Starting phenix.real_space_refine
on Tue Mar  3 14:06:39 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7uvp_26815/03_2026/7uvp_26815.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7uvp_26815/03_2026/7uvp_26815.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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2026/7uvp_26815.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2026/7uvp_26815.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2026/7uvp_26815.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7uvp_26815/03_2026/7uvp_26815.cif"
  }
  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=   0.061
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       3      5.49       5
     Mg      1      5.21       5
     S      33      5.16       5
     C    3589      2.51       5
     N     951      2.21       5
     O    1094      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5671
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5637
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 718, 5637
          Classifications: {'peptide': 718}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 32, 'TRANS': 685}
    Chain: "A"
      Number of atoms: 34
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 34
          Unusual residues: {' MG': 1, 'GTP': 1}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}
  Time building chain proxies: 1.27, per 1000 atoms: 0.22
  Number of scatterers: 5671
  At special positions: 0
  Unit cell: (73.692, 73.692, 128.16, 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      33     16.00
     P       3     15.00
     Mg      1     11.99
     O    1094      8.00
     N     951      7.00
     C    3589      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: 0.46
  Conformation dependent library (CDL) restraints added in 277.6 milliseconds
  

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1312

  Finding SS restraints...
    Secondary structure from input PDB file:
      17 helices and 10 sheets defined
      31.9% alpha, 23.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.28
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 33
    Processing helix  chain 'A' and resid 52 through 59
      removed outlier: 3.758A  pdb=" N   GLY A  59 " --> pdb=" O   GLU A  55 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 98
      removed outlier: 3.805A  pdb=" N   THR A  91 " --> pdb=" O   PHE A  87 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A  97 " --> pdb=" O   THR A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 126
      removed outlier: 3.519A  pdb=" N   GLN A 116 " --> pdb=" O   GLU A 112 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   TYR A 121 " --> pdb=" O   ASN A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 142 through 154
      removed outlier: 4.217A  pdb=" N   GLU A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   ALA A 153 " --> pdb=" O   GLN A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 218
      removed outlier: 3.981A  pdb=" N   ASP A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 4.450A  pdb=" N   LYS A 204 " --> pdb=" O   GLU A 200 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   MET A 206 " --> pdb=" O   MET A 202 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   GLU A 207 " --> pdb=" O   ASP A 203 " (cutoff:3.500A)
      removed outlier: 4.283A  pdb=" N   MET A 208 " --> pdb=" O   LYS A 204 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU A 218 " --> pdb=" O   GLU A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 231
    Processing helix  chain 'A' and resid 236 through 249
      removed outlier: 3.583A  pdb=" N   GLU A 240 " --> pdb=" O   ASP A 236 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   GLY A 241 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ILE A 242 " --> pdb=" O   MET A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 275
    Processing helix  chain 'A' and resid 411 through 426
    Processing helix  chain 'A' and resid 446 through 460
      removed outlier: 3.542A  pdb=" N   LEU A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 573
      removed outlier: 4.087A  pdb=" N   ILE A 562 " --> pdb=" O   PHE A 558 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN A 572 " --> pdb=" O   SER A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 617
      removed outlier: 3.523A  pdb=" N   ALA A 613 " --> pdb=" O   ALA A 609 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   PHE A 614 " --> pdb=" O   PHE A 610 " (cutoff:3.500A)
      removed outlier: 4.600A  pdb=" N   LYS A 615 " --> pdb=" O   SER A 611 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ASN A 616 " --> pdb=" O   GLU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 646
    Processing helix  chain 'A' and resid 670 through 673
    Processing helix  chain 'A' and resid 674 through 684
      removed outlier: 3.515A  pdb=" N   ALA A 678 " --> pdb=" O   SER A 674 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 716
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 70
      removed outlier: 3.551A  pdb=" N   THR A  65 " --> pdb=" O   ASP A  80 " (cutoff:3.500A)
      removed outlier: 6.938A  pdb=" N   ALA A 101 " --> pdb=" O   ILE A 130 " (cutoff:3.500A)
      removed outlier: 7.755A  pdb=" N   LEU A 132 " --> pdb=" O   ALA A 101 " (cutoff:3.500A)
      removed outlier: 6.219A  pdb=" N   ILE A 103 " --> pdb=" O   LEU A 132 " (cutoff:3.500A)
      removed outlier: 7.132A  pdb=" N   ASN A 134 " --> pdb=" O   ILE A 103 " (cutoff:3.500A)
      removed outlier: 6.178A  pdb=" N   LEU A 105 " --> pdb=" O   ASN A 134 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 162 through 164
      removed outlier: 4.027A  pdb=" N   LYS A 181 " --> pdb=" O   ASP A 176 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286
      removed outlier: 3.522A  pdb=" N   VAL A 285 " --> pdb=" O   VAL A 293 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 335
      removed outlier: 7.276A  pdb=" N   SER A 302 " --> pdb=" O   MET A 323 " (cutoff:3.500A)
      removed outlier: 8.729A  pdb=" N   ILE A 366 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL A 350 " --> pdb=" O   ILE A 366 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 326 through 328
    Processing sheet with id=AA6, first strand: chain 'A' and resid 430 through 434
      removed outlier: 3.808A  pdb=" N   SER A 434 " --> pdb=" O   GLN A 439 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   GLN A 439 " --> pdb=" O   SER A 434 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   THR A 440 " --> pdb=" O   ILE A 404 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 475 through 478
      removed outlier: 3.575A  pdb=" N   ARG A 475 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   GLU A 657 " --> pdb=" O   PHE A 660 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   VAL A 664 " --> pdb=" O   GLY A 653 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   GLY A 653 " --> pdb=" O   VAL A 664 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 475 through 478
      removed outlier: 3.575A  pdb=" N   ARG A 475 " --> pdb=" O   LEU A 622 " (cutoff:3.500A)
      removed outlier: 6.247A  pdb=" N   GLU A 623 " --> pdb=" O   TYR A 696 " (cutoff:3.500A)
      removed outlier: 5.220A  pdb=" N   TYR A 696 " --> pdb=" O   GLU A 623 " (cutoff:3.500A)
      removed outlier: 5.292A  pdb=" N   ILE A 625 " --> pdb=" O   ALA A 694 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 482 through 488
      removed outlier: 3.682A  pdb=" N   ALA A 484 " --> pdb=" O   LEU A 503 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   LEU A 503 " --> pdb=" O   ALA A 484 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   TYR A 486 " --> pdb=" O   VAL A 501 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   GLU A 500 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 4.563A  pdb=" N   GLY A 590 " --> pdb=" O   GLU A 500 " (cutoff:3.500A)
      removed outlier: 7.042A  pdb=" N   HIS A 502 " --> pdb=" O   TYR A 588 " (cutoff:3.500A)
      removed outlier: 6.520A  pdb=" N   LYS A 542 " --> pdb=" O   VAL A 583 " (cutoff:3.500A)
      removed outlier: 7.697A  pdb=" N   VAL A 585 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 5.891A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 585 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   VAL A 587 " --> pdb=" O   VAL A 544 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   ILE A 546 " --> pdb=" O   VAL A 587 " (cutoff:3.500A)
      removed outlier: 8.619A  pdb=" N   ASP A 589 " --> pdb=" O   ILE A 546 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 517 through 519
      removed outlier: 3.982A  pdb=" N   TYR A 518 " --> pdb=" O   PHE A 525 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   PHE A 525 " --> pdb=" O   TYR A 518 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    224 hydrogen bonds defined for protein.
    651 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.98

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1864
        1.34 -     1.46: 1135
        1.46 -     1.58: 2714
        1.58 -     1.69: 5
        1.69 -     1.81: 61
  Bond restraints: 5779
  Sorted by residual:
  bond pdb=" CB  PHE A 255 "
       pdb=" CG  PHE A 255 "
    ideal  model  delta    sigma   weight residual
    1.502  1.481  0.021 2.30e-02 1.89e+03 8.08e-01
  bond pdb=" C   LYS A 471 "
       pdb=" N   ILE A 472 "
    ideal  model  delta    sigma   weight residual
    1.329  1.323  0.006 7.30e-03 1.88e+04 5.97e-01
  bond pdb=" CA  LYS A 405 "
       pdb=" C   LYS A 405 "
    ideal  model  delta    sigma   weight residual
    1.517  1.525 -0.008 1.07e-02 8.73e+03 5.04e-01
  bond pdb=" C2' GTP A 901 "
       pdb=" C3' GTP A 901 "
    ideal  model  delta    sigma   weight residual
    1.524  1.511  0.013 2.00e-02 2.50e+03 4.15e-01
  bond pdb=" CE1 PHE A 255 "
       pdb=" CZ  PHE A 255 "
    ideal  model  delta    sigma   weight residual
    1.382  1.363  0.019 3.00e-02 1.11e+03 3.90e-01
  ... (remaining 5774 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.30: 7583
        1.30 -     2.60: 164
        2.60 -     3.89: 41
        3.89 -     5.19: 4
        5.19 -     6.49: 3
  Bond angle restraints: 7795
  Sorted by residual:
  angle pdb=" C   GLU A 534 "
        pdb=" N   ILE A 535 "
        pdb=" CA  ILE A 535 "
      ideal   model   delta    sigma   weight residual
     122.59  120.56    2.03 7.20e-01 1.93e+00 7.98e+00
  angle pdb=" C1' GTP A 901 "
        pdb=" C2' GTP A 901 "
        pdb=" C3' GTP A 901 "
      ideal   model   delta    sigma   weight residual
     111.00  104.51    6.49 3.00e+00 1.11e-01 4.68e+00
  angle pdb=" N   VAL A 275 "
        pdb=" CA  VAL A 275 "
        pdb=" C   VAL A 275 "
      ideal   model   delta    sigma   weight residual
     106.42  109.51   -3.09 1.51e+00 4.39e-01 4.19e+00
  angle pdb=" CA  MET A 282 "
        pdb=" CB  MET A 282 "
        pdb=" CG  MET A 282 "
      ideal   model   delta    sigma   weight residual
     114.10  117.75   -3.65 2.00e+00 2.50e-01 3.33e+00
  angle pdb=" CA  LYS A 124 "
        pdb=" CB  LYS A 124 "
        pdb=" CG  LYS A 124 "
      ideal   model   delta    sigma   weight residual
     114.10  117.42   -3.32 2.00e+00 2.50e-01 2.75e+00
  ... (remaining 7790 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.29: 3424
       35.29 -    70.58: 80
       70.58 -   105.86: 8
      105.86 -   141.15: 2
      141.15 -   176.44: 1
  Dihedral angle restraints: 3515
    sinusoidal: 1461
      harmonic: 2054
  Sorted by residual:
  dihedral pdb=" C8  GTP A 901 "
           pdb=" C1' GTP A 901 "
           pdb=" N9  GTP A 901 "
           pdb=" O4' GTP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59  -78.97 -176.44     1      2.00e+01 2.50e-03 4.80e+01
  dihedral pdb=" O3B GTP A 901 "
           pdb=" O3A GTP A 901 "
           pdb=" PB  GTP A 901 "
           pdb=" PA  GTP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  179.75  111.33     1      2.00e+01 2.50e-03 3.27e+01
  dihedral pdb=" C4' GTP A 901 "
           pdb=" C5' GTP A 901 "
           pdb=" O5' GTP A 901 "
           pdb=" PA  GTP A 901 "
      ideal   model   delta sinusoidal    sigma   weight residual
     260.87  150.29  110.58     1      2.00e+01 2.50e-03 3.24e+01
  ... (remaining 3512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 514
       0.031 -    0.062: 213
       0.062 -    0.093: 67
       0.093 -    0.124: 47
       0.124 -    0.156: 5
  Chirality restraints: 846
  Sorted by residual:
  chirality pdb=" CB  ILE A 535 "
            pdb=" CA  ILE A 535 "
            pdb=" CG1 ILE A 535 "
            pdb=" CG2 ILE A 535 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.49    0.16 2.00e-01 2.50e+01 6.05e-01
  chirality pdb=" CB  VAL A 310 "
            pdb=" CA  VAL A 310 "
            pdb=" CG1 VAL A 310 "
            pdb=" CG2 VAL A 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.50   -0.13 2.00e-01 2.50e+01 4.35e-01
  chirality pdb=" CA  VAL A 667 "
            pdb=" N   VAL A 667 "
            pdb=" C   VAL A 667 "
            pdb=" CB  VAL A 667 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.33e-01
  ... (remaining 843 not shown)

  Planarity restraints: 1012
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 276 "    0.034 5.00e-02 4.00e+02   5.22e-02 4.36e+00
        pdb=" N   PRO A 277 "   -0.090 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 282 "    0.033 5.00e-02 4.00e+02   5.08e-02 4.12e+00
        pdb=" N   PRO A 283 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 283 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 283 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 271 "    0.010 2.00e-02 2.50e+03   1.35e-02 3.19e+00
        pdb=" CG  PHE A 271 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 271 "    0.015 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 271 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 271 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 271 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 271 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1009 not shown)

  Histogram of nonbonded interaction distances:
        1.94 -     2.53: 37
        2.53 -     3.13: 4299
        3.13 -     3.72: 8534
        3.72 -     4.31: 11805
        4.31 -     4.90: 19835
  Nonbonded interactions: 44510
  Sorted by model distance:
  nonbonded pdb=" O1B GTP A 901 "
            pdb="MG    MG A 902 "
     model   vdw
     1.942 2.170
  nonbonded pdb=" O3G GTP A 901 "
            pdb="MG    MG A 902 "
     model   vdw
     1.987 2.170
  nonbonded pdb=" O3B GTP A 901 "
            pdb="MG    MG A 902 "
     model   vdw
     2.049 2.170
  nonbonded pdb=" O   LEU A 604 "
            pdb=" ND2 ASN A 608 "
     model   vdw
     2.203 3.120
  nonbonded pdb=" NH1 ARG A 636 "
            pdb=" O   THR A 683 "
     model   vdw
     2.260 3.120
  ... (remaining 44505 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.970
  Find NCS groups from input model:        0.020
  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:1.430
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7500
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      :  0.002   0.021   5779  Z= 0.110
  Angle     :  0.506   6.490   7795  Z= 0.265
  Chirality :  0.043   0.156    846
  Planarity :  0.004   0.052   1012
  Dihedral  : 15.709 176.438   2203
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 7.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.03 %
    Favored  : 94.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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: -1.10 (0.31), residues: 716
  helix:  0.91 (0.39), residues: 193
  sheet: -1.35 (0.40), residues: 196
  loop : -1.26 (0.31), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 239 
 TYR   0.011   0.001   TYR A 163 
 PHE   0.030   0.001   PHE A 271 
 TRP   0.004   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 5779)
  covalent geometry    : angle       0.50624 ( 7795)
  hydrogen bonds       : bond        0.28670 (  221)
  hydrogen bonds       : angle       9.16986 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.204 
Fit side-chains
REVERT: A  500 GLU cc_start: 0.4967 (tt0) cc_final: 0.4642 (tt0)
REVERT: A  558 PHE cc_start: 0.6467 (m-10) cc_final: 0.6053 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 144
  average time/residue: 0.0782
  time to fit residues: 14.7076
Evaluate side-chains
  120 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
A 219 ASN
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 362 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 502 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.173692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.139026 restraints weight = 7091.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.142666 restraints weight = 3969.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.144839 restraints weight = 2666.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.146523 restraints weight = 2084.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.147416 restraints weight = 1771.007|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5779  Z= 0.165
  Angle     :  0.580   6.807   7795  Z= 0.304
  Chirality :  0.047   0.166    846
  Planarity :  0.005   0.055   1012
  Dihedral  : 10.434 175.053    787
  Min Nonbonded Distance : 1.834

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.38 %
    Favored  : 85.15 %
  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: -1.08 (0.32), residues: 716
  helix:  1.23 (0.37), residues: 212
  sheet: -1.48 (0.38), residues: 197
  loop : -1.53 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 120 
 TYR   0.030   0.002   TYR A 163 
 PHE   0.032   0.002   PHE A 693 
 TRP   0.008   0.002   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 5779)
  covalent geometry    : angle       0.57950 ( 7795)
  hydrogen bonds       : bond        0.04706 (  221)
  hydrogen bonds       : angle       5.94336 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 138
  time to evaluate  : 0.211 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6667 (tmm) cc_final: 0.6241 (tmm)
REVERT: A  558 PHE cc_start: 0.6116 (m-10) cc_final: 0.5835 (m-10)
REVERT: A  706 LYS cc_start: 0.7623 (tptp) cc_final: 0.7384 (tptp)
  outliers start: 9
  outliers final: 7
  residues processed: 141
  average time/residue: 0.0874
  time to fit residues: 15.6223
Evaluate side-chains
  132 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 125
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  683 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0470
   chunk 33 optimal weight:    7.9990
   chunk 44 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 28 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   overall best weight:    0.7280

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
A 274 ASN
A 362 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.173240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.138569 restraints weight = 7039.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.141942 restraints weight = 3966.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.144316 restraints weight = 2712.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.145638 restraints weight = 2118.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.146698 restraints weight = 1820.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   5779  Z= 0.152
  Angle     :  0.546   6.756   7795  Z= 0.285
  Chirality :  0.045   0.143    846
  Planarity :  0.005   0.056   1012
  Dihedral  : 10.429 176.137    787
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 13.87 %
    Favored  : 81.57 %
  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: -1.04 (0.32), residues: 716
  helix:  1.27 (0.37), residues: 213
  sheet: -1.48 (0.38), residues: 196
  loop : -1.50 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 456 
 TYR   0.023   0.002   TYR A 319 
 PHE   0.032   0.002   PHE A 693 
 TRP   0.009   0.002   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 ( 5779)
  covalent geometry    : angle       0.54599 ( 7795)
  hydrogen bonds       : bond        0.03993 (  221)
  hydrogen bonds       : angle       5.32147 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 0.219 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6674 (tmm) cc_final: 0.6201 (tmm)
  outliers start: 28
  outliers final: 17
  residues processed: 145
  average time/residue: 0.0943
  time to fit residues: 17.2101
Evaluate side-chains
  139 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  629 GLU
Chi-restraints excluded: chain A residue  648 ARG
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  683 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9990
   chunk 63 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 29 optimal weight:    6.9990
   chunk 37 optimal weight:    0.1980
   chunk 20 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   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  68 HIS
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.176675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.142570 restraints weight = 7063.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.146002 restraints weight = 4014.975|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.148106 restraints weight = 2745.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.149719 restraints weight = 2160.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.150558 restraints weight = 1844.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5779  Z= 0.142
  Angle     :  0.533   6.671   7795  Z= 0.281
  Chirality :  0.045   0.140    846
  Planarity :  0.004   0.055   1012
  Dihedral  : 10.387 176.841    787
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 17.13 %
    Favored  : 79.28 %
  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: -0.92 (0.32), residues: 716
  helix:  1.44 (0.37), residues: 213
  sheet: -1.44 (0.37), residues: 196
  loop : -1.46 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 456 
 TYR   0.020   0.002   TYR A 319 
 PHE   0.017   0.001   PHE A 271 
 TRP   0.008   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 5779)
  covalent geometry    : angle       0.53255 ( 7795)
  hydrogen bonds       : bond        0.03530 (  221)
  hydrogen bonds       : angle       4.97617 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.224 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6650 (tmm) cc_final: 0.6377 (tpt)
REVERT: A  413 GLU cc_start: 0.7598 (pt0) cc_final: 0.7395 (pt0)
REVERT: A  592 MET cc_start: 0.6327 (tmm) cc_final: 0.5732 (tmm)
  outliers start: 22
  outliers final: 15
  residues processed: 141
  average time/residue: 0.0895
  time to fit residues: 15.8031
Evaluate side-chains
  137 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 122
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  428 THR
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  683 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 7 optimal weight:    0.0770
   chunk 52 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 29 optimal weight:    7.9990
   chunk 45 optimal weight:    1.9990
   chunk 60 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 274 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 = 0.3800 r_free = 0.3800 target = 0.174486 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.140135 restraints weight = 7220.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.143548 restraints weight = 4069.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.145644 restraints weight = 2791.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.147227 restraints weight = 2194.617|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.148021 restraints weight = 1873.267|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7460
moved from start:          0.2210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5779  Z= 0.138
  Angle     :  0.533   6.680   7795  Z= 0.278
  Chirality :  0.045   0.136    846
  Planarity :  0.004   0.053   1012
  Dihedral  : 10.376 177.248    787
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 18.43 %
    Favored  : 77.49 %
  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: -0.82 (0.32), residues: 716
  helix:  1.51 (0.37), residues: 214
  sheet: -1.40 (0.37), residues: 196
  loop : -1.39 (0.33), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 456 
 TYR   0.016   0.002   TYR A 163 
 PHE   0.034   0.002   PHE A 693 
 TRP   0.008   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 5779)
  covalent geometry    : angle       0.53344 ( 7795)
  hydrogen bonds       : bond        0.03375 (  221)
  hydrogen bonds       : angle       4.82611 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.239 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6663 (tmm) cc_final: 0.6379 (tpt)
REVERT: A  238 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.6595 (ppp)
REVERT: A  592 MET cc_start: 0.6289 (tmm) cc_final: 0.5779 (tmm)
REVERT: A  663 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8474 (tp)
REVERT: A  706 LYS cc_start: 0.7590 (tptp) cc_final: 0.7355 (tptp)
  outliers start: 25
  outliers final: 16
  residues processed: 134
  average time/residue: 0.0935
  time to fit residues: 15.9351
Evaluate side-chains
  139 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 121
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  648 ARG
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  683 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 28 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  68 HIS
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 274 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 = 0.3783 r_free = 0.3783 target = 0.172762 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.138761 restraints weight = 7141.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.141865 restraints weight = 4146.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.144095 restraints weight = 2905.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.145463 restraints weight = 2306.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.146157 restraints weight = 1992.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7499
moved from start:          0.2285

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5779  Z= 0.151
  Angle     :  0.534   6.736   7795  Z= 0.279
  Chirality :  0.045   0.144    846
  Planarity :  0.004   0.050   1012
  Dihedral  : 10.377 177.039    787
  Min Nonbonded Distance : 1.835

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 18.43 %
    Favored  : 76.35 %
  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: -0.82 (0.31), residues: 716
  helix:  1.58 (0.36), residues: 213
  sheet: -1.41 (0.37), residues: 196
  loop : -1.43 (0.33), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 456 
 TYR   0.017   0.002   TYR A 319 
 PHE   0.021   0.001   PHE A 631 
 TRP   0.007   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 5779)
  covalent geometry    : angle       0.53350 ( 7795)
  hydrogen bonds       : bond        0.03322 (  221)
  hydrogen bonds       : angle       4.79099 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6726 (tmm) cc_final: 0.6385 (tpt)
REVERT: A  238 MET cc_start: 0.8045 (OUTLIER) cc_final: 0.6749 (ppp)
REVERT: A  697 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6141 (mp0)
REVERT: A  706 LYS cc_start: 0.7569 (tptp) cc_final: 0.7369 (tptp)
  outliers start: 32
  outliers final: 20
  residues processed: 145
  average time/residue: 0.0848
  time to fit residues: 15.8380
Evaluate side-chains
  146 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  587 VAL
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  629 GLU
Chi-restraints excluded: chain A residue  648 ARG
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  697 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 41 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 70 optimal weight:    0.7980
   chunk 25 optimal weight:    0.5980
   chunk 29 optimal weight:    6.9990
   chunk 37 optimal weight:    1.9990
   chunk 21 optimal weight:    5.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 274 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 = 0.3781 r_free = 0.3781 target = 0.172442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.138367 restraints weight = 7210.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.141644 restraints weight = 4171.903|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.143659 restraints weight = 2896.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.145179 restraints weight = 2302.419|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.145929 restraints weight = 1982.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5779  Z= 0.143
  Angle     :  0.532   6.693   7795  Z= 0.278
  Chirality :  0.045   0.136    846
  Planarity :  0.004   0.049   1012
  Dihedral  : 10.392 177.250    787
  Min Nonbonded Distance : 1.845

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.61 %
    Favored  : 95.39 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 18.76 %
    Favored  : 76.18 %
  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: -0.77 (0.31), residues: 716
  helix:  1.54 (0.36), residues: 214
  sheet: -1.24 (0.38), residues: 194
  loop : -1.46 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 456 
 TYR   0.016   0.002   TYR A 319 
 PHE   0.037   0.001   PHE A 693 
 TRP   0.007   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 5779)
  covalent geometry    : angle       0.53239 ( 7795)
  hydrogen bonds       : bond        0.03214 (  221)
  hydrogen bonds       : angle       4.73402 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6714 (tmm) cc_final: 0.6374 (tpt)
REVERT: A  238 MET cc_start: 0.8032 (OUTLIER) cc_final: 0.6760 (ppp)
REVERT: A  424 GLU cc_start: 0.7989 (tp30) cc_final: 0.7639 (tp30)
REVERT: A  697 GLU cc_start: 0.7484 (OUTLIER) cc_final: 0.6091 (mp0)
  outliers start: 31
  outliers final: 21
  residues processed: 143
  average time/residue: 0.0898
  time to fit residues: 16.3860
Evaluate side-chains
  143 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  629 GLU
Chi-restraints excluded: chain A residue  648 ARG
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  697 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    0.9990
   chunk 43 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 45 optimal weight:    0.5980
   chunk 66 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 274 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 = 0.3768 r_free = 0.3768 target = 0.171107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.137355 restraints weight = 7118.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.140570 restraints weight = 4141.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.142698 restraints weight = 2876.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.143907 restraints weight = 2288.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.144764 restraints weight = 1989.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7513
moved from start:          0.2425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   5779  Z= 0.162
  Angle     :  0.560   6.798   7795  Z= 0.292
  Chirality :  0.045   0.137    846
  Planarity :  0.004   0.049   1012
  Dihedral  : 10.406 177.036    787
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 20.72 %
    Favored  : 74.39 %
  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: -0.81 (0.31), residues: 716
  helix:  1.55 (0.36), residues: 213
  sheet: -1.30 (0.38), residues: 195
  loop : -1.47 (0.32), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 456 
 TYR   0.017   0.002   TYR A 319 
 PHE   0.036   0.002   PHE A 693 
 TRP   0.007   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 5779)
  covalent geometry    : angle       0.55965 ( 7795)
  hydrogen bonds       : bond        0.03308 (  221)
  hydrogen bonds       : angle       4.72566 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.258 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6731 (tmm) cc_final: 0.6394 (tpt)
REVERT: A  238 MET cc_start: 0.7895 (OUTLIER) cc_final: 0.6756 (ppp)
REVERT: A  424 GLU cc_start: 0.7927 (tp30) cc_final: 0.7685 (tp30)
REVERT: A  539 TRP cc_start: 0.7591 (p90) cc_final: 0.6865 (p90)
REVERT: A  697 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.6142 (mp0)
  outliers start: 30
  outliers final: 20
  residues processed: 140
  average time/residue: 0.0877
  time to fit residues: 15.8232
Evaluate side-chains
  143 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 121
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  629 GLU
Chi-restraints excluded: chain A residue  648 ARG
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  697 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 19 optimal weight:    0.5980
   chunk 12 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 45 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 274 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 = 0.3780 r_free = 0.3780 target = 0.172588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.137989 restraints weight = 7143.059|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.141470 restraints weight = 4010.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.143776 restraints weight = 2729.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.145312 restraints weight = 2124.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.146103 restraints weight = 1801.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3500
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5779  Z= 0.131
  Angle     :  0.545   8.296   7795  Z= 0.282
  Chirality :  0.045   0.134    846
  Planarity :  0.004   0.049   1012
  Dihedral  : 10.389 177.581    787
  Min Nonbonded Distance : 1.857

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 21.21 %
    Favored  : 74.55 %
  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: -0.79 (0.31), residues: 716
  helix:  1.63 (0.36), residues: 214
  sheet: -1.35 (0.37), residues: 200
  loop : -1.48 (0.32), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 456 
 TYR   0.015   0.001   TYR A 319 
 PHE   0.037   0.001   PHE A 693 
 TRP   0.008   0.001   TRP A 185 
 HIS   0.003   0.001   HIS A 443 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 5779)
  covalent geometry    : angle       0.54532 ( 7795)
  hydrogen bonds       : bond        0.03113 (  221)
  hydrogen bonds       : angle       4.59411 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 0.246 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6614 (tmm) cc_final: 0.6311 (tpt)
REVERT: A  238 MET cc_start: 0.7914 (OUTLIER) cc_final: 0.6706 (ppp)
REVERT: A  424 GLU cc_start: 0.7902 (tp30) cc_final: 0.7676 (tp30)
REVERT: A  539 TRP cc_start: 0.7628 (p90) cc_final: 0.7193 (p90)
REVERT: A  697 GLU cc_start: 0.7468 (OUTLIER) cc_final: 0.6046 (mp0)
  outliers start: 26
  outliers final: 21
  residues processed: 133
  average time/residue: 0.0951
  time to fit residues: 16.0319
Evaluate side-chains
  143 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  629 GLU
Chi-restraints excluded: chain A residue  648 ARG
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  697 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 4 optimal weight:    0.2980
   chunk 48 optimal weight:    7.9990
   chunk 54 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.4386

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

Flipped N/Q/H residues before XYZ refinement:
** A  96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 274 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 = 0.3731 r_free = 0.3731 target = 0.167408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.133625 restraints weight = 7270.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.136541 restraints weight = 4268.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.138752 restraints weight = 3010.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.140046 restraints weight = 2389.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.140897 restraints weight = 2062.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7571
moved from start:          0.2510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   5779  Z= 0.252
  Angle     :  0.650   8.591   7795  Z= 0.338
  Chirality :  0.048   0.150    846
  Planarity :  0.005   0.049   1012
  Dihedral  : 10.514 174.199    787
  Min Nonbonded Distance : 1.767

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.84 %
    Favored  : 93.16 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 21.21 %
    Favored  : 74.06 %
  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: -1.13 (0.31), residues: 716
  helix:  1.30 (0.36), residues: 212
  sheet: -1.47 (0.37), residues: 195
  loop : -1.69 (0.31), residues: 309

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 249 
 TYR   0.024   0.002   TYR A 319 
 PHE   0.040   0.002   PHE A 693 
 TRP   0.010   0.002   TRP A 185 
 HIS   0.003   0.001   HIS A 593 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 ( 5779)
  covalent geometry    : angle       0.64984 ( 7795)
  hydrogen bonds       : bond        0.03764 (  221)
  hydrogen bonds       : angle       5.01017 (  651)

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

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

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1432 Ramachandran restraints generated.
    716 Oldfield, 0 Emsley, 716 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  224 MET cc_start: 0.6792 (tmm) cc_final: 0.6427 (tpt)
REVERT: A  236 ASP cc_start: 0.6978 (t70) cc_final: 0.6701 (t0)
REVERT: A  238 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.6799 (ppp)
REVERT: A  424 GLU cc_start: 0.8042 (tp30) cc_final: 0.7798 (tp30)
REVERT: A  697 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6160 (mp0)
REVERT: A  707 LEU cc_start: 0.8358 (OUTLIER) cc_final: 0.7994 (mt)
  outliers start: 29
  outliers final: 21
  residues processed: 139
  average time/residue: 0.0878
  time to fit residues: 15.7584
Evaluate side-chains
  147 residues out of total 613 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 123
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    6 THR
Chi-restraints excluded: chain A residue   26 VAL
Chi-restraints excluded: chain A residue   54 VAL
Chi-restraints excluded: chain A residue   69 VAL
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  228 PHE
Chi-restraints excluded: chain A residue  238 MET
Chi-restraints excluded: chain A residue  297 VAL
Chi-restraints excluded: chain A residue  329 GLU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  441 LEU
Chi-restraints excluded: chain A residue  479 THR
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  514 VAL
Chi-restraints excluded: chain A residue  586 ILE
Chi-restraints excluded: chain A residue  604 LEU
Chi-restraints excluded: chain A residue  629 GLU
Chi-restraints excluded: chain A residue  648 ARG
Chi-restraints excluded: chain A residue  650 MET
Chi-restraints excluded: chain A residue  654 MET
Chi-restraints excluded: chain A residue  658 LYS
Chi-restraints excluded: chain A residue  683 THR
Chi-restraints excluded: chain A residue  697 GLU
Chi-restraints excluded: chain A residue  707 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9980
   chunk 13 optimal weight:    0.5980
   chunk 38 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 5 optimal weight:    0.0270
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 44 optimal weight:    0.5980
   chunk 48 optimal weight:    2.9990
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 138 ASN
** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 449 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.173212 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.139322 restraints weight = 7065.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.142748 restraints weight = 3991.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.145087 restraints weight = 2702.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.146568 restraints weight = 2104.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.147370 restraints weight = 1792.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5779  Z= 0.129
  Angle     :  0.566   7.635   7795  Z= 0.295
  Chirality :  0.045   0.136    846
  Planarity :  0.005   0.050   1012
  Dihedral  : 10.447 178.630    787
  Min Nonbonded Distance : 1.865

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 22.68 %
    Favored  : 73.57 %
  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: -0.94 (0.31), residues: 716
  helix:  1.51 (0.36), residues: 214
  sheet: -1.45 (0.37), residues: 200
  loop : -1.57 (0.31), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 456 
 TYR   0.035   0.002   TYR A 163 
 PHE   0.036   0.001   PHE A 693 
 TRP   0.009   0.001   TRP A 185 
 HIS   0.004   0.001   HIS A 449 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 5779)
  covalent geometry    : angle       0.56613 ( 7795)
  hydrogen bonds       : bond        0.03154 (  221)
  hydrogen bonds       : angle       4.57593 (  651)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1147.99 seconds
wall clock time: 20 minutes 26.61 seconds (1226.61 seconds total)