Starting phenix.real_space_refine
on Thu Jul 24 10:34:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7to1_26026/07_2025/7to1_26026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7to1_26026/07_2025/7to1_26026.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2025/7to1_26026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2025/7to1_26026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2025/7to1_26026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7to1_26026/07_2025/7to1_26026.cif"
  }
  resolution = 3.66
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      24      5.49       5
     S      31      5.16       5
     C    3492      2.51       5
     N     947      2.21       5
     O    1106      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 5601
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5123
          Classifications: {'peptide': 635}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 27, 'TRANS': 607}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 477
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 21, 'undetermined': 1}
          Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 20, None: 1}
            Not linked:
              pdbres="GTP B   1 "
              pdbres="  G B   2 "
          Chain breaks: 1
    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   4191  SG  CYS A 810      43.045  22.013  23.953  1.00 50.21           S
  ATOM   4630  SG  CYS A 864      42.729  20.263  20.098  1.00 64.66           S
  ATOM   4669  SG  CYS A 869      39.685  21.192  21.887  1.00 60.38           S

  Time building chain proxies: 4.05, per 1000 atoms: 0.72
  Number of scatterers: 5601
  At special positions: 0
  Unit cell: (89.25, 94.5, 66.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      31     16.00
     P      24     15.00
     O    1106      8.00
     N     947      7.00
     C    3492      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.48
  Conformation dependent library (CDL) restraints added in 853.4 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 869 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 810 "


  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1220

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 5 sheets defined
      50.2% alpha, 8.7% beta
      10 base pairs and 15 stacking pairs defined.
    Time for finding SS restraints: 1.83
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 256
      removed outlier: 3.711A  pdb=" N   LEU A 250 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.725A  pdb=" N   LYS A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 284
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 3.534A  pdb=" N   LEU A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 377
    Processing helix  chain 'A' and resid 381 through 396
    Processing helix  chain 'A' and resid 419 through 434
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 4.068A  pdb=" N   GLN A 451 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL A 452 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 452'
    Processing helix  chain 'A' and resid 469 through 487
    Processing helix  chain 'A' and resid 492 through 497
      removed outlier: 4.366A  pdb=" N   SER A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 521
    Processing helix  chain 'A' and resid 529 through 558
      removed outlier: 3.674A  pdb=" N   ARG A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 576
      removed outlier: 3.698A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 602
      removed outlier: 3.598A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   SER A 599 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 3.960A  pdb=" N   GLU A 607 " --> pdb=" O   PRO A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 650
      removed outlier: 3.714A  pdb=" N   VAL A 640 " --> pdb=" O   THR A 636 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASP A 641 " --> pdb=" O   ARG A 637 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS A 644 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 771
      removed outlier: 4.107A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 794
    Processing helix  chain 'A' and resid 835 through 840
      removed outlier: 3.561A  pdb=" N   LYS A 839 " --> pdb=" O   GLY A 835 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLU A 840 " --> pdb=" O   ASP A 836 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 835 through 840'
    Processing helix  chain 'A' and resid 889 through 892
    Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296
      removed outlier: 7.202A  pdb=" N   LEU A 408 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   PHE A 371 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 461 through 462
      removed outlier: 3.744A  pdb=" N   THR A 742 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   VAL A 712 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   LEU A 741 " --> pdb=" O   VAL A 712 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU A 714 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ILE A 631 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   TYR A 715 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   PHE A 633 " --> pdb=" O   TYR A 715 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   THR A 630 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ALA A 696 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU A 632 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819
      removed outlier: 3.857A  pdb=" N   CYS A 818 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833
      removed outlier: 4.405A  pdb=" N   ILE A 916 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846
      removed outlier: 5.729A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   LYS A 878 " --> pdb=" O   LYS A 858 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A 862 " --> pdb=" O   GLY A 874 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY A 874 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   CYS A 864 " --> pdb=" O   ASP A 872 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ASP A 872 " --> pdb=" O   CYS A 864 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    687 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      15 stacking parallelities
  Total time for adding SS restraints: 1.96

  Time building geometry restraints manager: 1.81 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 895
        1.32 -     1.44: 1579
        1.44 -     1.57: 3195
        1.57 -     1.69: 46
        1.69 -     1.82: 43
  Bond restraints: 5758
  Sorted by residual:
  bond pdb=" C1' GTP B   1 "
       pdb=" C2' GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.524  1.285  0.239 2.00e-02 2.50e+03 1.43e+02
  bond pdb=" C1' GTP B   1 "
       pdb=" O4' GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.613 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C5  GTP B   1 "
       pdb=" C6  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.544 -0.154 2.00e-02 2.50e+03 5.91e+01
  bond pdb=" C4  GTP B   1 "
       pdb=" N3  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.355  1.490 -0.135 2.00e-02 2.50e+03 4.54e+01
  bond pdb=" C2  GTP B   1 "
       pdb=" N2  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.330  1.452 -0.122 2.00e-02 2.50e+03 3.73e+01
  ... (remaining 5753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 6868
        1.63 -     3.27: 981
        3.27 -     4.90: 18
        4.90 -     6.54: 2
        6.54 -     8.17: 3
  Bond angle restraints: 7872
  Sorted by residual:
  angle pdb=" CA  GLY A 835 "
        pdb=" C   GLY A 835 "
        pdb=" O   GLY A 835 "
      ideal   model   delta    sigma   weight residual
     121.41  118.49    2.92 8.80e-01 1.29e+00 1.10e+01
  angle pdb=" C   VAL A 453 "
        pdb=" N   TYR A 454 "
        pdb=" CA  TYR A 454 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" CA  VAL A 414 "
        pdb=" C   VAL A 414 "
        pdb=" O   VAL A 414 "
      ideal   model   delta    sigma   weight residual
     120.34  117.52    2.82 9.10e-01 1.21e+00 9.62e+00
  angle pdb=" N   ILE A 489 "
        pdb=" CA  ILE A 489 "
        pdb=" C   ILE A 489 "
      ideal   model   delta    sigma   weight residual
     113.53  110.85    2.68 9.80e-01 1.04e+00 7.50e+00
  angle pdb=" C2' GTP B   1 "
        pdb=" C3' GTP B   1 "
        pdb=" C4' GTP B   1 "
      ideal   model   delta    sigma   weight residual
     111.00  102.83    8.17 3.00e+00 1.11e-01 7.42e+00
  ... (remaining 7867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.24: 3236
       20.24 -    40.47: 228
       40.47 -    60.70: 43
       60.70 -    80.93: 26
       80.93 -   101.17: 2
  Dihedral angle restraints: 3535
    sinusoidal: 1663
      harmonic: 1872
  Sorted by residual:
  dihedral pdb=" C8  GTP B   1 "
           pdb=" C1' GTP B   1 "
           pdb=" N9  GTP B   1 "
           pdb=" O4' GTP B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59    3.43  101.17     1      2.00e+01 2.50e-03 2.86e+01
  dihedral pdb=" C4' GTP B   1 "
           pdb=" C5' GTP B   1 "
           pdb=" O5' GTP B   1 "
           pdb=" PA  GTP B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -99.13 -165.63   66.50     1      2.00e+01 2.50e-03 1.44e+01
  dihedral pdb=" CA  LEU A 449 "
           pdb=" C   LEU A 449 "
           pdb=" N   GLU A 450 "
           pdb=" CA  GLU A 450 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.31  -18.69     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 411
       0.041 -    0.081: 265
       0.081 -    0.122: 188
       0.122 -    0.162: 27
       0.162 -    0.203: 2
  Chirality restraints: 893
  Sorted by residual:
  chirality pdb=" CA  ILE A 360 "
            pdb=" N   ILE A 360 "
            pdb=" C   ILE A 360 "
            pdb=" CB  ILE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ILE A 261 "
            pdb=" N   ILE A 261 "
            pdb=" C   ILE A 261 "
            pdb=" CB  ILE A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.10e-01
  chirality pdb=" CA  ILE A 386 "
            pdb=" N   ILE A 386 "
            pdb=" C   ILE A 386 "
            pdb=" CB  ILE A 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.52e-01
  ... (remaining 890 not shown)

  Planarity restraints: 924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  62 "    0.028 2.00e-02 2.50e+03   1.31e-02 3.86e+00
        pdb=" N1    U B  62 "   -0.011 2.00e-02 2.50e+03
        pdb=" C2    U B  62 "   -0.010 2.00e-02 2.50e+03
        pdb=" O2    U B  62 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    U B  62 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    U B  62 "    0.004 2.00e-02 2.50e+03
        pdb=" O4    U B  62 "    0.014 2.00e-02 2.50e+03
        pdb=" C5    U B  62 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6    U B  62 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 697 "   -0.006 2.00e-02 2.50e+03   1.20e-02 1.43e+00
        pdb=" C   THR A 697 "    0.021 2.00e-02 2.50e+03
        pdb=" O   THR A 697 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   SER A 698 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  60 "    0.017 2.00e-02 2.50e+03   6.79e-03 1.38e+00
        pdb=" N9    G B  60 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8    G B  60 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7    G B  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  60 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  60 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G B  60 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G B  60 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G B  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  60 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    G B  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G B  60 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 921 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1634
        2.83 -     3.35: 5465
        3.35 -     3.87: 9347
        3.87 -     4.38: 10237
        4.38 -     4.90: 17565
  Nonbonded interactions: 44248
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 557 "
            pdb=" OH  TYR A 715 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OH  TYR A 622 "
            pdb=" OD1 ASN A 692 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" NH1 ARG A 811 "
            pdb=" O   GLU A 890 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   ILE A 337 "
            pdb=" ND2 ASN A 341 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" OG  SER A 362 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.364 3.040
  ... (remaining 44243 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:             1.520
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.210
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     21.110
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
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      :  0.015   0.676   5762  Z= 0.890
  Angle     :  1.047   8.173   7872  Z= 0.756
  Chirality :  0.063   0.203    893
  Planarity :  0.004   0.019    924
  Dihedral  : 15.282 101.166   2315
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.28 (0.31), residues: 627
  helix:  0.24 (0.29), residues: 282
  sheet: -3.75 (0.50), residues: 67
  loop : -2.85 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.003   TRP A 873 
 HIS   0.005   0.002   HIS A 782 
 PHE   0.016   0.003   PHE A 460 
 TYR   0.015   0.003   TYR A 390 
 ARG   0.008   0.001   ARG A 316 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13076 (  260)
  hydrogen bonds       : angle       5.07344 (  737)
  metal coordination   : bond        0.40819 (    3)
  covalent geometry    : bond        0.01213 ( 5758)
  covalent geometry    : angle       1.04703 ( 7872)
  Misc. bond           : bond        0.00023 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8600 (mptt)
REVERT: A  287 GLN cc_start: 0.8710 (tp40) cc_final: 0.8243 (pm20)
REVERT: A  298 ASN cc_start: 0.8024 (t0) cc_final: 0.7807 (t0)
REVERT: A  373 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7668 (mt-10)
REVERT: A  388 PHE cc_start: 0.8300 (m-10) cc_final: 0.7722 (m-80)
REVERT: A  481 ASP cc_start: 0.7314 (m-30) cc_final: 0.7111 (m-30)
REVERT: A  525 MET cc_start: 0.7566 (mmt) cc_final: 0.7181 (mmp)
REVERT: A  531 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8079 (tt0)
REVERT: A  556 GLU cc_start: 0.7822 (tt0) cc_final: 0.7565 (mt-10)
REVERT: A  598 GLU cc_start: 0.8597 (tp30) cc_final: 0.8378 (tp30)
REVERT: A  603 ASP cc_start: 0.8437 (t0) cc_final: 0.7931 (t70)
REVERT: A  773 GLU cc_start: 0.7947 (tt0) cc_final: 0.7544 (tm-30)
REVERT: A  803 LYS cc_start: 0.8941 (mmmt) cc_final: 0.8739 (mmmt)
REVERT: A  907 LYS cc_start: 0.8642 (mttt) cc_final: 0.8119 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.2308
  time to fit residues: 37.4097
Evaluate side-chains
  87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 54 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    0.4980
   chunk 16 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 50 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 59 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 380 GLN
A 495 ASN
A 517 GLN
A 557 HIS
A 595 GLN
A 769 GLN
A 784 GLN
A 876 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.138615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112725 restraints weight = 6877.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.116295 restraints weight = 4329.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.118837 restraints weight = 3159.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.1570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5762  Z= 0.128
  Angle     :  0.541   8.079   7872  Z= 0.269
  Chirality :  0.039   0.234    893
  Planarity :  0.004   0.041    924
  Dihedral  : 13.612  89.007   1009
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.96 %
    Favored  : 85.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.34), residues: 627
  helix:  1.26 (0.31), residues: 292
  sheet: -3.33 (0.54), residues: 74
  loop : -2.60 (0.35), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 771 
 HIS   0.006   0.001   HIS A 280 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.013   0.002   TYR A 622 
 ARG   0.008   0.001   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03934 (  260)
  hydrogen bonds       : angle       3.76778 (  737)
  metal coordination   : bond        0.00385 (    3)
  covalent geometry    : bond        0.00291 ( 5758)
  covalent geometry    : angle       0.54067 ( 7872)
  Misc. bond           : bond        0.00046 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.8028 (t0) cc_final: 0.7814 (t0)
REVERT: A  511 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7562 (tm-30)
REVERT: A  529 ASP cc_start: 0.8118 (t0) cc_final: 0.7868 (t0)
REVERT: A  541 TYR cc_start: 0.8120 (m-80) cc_final: 0.7850 (m-80)
REVERT: A  596 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8190 (tm-30)
REVERT: A  598 GLU cc_start: 0.8093 (tp30) cc_final: 0.7789 (tp30)
REVERT: A  907 LYS cc_start: 0.8600 (mttt) cc_final: 0.8096 (mtmm)
  outliers start: 11
  outliers final: 6
  residues processed: 96
  average time/residue: 0.1873
  time to fit residues: 23.2670
Evaluate side-chains
  81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  890 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 20 optimal weight:    3.9990
   chunk 51 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 41 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
A 608 ASN
A 619 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.154280 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.129979 restraints weight = 6440.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.133520 restraints weight = 4556.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.134897 restraints weight = 3757.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5762  Z= 0.134
  Angle     :  0.541   7.555   7872  Z= 0.270
  Chirality :  0.039   0.178    893
  Planarity :  0.003   0.036    924
  Dihedral  : 13.497  89.460   1009
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.29 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.35), residues: 627
  helix:  1.66 (0.31), residues: 287
  sheet: -3.30 (0.57), residues: 68
  loop : -2.35 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 512 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.012   0.002   TYR A 622 
 ARG   0.004   0.001   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03905 (  260)
  hydrogen bonds       : angle       3.73281 (  737)
  metal coordination   : bond        0.00296 (    3)
  covalent geometry    : bond        0.00312 ( 5758)
  covalent geometry    : angle       0.54087 ( 7872)
  Misc. bond           : bond        0.00019 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.7847 (tp30) cc_final: 0.7631 (tp30)
REVERT: A  283 LYS cc_start: 0.8802 (tppt) cc_final: 0.8355 (mmtt)
REVERT: A  298 ASN cc_start: 0.8030 (t0) cc_final: 0.7787 (t0)
REVERT: A  511 GLN cc_start: 0.8047 (tm-30) cc_final: 0.7690 (tm-30)
REVERT: A  529 ASP cc_start: 0.8033 (t0) cc_final: 0.7759 (t0)
REVERT: A  541 TYR cc_start: 0.8050 (m-80) cc_final: 0.7779 (m-80)
REVERT: A  907 LYS cc_start: 0.8587 (mttt) cc_final: 0.8241 (mtmm)
  outliers start: 15
  outliers final: 11
  residues processed: 95
  average time/residue: 0.1888
  time to fit residues: 23.3510
Evaluate side-chains
  87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 76
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9980
   chunk 43 optimal weight:    0.1980
   chunk 29 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 15 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 24 optimal weight:    4.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 384 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.154557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130185 restraints weight = 6515.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.133595 restraints weight = 4577.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.134731 restraints weight = 3767.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5762  Z= 0.117
  Angle     :  0.525   7.388   7872  Z= 0.265
  Chirality :  0.038   0.150    893
  Planarity :  0.004   0.045    924
  Dihedral  : 13.462  88.915   1009
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 17.16 %
    Favored  : 79.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.35), residues: 627
  helix:  1.78 (0.31), residues: 293
  sheet: -3.17 (0.59), residues: 68
  loop : -2.35 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 512 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.011   0.001   TYR A 622 
 ARG   0.004   0.001   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03692 (  260)
  hydrogen bonds       : angle       3.61867 (  737)
  metal coordination   : bond        0.00221 (    3)
  covalent geometry    : bond        0.00266 ( 5758)
  covalent geometry    : angle       0.52489 ( 7872)
  Misc. bond           : bond        0.00016 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 83
  time to evaluate  : 0.613 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8833 (tppt) cc_final: 0.8482 (mmtt)
REVERT: A  298 ASN cc_start: 0.8047 (t0) cc_final: 0.7776 (t0)
REVERT: A  511 GLN cc_start: 0.8055 (tm-30) cc_final: 0.7646 (tm-30)
REVERT: A  529 ASP cc_start: 0.8027 (t0) cc_final: 0.7709 (t0)
REVERT: A  907 LYS cc_start: 0.8573 (mttt) cc_final: 0.8221 (mtmm)
  outliers start: 20
  outliers final: 12
  residues processed: 98
  average time/residue: 0.1819
  time to fit residues: 23.1371
Evaluate side-chains
  87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 17 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0980
   chunk 50 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.1384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.151628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.127788 restraints weight = 6460.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.130214 restraints weight = 4462.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.131586 restraints weight = 4215.272|
|-----------------------------------------------------------------------------|
r_work (final): 0.3576
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7765
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5762  Z= 0.141
  Angle     :  0.553   7.723   7872  Z= 0.279
  Chirality :  0.039   0.155    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.387  89.107   1009
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.09 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.35), residues: 627
  helix:  1.84 (0.31), residues: 292
  sheet: -2.95 (0.63), residues: 66
  loop : -2.29 (0.37), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 646 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.011   0.001   PHE A 295 
 TYR   0.013   0.001   TYR A 622 
 ARG   0.003   0.001   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03858 (  260)
  hydrogen bonds       : angle       3.66554 (  737)
  metal coordination   : bond        0.00282 (    3)
  covalent geometry    : bond        0.00325 ( 5758)
  covalent geometry    : angle       0.55272 ( 7872)
  Misc. bond           : bond        0.00015 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8884 (tppt) cc_final: 0.8479 (mmtt)
REVERT: A  298 ASN cc_start: 0.8108 (t0) cc_final: 0.7826 (t0)
REVERT: A  511 GLN cc_start: 0.8136 (tm-30) cc_final: 0.7735 (tm-30)
REVERT: A  528 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8469 (mmmt)
REVERT: A  529 ASP cc_start: 0.8054 (t0) cc_final: 0.7715 (t0)
REVERT: A  907 LYS cc_start: 0.8587 (mttt) cc_final: 0.8222 (mtmm)
  outliers start: 17
  outliers final: 13
  residues processed: 94
  average time/residue: 0.1711
  time to fit residues: 21.2430
Evaluate side-chains
  90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 2 optimal weight:    0.1980
   chunk 44 optimal weight:    6.9990
   chunk 4 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0000
   chunk 39 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 58 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    0.5584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.155897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.132175 restraints weight = 6454.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.135662 restraints weight = 4349.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.136967 restraints weight = 3724.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.2439

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5762  Z= 0.107
  Angle     :  0.528   7.222   7872  Z= 0.266
  Chirality :  0.038   0.136    893
  Planarity :  0.003   0.036    924
  Dihedral  : 13.406  88.645   1009
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.39 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.36), residues: 627
  helix:  1.95 (0.31), residues: 294
  sheet: -2.77 (0.61), residues: 73
  loop : -2.12 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 646 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.007   0.001   PHE A 295 
 TYR   0.012   0.001   TYR A 390 
 ARG   0.003   0.000   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03506 (  260)
  hydrogen bonds       : angle       3.54341 (  737)
  metal coordination   : bond        0.00147 (    3)
  covalent geometry    : bond        0.00238 ( 5758)
  covalent geometry    : angle       0.52835 ( 7872)
  Misc. bond           : bond        0.00011 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 83
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8906 (tppt) cc_final: 0.8523 (mmtt)
REVERT: A  298 ASN cc_start: 0.8060 (t0) cc_final: 0.7756 (t0)
REVERT: A  511 GLN cc_start: 0.8081 (tm-30) cc_final: 0.7652 (tm-30)
REVERT: A  528 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8432 (mmmt)
REVERT: A  529 ASP cc_start: 0.8099 (t0) cc_final: 0.7739 (t0)
REVERT: A  907 LYS cc_start: 0.8517 (mttt) cc_final: 0.8111 (mtmm)
  outliers start: 18
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1720
  time to fit residues: 21.5299
Evaluate side-chains
  95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.614 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0370
   chunk 8 optimal weight:    0.0270
   chunk 34 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 31 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 47 optimal weight:    0.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 517 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.155317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.131805 restraints weight = 6544.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.134587 restraints weight = 4597.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.136060 restraints weight = 4145.155|
|-----------------------------------------------------------------------------|
r_work (final): 0.3632
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5762  Z= 0.108
  Angle     :  0.526   7.332   7872  Z= 0.265
  Chirality :  0.038   0.154    893
  Planarity :  0.003   0.036    924
  Dihedral  : 13.355  88.386   1009
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.91 %
    Favored  : 78.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.35 (0.36), residues: 627
  helix:  2.02 (0.31), residues: 294
  sheet: -2.95 (0.56), residues: 86
  loop : -2.05 (0.39), residues: 247

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 646 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.007   0.001   PHE A 295 
 TYR   0.015   0.001   TYR A 390 
 ARG   0.004   0.000   ARG A 811 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03481 (  260)
  hydrogen bonds       : angle       3.55767 (  737)
  metal coordination   : bond        0.00110 (    3)
  covalent geometry    : bond        0.00241 ( 5758)
  covalent geometry    : angle       0.52602 ( 7872)
  Misc. bond           : bond        0.00013 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.8010 (t0) cc_final: 0.7695 (t0)
REVERT: A  511 GLN cc_start: 0.8147 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: A  525 MET cc_start: 0.6570 (mmt) cc_final: 0.6147 (tpt)
REVERT: A  529 ASP cc_start: 0.8085 (t0) cc_final: 0.7696 (t0)
REVERT: A  907 LYS cc_start: 0.8499 (mttt) cc_final: 0.8193 (mtmm)
  outliers start: 17
  outliers final: 15
  residues processed: 94
  average time/residue: 0.1615
  time to fit residues: 20.3423
Evaluate side-chains
  90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.624 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 14 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 41 optimal weight:    0.5980
   chunk 57 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    7.9990
   chunk 4 optimal weight:    0.0010
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.6788

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

Flipped N/Q/H residues before XYZ refinement:
A 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.154990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.131509 restraints weight = 6459.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135327 restraints weight = 4407.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.136300 restraints weight = 3564.798|
|-----------------------------------------------------------------------------|
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7700
moved from start:          0.2605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5762  Z= 0.113
  Angle     :  0.543   7.695   7872  Z= 0.272
  Chirality :  0.038   0.164    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.325  88.045   1009
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.61 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.36), residues: 627
  helix:  2.08 (0.31), residues: 292
  sheet: -2.85 (0.60), residues: 80
  loop : -1.90 (0.39), residues: 255

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 512 
 HIS   0.003   0.000   HIS A 280 
 PHE   0.007   0.001   PHE A 295 
 TYR   0.012   0.001   TYR A 390 
 ARG   0.002   0.000   ARG A 320 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03535 (  260)
  hydrogen bonds       : angle       3.55900 (  737)
  metal coordination   : bond        0.00116 (    3)
  covalent geometry    : bond        0.00257 ( 5758)
  covalent geometry    : angle       0.54309 ( 7872)
  Misc. bond           : bond        0.00012 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7871 (t0) cc_final: 0.7509 (t0)
REVERT: A  511 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7748 (tm-30)
REVERT: A  529 ASP cc_start: 0.8031 (t0) cc_final: 0.7650 (t0)
REVERT: A  907 LYS cc_start: 0.8523 (mttt) cc_final: 0.8219 (mtmm)
  outliers start: 17
  outliers final: 16
  residues processed: 95
  average time/residue: 0.1656
  time to fit residues: 20.9874
Evaluate side-chains
  95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   chunk 2 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   chunk 39 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 9 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 18 optimal weight:    0.6980
   chunk 53 optimal weight:    5.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 588 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.137025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.113097 restraints weight = 7106.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.115503 restraints weight = 4604.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116498 restraints weight = 3756.597|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.2730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5762  Z= 0.142
  Angle     :  0.581   8.165   7872  Z= 0.292
  Chirality :  0.039   0.158    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.293  87.990   1009
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.84 %
    Favored  : 76.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.23 (0.36), residues: 627
  helix:  2.04 (0.31), residues: 292
  sheet: -2.98 (0.63), residues: 74
  loop : -1.91 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.009   0.001   PHE A 295 
 TYR   0.016   0.001   TYR A 622 
 ARG   0.003   0.000   ARG A 602 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  260)
  hydrogen bonds       : angle       3.66340 (  737)
  metal coordination   : bond        0.00173 (    3)
  covalent geometry    : bond        0.00332 ( 5758)
  covalent geometry    : angle       0.58118 ( 7872)
  Misc. bond           : bond        0.00011 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7935 (t0) cc_final: 0.7526 (t0)
REVERT: A  511 GLN cc_start: 0.8215 (tm-30) cc_final: 0.7767 (tm-30)
REVERT: A  529 ASP cc_start: 0.8239 (t0) cc_final: 0.7785 (t0)
REVERT: A  749 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7184 (mp0)
REVERT: A  907 LYS cc_start: 0.8540 (mttt) cc_final: 0.8140 (mtmm)
  outliers start: 18
  outliers final: 15
  residues processed: 94
  average time/residue: 0.1732
  time to fit residues: 21.6324
Evaluate side-chains
  90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.631 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 55 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 59 optimal weight:    0.7980
   chunk 26 optimal weight:    0.7980
   chunk 25 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0030
   chunk 54 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    0.6190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.140031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.116131 restraints weight = 7117.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.119717 restraints weight = 4422.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.120733 restraints weight = 3368.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.2782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5762  Z= 0.115
  Angle     :  0.568   7.503   7872  Z= 0.285
  Chirality :  0.038   0.155    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.320  87.864   1009
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 20.67 %
    Favored  : 76.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.36), residues: 627
  helix:  2.10 (0.31), residues: 292
  sheet: -2.95 (0.63), residues: 74
  loop : -1.88 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 512 
 HIS   0.002   0.000   HIS A 281 
 PHE   0.007   0.001   PHE A 460 
 TYR   0.016   0.001   TYR A 541 
 ARG   0.003   0.000   ARG A 589 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03572 (  260)
  hydrogen bonds       : angle       3.61470 (  737)
  metal coordination   : bond        0.00147 (    3)
  covalent geometry    : bond        0.00264 ( 5758)
  covalent geometry    : angle       0.56836 ( 7872)
  Misc. bond           : bond        0.00009 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7912 (t0) cc_final: 0.7507 (t0)
REVERT: A  511 GLN cc_start: 0.8185 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: A  529 ASP cc_start: 0.8141 (t0) cc_final: 0.7778 (t0)
REVERT: A  749 GLU cc_start: 0.7377 (mm-30) cc_final: 0.7142 (mp0)
REVERT: A  907 LYS cc_start: 0.8550 (mttt) cc_final: 0.8117 (mtmm)
  outliers start: 17
  outliers final: 16
  residues processed: 89
  average time/residue: 0.1563
  time to fit residues: 18.8927
Evaluate side-chains
  90 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  527 ASP
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 44 optimal weight:    8.9990
   chunk 59 optimal weight:    0.6980
   chunk 4 optimal weight:    0.4980
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
A 517 GLN
A 588 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.139368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.113776 restraints weight = 7128.750|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.117465 restraints weight = 4382.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.119969 restraints weight = 3171.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.2845

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5762  Z= 0.122
  Angle     :  0.565   7.502   7872  Z= 0.284
  Chirality :  0.038   0.153    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.295  87.710   1009
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 21.54 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.36), residues: 627
  helix:  2.09 (0.31), residues: 293
  sheet: -2.97 (0.64), residues: 74
  loop : -1.86 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 512 
 HIS   0.002   0.000   HIS A 281 
 PHE   0.008   0.001   PHE A 295 
 TYR   0.015   0.001   TYR A 390 
 ARG   0.003   0.000   ARG A 589 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03649 (  260)
  hydrogen bonds       : angle       3.62762 (  737)
  metal coordination   : bond        0.00138 (    3)
  covalent geometry    : bond        0.00281 ( 5758)
  covalent geometry    : angle       0.56508 ( 7872)
  Misc. bond           : bond        0.00010 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2017.50 seconds
wall clock time: 36 minutes 5.52 seconds (2165.52 seconds total)