Starting phenix.real_space_refine
on Wed Sep 17 06:33:48 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gz3_51721/09_2025/9gz3_51721.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gz3_51721/09_2025/9gz3_51721.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gz3_51721/09_2025/9gz3_51721.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gz3_51721/09_2025/9gz3_51721.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gz3_51721/09_2025/9gz3_51721.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gz3_51721/09_2025/9gz3_51721.cif"
  }
  resolution = 3.4
  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=   0.000 sd=   0.046
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      32      5.16       5
     C    3941      2.51       5
     N    1051      2.21       5
     O    1152      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 55 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6180
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 764, 6147
          Classifications: {'peptide': 764}
          Link IDs: {'PTRANS': 29, 'TRANS': 734}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.73, per 1000 atoms: 0.28
  Number of scatterers: 6180
  At special positions: 0
  Unit cell: (71.514, 92.064, 129.876, 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      32     16.00
     P       3     15.00
     Mg      1     11.99
     O    1152      8.00
     N    1051      7.00
     C    3941      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: 0.51
  Conformation dependent library (CDL) restraints added in 380.4 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1434

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 6 sheets defined
      54.1% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.25
  Creating SS restraints...
    Processing helix  chain 'A' and resid 4 through 16
      removed outlier: 4.430A  pdb=" N   VAL A   8 " --> pdb=" O   GLU A   5 " (cutoff:3.500A)
      removed outlier: 6.839A  pdb=" N   ALA A  11 " --> pdb=" O   VAL A   8 " (cutoff:3.500A)
      Proline residue:  A  14  - end of helix
    Processing helix  chain 'A' and resid 21 through 26
    Processing helix  chain 'A' and resid 27 through 29
      No H-bonds generated for 'chain 'A' and resid 27 through 29'
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 89 through 93
    Processing helix  chain 'A' and resid 97 through 110
    Processing helix  chain 'A' and resid 131 through 134
      removed outlier: 3.938A  pdb=" N   TYR A 134 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 131 through 134'
    Processing helix  chain 'A' and resid 135 through 143
      removed outlier: 3.780A  pdb=" N   VAL A 139 " --> pdb=" O   THR A 135 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ALA A 140 " --> pdb=" O   PRO A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 153 through 169
    Processing helix  chain 'A' and resid 183 through 202
    Processing helix  chain 'A' and resid 215 through 232
      removed outlier: 3.891A  pdb=" N   ILE A 221 " --> pdb=" O   GLU A 217 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   ASN A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      Proline residue:  A 225  - end of helix
      removed outlier: 3.869A  pdb=" N   PHE A 230 " --> pdb=" O   ALA A 226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 274
      removed outlier: 3.532A  pdb=" N   VAL A 273 " --> pdb=" O   LYS A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 292
      removed outlier: 4.047A  pdb=" N   TYR A 287 " --> pdb=" O   TYR A 283 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 290 " --> pdb=" O   PHE A 286 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN A 292 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 299
    Processing helix  chain 'A' and resid 306 through 310
      removed outlier: 3.990A  pdb=" N   ASP A 309 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 339
      removed outlier: 4.247A  pdb=" N   MET A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 360
      removed outlier: 3.555A  pdb=" N   TYR A 350 " --> pdb=" O   LYS A 346 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   MET A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   GLY A 360 " --> pdb=" O   ILE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 388
    Processing helix  chain 'A' and resid 391 through 401
    Processing helix  chain 'A' and resid 416 through 448
    Processing helix  chain 'A' and resid 472 through 495
      removed outlier: 3.548A  pdb=" N   LEU A 476 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 4.074A  pdb=" N   ILE A 478 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 495 through 504
      removed outlier: 4.203A  pdb=" N   TYR A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   LYS A 502 " --> pdb=" O   GLN A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 525
      removed outlier: 4.016A  pdb=" N   LEU A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A 524 " --> pdb=" O   CYS A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 537
      removed outlier: 4.040A  pdb=" N   GLU A 535 " --> pdb=" O   MET A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 557
    Processing helix  chain 'A' and resid 592 through 597
    Processing helix  chain 'A' and resid 602 through 610
    Processing helix  chain 'A' and resid 614 through 621
    Processing helix  chain 'A' and resid 646 through 662
    Processing helix  chain 'A' and resid 663 through 665
      No H-bonds generated for 'chain 'A' and resid 663 through 665'
    Processing helix  chain 'A' and resid 685 through 696
    Processing helix  chain 'A' and resid 697 through 708
      removed outlier: 4.032A  pdb=" N   CYS A 705 " --> pdb=" O   GLY A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 723
    Processing helix  chain 'A' and resid 737 through 748
      removed outlier: 4.024A  pdb=" N   SER A 747 " --> pdb=" O   GLU A 743 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   SER A 748 " --> pdb=" O   LYS A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 768 through 796
    Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72
      removed outlier: 7.162A  pdb=" N   LYS A  58 " --> pdb=" O   ARG A  54 " (cutoff:3.500A)
      removed outlier: 5.374A  pdb=" N   ARG A  54 " --> pdb=" O   LYS A  58 " (cutoff:3.500A)
      removed outlier: 6.916A  pdb=" N   THR A  60 " --> pdb=" O   VAL A  52 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 115 through 117
      removed outlier: 6.137A  pdb=" N   CYS A 122 " --> pdb=" O   ARG A 671 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   ILE A 673 " --> pdb=" O   CYS A 122 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   THR A 124 " --> pdb=" O   ILE A 673 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   SER A 173 " --> pdb=" O   HIS A 668 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   VAL A 670 " --> pdb=" O   SER A 173 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU A 175 " --> pdb=" O   VAL A 670 " (cutoff:3.500A)
      removed outlier: 7.315A  pdb=" N   CYS A 672 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   THR A 177 " --> pdb=" O   CYS A 672 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   GLN A 172 " --> pdb=" O   GLY A 458 " (cutoff:3.500A)
      removed outlier: 8.381A  pdb=" N   LEU A 460 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
      removed outlier: 6.882A  pdb=" N   ILE A 174 " --> pdb=" O   LEU A 460 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   GLY A 245 " --> pdb=" O   TYR A 266 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 364 through 366
    Processing sheet with id=AA4, first strand: chain 'A' and resid 403 through 406
    Processing sheet with id=AA5, first strand: chain 'A' and resid 563 through 564
    Processing sheet with id=AA6, first strand: chain 'A' and resid 711 through 714
      removed outlier: 3.641A  pdb=" N   ASN A 711 " --> pdb=" O   PHE A 765 " (cutoff:3.500A)

    295 hydrogen bonds defined for protein.
    837 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: 1.01

  Time building geometry restraints manager: 0.68 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1498
        1.33 -     1.45: 1233
        1.45 -     1.57: 3518
        1.57 -     1.69: 5
        1.69 -     1.80: 56
  Bond restraints: 6310
  Sorted by residual:
  bond pdb=" O3  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.569  1.508  0.061 2.00e-02 2.50e+03 9.42e+00
  bond pdb=" O4  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.568  1.507  0.061 2.00e-02 2.50e+03 9.41e+00
  bond pdb=" O2  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.567  1.508  0.059 2.00e-02 2.50e+03 8.80e+00
  bond pdb=" O1  PO4 A1203 "
       pdb=" P   PO4 A1203 "
    ideal  model  delta    sigma   weight residual
    1.565  1.508  0.057 2.00e-02 2.50e+03 7.99e+00
  bond pdb=" N   LYS A 572 "
       pdb=" CA  LYS A 572 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.41e-02 5.03e+03 5.05e+00
  ... (remaining 6305 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 8128
        2.36 -     4.72: 341
        4.72 -     7.07: 38
        7.07 -     9.43: 5
        9.43 -    11.79: 1
  Bond angle restraints: 8513
  Sorted by residual:
  angle pdb=" CA  LYS A 542 "
        pdb=" CB  LYS A 542 "
        pdb=" CG  LYS A 542 "
      ideal   model   delta    sigma   weight residual
     114.10  122.70   -8.60 2.00e+00 2.50e-01 1.85e+01
  angle pdb=" C2' ADP A1202 "
        pdb=" C3' ADP A1202 "
        pdb=" C4' ADP A1202 "
      ideal   model   delta    sigma   weight residual
     111.00   99.21   11.79 3.00e+00 1.11e-01 1.54e+01
  angle pdb=" N   ILE A 591 "
        pdb=" CA  ILE A 591 "
        pdb=" C   ILE A 591 "
      ideal   model   delta    sigma   weight residual
     108.93  114.14   -5.21 1.35e+00 5.49e-01 1.49e+01
  angle pdb=" C   LYS A 598 "
        pdb=" N   ASP A 599 "
        pdb=" CA  ASP A 599 "
      ideal   model   delta    sigma   weight residual
     121.80  130.24   -8.44 2.44e+00 1.68e-01 1.20e+01
  angle pdb=" C   LEU A 749 "
        pdb=" N   ASP A 750 "
        pdb=" CA  ASP A 750 "
      ideal   model   delta    sigma   weight residual
     122.46  127.20   -4.74 1.41e+00 5.03e-01 1.13e+01
  ... (remaining 8508 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 3462
       17.63 -    35.26: 265
       35.26 -    52.89: 49
       52.89 -    70.52: 15
       70.52 -    88.15: 16
  Dihedral angle restraints: 3807
    sinusoidal: 1581
      harmonic: 2226
  Sorted by residual:
  dihedral pdb=" CA  LYS A 367 "
           pdb=" C   LYS A 367 "
           pdb=" N   GLN A 368 "
           pdb=" CA  GLN A 368 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.70  -27.30     0      5.00e+00 4.00e-02 2.98e+01
  dihedral pdb=" CA  GLN A  44 "
           pdb=" C   GLN A  44 "
           pdb=" N   GLU A  45 "
           pdb=" CA  GLU A  45 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.57  -26.43     0      5.00e+00 4.00e-02 2.79e+01
  dihedral pdb=" CA  ARG A 281 "
           pdb=" C   ARG A 281 "
           pdb=" N   ASP A 282 "
           pdb=" CA  ASP A 282 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.73   26.27     0      5.00e+00 4.00e-02 2.76e+01
  ... (remaining 3804 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 578
       0.051 -    0.101: 243
       0.101 -    0.152: 79
       0.152 -    0.203: 17
       0.203 -    0.253: 5
  Chirality restraints: 922
  Sorted by residual:
  chirality pdb=" CA  ASN A 224 "
            pdb=" N   ASN A 224 "
            pdb=" C   ASN A 224 "
            pdb=" CB  ASN A 224 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CB  ILE A 730 "
            pdb=" CA  ILE A 730 "
            pdb=" CG1 ILE A 730 "
            pdb=" CG2 ILE A 730 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.23 2.00e-01 2.50e+01 1.31e+00
  chirality pdb=" CB  VAL A 763 "
            pdb=" CA  VAL A 763 "
            pdb=" CG1 VAL A 763 "
            pdb=" CG2 VAL A 763 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.18e+00
  ... (remaining 919 not shown)

  Planarity restraints: 1097
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 712 "    0.263 9.50e-02 1.11e+02   1.22e-01 2.03e+01
        pdb=" NE  ARG A 712 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 712 "   -0.062 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 712 "    0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 712 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A 570 "    0.017 2.00e-02 2.50e+03   3.42e-02 1.17e+01
        pdb=" C   LYS A 570 "   -0.059 2.00e-02 2.50e+03
        pdb=" O   LYS A 570 "    0.023 2.00e-02 2.50e+03
        pdb=" N   GLY A 571 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 671 "   -0.191 9.50e-02 1.11e+02   8.76e-02 9.21e+00
        pdb=" NE  ARG A 671 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 671 "    0.040 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 671 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 671 "   -0.019 2.00e-02 2.50e+03
  ... (remaining 1094 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 81
        2.65 -     3.21: 5659
        3.21 -     3.78: 9356
        3.78 -     4.34: 13042
        4.34 -     4.90: 21332
  Nonbonded interactions: 49470
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 242 "
            pdb="MG    MG A1201 "
     model   vdw
     2.088 2.170
  nonbonded pdb="MG    MG A1201 "
            pdb=" O1B ADP A1202 "
     model   vdw
     2.093 2.170
  nonbonded pdb=" OG1 THR A 185 "
            pdb="MG    MG A1201 "
     model   vdw
     2.147 2.170
  nonbonded pdb=" OG1 THR A 185 "
            pdb=" O1B ADP A1202 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   SER A 664 "
            pdb=" OG  SER A 664 "
     model   vdw
     2.300 3.040
  ... (remaining 49465 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 individual isotropic
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:             3.160
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.730
  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:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
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      :  0.007   0.094   6310  Z= 0.305
  Angle     :  1.067  11.790   8513  Z= 0.612
  Chirality :  0.063   0.253    922
  Planarity :  0.009   0.122   1097
  Dihedral  : 14.737  88.150   2373
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 1.46
  Ramachandran Plot:
    Outliers :  0.26 %
    Allowed  :  3.56 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.15 %
    Allowed  :  1.81 %
    Favored  : 98.04 %
  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 aren not related in a simple way.
  whole: -1.99 (0.27), residues: 758
  helix: -1.53 (0.23), residues: 359
  sheet: -1.52 (0.59), residues: 69
  loop : -0.80 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.059   0.006   ARG A 712 
 TYR   0.027   0.004   TYR A 117 
 PHE   0.028   0.003   PHE A 489 
 TRP   0.015   0.002   TRP A 438 
 HIS   0.008   0.002   HIS A 576 

Details of bonding type rmsd
  covalent geometry    : bond        0.00695 ( 6310)
  covalent geometry    : angle       1.06737 ( 8513)
  hydrogen bonds       : bond        0.22728 (  295)
  hydrogen bonds       : angle       8.14992 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.192 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.7518 (tm-30) cc_final: 0.7279 (tm-30)
REVERT: A  470 PHE cc_start: 0.7779 (t80) cc_final: 0.7491 (t80)
  outliers start: 1
  outliers final: 1
  residues processed: 122
  average time/residue: 0.0958
  time to fit residues: 14.7833
Evaluate side-chains
  78 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 77
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  572 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.0870
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 104 ASN
A 160 ASN
A 471 ASN
A 490 ASN
A 492 HIS
** A 576 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 668 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.174022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.143134 restraints weight = 7886.348|
|-----------------------------------------------------------------------------|
r_work (start): 0.3766 rms_B_bonded: 2.27
r_work: 0.3657 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.3505 rms_B_bonded: 5.00 restraints_weight: 0.2500
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6310  Z= 0.144
  Angle     :  0.621   6.852   8513  Z= 0.318
  Chirality :  0.044   0.135    922
  Planarity :  0.004   0.031   1097
  Dihedral  :  6.440  67.492    843
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  6.79 %
    Favored  : 92.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.10 (0.30), residues: 758
  helix:  0.42 (0.27), residues: 366
  sheet: -1.07 (0.63), residues: 63
  loop : -0.25 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 780 
 TYR   0.013   0.002   TYR A 117 
 PHE   0.016   0.001   PHE A 252 
 TRP   0.005   0.001   TRP A 593 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 6310)
  covalent geometry    : angle       0.62066 ( 8513)
  hydrogen bonds       : bond        0.04357 (  295)
  hydrogen bonds       : angle       4.82721 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8083 (tm-30)
REVERT: A   77 MET cc_start: 0.5887 (ptm) cc_final: 0.5684 (ptp)
REVERT: A  146 LYS cc_start: 0.8482 (mmmm) cc_final: 0.8060 (mtmt)
REVERT: A  195 PHE cc_start: 0.7346 (m-80) cc_final: 0.7137 (m-80)
REVERT: A  386 TYR cc_start: 0.8139 (t80) cc_final: 0.7923 (t80)
REVERT: A  433 GLU cc_start: 0.8274 (tm-30) cc_final: 0.7900 (tt0)
  outliers start: 8
  outliers final: 3
  residues processed: 95
  average time/residue: 0.0942
  time to fit residues: 11.6867
Evaluate side-chains
  75 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  263 ILE
Chi-restraints excluded: chain A residue  698 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 42 optimal weight:    0.7980
   chunk 14 optimal weight:    0.2980
   chunk 36 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 38 optimal weight:    0.8980
   chunk 73 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A 288 GLN
A 576 HIS
** A 597 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 = 0.4063 r_free = 0.4063 target = 0.171510 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.140015 restraints weight = 7916.881|
|-----------------------------------------------------------------------------|
r_work (start): 0.3744 rms_B_bonded: 2.38
r_work: 0.3626 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6310  Z= 0.144
  Angle     :  0.583   7.325   8513  Z= 0.292
  Chirality :  0.044   0.132    922
  Planarity :  0.003   0.033   1097
  Dihedral  :  5.777  60.400    839
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 5.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  9.05 %
    Favored  : 88.84 %
  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 aren not related in a simple way.
  whole:  0.05 (0.30), residues: 758
  helix:  0.60 (0.27), residues: 373
  sheet: -0.99 (0.67), residues: 58
  loop : -0.29 (0.35), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.012   0.001   TYR A 266 
 PHE   0.012   0.001   PHE A 252 
 TRP   0.003   0.001   TRP A 508 
 HIS   0.005   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6310)
  covalent geometry    : angle       0.58331 ( 8513)
  hydrogen bonds       : bond        0.03768 (  295)
  hydrogen bonds       : angle       4.48156 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8328 (tm-30) cc_final: 0.8032 (tm-30)
REVERT: A   92 MET cc_start: 0.7541 (mmm) cc_final: 0.7116 (mmp)
REVERT: A  330 MET cc_start: 0.7330 (mtt) cc_final: 0.7075 (mtt)
REVERT: A  378 THR cc_start: 0.8983 (OUTLIER) cc_final: 0.8752 (m)
REVERT: A  433 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7671 (tt0)
REVERT: A  574 GLU cc_start: 0.6156 (tp30) cc_final: 0.5464 (pt0)
  outliers start: 14
  outliers final: 8
  residues processed: 90
  average time/residue: 0.0892
  time to fit residues: 10.6914
Evaluate side-chains
  84 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  304 THR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  482 ASN
Chi-restraints excluded: chain A residue  674 ILE
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  723 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 13 optimal weight:    0.7980
   chunk 50 optimal weight:    0.2980
   chunk 31 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 29 optimal weight:    0.2980
   chunk 39 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 49 optimal weight:    0.7980
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    0.5980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 419 GLN
A 581 HIS
** A 597 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 = 0.4093 r_free = 0.4093 target = 0.174951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.143083 restraints weight = 7900.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.3758 rms_B_bonded: 2.39
r_work: 0.3635 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6310  Z= 0.120
  Angle     :  0.536   6.788   8513  Z= 0.267
  Chirality :  0.042   0.130    922
  Planarity :  0.003   0.027   1097
  Dihedral  :  5.443  53.711    839
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 10.11 %
    Favored  : 87.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.30 (0.31), residues: 758
  helix:  0.82 (0.27), residues: 371
  sheet: -0.99 (0.69), residues: 58
  loop : -0.16 (0.35), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  23 
 TYR   0.012   0.001   TYR A 266 
 PHE   0.012   0.001   PHE A 252 
 TRP   0.003   0.001   TRP A 130 
 HIS   0.002   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6310)
  covalent geometry    : angle       0.53600 ( 8513)
  hydrogen bonds       : bond        0.03324 (  295)
  hydrogen bonds       : angle       4.28915 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8056 (tm-30)
REVERT: A  349 MET cc_start: 0.7890 (mtp) cc_final: 0.7653 (mtt)
REVERT: A  378 THR cc_start: 0.8924 (OUTLIER) cc_final: 0.8680 (m)
REVERT: A  433 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7689 (tt0)
REVERT: A  574 GLU cc_start: 0.6365 (tp30) cc_final: 0.5636 (pt0)
  outliers start: 16
  outliers final: 7
  residues processed: 89
  average time/residue: 0.0803
  time to fit residues: 9.7411
Evaluate side-chains
  79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  723 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    0.0970
   chunk 62 optimal weight:    1.9990
   chunk 20 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 30 optimal weight:    3.9990
   chunk 22 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 2 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.171816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.140437 restraints weight = 7967.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.3748 rms_B_bonded: 2.37
r_work: 0.3623 rms_B_bonded: 3.16 restraints_weight: 0.5000
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3037

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6310  Z= 0.123
  Angle     :  0.538   7.344   8513  Z= 0.267
  Chirality :  0.042   0.132    922
  Planarity :  0.003   0.038   1097
  Dihedral  :  5.353  51.764    839
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 11.01 %
    Favored  : 86.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.36 (0.31), residues: 758
  helix:  0.88 (0.27), residues: 371
  sheet: -1.06 (0.70), residues: 58
  loop : -0.10 (0.34), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.012   0.001   TYR A 266 
 PHE   0.013   0.001   PHE A 252 
 TRP   0.003   0.001   TRP A 130 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6310)
  covalent geometry    : angle       0.53823 ( 8513)
  hydrogen bonds       : bond        0.03218 (  295)
  hydrogen bonds       : angle       4.20097 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8368 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: A   92 MET cc_start: 0.7556 (mmp) cc_final: 0.6833 (mtm)
REVERT: A  330 MET cc_start: 0.7222 (mtt) cc_final: 0.7015 (mtt)
REVERT: A  378 THR cc_start: 0.8873 (OUTLIER) cc_final: 0.8636 (m)
REVERT: A  433 GLU cc_start: 0.7956 (tm-30) cc_final: 0.7708 (tt0)
  outliers start: 16
  outliers final: 8
  residues processed: 93
  average time/residue: 0.0838
  time to fit residues: 10.4920
Evaluate side-chains
  79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  723 ARG
Chi-restraints excluded: chain A residue  784 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9990
   chunk 2 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0980
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   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 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.173746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.142133 restraints weight = 7855.017|
|-----------------------------------------------------------------------------|
r_work (start): 0.3719 rms_B_bonded: 2.37
r_work: 0.3600 rms_B_bonded: 3.11 restraints_weight: 0.5000
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6310  Z= 0.126
  Angle     :  0.555   7.521   8513  Z= 0.272
  Chirality :  0.042   0.129    922
  Planarity :  0.003   0.040   1097
  Dihedral  :  5.174  49.212    839
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.24 %
    Favored  : 97.76 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 12.22 %
    Favored  : 85.67 %
  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 aren not related in a simple way.
  whole:  0.42 (0.31), residues: 758
  helix:  0.95 (0.27), residues: 370
  sheet: -1.26 (0.68), residues: 58
  loop : -0.06 (0.35), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  23 
 TYR   0.012   0.001   TYR A 422 
 PHE   0.011   0.001   PHE A 473 
 TRP   0.004   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6310)
  covalent geometry    : angle       0.55460 ( 8513)
  hydrogen bonds       : bond        0.03190 (  295)
  hydrogen bonds       : angle       4.10665 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8332 (tm-30) cc_final: 0.8007 (tm-30)
REVERT: A   92 MET cc_start: 0.7596 (mmp) cc_final: 0.6861 (mtm)
REVERT: A  195 PHE cc_start: 0.7297 (m-80) cc_final: 0.7069 (m-10)
REVERT: A  378 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8625 (m)
REVERT: A  433 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7685 (tt0)
REVERT: A  574 GLU cc_start: 0.6079 (tp30) cc_final: 0.5427 (pt0)
  outliers start: 14
  outliers final: 8
  residues processed: 80
  average time/residue: 0.0853
  time to fit residues: 9.1854
Evaluate side-chains
  78 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  378 THR
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  723 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 31 optimal weight:    2.9990
   chunk 22 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 70 optimal weight:    7.9990
   chunk 13 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 61 optimal weight:    0.6980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.172176 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.140578 restraints weight = 7886.013|
|-----------------------------------------------------------------------------|
r_work (start): 0.3713 rms_B_bonded: 2.37
r_work: 0.3595 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3595
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   6310  Z= 0.141
  Angle     :  0.565   8.932   8513  Z= 0.276
  Chirality :  0.043   0.130    922
  Planarity :  0.003   0.038   1097
  Dihedral  :  5.048  42.459    839
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 6.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 12.22 %
    Favored  : 85.52 %
  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 aren not related in a simple way.
  whole:  0.34 (0.31), residues: 758
  helix:  0.91 (0.27), residues: 373
  sheet: -1.36 (0.66), residues: 58
  loop : -0.13 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  23 
 TYR   0.012   0.001   TYR A 266 
 PHE   0.011   0.001   PHE A 473 
 TRP   0.004   0.001   TRP A 593 
 HIS   0.004   0.001   HIS A 753 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6310)
  covalent geometry    : angle       0.56451 ( 8513)
  hydrogen bonds       : bond        0.03237 (  295)
  hydrogen bonds       : angle       4.12826 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8287 (tm-30) cc_final: 0.7963 (tm-30)
REVERT: A  195 PHE cc_start: 0.7261 (m-80) cc_final: 0.7040 (m-10)
REVERT: A  374 GLU cc_start: 0.7097 (mm-30) cc_final: 0.6495 (tt0)
REVERT: A  433 GLU cc_start: 0.7984 (tm-30) cc_final: 0.7737 (tt0)
REVERT: A  574 GLU cc_start: 0.6082 (tp30) cc_final: 0.5530 (pt0)
REVERT: A  753 HIS cc_start: 0.7273 (m-70) cc_final: 0.7050 (m-70)
  outliers start: 15
  outliers final: 9
  residues processed: 82
  average time/residue: 0.0834
  time to fit residues: 9.2386
Evaluate side-chains
  77 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   76 VAL
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  698 VAL
Chi-restraints excluded: chain A residue  723 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 36 optimal weight:    0.3980
   chunk 65 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0770
   chunk 74 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 54 optimal weight:    0.2980
   chunk 24 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 22 optimal weight:    0.5980
   overall best weight:    0.4338

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.173553 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.141779 restraints weight = 7862.276|
|-----------------------------------------------------------------------------|
r_work (start): 0.3746 rms_B_bonded: 2.39
r_work: 0.3629 rms_B_bonded: 3.14 restraints_weight: 0.5000
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6310  Z= 0.110
  Angle     :  0.552   9.516   8513  Z= 0.268
  Chirality :  0.041   0.130    922
  Planarity :  0.003   0.039   1097
  Dihedral  :  4.895  41.411    839
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 13.27 %
    Favored  : 85.37 %
  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 aren not related in a simple way.
  whole:  0.46 (0.31), residues: 758
  helix:  1.03 (0.27), residues: 373
  sheet: -1.28 (0.65), residues: 58
  loop : -0.10 (0.34), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  23 
 TYR   0.011   0.001   TYR A 266 
 PHE   0.011   0.001   PHE A 473 
 TRP   0.004   0.001   TRP A 130 
 HIS   0.003   0.000   HIS A  97 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6310)
  covalent geometry    : angle       0.55190 ( 8513)
  hydrogen bonds       : bond        0.02993 (  295)
  hydrogen bonds       : angle       4.02400 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 79
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7957 (tm-30)
REVERT: A   92 MET cc_start: 0.7415 (mmp) cc_final: 0.6855 (mtm)
REVERT: A  195 PHE cc_start: 0.7232 (m-80) cc_final: 0.7002 (m-10)
REVERT: A  374 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6311 (tt0)
REVERT: A  470 PHE cc_start: 0.7834 (t80) cc_final: 0.7471 (t80)
REVERT: A  574 GLU cc_start: 0.6000 (tp30) cc_final: 0.5531 (pt0)
REVERT: A  753 HIS cc_start: 0.7281 (m-70) cc_final: 0.7054 (m-70)
  outliers start: 9
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0887
  time to fit residues: 9.9009
Evaluate side-chains
  79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  723 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 67 optimal weight:    0.0070
   chunk 32 optimal weight:    2.9990
   chunk 50 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   chunk 18 optimal weight:    0.9980
   chunk 68 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.7198

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.172874 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.141353 restraints weight = 7886.520|
|-----------------------------------------------------------------------------|
r_work (start): 0.3737 rms_B_bonded: 2.37
r_work: 0.3613 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.3435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6310  Z= 0.138
  Angle     :  0.572  10.163   8513  Z= 0.276
  Chirality :  0.042   0.128    922
  Planarity :  0.003   0.036   1097
  Dihedral  :  4.970  41.085    839
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.42 %
    Favored  : 85.07 %
  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 aren not related in a simple way.
  whole:  0.35 (0.30), residues: 758
  helix:  0.94 (0.27), residues: 374
  sheet: -1.33 (0.65), residues: 58
  loop : -0.16 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.011   0.001   TYR A 266 
 PHE   0.011   0.001   PHE A 473 
 TRP   0.004   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6310)
  covalent geometry    : angle       0.57191 ( 8513)
  hydrogen bonds       : bond        0.03163 (  295)
  hydrogen bonds       : angle       4.08745 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8285 (tm-30) cc_final: 0.7965 (tm-30)
REVERT: A   92 MET cc_start: 0.7436 (mmp) cc_final: 0.6872 (mtm)
REVERT: A  195 PHE cc_start: 0.7195 (m-80) cc_final: 0.6994 (m-10)
REVERT: A  374 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6339 (tt0)
REVERT: A  388 MET cc_start: 0.8556 (mtt) cc_final: 0.8296 (mtt)
REVERT: A  517 LEU cc_start: 0.7657 (mt) cc_final: 0.7444 (mt)
REVERT: A  574 GLU cc_start: 0.6029 (tp30) cc_final: 0.5546 (pt0)
  outliers start: 10
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0897
  time to fit residues: 9.1769
Evaluate side-chains
  79 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  723 ARG
Chi-restraints excluded: chain A residue  730 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 2 optimal weight:    0.9990
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   chunk 32 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.171773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.139971 restraints weight = 7861.388|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 2.37
r_work: 0.3594 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.3503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6310  Z= 0.151
  Angle     :  0.594  10.459   8513  Z= 0.290
  Chirality :  0.043   0.131    922
  Planarity :  0.003   0.036   1097
  Dihedral  :  5.072  41.149    839
  Min Nonbonded Distance : 2.042

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 13.27 %
    Favored  : 85.07 %
  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 aren not related in a simple way.
  whole:  0.27 (0.30), residues: 758
  helix:  0.88 (0.27), residues: 374
  sheet: -1.41 (0.65), residues: 58
  loop : -0.21 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.012   0.001   TYR A 310 
 PHE   0.011   0.001   PHE A  38 
 TRP   0.004   0.001   TRP A 130 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6310)
  covalent geometry    : angle       0.59415 ( 8513)
  hydrogen bonds       : bond        0.03244 (  295)
  hydrogen bonds       : angle       4.14386 (  837)

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

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

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1516 Ramachandran restraints generated.
    758 Oldfield, 0 Emsley, 758 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   73 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7926 (tm-30)
REVERT: A   92 MET cc_start: 0.7443 (mmp) cc_final: 0.6853 (mtm)
REVERT: A  195 PHE cc_start: 0.7241 (m-80) cc_final: 0.7010 (m-10)
REVERT: A  374 GLU cc_start: 0.6938 (mm-30) cc_final: 0.6188 (tt0)
REVERT: A  470 PHE cc_start: 0.7954 (t80) cc_final: 0.7592 (t80)
REVERT: A  517 LEU cc_start: 0.7716 (mt) cc_final: 0.7503 (mt)
REVERT: A  574 GLU cc_start: 0.6064 (tp30) cc_final: 0.5551 (pt0)
REVERT: A  783 ARG cc_start: 0.8769 (tmm-80) cc_final: 0.8561 (ttm110)
  outliers start: 11
  outliers final: 8
  residues processed: 78
  average time/residue: 0.0864
  time to fit residues: 9.0425
Evaluate side-chains
  81 residues out of total 663 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 73
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 MET
Chi-restraints excluded: chain A residue  177 THR
Chi-restraints excluded: chain A residue  308 TYR
Chi-restraints excluded: chain A residue  420 VAL
Chi-restraints excluded: chain A residue  481 THR
Chi-restraints excluded: chain A residue  695 CYS
Chi-restraints excluded: chain A residue  723 ARG
Chi-restraints excluded: chain A residue  730 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 54 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 67 optimal weight:    0.0870
   chunk 75 optimal weight:    0.9980
   overall best weight:    0.7558

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

Flipped N/Q/H residues before XYZ refinement:
** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.170080 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.138477 restraints weight = 7825.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3723 rms_B_bonded: 2.36
r_work: 0.3601 rms_B_bonded: 3.09 restraints_weight: 0.5000
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6310  Z= 0.146
  Angle     :  0.599  10.647   8513  Z= 0.290
  Chirality :  0.043   0.129    922
  Planarity :  0.003   0.036   1097
  Dihedral  :  5.077  41.082    839
  Min Nonbonded Distance : 2.046

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 13.27 %
    Favored  : 84.77 %
  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 aren not related in a simple way.
  whole:  0.27 (0.31), residues: 758
  helix:  0.90 (0.27), residues: 374
  sheet: -1.42 (0.66), residues: 58
  loop : -0.23 (0.34), residues: 326

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 243 
 TYR   0.012   0.001   TYR A 266 
 PHE   0.011   0.001   PHE A 473 
 TRP   0.004   0.001   TRP A 130 
 HIS   0.002   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 6310)
  covalent geometry    : angle       0.59933 ( 8513)
  hydrogen bonds       : bond        0.03265 (  295)
  hydrogen bonds       : angle       4.15544 (  837)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1540.35 seconds
wall clock time: 27 minutes 10.59 seconds (1630.59 seconds total)