28 (    8)
  hydrogen bonds       : bond        0.03476 /  2.21 (  265)
  hydrogen bonds       : angle       4.77344 /  3.27 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 93
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6788 (mm110)
REVERT: A  114 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7287 (mm-30)
REVERT: A  143 LYS cc_start: 0.6322 (mttp) cc_final: 0.5964 (mttm)
REVERT: A  208 TYR cc_start: 0.8248 (t80) cc_final: 0.8045 (t80)
REVERT: A  408 GLN cc_start: 0.6391 (OUTLIER) cc_final: 0.6146 (tt0)
REVERT: A  413 LYS cc_start: 0.4782 (ttmt) cc_final: 0.4372 (ttmm)
REVERT: A  447 TRP cc_start: 0.7950 (OUTLIER) cc_final: 0.7611 (m-10)
REVERT: A  504 GLU cc_start: 0.7373 (tp30) cc_final: 0.7136 (mm-30)
REVERT: A  688 ARG cc_start: 0.7254 (ttp-110) cc_final: 0.6990 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7831 (mttt) cc_final: 0.7242 (mptt)
REVERT: A  784 GLU cc_start: 0.6519 (pp20) cc_final: 0.6080 (pp20)
REVERT: A  853 ARG cc_start: 0.5585 (OUTLIER) cc_final: 0.5247 (ttm170)
REVERT: A  858 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6161 (mp0)
REVERT: A  864 TYR cc_start: 0.6069 (OUTLIER) cc_final: 0.5736 (m-80)
  outliers start: 29
  outliers final: 19
  residues processed: 112
  average time/residue: 0.3292
  time to fit residues: 39.5972
Evaluate side-chains
  114 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 89
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  203 LYS
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  408 GLN
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  765 LEU
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  858 GLU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Chi-restraints excluded: chain C residue  123 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 10 optimal weight:    7.9990
   chunk 8 optimal weight:    0.0870
   chunk 6 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   overall best weight:    0.4960

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 408 GLN
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4368 r_free = 0.4368 target = 0.176980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.150870 restraints weight = 31631.563|
|-----------------------------------------------------------------------------|
r_work (start): 0.4085 rms_B_bonded: 3.84
r_work: 0.3957 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3963
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3963 r_free = 0.3963    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3963 r_free = 0.3963    target_work(ls_wunit_k1) = 0.139         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3963
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7279
moved from start:          0.3156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7055  Z= 0.115
  Angle     :  0.567   8.151   9573  Z= 0.295
  Chirality :  0.042   0.154   1016
  Planarity :  0.004   0.033   1212
  Dihedral  :  6.217  52.158    952
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 24.12 %
    Favored  : 72.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.30), residues: 820
  helix:  0.68 (0.29), residues: 318
  sheet: -1.01 (0.53), residues: 108
  loop : -0.06 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  38 
 TYR   0.020   0.001   TYR A 680 
 PHE   0.043   0.001   PHE A 339 
 TRP   0.041   0.002   TRP A 391 
 HIS   0.005   0.001   HIS A 716 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 ( 7051)
  covalent geometry    : angle       0.56744 /  0.29 ( 9565)
  SS BOND              : bond        0.00130 /  0.08 (    4)
  SS BOND              : angle       0.36802 /  0.23 (    8)
  hydrogen bonds       : bond        0.03370 /  2.14 (  265)
  hydrogen bonds       : angle       4.71646 /  3.22 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 94
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7228 (mm-40) cc_final: 0.6815 (mm-40)
REVERT: A  110 LYS cc_start: 0.6811 (mmmt) cc_final: 0.6203 (mptt)
REVERT: A  114 GLU cc_start: 0.7525 (OUTLIER) cc_final: 0.7273 (mm-30)
REVERT: A  143 LYS cc_start: 0.6310 (mttp) cc_final: 0.5964 (mttm)
REVERT: A  208 TYR cc_start: 0.8250 (t80) cc_final: 0.8044 (t80)
REVERT: A  413 LYS cc_start: 0.4866 (ttmt) cc_final: 0.4614 (ttmm)
REVERT: A  447 TRP cc_start: 0.7923 (OUTLIER) cc_final: 0.7695 (m-10)
REVERT: A  504 GLU cc_start: 0.7374 (tp30) cc_final: 0.7151 (mm-30)
REVERT: A  688 ARG cc_start: 0.7235 (ttp-110) cc_final: 0.6978 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7832 (mttt) cc_final: 0.7248 (mptt)
REVERT: A  781 LEU cc_start: 0.7304 (OUTLIER) cc_final: 0.7097 (tt)
REVERT: A  784 GLU cc_start: 0.6549 (pp20) cc_final: 0.6121 (pp20)
REVERT: A  853 ARG cc_start: 0.5579 (OUTLIER) cc_final: 0.5260 (ttm170)
REVERT: A  858 GLU cc_start: 0.6595 (OUTLIER) cc_final: 0.6157 (mp0)
REVERT: A  864 TYR cc_start: 0.6073 (OUTLIER) cc_final: 0.5740 (m-80)
  outliers start: 27
  outliers final: 13
  residues processed: 113
  average time/residue: 0.3740
  time to fit residues: 45.0730
Evaluate side-chains
  107 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  447 TRP
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  716 HIS
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  829 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  858 GLU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain A residue  864 TYR
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 44 optimal weight:    5.9990
   chunk 81 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 42 optimal weight:    0.0050
   chunk 24 optimal weight:    0.0980
   chunk 41 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.4994

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.177590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.152045 restraints weight = 27465.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.4098 rms_B_bonded: 3.61
r_work: 0.3974 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3974
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3980
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3980 r_free = 0.3980    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3980
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7264
moved from start:          0.3179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7055  Z= 0.117
  Angle     :  0.564   7.670   9573  Z= 0.296
  Chirality :  0.043   0.178   1016
  Planarity :  0.004   0.034   1212
  Dihedral  :  6.217  51.537    952
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 24.25 %
    Favored  : 72.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.11 (0.31), residues: 820
  helix:  0.75 (0.30), residues: 317
  sheet: -0.97 (0.51), residues: 116
  loop : -0.00 (0.34), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 557 
 TYR   0.024   0.001   TYR A 680 
 PHE   0.013   0.001   PHE C 108 
 TRP   0.040   0.002   TRP A 391 
 HIS   0.004   0.001   HIS A 419 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 ( 7051)
  covalent geometry    : angle       0.56429 /  0.30 ( 9565)
  SS BOND              : bond        0.00123 /  0.08 (    4)
  SS BOND              : angle       0.35478 /  0.22 (    8)
  hydrogen bonds       : bond        0.03313 /  2.11 (  265)
  hydrogen bonds       : angle       4.70862 /  3.22 (  759)

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

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

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1640 Ramachandran restraints generated.
    820 Oldfield, 0 Emsley, 820 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 92
  time to evaluate  : 0.181 
Fit side-chains
   revert: symmetry clash
REVERT: A   98 GLN cc_start: 0.7244 (mm-40) cc_final: 0.6830 (mm-40)
REVERT: A  110 LYS cc_start: 0.6765 (mmmt) cc_final: 0.6162 (mptt)
REVERT: A  114 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7284 (mm-30)
REVERT: A  143 LYS cc_start: 0.6322 (mttp) cc_final: 0.5982 (mttm)
REVERT: A  208 TYR cc_start: 0.8248 (t80) cc_final: 0.8045 (t80)
REVERT: A  413 LYS cc_start: 0.4746 (ttmt) cc_final: 0.4341 (ttmm)
REVERT: A  504 GLU cc_start: 0.7320 (tp30) cc_final: 0.7113 (mm-30)
REVERT: A  688 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.6977 (ptt-90)
REVERT: A  743 LYS cc_start: 0.7798 (mttt) cc_final: 0.7240 (mptt)
REVERT: A  781 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.7043 (tt)
REVERT: A  784 GLU cc_start: 0.6545 (pp20) cc_final: 0.6135 (pp20)
REVERT: A  853 ARG cc_start: 0.5611 (OUTLIER) cc_final: 0.5306 (ttm170)
REVERT: A  858 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6159 (mp0)
  outliers start: 23
  outliers final: 12
  residues processed: 108
  average time/residue: 0.3460
  time to fit residues: 39.9484
Evaluate side-chains
  104 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  114 GLU
Chi-restraints excluded: chain A residue  136 ILE
Chi-restraints excluded: chain A residue  267 VAL
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  516 LEU
Chi-restraints excluded: chain A residue  701 THR
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  781 LEU
Chi-restraints excluded: chain A residue  853 ARG
Chi-restraints excluded: chain A residue  858 GLU
Chi-restraints excluded: chain A residue  862 LEU
Chi-restraints excluded: chain C residue   29 VAL
Chi-restraints excluded: chain C residue   48 VAL
Chi-restraints excluded: chain C residue  112 SER
Chi-restraints excluded: chain C residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 83
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 2 optimal weight:    0.0980
   chunk 74 optimal weight:    0.0270
   chunk 79 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 30 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 41 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.5638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  95 GLN
** A 393 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 408 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 720 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 769 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.177876 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.152297 restraints weight = 29088.228|
|-----------------------------------------------------------------------------|
r_work (start): 0.4102 rms_B_bonded: 3.56
r_work: 0.3980 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3986
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3986 r_free = 0.3986    target_work(ls_wunit_k1) = 0.141         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.3986
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7260
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7055  Z= 0.118
  Angle     :  0.565   7.410   9573  Z= 0.296
  Chirality :  0.043   0.168   1016
  Planarity :  0.004   0.033   1212
  Dihedral  :  5.985  51.108    950
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 25.61 %
    Favored  : 71.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.13 (0.31), residues: 820
  helix:  0.75 (0.29), residues: 317
  sheet: -0.94 (0.51), residues: 116
  loop :  0.02 (0.34), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C  38 
 TYR   0.027   0.001   TYR A 680 
 PHE   0.046   0.001   PHE A 339 
 TRP   0.046   0.002   TRP A 391 
 HIS   0.005   0.001   HIS A 720 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00269 /  0.12 ( 7051)
  covalent geometry    : angle       0.56472 /  0.30 ( 9565)
  SS BOND              : bond        0.00119 /  0.08 (    4)
  SS BOND              : angle       0.35215 /  0.22 (    8)
  hydrogen bonds       : bond        0.03362 /  2.14 (  265)
  hydrogen bonds       : angle       4.69114 /  3.21 (  759)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2529.59 seconds
wall clock time: 43 minutes 48.87 seconds (2628.87 seconds total)