Starting phenix.real_space_refine
on Tue Feb  3 21:42:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nhb_49407/02_2026/9nhb_49407.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhb_49407/02_2026/9nhb_49407.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhb_49407/02_2026/9nhb_49407.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhb_49407/02_2026/9nhb_49407.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nhb_49407/02_2026/9nhb_49407.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhb_49407/02_2026/9nhb_49407.map"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.071
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
     P      46      5.49       5
     Mg      1      5.21       5
     S      28      5.16       5
     C    4311      2.51       5
     N    1232      2.21       5
     O    1439      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 51 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7057
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 6040
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 748, 6040
          Classifications: {'peptide': 748}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 34, 'TRANS': 713}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 498
          Classifications: {'RNA': 23}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 7}
          Link IDs: {'rna2p': 2, 'rna3p': 20}
    Chain: "C"
      Number of atoms: 479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 23, 479
          Classifications: {'RNA': 23}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 12}
          Link IDs: {'rna2p': 2, 'rna3p': 20}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 39
          Classifications: {'peptide': 4}
          Link IDs: {'TRANS': 3}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' MG': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.49, per 1000 atoms: 0.21
  Number of scatterers: 7057
  At special positions: 0
  Unit cell: (73.71, 88.27, 107.38, 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)
     S      28     16.00
     P      46     15.00
     Mg      1     11.99
     O    1439      8.00
     N    1232      7.00
     C    4311      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 229.8 milliseconds
  

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1426

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 12 sheets defined
      33.8% alpha, 20.1% beta
      14 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 0.99
  Creating SS restraints...
    Processing helix  chain 'A' and resid 181 through 190
    Processing helix  chain 'A' and resid 191 through 193
      No H-bonds generated for 'chain 'A' and resid 191 through 193'
    Processing helix  chain 'A' and resid 246 through 262
      removed outlier: 3.869A  pdb=" N   ASN A 252 " --> pdb=" O   ILE A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 330
      removed outlier: 3.520A  pdb=" N   MET A 321 " --> pdb=" O   THR A 317 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 333 through 342
      removed outlier: 3.518A  pdb=" N   VAL A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 435 through 447
      removed outlier: 3.523A  pdb=" N   ASP A 443 " --> pdb=" O   MET A 439 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 467
      removed outlier: 3.651A  pdb=" N   PHE A 464 " --> pdb=" O   PHE A 460 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   THR A 465 " --> pdb=" O   ASN A 461 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 477
      removed outlier: 3.534A  pdb=" N   TRP A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 558
      removed outlier: 3.722A  pdb=" N   LEU A 551 " --> pdb=" O   SER A 547 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   GLY A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 591
      removed outlier: 3.545A  pdb=" N   TYR A 579 " --> pdb=" O   GLY A 575 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ALA A 580 " --> pdb=" O   PRO A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 615
      removed outlier: 4.048A  pdb=" N   TYR A 607 " --> pdb=" O   TYR A 603 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 630
    Processing helix  chain 'A' and resid 634 through 650
    Processing helix  chain 'A' and resid 710 through 729
      removed outlier: 3.917A  pdb=" N   GLY A 714 " --> pdb=" O   SER A 710 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 754
      removed outlier: 3.857A  pdb=" N   SER A 752 " --> pdb=" O   PRO A 748 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 842 through 853
    Processing helix  chain 'A' and resid 867 through 883
    Processing helix  chain 'A' and resid 889 through 893
      removed outlier: 4.010A  pdb=" N   ASN A 893 " --> pdb=" O   TYR A 890 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 150
      removed outlier: 6.866A  pdb=" N   PHE A 775 " --> pdb=" O   ILE A 835 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   ASP A 837 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LEU A 773 " --> pdb=" O   ASP A 837 " (cutoff:3.500A)
      removed outlier: 6.846A  pdb=" N   ILE A 735 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   ILE A 776 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
      removed outlier: 5.877A  pdb=" N   ILE A 737 " --> pdb=" O   ILE A 776 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   VAL A 778 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 6.642A  pdb=" N   ARG A 739 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
      removed outlier: 6.371A  pdb=" N   MET A 665 " --> pdb=" O   PHE A 736 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   TYR A 738 " --> pdb=" O   MET A 665 " (cutoff:3.500A)
      removed outlier: 6.995A  pdb=" N   VAL A 667 " --> pdb=" O   TYR A 738 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 487 through 488
      removed outlier: 3.572A  pdb=" N   SER A 793 " --> pdb=" O   ARG A 790 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 157 through 159
      removed outlier: 3.724A  pdb=" N   ASN A 296 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR A 271 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 157 through 159
      removed outlier: 3.724A  pdb=" N   ASN A 296 " --> pdb=" O   LEU A 303 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LEU A 285 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 205 through 208
    Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 356
    Processing sheet with id=AA7, first strand: chain 'A' and resid 369 through 371
    Processing sheet with id=AA8, first strand: chain 'A' and resid 399 through 401
    Processing sheet with id=AA9, first strand: chain 'A' and resid 497 through 500
      removed outlier: 3.730A  pdb=" N   TYR A 506 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   VAL A 504 " --> pdb=" O   GLN A 500 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 569 through 571
      removed outlier: 6.356A  pdb=" N   VAL A 535 " --> pdb=" O   VAL A 569 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   ILE A 571 " --> pdb=" O   VAL A 535 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   THR A 537 " --> pdb=" O   ILE A 571 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   VAL A 534 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   VAL A 598 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.942A  pdb=" N   ILE A 536 " --> pdb=" O   VAL A 598 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE A 595 " --> pdb=" O   GLN A 623 " (cutoff:3.500A)
      removed outlier: 8.070A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   CYS A 597 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 672 through 673
    Processing sheet with id=AB3, first strand: chain 'A' and resid 687 through 688

    248 hydrogen bonds defined for protein.
    684 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      34 hydrogen bonds
      68 hydrogen bond angles
      0 basepair planarities
      14 basepair parallelities
      32 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 0.95 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1598
        1.33 -     1.45: 1733
        1.45 -     1.57: 3828
        1.57 -     1.69: 90
        1.69 -     1.82: 45
  Bond restraints: 7294
  Sorted by residual:
  bond pdb=" C5'   A C  20 "
       pdb=" C4'   A C  20 "
    ideal  model  delta    sigma   weight residual
    1.508  1.567 -0.059 1.50e-02 4.44e+03 1.55e+01
  bond pdb=" CA  ASN A 591 "
       pdb=" C   ASN A 591 "
    ideal  model  delta    sigma   weight residual
    1.531  1.554 -0.023 7.40e-03 1.83e+04 9.65e+00
  bond pdb=" CZ  ARG A 223 "
       pdb=" NH2 ARG A 223 "
    ideal  model  delta    sigma   weight residual
    1.330  1.291  0.039 1.30e-02 5.92e+03 9.23e+00
  bond pdb=" CA  ASN A 591 "
       pdb=" CB  ASN A 591 "
    ideal  model  delta    sigma   weight residual
    1.522  1.543 -0.020 7.00e-03 2.04e+04 8.48e+00
  bond pdb=" CZ  ARG A 440 "
       pdb=" NH2 ARG A 440 "
    ideal  model  delta    sigma   weight residual
    1.330  1.292  0.038 1.30e-02 5.92e+03 8.36e+00
  ... (remaining 7289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.61: 9727
        3.61 -     7.22: 343
        7.22 -    10.83: 13
       10.83 -    14.44: 3
       14.44 -    18.05: 2
  Bond angle restraints: 10088
  Sorted by residual:
  angle pdb=" C3'   G B  22 "
        pdb=" O3'   G B  22 "
        pdb=" P     A B  23 "
      ideal   model   delta    sigma   weight residual
     120.20  102.15   18.05 1.50e+00 4.44e-01 1.45e+02
  angle pdb=" C3'   U B  21 "
        pdb=" O3'   U B  21 "
        pdb=" P     G B  22 "
      ideal   model   delta    sigma   weight residual
     120.20  106.68   13.52 1.50e+00 4.44e-01 8.13e+01
  angle pdb=" C3'   U B  20 "
        pdb=" O3'   U B  20 "
        pdb=" P     U B  21 "
      ideal   model   delta    sigma   weight residual
     120.20  107.11   13.09 1.50e+00 4.44e-01 7.62e+01
  angle pdb=" O4'   A C  20 "
        pdb=" C4'   A C  20 "
        pdb=" C3'   A C  20 "
      ideal   model   delta    sigma   weight residual
     104.00  112.11   -8.11 1.00e+00 1.00e+00 6.58e+01
  angle pdb=" C3'   U C  22 "
        pdb=" O3'   U C  22 "
        pdb=" P     C C  23 "
      ideal   model   delta    sigma   weight residual
     120.20  108.53   11.67 1.50e+00 4.44e-01 6.05e+01
  ... (remaining 10083 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.02: 4070
       23.02 -    46.04: 298
       46.04 -    69.06: 91
       69.06 -    92.07: 16
       92.07 -   115.09: 2
  Dihedral angle restraints: 4477
    sinusoidal: 2264
      harmonic: 2213
  Sorted by residual:
  dihedral pdb=" O4'   U C   3 "
           pdb=" C2'   U C   3 "
           pdb=" C1'   U C   3 "
           pdb=" C3'   U C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
      25.00  -16.74   41.74     1      8.00e+00 1.56e-02 3.81e+01
  dihedral pdb=" C4'   U C   3 "
           pdb=" O4'   U C   3 "
           pdb=" C1'   U C   3 "
           pdb=" C2'   U C   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
       3.00  -36.09   39.09     1      8.00e+00 1.56e-02 3.36e+01
  dihedral pdb=" CA  THR A 537 "
           pdb=" C   THR A 537 "
           pdb=" N   PRO A 538 "
           pdb=" CA  PRO A 538 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.51   27.49     0      5.00e+00 4.00e-02 3.02e+01
  ... (remaining 4474 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.118: 1005
       0.118 -    0.236: 135
       0.236 -    0.354: 22
       0.354 -    0.472: 7
       0.472 -    0.590: 3
  Chirality restraints: 1172
  Sorted by residual:
  chirality pdb=" P     A C  25 "
            pdb=" OP1   A C  25 "
            pdb=" OP2   A C  25 "
            pdb=" O5'   A C  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -3.00   -0.59 2.00e-01 2.50e+01 8.70e+00
  chirality pdb=" P     U C   3 "
            pdb=" OP1   U C   3 "
            pdb=" OP2   U C   3 "
            pdb=" O5'   U C   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.93   -0.52 2.00e-01 2.50e+01 6.77e+00
  chirality pdb=" P     U B   1 "
            pdb=" OP1   U B   1 "
            pdb=" OP2   U B   1 "
            pdb=" O5'   U B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.89   -0.48 2.00e-01 2.50e+01 5.86e+00
  ... (remaining 1169 not shown)

  Planarity restraints: 1113
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B   7 "   -0.108 2.00e-02 2.50e+03   7.38e-02 1.63e+02
        pdb=" N9    G B   7 "   -0.017 2.00e-02 2.50e+03
        pdb=" C8    G B   7 "    0.145 2.00e-02 2.50e+03
        pdb=" N7    G B   7 "    0.082 2.00e-02 2.50e+03
        pdb=" C5    G B   7 "   -0.029 2.00e-02 2.50e+03
        pdb=" C6    G B   7 "   -0.055 2.00e-02 2.50e+03
        pdb=" O6    G B   7 "   -0.065 2.00e-02 2.50e+03
        pdb=" N1    G B   7 "   -0.013 2.00e-02 2.50e+03
        pdb=" C2    G B   7 "   -0.002 2.00e-02 2.50e+03
        pdb=" N2    G B   7 "    0.124 2.00e-02 2.50e+03
        pdb=" N3    G B   7 "   -0.026 2.00e-02 2.50e+03
        pdb=" C4    G B   7 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  16 "   -0.093 2.00e-02 2.50e+03   5.85e-02 1.03e+02
        pdb=" N9    G B  16 "    0.006 2.00e-02 2.50e+03
        pdb=" C8    G B  16 "    0.094 2.00e-02 2.50e+03
        pdb=" N7    G B  16 "    0.068 2.00e-02 2.50e+03
        pdb=" C5    G B  16 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    G B  16 "   -0.040 2.00e-02 2.50e+03
        pdb=" O6    G B  16 "   -0.056 2.00e-02 2.50e+03
        pdb=" N1    G B  16 "   -0.021 2.00e-02 2.50e+03
        pdb=" C2    G B  16 "   -0.020 2.00e-02 2.50e+03
        pdb=" N2    G B  16 "    0.111 2.00e-02 2.50e+03
        pdb=" N3    G B  16 "   -0.025 2.00e-02 2.50e+03
        pdb=" C4    G B  16 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 749 "   -0.092 2.00e-02 2.50e+03   5.02e-02 5.04e+01
        pdb=" CG  TYR A 749 "    0.029 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 749 "    0.034 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 749 "    0.050 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 749 "    0.037 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 749 "    0.020 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 749 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A 749 "   -0.074 2.00e-02 2.50e+03
  ... (remaining 1110 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 25
        2.51 -     3.11: 4793
        3.11 -     3.71: 10772
        3.71 -     4.30: 15050
        4.30 -     4.90: 24953
  Nonbonded interactions: 55593
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 670 "
            pdb="MG    MG A 901 "
     model   vdw
     1.913 2.170
  nonbonded pdb=" OD1 ASP A 670 "
            pdb="MG    MG A 901 "
     model   vdw
     1.939 2.170
  nonbonded pdb=" OD2 ASP A 740 "
            pdb="MG    MG A 901 "
     model   vdw
     2.006 2.170
  nonbonded pdb=" OP1   U C  16 "
            pdb="MG    MG A 901 "
     model   vdw
     2.031 2.170
  nonbonded pdb=" OD2 ASP A 690 "
            pdb=" OG1 THR A 694 "
     model   vdw
     2.177 3.040
  ... (remaining 55588 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:             2.240
  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:          0.100
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.880
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
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      :  0.010   0.059   7294  Z= 0.582
  Angle     :  1.537  18.046  10088  Z= 1.004
  Chirality :  0.092   0.590   1172
  Planarity :  0.013   0.164   1113
  Dihedral  : 17.435 115.092   3051
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  : 11.14 %
    Favored  : 88.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.00 (0.29), residues: 742
  helix: -0.79 (0.33), residues: 226
  sheet: -1.22 (0.39), residues: 170
  loop : -1.66 (0.31), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 269 
 TYR   0.092   0.011   TYR A 749 
 PHE   0.043   0.006   PHE A 878 
 TRP   0.088   0.018   TRP A 166 
 HIS   0.009   0.002   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00977 ( 7294)
  covalent geometry    : angle       1.53742 (10088)
  hydrogen bonds       : bond        0.19025 (  269)
  hydrogen bonds       : angle       8.11175 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 0
  residues processed: 113
  average time/residue: 0.1017
  time to fit residues: 14.6080
Evaluate side-chains
  72 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.3980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 376 ASN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.162809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.140924 restraints weight = 8956.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.144032 restraints weight = 5529.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.145967 restraints weight = 3935.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.147573 restraints weight = 3113.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.148455 restraints weight = 2603.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7744
moved from start:          0.1509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7294  Z= 0.139
  Angle     :  0.619   8.654  10088  Z= 0.322
  Chirality :  0.043   0.188   1172
  Planarity :  0.004   0.043   1113
  Dihedral  : 16.789 103.688   1537
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 13.37 %
    Favored  : 84.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.30), residues: 742
  helix:  0.68 (0.35), residues: 228
  sheet: -0.88 (0.38), residues: 181
  loop : -1.24 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 848 
 TYR   0.011   0.001   TYR A 245 
 PHE   0.011   0.001   PHE A 370 
 TRP   0.009   0.002   TRP A 166 
 HIS   0.003   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7294)
  covalent geometry    : angle       0.61936 (10088)
  hydrogen bonds       : bond        0.04814 (  269)
  hydrogen bonds       : angle       5.60965 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.240 
Fit side-chains
REVERT: A  189 MET cc_start: 0.7425 (ttp) cc_final: 0.7013 (tmm)
REVERT: A  234 ILE cc_start: 0.8940 (mt) cc_final: 0.8633 (tt)
REVERT: A  779 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8282 (p)
REVERT: A  799 PRO cc_start: 0.8561 (Cg_exo) cc_final: 0.8191 (Cg_endo)
  outliers start: 15
  outliers final: 14
  residues processed: 94
  average time/residue: 0.0879
  time to fit residues: 10.6928
Evaluate side-chains
  87 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 VAL
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  779 SER
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  860 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 71 optimal weight:    0.7980
   chunk 36 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0980
   chunk 26 optimal weight:    5.9990
   chunk 8 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 23 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9980
   chunk 13 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 376 ASN
A 425 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.161784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.141848 restraints weight = 8912.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.145529 restraints weight = 5646.412|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.145860 restraints weight = 3478.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.146992 restraints weight = 3337.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.147060 restraints weight = 2773.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   7294  Z= 0.127
  Angle     :  0.538   6.512  10088  Z= 0.280
  Chirality :  0.041   0.138   1172
  Planarity :  0.004   0.038   1113
  Dihedral  : 16.502 103.500   1537
  Min Nonbonded Distance : 1.898

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 13.82 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.30), residues: 742
  helix:  0.96 (0.35), residues: 235
  sheet: -0.54 (0.39), residues: 173
  loop : -1.29 (0.32), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 406 
 TYR   0.010   0.001   TYR A 669 
 PHE   0.008   0.001   PHE A 370 
 TRP   0.009   0.001   TRP A 533 
 HIS   0.002   0.001   HIS A 445 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7294)
  covalent geometry    : angle       0.53818 (10088)
  hydrogen bonds       : bond        0.03763 (  269)
  hydrogen bonds       : angle       5.08165 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 86
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  234 ILE cc_start: 0.8936 (mt) cc_final: 0.8669 (tt)
REVERT: A  567 ASP cc_start: 0.6773 (t0) cc_final: 0.6527 (t0)
REVERT: A  669 TYR cc_start: 0.7084 (m-10) cc_final: 0.5972 (m-80)
REVERT: A  779 SER cc_start: 0.8515 (OUTLIER) cc_final: 0.8303 (p)
REVERT: A  799 PRO cc_start: 0.8484 (Cg_exo) cc_final: 0.8136 (Cg_endo)
  outliers start: 21
  outliers final: 14
  residues processed: 103
  average time/residue: 0.0822
  time to fit residues: 11.2373
Evaluate side-chains
  91 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  779 SER
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  860 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.157802 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135850 restraints weight = 9167.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.138775 restraints weight = 5762.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.140825 restraints weight = 4158.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.142240 restraints weight = 3288.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.143211 restraints weight = 2766.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3654
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7829
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   7294  Z= 0.210
  Angle     :  0.609   5.697  10088  Z= 0.316
  Chirality :  0.044   0.148   1172
  Planarity :  0.004   0.039   1113
  Dihedral  : 16.391  99.772   1537
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.99 %
    Favored  : 95.01 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 15.01 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.30), residues: 742
  helix:  0.63 (0.34), residues: 236
  sheet: -0.76 (0.39), residues: 173
  loop : -1.41 (0.32), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 739 
 TYR   0.015   0.002   TYR A 350 
 PHE   0.009   0.001   PHE A 370 
 TRP   0.012   0.001   TRP A 533 
 HIS   0.004   0.001   HIS A 855 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 7294)
  covalent geometry    : angle       0.60864 (10088)
  hydrogen bonds       : bond        0.04395 (  269)
  hydrogen bonds       : angle       5.25990 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 76
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  799 PRO cc_start: 0.8542 (Cg_exo) cc_final: 0.8250 (Cg_endo)
  outliers start: 28
  outliers final: 20
  residues processed: 94
  average time/residue: 0.0868
  time to fit residues: 10.6409
Evaluate side-chains
  96 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  519 MET
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  577 ILE
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  615 THR
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  860 CYS
Chi-restraints excluded: chain A residue  892 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 74 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 8 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.158756 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138243 restraints weight = 9047.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.140566 restraints weight = 6002.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.143047 restraints weight = 4331.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.143403 restraints weight = 3323.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.143538 restraints weight = 2884.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7817
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   7294  Z= 0.160
  Angle     :  0.557   8.843  10088  Z= 0.288
  Chirality :  0.042   0.155   1172
  Planarity :  0.004   0.037   1113
  Dihedral  : 16.301  98.419   1537
  Min Nonbonded Distance : 1.936

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 16.64 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.91 (0.30), residues: 742
  helix:  0.65 (0.34), residues: 236
  sheet: -0.85 (0.39), residues: 179
  loop : -1.33 (0.32), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 390 
 TYR   0.019   0.001   TYR A 669 
 PHE   0.008   0.001   PHE A 370 
 TRP   0.009   0.001   TRP A 533 
 HIS   0.003   0.001   HIS A 855 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 7294)
  covalent geometry    : angle       0.55685 (10088)
  hydrogen bonds       : bond        0.03909 (  269)
  hydrogen bonds       : angle       5.03043 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 83
  time to evaluate  : 0.290 
Fit side-chains
REVERT: A  567 ASP cc_start: 0.6769 (t0) cc_final: 0.6540 (t0)
REVERT: A  799 PRO cc_start: 0.8495 (Cg_exo) cc_final: 0.8205 (Cg_endo)
  outliers start: 25
  outliers final: 19
  residues processed: 98
  average time/residue: 0.0774
  time to fit residues: 10.1388
Evaluate side-chains
  94 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  860 CYS
Chi-restraints excluded: chain A residue  892 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 42 optimal weight:    6.9990
   chunk 58 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 2 optimal weight:    0.4980
   chunk 69 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9990
   chunk 52 optimal weight:    5.9990
   chunk 67 optimal weight:    1.9990
   chunk 25 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.158750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.138282 restraints weight = 9060.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.141217 restraints weight = 5585.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.142932 restraints weight = 3938.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.143475 restraints weight = 3023.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.143878 restraints weight = 2619.177|
|-----------------------------------------------------------------------------|
r_work (final): 0.3698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
moved from start:          0.2591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7294  Z= 0.133
  Angle     :  0.538   8.049  10088  Z= 0.278
  Chirality :  0.041   0.153   1172
  Planarity :  0.004   0.052   1113
  Dihedral  : 16.141  95.250   1537
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.09 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.30), residues: 742
  helix:  0.77 (0.34), residues: 236
  sheet: -0.82 (0.38), residues: 179
  loop : -1.27 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 211 
 TYR   0.016   0.001   TYR A 669 
 PHE   0.007   0.001   PHE A 370 
 TRP   0.007   0.001   TRP A 533 
 HIS   0.003   0.001   HIS A 855 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7294)
  covalent geometry    : angle       0.53758 (10088)
  hydrogen bonds       : bond        0.03631 (  269)
  hydrogen bonds       : angle       4.90119 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.235 
Fit side-chains
REVERT: A  567 ASP cc_start: 0.6796 (t0) cc_final: 0.6530 (t0)
REVERT: A  799 PRO cc_start: 0.8472 (Cg_exo) cc_final: 0.8190 (Cg_endo)
REVERT: A  811 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7235 (pt0)
  outliers start: 26
  outliers final: 21
  residues processed: 101
  average time/residue: 0.0906
  time to fit residues: 12.1248
Evaluate side-chains
  100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  892 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 63 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 72 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 68 optimal weight:    0.8980
   chunk 44 optimal weight:    0.0870
   chunk 2 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7158

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.158851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.138471 restraints weight = 8981.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.141138 restraints weight = 5537.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.142258 restraints weight = 4064.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.143051 restraints weight = 3281.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.143158 restraints weight = 2819.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7294  Z= 0.123
  Angle     :  0.519   7.056  10088  Z= 0.269
  Chirality :  0.041   0.156   1172
  Planarity :  0.004   0.044   1113
  Dihedral  : 16.045  93.740   1537
  Min Nonbonded Distance : 1.992

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 16.64 %
    Favored  : 79.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.68 (0.30), residues: 742
  helix:  0.90 (0.34), residues: 236
  sheet: -0.78 (0.38), residues: 178
  loop : -1.21 (0.32), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 562 
 TYR   0.009   0.001   TYR A 298 
 PHE   0.006   0.001   PHE A 370 
 TRP   0.007   0.001   TRP A 533 
 HIS   0.003   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7294)
  covalent geometry    : angle       0.51853 (10088)
  hydrogen bonds       : bond        0.03444 (  269)
  hydrogen bonds       : angle       4.79024 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 81
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  543 ARG cc_start: 0.7087 (OUTLIER) cc_final: 0.6522 (mtm180)
REVERT: A  567 ASP cc_start: 0.6786 (t0) cc_final: 0.6517 (t0)
REVERT: A  799 PRO cc_start: 0.8421 (Cg_exo) cc_final: 0.8138 (Cg_endo)
REVERT: A  811 GLU cc_start: 0.7546 (OUTLIER) cc_final: 0.7199 (pt0)
REVERT: A  814 ASP cc_start: 0.8345 (t0) cc_final: 0.8129 (t0)
  outliers start: 26
  outliers final: 20
  residues processed: 101
  average time/residue: 0.0957
  time to fit residues: 12.6024
Evaluate side-chains
  98 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 76
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  860 CYS
Chi-restraints excluded: chain A residue  892 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 42 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 19 optimal weight:    4.9990
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 27 optimal weight:    4.9990
   chunk 56 optimal weight:    0.6980
   chunk 53 optimal weight:    2.9990
   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 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.156836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.135422 restraints weight = 9072.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.138398 restraints weight = 5526.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.140333 restraints weight = 3910.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.141773 restraints weight = 3073.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.142596 restraints weight = 2578.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7811
moved from start:          0.2763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7294  Z= 0.178
  Angle     :  0.565   7.094  10088  Z= 0.292
  Chirality :  0.042   0.186   1172
  Planarity :  0.004   0.044   1113
  Dihedral  : 15.975  94.123   1537
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 16.79 %
    Favored  : 79.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.80 (0.30), residues: 742
  helix:  0.83 (0.34), residues: 234
  sheet: -0.97 (0.38), residues: 180
  loop : -1.21 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 562 
 TYR   0.013   0.001   TYR A 350 
 PHE   0.007   0.001   PHE A 370 
 TRP   0.009   0.001   TRP E 103 
 HIS   0.003   0.001   HIS A 855 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 7294)
  covalent geometry    : angle       0.56470 (10088)
  hydrogen bonds       : bond        0.03877 (  269)
  hydrogen bonds       : angle       4.94346 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 78
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  543 ARG cc_start: 0.6959 (OUTLIER) cc_final: 0.6405 (mtm180)
REVERT: A  567 ASP cc_start: 0.6819 (t0) cc_final: 0.6550 (t0)
REVERT: A  799 PRO cc_start: 0.8477 (Cg_exo) cc_final: 0.8203 (Cg_endo)
REVERT: A  811 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.7244 (pt0)
  outliers start: 27
  outliers final: 25
  residues processed: 99
  average time/residue: 0.0911
  time to fit residues: 11.7552
Evaluate side-chains
  103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 76
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  860 CYS
Chi-restraints excluded: chain A residue  892 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 52 optimal weight:    0.0020
   chunk 18 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 9 optimal weight:    7.9990
   chunk 38 optimal weight:    2.9990
   chunk 15 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9990
   chunk 68 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 10 optimal weight:    0.5980
   chunk 0 optimal weight:    6.9990
   overall best weight:    0.6188

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.162433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.141597 restraints weight = 8982.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.144210 restraints weight = 5798.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.145363 restraints weight = 4248.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.146154 restraints weight = 3452.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.146186 restraints weight = 2984.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3709
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7294  Z= 0.114
  Angle     :  0.517   6.865  10088  Z= 0.268
  Chirality :  0.040   0.155   1172
  Planarity :  0.004   0.042   1113
  Dihedral  : 15.915  92.489   1537
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 17.38 %
    Favored  : 78.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.64 (0.31), residues: 742
  helix:  0.93 (0.34), residues: 236
  sheet: -0.81 (0.38), residues: 178
  loop : -1.14 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 562 
 TYR   0.008   0.001   TYR A 298 
 PHE   0.006   0.001   PHE A 370 
 TRP   0.008   0.001   TRP E 103 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 7294)
  covalent geometry    : angle       0.51740 (10088)
  hydrogen bonds       : bond        0.03331 (  269)
  hydrogen bonds       : angle       4.75154 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 77
  time to evaluate  : 0.272 
Fit side-chains
REVERT: A  543 ARG cc_start: 0.7082 (OUTLIER) cc_final: 0.6527 (mtm180)
REVERT: A  567 ASP cc_start: 0.6802 (t0) cc_final: 0.6542 (t0)
REVERT: A  799 PRO cc_start: 0.8398 (Cg_exo) cc_final: 0.8140 (Cg_endo)
REVERT: A  811 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7257 (pt0)
  outliers start: 26
  outliers final: 21
  residues processed: 97
  average time/residue: 0.1040
  time to fit residues: 12.9686
Evaluate side-chains
  97 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 74
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  892 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9990
   chunk 65 optimal weight:    2.9990
   chunk 44 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 19 optimal weight:    4.9990
   chunk 18 optimal weight:    0.3980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.159437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.138916 restraints weight = 9013.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.141837 restraints weight = 5594.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.143421 restraints weight = 3915.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.144094 restraints weight = 3058.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.144475 restraints weight = 2635.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   7294  Z= 0.132
  Angle     :  0.529   6.719  10088  Z= 0.273
  Chirality :  0.041   0.193   1172
  Planarity :  0.004   0.042   1113
  Dihedral  : 15.851  92.372   1537
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.18 %
    Favored  : 95.82 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 17.83 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.62 (0.31), residues: 742
  helix:  0.95 (0.34), residues: 234
  sheet: -0.78 (0.38), residues: 178
  loop : -1.15 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 562 
 TYR   0.009   0.001   TYR A 298 
 PHE   0.006   0.001   PHE A 370 
 TRP   0.011   0.001   TRP E 103 
 HIS   0.004   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 7294)
  covalent geometry    : angle       0.52877 (10088)
  hydrogen bonds       : bond        0.03497 (  269)
  hydrogen bonds       : angle       4.77101 (  752)

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

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

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1484 Ramachandran restraints generated.
    742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 76
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  543 ARG cc_start: 0.7062 (OUTLIER) cc_final: 0.6471 (mtm180)
REVERT: A  567 ASP cc_start: 0.6774 (t0) cc_final: 0.6484 (t0)
REVERT: A  799 PRO cc_start: 0.8417 (Cg_exo) cc_final: 0.8154 (Cg_endo)
REVERT: A  811 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.7277 (pt0)
  outliers start: 25
  outliers final: 23
  residues processed: 95
  average time/residue: 0.1123
  time to fit residues: 13.6738
Evaluate side-chains
  100 residues out of total 673 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 75
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 VAL
Chi-restraints excluded: chain A residue  232 ILE
Chi-restraints excluded: chain A residue  238 CYS
Chi-restraints excluded: chain A residue  240 VAL
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  360 VAL
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  543 ARG
Chi-restraints excluded: chain A residue  568 LEU
Chi-restraints excluded: chain A residue  599 LEU
Chi-restraints excluded: chain A residue  648 CYS
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  699 ILE
Chi-restraints excluded: chain A residue  764 GLU
Chi-restraints excluded: chain A residue  782 ILE
Chi-restraints excluded: chain A residue  803 ILE
Chi-restraints excluded: chain A residue  811 GLU
Chi-restraints excluded: chain A residue  817 LEU
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain A residue  854 THR
Chi-restraints excluded: chain A residue  892 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 4 optimal weight:    0.5980
   chunk 57 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 18 optimal weight:    6.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 500 GLN
** A 701 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.161555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.140452 restraints weight = 8996.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.143377 restraints weight = 5809.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.144659 restraints weight = 4261.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.145382 restraints weight = 3388.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.146170 restraints weight = 2901.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7781
moved from start:          0.2976

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7294  Z= 0.129
  Angle     :  0.525   6.603  10088  Z= 0.271
  Chirality :  0.041   0.178   1172
  Planarity :  0.004   0.042   1113
  Dihedral  : 15.801  91.639   1537
  Min Nonbonded Distance : 1.991

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 16.64 %
    Favored  : 79.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.31), residues: 742
  helix:  0.96 (0.35), residues: 234
  sheet: -0.80 (0.39), residues: 178
  loop : -1.11 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 229 
 TYR   0.009   0.001   TYR A 298 
 PHE   0.007   0.001   PHE A 561 
 TRP   0.007   0.001   TRP A 533 
 HIS   0.005   0.001   HIS A 712 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7294)
  covalent geometry    : angle       0.52533 (10088)
  hydrogen bonds       : bond        0.03415 (  269)
  hydrogen bonds       : angle       4.76588 (  752)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1037.15 seconds
wall clock time: 18 minutes 43.77 seconds (1123.77 seconds total)