Starting phenix.real_space_refine
on Tue Feb 11 14:24:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7to1_26026/02_2025/7to1_26026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7to1_26026/02_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_26026/02_2025/7to1_26026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7to1_26026/02_2025/7to1_26026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7to1_26026/02_2025/7to1_26026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7to1_26026/02_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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 3.53, per 1000 atoms: 0.63
  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: 1.50
  Conformation dependent library (CDL) restraints added in 914.9 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: 2.02
  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: 2.01

  Time building geometry restraints manager: 1.73 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:             0.560
  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:          0.230
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.640
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.190
-------------------------------------------------------------------------------
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      :  0.012   0.239   5758  Z= 0.795
  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 

*********************** 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  : 0.639 
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: 0.2270
  time to fit residues: 36.7507
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  : 0.583 
-------------------------------------------------------------------------------
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 = 43)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.112729 restraints weight = 6877.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.116310 restraints weight = 4328.566|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118919 restraints weight = 3152.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
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   5758  Z= 0.189
  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 

*********************** 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  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.8029 (t0) cc_final: 0.7815 (t0)
REVERT: A  511 GLN cc_start: 0.7953 (tm-30) cc_final: 0.7562 (tm-30)
REVERT: A  529 ASP cc_start: 0.8112 (t0) cc_final: 0.7863 (t0)
REVERT: A  541 TYR cc_start: 0.8120 (m-80) cc_final: 0.7850 (m-80)
REVERT: A  596 GLU cc_start: 0.8461 (tm-30) cc_final: 0.8188 (tm-30)
REVERT: A  598 GLU cc_start: 0.8092 (tp30) cc_final: 0.7788 (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: 0.1879
  time to fit residues: 23.2939
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  : 0.594 
-------------------------------------------------------------------------------
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:    5.9990
   chunk 36 optimal weight:    3.9990
   chunk 19 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 59 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 384 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
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 = 0.3801 r_free = 0.3801 target = 0.152386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.127969 restraints weight = 6467.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.131110 restraints weight = 4620.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.132228 restraints weight = 3835.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3584
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5758  Z= 0.233
  Angle     :  0.560   7.829   7872  Z= 0.281
  Chirality :  0.039   0.176    893
  Planarity :  0.003   0.036    924
  Dihedral  : 13.468  89.567   1009
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.29 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.35), residues: 627
  helix:  1.63 (0.31), residues: 286
  sheet: -3.38 (0.56), residues: 69
  loop : -2.34 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 280 
 PHE   0.011   0.001   PHE A 295 
 TYR   0.013   0.002   TYR A 622 
 ARG   0.005   0.001   ARG A 602 

*********************** 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
  100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.624 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8824 (tppt) cc_final: 0.8401 (mmtt)
REVERT: A  298 ASN cc_start: 0.8046 (t0) cc_final: 0.7785 (t0)
REVERT: A  511 GLN cc_start: 0.8089 (tm-30) cc_final: 0.7733 (tm-30)
REVERT: A  529 ASP cc_start: 0.8029 (t0) cc_final: 0.7826 (t0)
REVERT: A  541 TYR cc_start: 0.8080 (m-80) cc_final: 0.7811 (m-80)
REVERT: A  907 LYS cc_start: 0.8589 (mttt) cc_final: 0.8250 (mtmm)
  outliers start: 17
  outliers final: 11
  residues processed: 96
  average time/residue: 0.1835
  time to fit residues: 23.0939
Evaluate side-chains
  84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 28 optimal weight:    0.2980
   chunk 47 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0970
   chunk 29 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 41 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 63 optimal weight:    4.9990
   chunk 49 optimal weight:    6.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.5778

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

Flipped N/Q/H residues before XYZ refinement:
A 384 ASN
A 876 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.154993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.130896 restraints weight = 6514.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.134739 restraints weight = 4470.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.135812 restraints weight = 3549.054|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7690
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   5758  Z= 0.152
  Angle     :  0.516   7.192   7872  Z= 0.260
  Chirality :  0.038   0.152    893
  Planarity :  0.003   0.040    924
  Dihedral  : 13.464  88.888   1009
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.22 %
    Favored  : 93.78 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 16.99 %
    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: -0.57 (0.35), residues: 627
  helix:  1.84 (0.31), residues: 293
  sheet: -2.94 (0.58), residues: 72
  loop : -2.30 (0.37), residues: 262

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   0.008   0.001   PHE A 295 
 TYR   0.012   0.001   TYR A 622 
 ARG   0.005   0.001   ARG A 602 

*********************** 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
  108 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.618 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.7921 (tp30) cc_final: 0.7625 (tp30)
REVERT: A  283 LYS cc_start: 0.8873 (tppt) cc_final: 0.8462 (mmtt)
REVERT: A  298 ASN cc_start: 0.8116 (t0) cc_final: 0.7872 (t0)
REVERT: A  511 GLN cc_start: 0.8064 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: A  529 ASP cc_start: 0.8108 (t0) cc_final: 0.7767 (t0)
REVERT: A  907 LYS cc_start: 0.8571 (mttt) cc_final: 0.8160 (mtmm)
  outliers start: 21
  outliers final: 13
  residues processed: 101
  average time/residue: 0.1873
  time to fit residues: 24.6112
Evaluate side-chains
  89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.662 
-------------------------------------------------------------------------------
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  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:    5.9990
   chunk 20 optimal weight:    0.0870
   chunk 50 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 56 optimal weight:    0.8980
   chunk 54 optimal weight:    5.9990
   overall best weight:    1.1560

-------------------------------------------------------------------------------
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 = 0.3795 r_free = 0.3795 target = 0.151982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.128299 restraints weight = 6451.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.131272 restraints weight = 4438.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.132209 restraints weight = 4018.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7761
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5758  Z= 0.216
  Angle     :  0.568   7.791   7872  Z= 0.284
  Chirality :  0.039   0.157    893
  Planarity :  0.003   0.034    924
  Dihedral  : 13.368  89.216   1009
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 18.04 %
    Favored  : 78.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.54 (0.35), residues: 627
  helix:  1.85 (0.31), residues: 293
  sheet: -2.99 (0.63), residues: 66
  loop : -2.28 (0.37), residues: 268

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   0.010   0.001   PHE A 295 
 TYR   0.014   0.001   TYR A 622 
 ARG   0.003   0.000   ARG A 602 

*********************** 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
  97 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8883 (tppt) cc_final: 0.8515 (mmtt)
REVERT: A  298 ASN cc_start: 0.8084 (t0) cc_final: 0.7765 (t0)
REVERT: A  511 GLN cc_start: 0.8150 (tm-30) cc_final: 0.7741 (tm-30)
REVERT: A  529 ASP cc_start: 0.8016 (t0) cc_final: 0.7641 (t0)
REVERT: A  622 TYR cc_start: 0.8707 (m-10) cc_final: 0.8501 (m-10)
REVERT: A  907 LYS cc_start: 0.8585 (mttt) cc_final: 0.8212 (mtmm)
  outliers start: 18
  outliers final: 15
  residues processed: 92
  average time/residue: 0.1748
  time to fit residues: 21.4801
Evaluate side-chains
  89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 2 optimal weight:    0.9990
   chunk 44 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 39 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    1.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS
A 306 GLN
A 876 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.149760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.126681 restraints weight = 6507.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.129909 restraints weight = 4505.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.130594 restraints weight = 4022.585|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5758  Z= 0.242
  Angle     :  0.577   7.842   7872  Z= 0.290
  Chirality :  0.039   0.162    893
  Planarity :  0.004   0.039    924
  Dihedral  : 13.351  88.982   1009
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 18.91 %
    Favored  : 77.23 %
  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: -0.52 (0.35), residues: 627
  helix:  1.82 (0.31), residues: 294
  sheet: -3.02 (0.63), residues: 66
  loop : -2.21 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 512 
 HIS   0.004   0.001   HIS A 280 
 PHE   0.010   0.001   PHE A 295 
 TYR   0.013   0.001   TYR A 622 
 ARG   0.003   0.000   ARG A 602 

*********************** 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
  97 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 75
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8902 (tppt) cc_final: 0.8575 (mmtt)
REVERT: A  298 ASN cc_start: 0.7955 (t0) cc_final: 0.7566 (t0)
REVERT: A  511 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7731 (tm-30)
REVERT: A  529 ASP cc_start: 0.8029 (t0) cc_final: 0.7643 (t0)
REVERT: A  907 LYS cc_start: 0.8559 (mttt) cc_final: 0.8232 (mtmm)
  outliers start: 22
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1648
  time to fit residues: 20.2570
Evaluate side-chains
  86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.568 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 ASN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0970
   chunk 37 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.6778

-------------------------------------------------------------------------------
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 = 0.3717 r_free = 0.3717 target = 0.144858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.122694 restraints weight = 6785.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.125339 restraints weight = 4879.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.126462 restraints weight = 4128.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5758  Z= 0.163
  Angle     :  0.539   7.245   7872  Z= 0.269
  Chirality :  0.038   0.134    893
  Planarity :  0.003   0.034    924
  Dihedral  : 13.368  88.722   1009
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.61 %
    Favored  : 77.58 %
  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: -0.36 (0.36), residues: 627
  helix:  1.92 (0.31), residues: 295
  sheet: -2.99 (0.64), residues: 67
  loop : -2.08 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 646 
 HIS   0.004   0.000   HIS A 281 
 PHE   0.007   0.001   PHE A 460 
 TYR   0.014   0.001   TYR A 622 
 ARG   0.003   0.000   ARG A 602 

*********************** 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
  100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.656 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7890 (t0) cc_final: 0.7515 (t0)
REVERT: A  511 GLN cc_start: 0.8129 (tm-30) cc_final: 0.7736 (tm-30)
REVERT: A  525 MET cc_start: 0.6758 (mmt) cc_final: 0.6535 (tpt)
REVERT: A  529 ASP cc_start: 0.8061 (t0) cc_final: 0.7659 (t0)
REVERT: A  541 TYR cc_start: 0.8071 (m-80) cc_final: 0.7794 (m-80)
REVERT: A  907 LYS cc_start: 0.8535 (mttt) cc_final: 0.8166 (mtmm)
  outliers start: 16
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1774
  time to fit residues: 22.3158
Evaluate side-chains
  89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.608 
-------------------------------------------------------------------------------
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  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:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 50 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9980
   chunk 4 optimal weight:    0.0010
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7588

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.153452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130495 restraints weight = 6433.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.133944 restraints weight = 4456.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.135193 restraints weight = 3757.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.2650

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5758  Z= 0.178
  Angle     :  0.568  10.330   7872  Z= 0.280
  Chirality :  0.040   0.343    893
  Planarity :  0.004   0.041    924
  Dihedral  : 13.346  88.769   1009
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.96 %
    Favored  : 76.88 %
  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: -0.26 (0.36), residues: 627
  helix:  2.02 (0.31), residues: 292
  sheet: -3.12 (0.62), residues: 69
  loop : -1.93 (0.38), residues: 266

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 295 
 TYR   0.016   0.001   TYR A 390 
 ARG   0.006   0.001   ARG A 811 

*********************** 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: 18
    poor density    : 82
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7867 (t0) cc_final: 0.7486 (t0)
REVERT: A  511 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7764 (tm-30)
REVERT: A  529 ASP cc_start: 0.8028 (t0) cc_final: 0.7731 (t0)
REVERT: A  907 LYS cc_start: 0.8534 (mttt) cc_final: 0.8227 (mtmm)
  outliers start: 18
  outliers final: 16
  residues processed: 95
  average time/residue: 0.1656
  time to fit residues: 20.8784
Evaluate side-chains
  87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 71
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
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  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  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:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 39 optimal weight:    0.4980
   chunk 8 optimal weight:    0.6980
   chunk 9 optimal weight:    0.0020
   chunk 57 optimal weight:    0.9990
   chunk 51 optimal weight:    0.4980
   chunk 18 optimal weight:    0.9980
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.5388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.141138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.117395 restraints weight = 6965.862|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120369 restraints weight = 4380.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.121483 restraints weight = 3585.060|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5758  Z= 0.164
  Angle     :  0.588  10.222   7872  Z= 0.287
  Chirality :  0.040   0.356    893
  Planarity :  0.004   0.056    924
  Dihedral  : 13.354  88.217   1009
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.38 %
    Favored  : 93.62 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 20.32 %
    Favored  : 76.53 %
  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:  2.06 (0.31), residues: 292
  sheet: -2.91 (0.60), residues: 75
  loop : -1.85 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 512 
 HIS   0.003   0.000   HIS A 281 
 PHE   0.008   0.001   PHE A 272 
 TYR   0.014   0.001   TYR A 622 
 ARG   0.006   0.000   ARG A 811 

*********************** 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
  99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 81
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7871 (t0) cc_final: 0.7480 (t0)
REVERT: A  511 GLN cc_start: 0.8182 (tm-30) cc_final: 0.7734 (tm-30)
REVERT: A  529 ASP cc_start: 0.8142 (t0) cc_final: 0.7710 (t0)
REVERT: A  556 GLU cc_start: 0.7382 (tt0) cc_final: 0.7141 (mt-10)
REVERT: A  759 LYS cc_start: 0.8490 (tppp) cc_final: 0.8094 (tppt)
REVERT: A  907 LYS cc_start: 0.8513 (mttt) cc_final: 0.8103 (mtmm)
  outliers start: 18
  outliers final: 17
  residues processed: 94
  average time/residue: 0.1760
  time to fit residues: 21.8260
Evaluate side-chains
  93 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 59 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0010
   chunk 54 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   overall best weight:    0.7186

-------------------------------------------------------------------------------
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 = 0.3664 r_free = 0.3664 target = 0.139787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.115699 restraints weight = 7167.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.118652 restraints weight = 4509.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.119562 restraints weight = 3531.451|
|-----------------------------------------------------------------------------|
r_work (final): 0.3437
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2814

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5758  Z= 0.179
  Angle     :  0.588   9.998   7872  Z= 0.290
  Chirality :  0.040   0.349    893
  Planarity :  0.003   0.034    924
  Dihedral  : 13.306  87.741   1009
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 20.67 %
    Favored  : 75.66 %
  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: -0.22 (0.36), residues: 627
  helix:  2.04 (0.31), residues: 292
  sheet: -3.11 (0.62), residues: 69
  loop : -1.88 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 512 
 HIS   0.003   0.000   HIS A 281 
 PHE   0.008   0.001   PHE A 460 
 TYR   0.016   0.001   TYR A 390 
 ARG   0.003   0.000   ARG A 589 

********************** 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: 21
    poor density    : 73
  time to evaluate  : 0.627 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7888 (t0) cc_final: 0.7485 (t0)
REVERT: A  511 GLN cc_start: 0.8208 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: A  541 TYR cc_start: 0.8066 (m-80) cc_final: 0.7858 (m-80)
REVERT: A  759 LYS cc_start: 0.8497 (tppp) cc_final: 0.8075 (tppt)
REVERT: A  907 LYS cc_start: 0.8566 (mttt) cc_final: 0.8130 (mtmm)
  outliers start: 21
  outliers final: 17
  residues processed: 90
  average time/residue: 0.1606
  time to fit residues: 19.5729
Evaluate side-chains
  91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  time to evaluate  : 0.672 
-------------------------------------------------------------------------------
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  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:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 44 optimal weight:    7.9990
   chunk 59 optimal weight:    1.9990
   chunk 4 optimal weight:    5.9990
   chunk 24 optimal weight:    0.9990
   chunk 10 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3657 r_free = 0.3657 target = 0.139049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.115245 restraints weight = 7178.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118108 restraints weight = 4554.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.119035 restraints weight = 3631.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3428
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7676
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5758  Z= 0.189
  Angle     :  0.612   9.990   7872  Z= 0.299
  Chirality :  0.041   0.351    893
  Planarity :  0.003   0.034    924
  Dihedral  : 13.286  87.613   1009
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  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: -0.29 (0.36), residues: 627
  helix:  2.02 (0.31), residues: 292
  sheet: -3.06 (0.59), residues: 80
  loop : -1.92 (0.38), residues: 255

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 460 
 TYR   0.014   0.001   TYR A 622 
 ARG   0.003   0.000   ARG A 589 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1741.51 seconds
wall clock time: 32 minutes 6.85 seconds (1926.85 seconds total)