Starting phenix.real_space_refine
on Sat Dec 20 00:33:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6g1x_4341/12_2025/6g1x_4341.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6g1x_4341/12_2025/6g1x_4341.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6g1x_4341/12_2025/6g1x_4341.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6g1x_4341/12_2025/6g1x_4341.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6g1x_4341/12_2025/6g1x_4341.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6g1x_4341/12_2025/6g1x_4341.cif"
  }
  resolution = 3.93
  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=   0.001 sd=   0.011
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      30      5.49       5
     S      35      5.16       5
     C    3572      2.51       5
     N    1010      2.21       5
     O    1159      1.98       5
     H    4182      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5913/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9989
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9349
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 648, 9349
          Classifications: {'peptide': 648}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'CIS': 2, 'PTRANS': 20, 'TRANS': 625}
          Chain breaks: 11
          Unresolved non-hydrogen bonds: 49
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 44
          Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'GLU:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 31
    Chain: "X"
      Number of atoms: 318
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 318
          Classifications: {'RNA': 15}
          Modifications used: {'rna3p_pur': 7, 'rna3p_pyr': 8}
          Link IDs: {'rna3p': 14}
    Chain: "Y"
      Number of atoms: 321
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 321
          Classifications: {'RNA': 15}
          Modifications used: {'rna3p_pur': 8, 'rna3p_pyr': 7}
          Link IDs: {'rna3p': 14}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7932  SG  CYS A 907      78.091  28.119  38.244  1.00123.87           S
  ATOM   7979  SG  CYS A 910      81.377  27.168  38.115  1.00130.12           S
  ATOM   8581  SG  CYS A 962      79.713  29.514  41.640  1.00127.98           S

  Time building chain proxies: 2.17, per 1000 atoms: 0.22
  Number of scatterers: 9989
  At special positions: 0
  Unit cell: (99.51, 83.46, 72.76, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      35     16.00
     P      30     15.00
     O    1159      8.00
     N    1010      7.00
     C    3572      6.00
     H    4182      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.06
  Conformation dependent library (CDL) restraints added in 215.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 910 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 962 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 907 "


  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 7 sheets defined
      53.2% alpha, 6.0% beta
      13 base pairs and 16 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 310 through 318
      removed outlier: 3.582A  pdb=" N   GLU A 315 " --> pdb=" O   PRO A 311 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL A 316 " --> pdb=" O   TYR A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 322
    Processing helix  chain 'A' and resid 335 through 355
      removed outlier: 4.276A  pdb=" N   VAL A 339 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ALA A 340 " --> pdb=" O   LYS A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 377
      removed outlier: 3.919A  pdb=" N   ALA A 370 " --> pdb=" O   LYS A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 383
    Processing helix  chain 'A' and resid 400 through 407
      removed outlier: 3.546A  pdb=" N   VAL A 404 " --> pdb=" O   SER A 400 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 427
      removed outlier: 4.010A  pdb=" N   LEU A 418 " --> pdb=" O   THR A 414 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLU A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 438
    Processing helix  chain 'A' and resid 445 through 449
    Processing helix  chain 'A' and resid 457 through 474
      removed outlier: 3.593A  pdb=" N   ARG A 461 " --> pdb=" O   ASN A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 499 through 514
      removed outlier: 3.736A  pdb=" N   ALA A 503 " --> pdb=" O   LYS A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 533
      removed outlier: 3.768A  pdb=" N   LEU A 529 " --> pdb=" O   ASN A 525 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 550 through 567
      removed outlier: 3.829A  pdb=" N   ILE A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 592
      removed outlier: 3.699A  pdb=" N   GLU A 580 " --> pdb=" O   THR A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 616
    Processing helix  chain 'A' and resid 620 through 643
    Processing helix  chain 'A' and resid 670 through 693
      removed outlier: 4.288A  pdb=" N   ASN A 683 " --> pdb=" O   LEU A 679 " (cutoff:3.500A)
      removed outlier: 4.689A  pdb=" N   LYS A 685 " --> pdb=" O   PHE A 681 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   MET A 686 " --> pdb=" O   ASP A 682 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   ASN A 693 " --> pdb=" O   LYS A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 715
      removed outlier: 5.022A  pdb=" N   GLN A 711 " --> pdb=" O   THR A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 741
    Processing helix  chain 'A' and resid 767 through 780
    Processing helix  chain 'A' and resid 812 through 823
      removed outlier: 3.705A  pdb=" N   ALA A 823 " --> pdb=" O   ALA A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 863
      removed outlier: 3.748A  pdb=" N   GLU A 844 " --> pdb=" O   VAL A 840 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   TYR A 855 " --> pdb=" O   GLU A 851 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ASN A 863 " --> pdb=" O   ASN A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 895
      removed outlier: 3.958A  pdb=" N   GLN A 895 " --> pdb=" O   SER A 891 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 938
    Processing helix  chain 'A' and resid 1002 through 1006
      removed outlier: 3.729A  pdb=" N   GLU A1005 " --> pdb=" O   LYS A1002 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   LEU A1006 " --> pdb=" O   TRP A1003 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1002 through 1006'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 328 through 329
      removed outlier: 6.403A  pdb=" N   ILE A 328 " --> pdb=" O   THR A 489 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 360 through 361
      removed outlier: 6.140A  pdb=" N   VAL A 360 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 440 through 441
    Processing sheet with id=AA4, first strand: chain 'A' and resid 751 through 753
      removed outlier: 7.107A  pdb=" N   HIS A 752 " --> pdb=" O   ILE A 787 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 912 through 916
      removed outlier: 6.418A  pdb=" N   LEU A 913 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
      removed outlier: 5.772A  pdb=" N   CYS A 907 " --> pdb=" O   LEU A 913 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 921 through 923
    Processing sheet with id=AA7, first strand: chain 'A' and resid 940 through 942
      removed outlier: 6.339A  pdb=" N   ILE A 960 " --> pdb=" O   TRP A 968 " (cutoff:3.500A)

    245 hydrogen bonds defined for protein.
    699 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      33 hydrogen bonds
      66 hydrogen bond angles
      0 basepair planarities
      13 basepair parallelities
      16 stacking parallelities
  Total time for adding SS restraints: 2.06

  Time building geometry restraints manager: 1.42 seconds

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

  Histogram of bond lengths:
        0.83 -     1.03: 4171
        1.03 -     1.22: 19
        1.22 -     1.42: 2475
        1.42 -     1.62: 3415
        1.62 -     1.81: 56
  Bond restraints: 10136
  Sorted by residual:
  bond pdb=" CG  ASN A 897 "
       pdb=" ND2 ASN A 897 "
    ideal  model  delta    sigma   weight residual
    1.328  1.249  0.079 2.10e-02 2.27e+03 1.42e+01
  bond pdb=" CB  MET A 459 "
       pdb=" CG  MET A 459 "
    ideal  model  delta    sigma   weight residual
    1.520  1.433  0.087 3.00e-02 1.11e+03 8.37e+00
  bond pdb=" CB  THR A 521 "
       pdb=" CG2 THR A 521 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.64e+00
  bond pdb=" CG  LEU A 418 "
       pdb=" CD1 LEU A 418 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.47e+00
  bond pdb=" CB  ILE A 507 "
       pdb=" CG2 ILE A 507 "
    ideal  model  delta    sigma   weight residual
    1.521  1.444  0.077 3.30e-02 9.18e+02 5.39e+00
  ... (remaining 10131 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    10.53: 17691
       10.53 -    21.06: 3
       21.06 -    31.59: 0
       31.59 -    42.12: 0
       42.12 -    52.65: 4
  Bond angle restraints: 17698
  Sorted by residual:
  angle pdb=" C   ALA A 497 "
        pdb=" N   LYS A 498 "
        pdb=" H   LYS A 498 "
      ideal   model   delta    sigma   weight residual
     124.56   71.91   52.65 3.00e+00 1.11e-01 3.08e+02
  angle pdb=" C   ILE A 399 "
        pdb=" N   SER A 400 "
        pdb=" H   SER A 400 "
      ideal   model   delta    sigma   weight residual
     124.71   72.94   51.77 3.00e+00 1.11e-01 2.98e+02
  angle pdb=" CA  SER A 400 "
        pdb=" N   SER A 400 "
        pdb=" H   SER A 400 "
      ideal   model   delta    sigma   weight residual
     114.41   63.13   51.29 3.00e+00 1.11e-01 2.92e+02
  angle pdb=" CA  LYS A 498 "
        pdb=" N   LYS A 498 "
        pdb=" H   LYS A 498 "
      ideal   model   delta    sigma   weight residual
     114.26   65.10   49.16 3.00e+00 1.11e-01 2.68e+02
  angle pdb=" C   ALA A 497 "
        pdb=" N   LYS A 498 "
        pdb=" CA  LYS A 498 "
      ideal   model   delta    sigma   weight residual
     121.18  137.00  -15.82 1.64e+00 3.72e-01 9.30e+01
  ... (remaining 17693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.72: 4629
       14.72 -    29.45: 318
       29.45 -    44.17: 80
       44.17 -    58.89: 42
       58.89 -    73.61: 33
  Dihedral angle restraints: 5102
    sinusoidal: 2956
      harmonic: 2146
  Sorted by residual:
  dihedral pdb=" CA  VAL A 810 "
           pdb=" C   VAL A 810 "
           pdb=" N   THR A 811 "
           pdb=" CA  THR A 811 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -143.86  -36.14     0      5.00e+00 4.00e-02 5.22e+01
  dihedral pdb=" CA  ILE A 411 "
           pdb=" C   ILE A 411 "
           pdb=" N   ILE A 412 "
           pdb=" CA  ILE A 412 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.11   29.89     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  LEU A 938 "
           pdb=" C   LEU A 938 "
           pdb=" N   TYR A 939 "
           pdb=" CA  TYR A 939 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.43  -29.57     0      5.00e+00 4.00e-02 3.50e+01
  ... (remaining 5099 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 787
       0.065 -    0.131: 145
       0.131 -    0.196: 21
       0.196 -    0.262: 3
       0.262 -    0.327: 1
  Chirality restraints: 957
  Sorted by residual:
  chirality pdb=" CB  ILE A 361 "
            pdb=" CA  ILE A 361 "
            pdb=" CG1 ILE A 361 "
            pdb=" CG2 ILE A 361 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.32    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CG  LEU A 508 "
            pdb=" CB  LEU A 508 "
            pdb=" CD1 LEU A 508 "
            pdb=" CD2 LEU A 508 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CB  ILE A 417 "
            pdb=" CA  ILE A 417 "
            pdb=" CG1 ILE A 417 "
            pdb=" CG2 ILE A 417 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.96e-01
  ... (remaining 954 not shown)

  Planarity restraints: 1459
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 968 "   -0.011 2.00e-02 2.50e+03   1.08e-02 4.70e+00
        pdb=" CG  TRP A 968 "    0.012 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 968 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 968 "   -0.003 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 968 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 968 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 968 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 968 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 968 "    0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 968 "    0.008 2.00e-02 2.50e+03
        pdb=" HD1 TRP A 968 "   -0.000 2.00e-02 2.50e+03
        pdb=" HE1 TRP A 968 "    0.011 2.00e-02 2.50e+03
        pdb=" HE3 TRP A 968 "   -0.004 2.00e-02 2.50e+03
        pdb=" HZ2 TRP A 968 "   -0.016 2.00e-02 2.50e+03
        pdb=" HZ3 TRP A 968 "    0.003 2.00e-02 2.50e+03
        pdb=" HH2 TRP A 968 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 960 "   -0.010 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" C   ILE A 960 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ILE A 960 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE A 961 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 599 "    0.008 9.50e-02 1.11e+02   1.39e-02 4.15e+00
        pdb=" NE  ARG A 599 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 599 "   -0.007 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 599 "   -0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 599 "    0.010 2.00e-02 2.50e+03
        pdb="HH11 ARG A 599 "    0.011 2.00e-02 2.50e+03
        pdb="HH12 ARG A 599 "   -0.017 2.00e-02 2.50e+03
        pdb="HH21 ARG A 599 "   -0.022 2.00e-02 2.50e+03
        pdb="HH22 ARG A 599 "    0.023 2.00e-02 2.50e+03
  ... (remaining 1456 not shown)

  Histogram of nonbonded interaction distances:
        1.53 -     2.14: 235
        2.14 -     2.76: 16986
        2.76 -     3.37: 24609
        3.37 -     3.99: 31881
        3.99 -     4.60: 49905
  Nonbonded interactions: 123616
  Sorted by model distance:
  nonbonded pdb=" H   LYS A 498 "
            pdb=" HA  LYS A 498 "
     model   vdw
     1.530 1.816
  nonbonded pdb=" H   SER A 400 "
            pdb=" HA  SER A 400 "
     model   vdw
     1.640 1.816
  nonbonded pdb=" O   ILE A 614 "
            pdb=" H   ILE A 618 "
     model   vdw
     1.671 2.450
  nonbonded pdb=" O   THR A 617 "
            pdb=" HH  TYR A 807 "
     model   vdw
     1.711 2.450
  nonbonded pdb=" HE2 HIS A 927 "
            pdb=" O2'   U X   5 "
     model   vdw
     1.720 2.450
  ... (remaining 123611 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.730
  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:             0.070
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.800
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.280
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
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      :  0.014   0.602   5957  Z= 0.574
  Angle     :  0.989  15.819   8144  Z= 0.545
  Chirality :  0.053   0.327    957
  Planarity :  0.005   0.046    914
  Dihedral  : 13.235  73.613   2477
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.66 %
    Favored  : 87.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.58 %
    Favored  : 98.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

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: -3.99 (0.28), residues: 624
  helix: -1.39 (0.26), residues: 286
  sheet: -4.67 (0.37), residues: 69
  loop : -3.47 (0.32), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 820 
 TYR   0.014   0.003   TYR A 312 
 PHE   0.020   0.003   PHE A 517 
 TRP   0.021   0.003   TRP A 968 
 HIS   0.006   0.002   HIS A 752 

Details of bonding type rmsd
  covalent geometry    : bond        0.01173 ( 5954)
  covalent geometry    : angle       0.98887 ( 8144)
  hydrogen bonds       : bond        0.13988 (  278)
  hydrogen bonds       : angle       6.45720 (  765)
  metal coordination   : bond        0.35014 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  180 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  504 GLU cc_start: 0.6905 (mt-10) cc_final: 0.6235 (mt-10)
REVERT: A  568 LYS cc_start: 0.7542 (mmtt) cc_final: 0.7313 (mmmt)
REVERT: A  587 GLU cc_start: 0.8525 (tt0) cc_final: 0.8177 (tm-30)
REVERT: A  599 ARG cc_start: 0.7606 (ptm-80) cc_final: 0.7178 (ptm160)
REVERT: A  615 ASN cc_start: 0.8771 (t0) cc_final: 0.8376 (t0)
REVERT: A  674 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8125 (mm-30)
REVERT: A  851 GLU cc_start: 0.8489 (tt0) cc_final: 0.8200 (tm-30)
REVERT: A  855 TYR cc_start: 0.8519 (m-10) cc_final: 0.8311 (m-10)
REVERT: A  923 ILE cc_start: 0.7920 (pp) cc_final: 0.7694 (mt)
REVERT: A  981 CYS cc_start: 0.7661 (t) cc_final: 0.7431 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.2194
  time to fit residues: 47.4177
Evaluate side-chains
  107 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
A 379 ASN
A 509 ASN
A 683 ASN
A 711 GLN
A 784 ASN
** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 974 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.148210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.121009 restraints weight = 28944.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.126305 restraints weight = 14015.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.129610 restraints weight = 8961.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131741 restraints weight = 6733.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133147 restraints weight = 5559.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   5957  Z= 0.138
  Angle     :  0.668  16.239   8144  Z= 0.359
  Chirality :  0.038   0.156    957
  Planarity :  0.004   0.046    914
  Dihedral  : 15.338  73.863   1152
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 16.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  :  7.36 %
    Favored  : 90.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -2.39 (0.32), residues: 624
  helix:  0.32 (0.30), residues: 293
  sheet: -4.61 (0.38), residues: 65
  loop : -3.04 (0.34), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 619 
 TYR   0.016   0.002   TYR A 342 
 PHE   0.008   0.001   PHE A 551 
 TRP   0.010   0.001   TRP A 582 
 HIS   0.010   0.002   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 5954)
  covalent geometry    : angle       0.66776 ( 8144)
  hydrogen bonds       : bond        0.04053 (  278)
  hydrogen bonds       : angle       4.81319 (  765)
  metal coordination   : bond        0.00682 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  133 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.283 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  431 ASP cc_start: 0.7021 (p0) cc_final: 0.6801 (p0)
REVERT: A  444 ASP cc_start: 0.7258 (t70) cc_final: 0.6563 (t70)
REVERT: A  465 GLN cc_start: 0.8314 (tt0) cc_final: 0.8000 (tp40)
REVERT: A  515 ASP cc_start: 0.7511 (t0) cc_final: 0.7204 (t0)
REVERT: A  568 LYS cc_start: 0.7669 (mmtt) cc_final: 0.7125 (mtpp)
REVERT: A  856 LYS cc_start: 0.8585 (mtpt) cc_final: 0.8267 (mtmm)
REVERT: A  972 MET cc_start: 0.7866 (ttp) cc_final: 0.7463 (ttp)
REVERT: A  981 CYS cc_start: 0.7593 (t) cc_final: 0.7191 (p)
  outliers start: 12
  outliers final: 11
  residues processed: 127
  average time/residue: 0.1846
  time to fit residues: 29.2771
Evaluate side-chains
  105 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  457 ASN
Chi-restraints excluded: chain A residue  509 ASN
Chi-restraints excluded: chain A residue  638 LYS
Chi-restraints excluded: chain A residue  683 ASN
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    9.9990
   chunk 1 optimal weight:    0.8980
   chunk 23 optimal weight:   10.0000
   chunk 39 optimal weight:    6.9990
   chunk 51 optimal weight:    6.9990
   chunk 60 optimal weight:    9.9990
   chunk 7 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 15 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 53 optimal weight:    0.4980
   overall best weight:    2.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 609 ASN
A 683 ASN
** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.142638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.115155 restraints weight = 28741.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.120297 restraints weight = 13735.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.123508 restraints weight = 8741.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.125555 restraints weight = 6569.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.126706 restraints weight = 5449.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.4387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5957  Z= 0.189
  Angle     :  0.653  16.255   8144  Z= 0.355
  Chirality :  0.039   0.143    957
  Planarity :  0.004   0.046    914
  Dihedral  : 15.103  74.241   1152
  Min Nonbonded Distance : 2.221

Molprobity Statistics.
  All-atom Clashscore : 20.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.62 %
    Favored  : 90.38 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 11.03 %
    Favored  : 87.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -1.84 (0.34), residues: 624
  helix:  0.94 (0.30), residues: 299
  sheet: -4.73 (0.38), residues: 66
  loop : -2.93 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 387 
 TYR   0.015   0.001   TYR A 342 
 PHE   0.010   0.001   PHE A 517 
 TRP   0.008   0.001   TRP A 582 
 HIS   0.006   0.001   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 5954)
  covalent geometry    : angle       0.65316 ( 8144)
  hydrogen bonds       : bond        0.03831 (  278)
  hydrogen bonds       : angle       4.68044 (  765)
  metal coordination   : bond        0.00284 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8698 (mmtp) cc_final: 0.8205 (pttt)
REVERT: A  444 ASP cc_start: 0.7291 (t70) cc_final: 0.6562 (t70)
REVERT: A  465 GLN cc_start: 0.8391 (tt0) cc_final: 0.8188 (tp40)
REVERT: A  515 ASP cc_start: 0.7753 (t0) cc_final: 0.7482 (t0)
REVERT: A  568 LYS cc_start: 0.7634 (mmtt) cc_final: 0.7156 (mtpp)
REVERT: A  750 LYS cc_start: 0.7437 (pmmt) cc_final: 0.7170 (tppt)
  outliers start: 10
  outliers final: 10
  residues processed: 108
  average time/residue: 0.1400
  time to fit residues: 20.1060
Evaluate side-chains
  105 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 95
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  457 ASN
Chi-restraints excluded: chain A residue  571 MET
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  683 ASN
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 41 optimal weight:    1.9990
   chunk 36 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 2 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0870
   chunk 29 optimal weight:    7.9990
   chunk 65 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.7762

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

Flipped N/Q/H residues before XYZ refinement:
A 615 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.145770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.117926 restraints weight = 28475.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.123166 restraints weight = 13857.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.126490 restraints weight = 8937.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.128558 restraints weight = 6740.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.129689 restraints weight = 5595.059|
|-----------------------------------------------------------------------------|
r_work (final): 0.3721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7645
moved from start:          0.4909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5957  Z= 0.110
  Angle     :  0.598  16.365   8144  Z= 0.322
  Chirality :  0.037   0.179    957
  Planarity :  0.003   0.029    914
  Dihedral  : 15.072  73.812   1152
  Min Nonbonded Distance : 2.330

Molprobity Statistics.
  All-atom Clashscore : 19.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.53 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.66 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -1.25 (0.35), residues: 624
  helix:  1.58 (0.31), residues: 294
  sheet: -4.45 (0.42), residues: 60
  loop : -2.83 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 387 
 TYR   0.014   0.001   TYR A 342 
 PHE   0.009   0.001   PHE A 551 
 TRP   0.007   0.001   TRP A 582 
 HIS   0.007   0.001   HIS A 974 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 5954)
  covalent geometry    : angle       0.59822 ( 8144)
  hydrogen bonds       : bond        0.03375 (  278)
  hydrogen bonds       : angle       4.28116 (  765)
  metal coordination   : bond        0.00119 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  110 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 101
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8626 (mmtp) cc_final: 0.8181 (pttt)
REVERT: A  444 ASP cc_start: 0.7436 (t70) cc_final: 0.6763 (t70)
REVERT: A  568 LYS cc_start: 0.7620 (mmtt) cc_final: 0.7168 (mtpp)
REVERT: A  586 MET cc_start: 0.7554 (mmm) cc_final: 0.7061 (mmm)
REVERT: A  673 ASP cc_start: 0.7924 (t0) cc_final: 0.7707 (t0)
REVERT: A  674 GLU cc_start: 0.7623 (mm-30) cc_final: 0.7312 (mm-30)
REVERT: A  865 LYS cc_start: 0.8710 (tppt) cc_final: 0.8420 (tptp)
REVERT: A  981 CYS cc_start: 0.7775 (t) cc_final: 0.7295 (p)
  outliers start: 9
  outliers final: 8
  residues processed: 107
  average time/residue: 0.1370
  time to fit residues: 19.8240
Evaluate side-chains
  102 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  770 GLU
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 52 optimal weight:    5.9990
   chunk 26 optimal weight:    7.9990
   chunk 22 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 41 optimal weight:    0.4980
   chunk 12 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 34 optimal weight:    8.9990
   chunk 15 optimal weight:    1.9990
   chunk 32 optimal weight:    7.9990
   overall best weight:    2.4988

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

Flipped N/Q/H residues before XYZ refinement:
A 509 ASN
A 615 ASN
A 784 ASN
A 863 ASN
** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.141311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.112941 restraints weight = 28479.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.117965 restraints weight = 14148.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121139 restraints weight = 9288.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.123139 restraints weight = 7080.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.124427 restraints weight = 5945.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.5526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5957  Z= 0.188
  Angle     :  0.647  16.326   8144  Z= 0.350
  Chirality :  0.039   0.154    957
  Planarity :  0.004   0.043    914
  Dihedral  : 15.041  74.734   1152
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 21.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.10 %
    Favored  : 89.90 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 13.13 %
    Favored  : 83.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -1.21 (0.34), residues: 624
  helix:  1.51 (0.30), residues: 301
  sheet: -4.50 (0.42), residues: 61
  loop : -2.75 (0.36), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 599 
 TYR   0.012   0.001   TYR A 342 
 PHE   0.013   0.001   PHE A 401 
 TRP   0.008   0.001   TRP A 582 
 HIS   0.005   0.001   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 5954)
  covalent geometry    : angle       0.64693 ( 8144)
  hydrogen bonds       : bond        0.03653 (  278)
  hydrogen bonds       : angle       4.46233 (  765)
  metal coordination   : bond        0.00124 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 99
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8611 (mmtp) cc_final: 0.8107 (pttt)
REVERT: A  431 ASP cc_start: 0.7564 (OUTLIER) cc_final: 0.7078 (p0)
REVERT: A  444 ASP cc_start: 0.7704 (t70) cc_final: 0.6979 (t70)
REVERT: A  568 LYS cc_start: 0.7918 (mmtt) cc_final: 0.7345 (mtpp)
REVERT: A  674 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7309 (mm-30)
REVERT: A  865 LYS cc_start: 0.8773 (tppt) cc_final: 0.8516 (tptp)
REVERT: A  981 CYS cc_start: 0.7904 (t) cc_final: 0.7455 (p)
  outliers start: 18
  outliers final: 16
  residues processed: 110
  average time/residue: 0.1354
  time to fit residues: 20.0534
Evaluate side-chains
  110 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  509 ASN
Chi-restraints excluded: chain A residue  571 MET
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  617 THR
Chi-restraints excluded: chain A residue  622 ASP
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  770 GLU
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 3 optimal weight:    6.9990
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   chunk 0 optimal weight:    7.9990
   chunk 43 optimal weight:    9.9990
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 928 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.141146 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.113482 restraints weight = 28005.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.118562 restraints weight = 13230.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121798 restraints weight = 8405.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.123839 restraints weight = 6287.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.125097 restraints weight = 5184.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.5821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5957  Z= 0.196
  Angle     :  0.635  16.300   8144  Z= 0.344
  Chirality :  0.039   0.147    957
  Planarity :  0.004   0.031    914
  Dihedral  : 14.964  74.598   1152
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 22.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.42 %
    Favored  : 89.58 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 15.24 %
    Favored  : 81.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -1.20 (0.35), residues: 624
  helix:  1.37 (0.30), residues: 308
  sheet: -4.39 (0.43), residues: 65
  loop : -2.63 (0.38), residues: 251

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 460 
 TYR   0.012   0.001   TYR A 342 
 PHE   0.012   0.001   PHE A 378 
 TRP   0.007   0.001   TRP A 582 
 HIS   0.005   0.001   HIS A 626 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 5954)
  covalent geometry    : angle       0.63477 ( 8144)
  hydrogen bonds       : bond        0.03658 (  278)
  hydrogen bonds       : angle       4.47556 (  765)
  metal coordination   : bond        0.00047 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 92
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8640 (mmtp) cc_final: 0.8125 (pttt)
REVERT: A  431 ASP cc_start: 0.7713 (OUTLIER) cc_final: 0.7171 (p0)
REVERT: A  444 ASP cc_start: 0.7775 (t70) cc_final: 0.7030 (t70)
REVERT: A  586 MET cc_start: 0.7735 (mmm) cc_final: 0.7344 (mmm)
REVERT: A  674 GLU cc_start: 0.7702 (mm-30) cc_final: 0.7351 (mm-30)
REVERT: A  912 MET cc_start: 0.8111 (ptt) cc_final: 0.7593 (ppp)
REVERT: A  981 CYS cc_start: 0.7968 (t) cc_final: 0.7505 (p)
  outliers start: 16
  outliers final: 13
  residues processed: 102
  average time/residue: 0.1375
  time to fit residues: 19.1246
Evaluate side-chains
  104 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 90
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  431 ASP
Chi-restraints excluded: chain A residue  571 MET
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  628 GLU
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  770 GLU
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 7 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 15 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0040
   chunk 6 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   overall best weight:    1.3396

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.143014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.115120 restraints weight = 28322.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.120294 restraints weight = 13892.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.123499 restraints weight = 9037.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.125515 restraints weight = 6849.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.126830 restraints weight = 5706.335|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.6058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   5957  Z= 0.118
  Angle     :  0.577  16.378   8144  Z= 0.310
  Chirality :  0.037   0.143    957
  Planarity :  0.003   0.031    914
  Dihedral  : 14.876  74.128   1152
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 19.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.46 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -0.78 (0.35), residues: 624
  helix:  1.74 (0.30), residues: 304
  sheet: -4.08 (0.50), residues: 55
  loop : -2.55 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 387 
 TYR   0.010   0.001   TYR A 342 
 PHE   0.008   0.001   PHE A 378 
 TRP   0.007   0.001   TRP A 582 
 HIS   0.006   0.001   HIS A 974 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 5954)
  covalent geometry    : angle       0.57697 ( 8144)
  hydrogen bonds       : bond        0.03280 (  278)
  hydrogen bonds       : angle       4.20601 (  765)
  metal coordination   : bond        0.00050 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  108 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8571 (mmtp) cc_final: 0.8106 (pttt)
REVERT: A  444 ASP cc_start: 0.7737 (t70) cc_final: 0.7065 (t70)
REVERT: A  674 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7356 (mm-30)
REVERT: A  912 MET cc_start: 0.8021 (ptt) cc_final: 0.7762 (ppp)
REVERT: A  981 CYS cc_start: 0.7926 (t) cc_final: 0.7388 (p)
  outliers start: 12
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1345
  time to fit residues: 19.0317
Evaluate side-chains
  104 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 94
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  571 MET
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  903 ILE
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    8.9990
   chunk 50 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 48 optimal weight:    4.9990
   chunk 19 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 58 optimal weight:    1.9990
   chunk 41 optimal weight:    0.0170
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.144226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.116342 restraints weight = 28120.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.121533 restraints weight = 13782.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.124832 restraints weight = 8907.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.126875 restraints weight = 6701.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.128230 restraints weight = 5572.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3689
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7673
moved from start:          0.6239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5957  Z= 0.096
  Angle     :  0.565  16.372   8144  Z= 0.303
  Chirality :  0.037   0.183    957
  Planarity :  0.003   0.027    914
  Dihedral  : 14.862  73.913   1152
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 18.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.01 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 16.46 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -0.53 (0.36), residues: 624
  helix:  2.11 (0.30), residues: 299
  sheet: -4.00 (0.50), residues: 55
  loop : -2.54 (0.37), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 387 
 TYR   0.013   0.001   TYR A1018 
 PHE   0.008   0.001   PHE A 551 
 TRP   0.007   0.001   TRP A 582 
 HIS   0.006   0.001   HIS A 974 

Details of bonding type rmsd
  covalent geometry    : bond        0.00207 ( 5954)
  covalent geometry    : angle       0.56508 ( 8144)
  hydrogen bonds       : bond        0.02988 (  278)
  hydrogen bonds       : angle       4.00462 (  765)
  metal coordination   : bond        0.00048 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  111 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8561 (mmtp) cc_final: 0.8109 (pttp)
REVERT: A  444 ASP cc_start: 0.7798 (t70) cc_final: 0.7026 (t70)
REVERT: A  562 ILE cc_start: 0.8900 (mt) cc_final: 0.8519 (tp)
REVERT: A  674 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7346 (mm-30)
REVERT: A  879 GLN cc_start: 0.8846 (mt0) cc_final: 0.8139 (tp-100)
REVERT: A  972 MET cc_start: 0.7712 (ttp) cc_final: 0.7398 (ttp)
REVERT: A  981 CYS cc_start: 0.7936 (t) cc_final: 0.7303 (p)
  outliers start: 13
  outliers final: 9
  residues processed: 106
  average time/residue: 0.1349
  time to fit residues: 19.2312
Evaluate side-chains
  103 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  571 MET
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  915 CYS
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 47 optimal weight:   10.0000
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 19 optimal weight:    2.9990
   chunk 48 optimal weight:    6.9990
   chunk 33 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 22 optimal weight:    8.9990
   chunk 44 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.143671 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.115024 restraints weight = 28022.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.120415 restraints weight = 13200.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.123692 restraints weight = 8381.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.125812 restraints weight = 6312.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.127165 restraints weight = 5223.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.6477

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5957  Z= 0.119
  Angle     :  0.579  16.316   8144  Z= 0.310
  Chirality :  0.037   0.157    957
  Planarity :  0.003   0.025    914
  Dihedral  : 14.825  74.210   1152
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 20.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.49 %
    Favored  : 91.51 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 17.16 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -0.52 (0.36), residues: 624
  helix:  2.03 (0.30), residues: 305
  sheet: -4.07 (0.47), residues: 60
  loop : -2.46 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 820 
 TYR   0.008   0.001   TYR A 342 
 PHE   0.008   0.001   PHE A 378 
 TRP   0.007   0.001   TRP A 582 
 HIS   0.006   0.001   HIS A 974 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5954)
  covalent geometry    : angle       0.57900 ( 8144)
  hydrogen bonds       : bond        0.03081 (  278)
  hydrogen bonds       : angle       4.04727 (  765)
  metal coordination   : bond        0.00088 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  104 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 95
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8556 (mmtp) cc_final: 0.8100 (pttp)
REVERT: A  444 ASP cc_start: 0.7753 (t70) cc_final: 0.7024 (t70)
REVERT: A  509 ASN cc_start: 0.8610 (t0) cc_final: 0.8346 (t0)
REVERT: A  586 MET cc_start: 0.7760 (mmm) cc_final: 0.7263 (mmm)
REVERT: A  674 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7348 (mm-30)
REVERT: A  766 MET cc_start: 0.8920 (mmm) cc_final: 0.8712 (mmm)
REVERT: A  972 MET cc_start: 0.7734 (ttp) cc_final: 0.7500 (ttp)
REVERT: A  981 CYS cc_start: 0.7969 (t) cc_final: 0.7418 (p)
  outliers start: 9
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1409
  time to fit residues: 18.9384
Evaluate side-chains
  100 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  571 MET
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 36 optimal weight:    3.9990
   chunk 32 optimal weight:    6.9990
   chunk 46 optimal weight:    6.9990
   chunk 37 optimal weight:    6.9990
   chunk 63 optimal weight:    0.1980
   chunk 24 optimal weight:    0.6980
   chunk 2 optimal weight:    0.4980
   chunk 60 optimal weight:    5.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.142594 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.116088 restraints weight = 27977.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.120986 restraints weight = 14685.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.122542 restraints weight = 8942.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.122749 restraints weight = 7972.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.123287 restraints weight = 7312.723|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.6642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5957  Z= 0.132
  Angle     :  0.594  16.345   8144  Z= 0.317
  Chirality :  0.038   0.151    957
  Planarity :  0.003   0.026    914
  Dihedral  : 14.795  74.322   1152
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 21.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.29 %
    Favored  : 90.71 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 17.69 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -0.56 (0.36), residues: 624
  helix:  2.08 (0.30), residues: 305
  sheet: -4.09 (0.44), residues: 73
  loop : -2.45 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 461 
 TYR   0.014   0.001   TYR A1018 
 PHE   0.010   0.001   PHE A 378 
 TRP   0.006   0.001   TRP A 582 
 HIS   0.005   0.001   HIS A 974 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 5954)
  covalent geometry    : angle       0.59442 ( 8144)
  hydrogen bonds       : bond        0.03116 (  278)
  hydrogen bonds       : angle       4.07819 (  765)
  metal coordination   : bond        0.00073 (    3)

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

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

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1248 Ramachandran restraints generated.
    624 Oldfield, 0 Emsley, 624 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue TYR  381 is missing expected H atoms. Skipping.
Residue LEU  397 is missing expected H atoms. Skipping.
Residue LYS  398 is missing expected H atoms. Skipping.
Residue ILE  399 is missing expected H atoms. Skipping.
Residue LYS  406 is missing expected H atoms. Skipping.
Residue LYS  451 is missing expected H atoms. Skipping.
Residue LEU  463 is missing expected H atoms. Skipping.
Residue LYS  464 is missing expected H atoms. Skipping.
Residue LYS  473 is missing expected H atoms. Skipping.
Residue LYS  474 is missing expected H atoms. Skipping.
Residue LYS  498 is missing expected H atoms. Skipping.
Residue LYS  505 is missing expected H atoms. Skipping.
Residue LYS  538 is missing expected H atoms. Skipping.
Residue LYS  552 is missing expected H atoms. Skipping.
Residue LYS  554 is missing expected H atoms. Skipping.
Residue LYS  568 is missing expected H atoms. Skipping.
Residue MET  571 is missing expected H atoms. Skipping.
Residue LYS  592 is missing expected H atoms. Skipping.
Residue LYS  607 is missing expected H atoms. Skipping.
Residue MET  620 is missing expected H atoms. Skipping.
Residue THR  672 is missing expected H atoms. Skipping.
Residue LYS  684 is missing expected H atoms. Skipping.
Residue LYS  685 is missing expected H atoms. Skipping.
Residue MET  686 is missing expected H atoms. Skipping.
Residue LYS  688 is missing expected H atoms. Skipping.
Residue LYS  689 is missing expected H atoms. Skipping.
Residue LYS  700 is missing expected H atoms. Skipping.
Residue MET  739 is missing expected H atoms. Skipping.
Residue LYS  764 is missing expected H atoms. Skipping.
Residue ILE  783 is missing expected H atoms. Skipping.
Residue LEU  785 is missing expected H atoms. Skipping.
Residue LEU  786 is missing expected H atoms. Skipping.
Residue ILE  787 is missing expected H atoms. Skipping.
Residue ALA  788 is missing expected H atoms. Skipping.
Residue THR  789 is missing expected H atoms. Skipping.
Residue THR  790 is missing expected H atoms. Skipping.
Residue ILE  798 is missing expected H atoms. Skipping.
Residue LYS  799 is missing expected H atoms. Skipping.
Residue SER  828 is missing expected H atoms. Skipping.
Residue THR  834 is missing expected H atoms. Skipping.
Residue SER  835 is missing expected H atoms. Skipping.
Residue SER  836 is missing expected H atoms. Skipping.
Residue LYS  856 is missing expected H atoms. Skipping.
Residue LYS  963 is missing expected H atoms. Skipping.
Residue MET  972 is missing expected H atoms. Skipping.
Residue VAL  973 is missing expected H atoms. Skipping.
Residue LYS  975 is missing expected H atoms. Skipping.
Residue LEU  979 is missing expected H atoms. Skipping.
Residue LEU 1013 is missing expected H atoms. Skipping.
Evaluate side-chains
  101 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.220 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LYS cc_start: 0.8523 (mmtp) cc_final: 0.8070 (pttt)
REVERT: A  403 GLU cc_start: 0.7808 (mp0) cc_final: 0.7589 (mp0)
REVERT: A  431 ASP cc_start: 0.7735 (p0) cc_final: 0.7257 (p0)
REVERT: A  444 ASP cc_start: 0.7761 (t70) cc_final: 0.7052 (t70)
REVERT: A  509 ASN cc_start: 0.8631 (t0) cc_final: 0.8376 (t0)
REVERT: A  586 MET cc_start: 0.7723 (mmm) cc_final: 0.7246 (mmm)
REVERT: A  674 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: A  972 MET cc_start: 0.7572 (ttp) cc_final: 0.7361 (ttp)
REVERT: A  981 CYS cc_start: 0.8003 (t) cc_final: 0.7488 (p)
  outliers start: 6
  outliers final: 6
  residues processed: 99
  average time/residue: 0.1329
  time to fit residues: 17.5830
Evaluate side-chains
  99 residues out of total 582 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 93
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 LEU
Chi-restraints excluded: chain A residue  571 MET
Chi-restraints excluded: chain A residue  610 GLU
Chi-restraints excluded: chain A residue  693 ASN
Chi-restraints excluded: chain A residue  786 LEU
Chi-restraints excluded: chain A residue  982 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 44 optimal weight:    0.0980
   chunk 37 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 41 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 10 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    2.0186

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

Flipped N/Q/H residues before XYZ refinement:
A 469 ASN
A 509 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.141383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.113264 restraints weight = 28324.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.118276 restraints weight = 14067.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.121394 restraints weight = 9195.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.123386 restraints weight = 7016.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.124669 restraints weight = 5870.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.6835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5957  Z= 0.151
  Angle     :  0.604  16.295   8144  Z= 0.324
  Chirality :  0.038   0.151    957
  Planarity :  0.003   0.025    914
  Dihedral  : 14.778  74.492   1152
  Min Nonbonded Distance : 2.216

Molprobity Statistics.
  All-atom Clashscore : 21.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.78 %
    Favored  : 90.22 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 17.69 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.32 %
    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: -0.57 (0.36), residues: 624
  helix:  2.07 (0.30), residues: 305
  sheet: -4.01 (0.46), residues: 73
  loop : -2.47 (0.40), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 460 
 TYR   0.012   0.001   TYR A1018 
 PHE   0.013   0.001   PHE A 378 
 TRP   0.006   0.001   TRP A 582 
 HIS   0.005   0.001   HIS A 974 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 5954)
  covalent geometry    : angle       0.60445 ( 8144)
  hydrogen bonds       : bond        0.03232 (  278)
  hydrogen bonds       : angle       4.13119 (  765)
  metal coordination   : bond        0.00036 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1882.01 seconds
wall clock time: 32 minutes 56.77 seconds (1976.77 seconds total)