Starting phenix.real_space_refine
on Wed Mar  4 08:34:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7m5o_23678/03_2026/7m5o_23678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7m5o_23678/03_2026/7m5o_23678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.54
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7m5o_23678/03_2026/7m5o_23678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7m5o_23678/03_2026/7m5o_23678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7m5o_23678/03_2026/7m5o_23678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7m5o_23678/03_2026/7m5o_23678.cif"
  }
  resolution = 3.54
  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=   0.173 sd=   0.984
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 261 atoms to isotropic.
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: 7
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      37      5.49       5
     S      20      5.16       5
     C    3633      2.51       5
     N    1104      2.21       5
     O    1218      1.98       5
     H    5635      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 49 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: 11648
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 10449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 655, 10449
          Classifications: {'peptide': 655}
          Link IDs: {'PTRANS': 39, 'TRANS': 615}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 1198
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 1198
          Classifications: {'RNA': 37}
          Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 4, 'rna3p_pur': 15, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 10, 'rna3p': 26}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   9735  SG  CYS A 667      47.731  13.611  37.310  1.00139.12           S
  ATOM   9782  SG  CYS A 670      48.241  12.976  33.639  1.00137.51           S
  ATOM   9984  SG  CYS A 685      44.845  12.824  35.611  1.00142.82           S
  ATOM  10024  SG  CYS A 688      47.103   9.939  35.540  1.00139.82           S

  Time building chain proxies: 2.22, per 1000 atoms: 0.19
  Number of scatterers: 11648
  At special positions: 0
  Unit cell: (79.165, 88.085, 111.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      1     29.99
     S      20     16.00
     P      37     15.00
     O    1218      8.00
     N    1104      7.00
     C    3633      6.00
     H    5635      1.00
    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: 1.05
  Conformation dependent library (CDL) restraints added in 419.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 801 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 688 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 670 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 685 "
        pdb="ZN    ZN A 801 " - pdb=" SG  CYS A 667 "
      Number of angles added : 6


  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1240

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 3 sheets defined
      45.8% alpha, 8.7% beta
      5 base pairs and 11 stacking pairs defined.
    Time for finding SS restraints: 1.51
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 75
    Processing helix  chain 'A' and resid 76 through 91
      removed outlier: 3.582A  pdb=" N   ALA A  91 " --> pdb=" O   ARG A  87 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 100
      removed outlier: 3.912A  pdb=" N   ARG A  97 " --> pdb=" O   SER A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 117
    Processing helix  chain 'A' and resid 129 through 169
      removed outlier: 3.999A  pdb=" N   LEU A 144 " --> pdb=" O   TYR A 140 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   VAL A 147 " --> pdb=" O   VAL A 143 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ASP A 167 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 252 through 256
      removed outlier: 3.650A  pdb=" N   ARG A 256 " --> pdb=" O   GLU A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 296
      removed outlier: 3.930A  pdb=" N   ASP A 296 " --> pdb=" O   GLU A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 323
      removed outlier: 3.994A  pdb=" N   ARG A 323 " --> pdb=" O   ASN A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 338
    Processing helix  chain 'A' and resid 373 through 383
      removed outlier: 4.085A  pdb=" N   ALA A 377 " --> pdb=" O   LYS A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 454
    Processing helix  chain 'A' and resid 456 through 466
      removed outlier: 3.658A  pdb=" N   GLN A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   ALA A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   GLU A 462 " --> pdb=" O   ALA A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 483
    Processing helix  chain 'A' and resid 499 through 509
      removed outlier: 3.613A  pdb=" N   GLU A 503 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 544
    Processing helix  chain 'A' and resid 549 through 567
      removed outlier: 3.965A  pdb=" N   LEU A 555 " --> pdb=" O   GLU A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 597
      removed outlier: 3.930A  pdb=" N   LEU A 571 " --> pdb=" O   SER A 567 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   VAL A 588 " --> pdb=" O   SER A 584 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 627
      removed outlier: 3.602A  pdb=" N   PHE A 626 " --> pdb=" O   TRP A 623 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   PHE A 627 " --> pdb=" O   ASP A 624 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 623 through 627'
    Processing helix  chain 'A' and resid 635 through 651
      removed outlier: 4.174A  pdb=" N   THR A 649 " --> pdb=" O   SER A 645 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG A 651 " --> pdb=" O   LEU A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 664
      removed outlier: 4.612A  pdb=" N   THR A 663 " --> pdb=" O   ARG A 659 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER A 664 " --> pdb=" O   PRO A 660 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 659 through 664'
    Processing helix  chain 'A' and resid 674 through 678
      removed outlier: 4.245A  pdb=" N   ARG A 678 " --> pdb=" O   VAL A 675 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 709
      removed outlier: 3.863A  pdb=" N   THR A 709 " --> pdb=" O   GLN A 705 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 197 through 199
      removed outlier: 5.543A  pdb=" N   VAL A  66 " --> pdb=" O   ASP A 312 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ASP A 312 " --> pdb=" O   VAL A  66 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   THR A  68 " --> pdb=" O   VAL A 310 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE A 304 " --> pdb=" O   ASP A 307 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 262
    Processing sheet with id=AA3, first strand: chain 'A' and resid 370 through 371
      removed outlier: 6.656A  pdb=" N   LEU A 370 " --> pdb=" O   GLU A 657 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 658 " --> pdb=" O   ILE A 605 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   VAL A 604 " --> pdb=" O   ALA A 389 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   VAL A 391 " --> pdb=" O   VAL A 604 " (cutoff:3.500A)
      removed outlier: 8.334A  pdb=" N   GLU A 606 " --> pdb=" O   VAL A 391 " (cutoff:3.500A)
      removed outlier: 8.498A  pdb=" N   ILE A 393 " --> pdb=" O   GLU A 606 " (cutoff:3.500A)
      removed outlier: 6.314A  pdb=" N   ARG A 407 " --> pdb=" O   PRO A 419 " (cutoff:3.500A)

    222 hydrogen bonds defined for protein.
    636 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      14 hydrogen bonds
      28 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      11 stacking parallelities
  Total time for adding SS restraints: 2.25

  Time building geometry restraints manager: 1.39 seconds

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

  Histogram of bond lengths:
        0.84 -     1.04: 5623
        1.04 -     1.23: 113
        1.23 -     1.43: 2616
        1.43 -     1.63: 3478
        1.63 -     1.82: 25
  Bond restraints: 11855
  Sorted by residual:
  bond pdb=" CA  PRO A 191 "
       pdb=" C   PRO A 191 "
    ideal  model  delta    sigma   weight residual
    1.517  1.523 -0.006 6.70e-03 2.23e+04 8.64e-01
  bond pdb=" CB  LYS A 669 "
       pdb=" CG  LYS A 669 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.57e-01
  bond pdb=" CB  CYS A 685 "
       pdb=" HB3 CYS A 685 "
    ideal  model  delta    sigma   weight residual
    0.970  0.987 -0.017 2.00e-02 2.50e+03 7.04e-01
  bond pdb=" N   ILE A 232 "
       pdb=" CA  ILE A 232 "
    ideal  model  delta    sigma   weight residual
    1.468  1.458  0.010 1.22e-02 6.72e+03 6.55e-01
  bond pdb=" CB  TRP A 287 "
       pdb=" CG  TRP A 287 "
    ideal  model  delta    sigma   weight residual
    1.498  1.473  0.025 3.10e-02 1.04e+03 6.39e-01
  ... (remaining 11850 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.99: 19576
        0.99 -     1.98: 1609
        1.98 -     2.98: 187
        2.98 -     3.97: 44
        3.97 -     4.96: 4
  Bond angle restraints: 21420
  Sorted by residual:
  angle pdb=" CA  CYS A 685 "
        pdb=" CB  CYS A 685 "
        pdb=" SG  CYS A 685 "
      ideal   model   delta    sigma   weight residual
     114.40  109.44    4.96 2.30e+00 1.89e-01 4.65e+00
  angle pdb=" N   ASP A 421 "
        pdb=" CA  ASP A 421 "
        pdb=" C   ASP A 421 "
      ideal   model   delta    sigma   weight residual
     108.13  111.72   -3.59 1.72e+00 3.38e-01 4.36e+00
  angle pdb=" CA  GLU A 632 "
        pdb=" CB  GLU A 632 "
        pdb=" CG  GLU A 632 "
      ideal   model   delta    sigma   weight residual
     114.10  118.03   -3.93 2.00e+00 2.50e-01 3.87e+00
  angle pdb=" N   GLU A 411 "
        pdb=" CA  GLU A 411 "
        pdb=" C   GLU A 411 "
      ideal   model   delta    sigma   weight residual
     109.50  106.54    2.96 1.58e+00 4.01e-01 3.52e+00
  angle pdb=" N   THR A 409 "
        pdb=" CA  THR A 409 "
        pdb=" C   THR A 409 "
      ideal   model   delta    sigma   weight residual
     110.80  106.89    3.91 2.13e+00 2.20e-01 3.37e+00
  ... (remaining 21415 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.17: 5210
       26.17 -    52.35: 288
       52.35 -    78.52: 102
       78.52 -   104.69: 9
      104.69 -   130.86: 3
  Dihedral angle restraints: 5612
    sinusoidal: 3413
      harmonic: 2199
  Sorted by residual:
  dihedral pdb=" CA  PRO A 660 "
           pdb=" C   PRO A 660 "
           pdb=" N   GLU A 661 "
           pdb=" CA  GLU A 661 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.91  -31.09     0      5.00e+00 4.00e-02 3.87e+01
  dihedral pdb=" CA  ASP A 421 "
           pdb=" C   ASP A 421 "
           pdb=" N   ARG A 422 "
           pdb=" CA  ARG A 422 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.54   25.46     0      5.00e+00 4.00e-02 2.59e+01
  dihedral pdb=" O4'   A B   8 "
           pdb=" C1'   A B   8 "
           pdb=" N9    A B   8 "
           pdb=" C4    A B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -106.00 -178.61   72.61     1      1.70e+01 3.46e-03 2.33e+01
  ... (remaining 5609 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 589
       0.025 -    0.050: 259
       0.050 -    0.075: 69
       0.075 -    0.100: 32
       0.100 -    0.124: 31
  Chirality restraints: 980
  Sorted by residual:
  chirality pdb=" CA  ILE A 351 "
            pdb=" N   ILE A 351 "
            pdb=" C   ILE A 351 "
            pdb=" CB  ILE A 351 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.87e-01
  chirality pdb=" CA  ILE A 232 "
            pdb=" N   ILE A 232 "
            pdb=" C   ILE A 232 "
            pdb=" CB  ILE A 232 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  chirality pdb=" CA  ILE A 325 "
            pdb=" N   ILE A 325 "
            pdb=" C   ILE A 325 "
            pdb=" CB  ILE A 325 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.81e-01
  ... (remaining 977 not shown)

  Planarity restraints: 1623
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 455 "    0.039 5.00e-02 4.00e+02   5.86e-02 5.49e+00
        pdb=" N   PRO A 456 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 456 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 456 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 276 "    0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO A 277 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 277 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 277 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 667 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.54e+00
        pdb=" N   PRO A 668 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 668 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 668 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1620 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.16: 492
        2.16 -     2.77: 21747
        2.77 -     3.38: 31525
        3.38 -     3.99: 38662
        3.99 -     4.60: 58960
  Nonbonded interactions: 151386
  Sorted by model distance:
  nonbonded pdb=" O   SER A 105 "
            pdb=" HD1 HIS A 109 "
     model   vdw
     1.545 2.450
  nonbonded pdb="HH21 ARG A 212 "
            pdb=" OE2 GLU A 214 "
     model   vdw
     1.593 2.450
  nonbonded pdb=" HE  ARG A 226 "
            pdb=" O   ALA A 297 "
     model   vdw
     1.598 2.450
  nonbonded pdb=" OD1 ASN A 497 "
            pdb=" HZ1 LYS A 536 "
     model   vdw
     1.605 2.450
  nonbonded pdb="HD21 ASN A 586 "
            pdb=" OP1   A B  -1 "
     model   vdw
     1.612 2.450
  ... (remaining 151381 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.050
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     15.400
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.270
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
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      :  0.004   0.163   6224  Z= 0.169
  Angle     :  0.619  19.241   8617  Z= 0.314
  Chirality :  0.036   0.124    980
  Planarity :  0.004   0.059    978
  Dihedral  : 18.446 130.863   2605
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  7.65 %
    Favored  : 91.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.03 (0.31), residues: 651
  helix: -0.30 (0.32), residues: 257
  sheet: -1.90 (0.53), residues: 87
  loop : -2.07 (0.32), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 139 
 TYR   0.005   0.001   TYR A  88 
 PHE   0.007   0.001   PHE A 626 
 TRP   0.008   0.001   TRP A  76 
 HIS   0.005   0.001   HIS A 672 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6220)
  covalent geometry    : angle       0.54475 ( 8611)
  hydrogen bonds       : bond        0.19162 (  236)
  hydrogen bonds       : angle       7.55376 (  664)
  metal coordination   : bond        0.10737 (    4)
  metal coordination   : angle      11.18386 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 134
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  148 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7174 (tm130)
REVERT: A  172 GLU cc_start: 0.7769 (tt0) cc_final: 0.7452 (tt0)
REVERT: A  276 SER cc_start: 0.8613 (p) cc_final: 0.8203 (m)
REVERT: A  578 GLU cc_start: 0.8108 (tp30) cc_final: 0.7493 (tp30)
REVERT: A  582 ARG cc_start: 0.8575 (mtt-85) cc_final: 0.8222 (mtt-85)
REVERT: A  590 GLU cc_start: 0.7518 (tp30) cc_final: 0.7064 (tp30)
  outliers start: 7
  outliers final: 3
  residues processed: 140
  average time/residue: 0.1679
  time to fit residues: 30.7650
Evaluate side-chains
  115 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 111
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  353 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    7.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    4.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 280 ASN
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** 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 = 0.3612 r_free = 0.3612 target = 0.101647 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.085961 restraints weight = 42636.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.089418 restraints weight = 15596.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.091414 restraints weight = 7603.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.092580 restraints weight = 4607.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.093267 restraints weight = 3375.231|
|-----------------------------------------------------------------------------|
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7588
moved from start:          0.1498

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   6224  Z= 0.176
  Angle     :  0.621  10.540   8617  Z= 0.324
  Chirality :  0.039   0.133    980
  Planarity :  0.005   0.052    978
  Dihedral  : 18.929 133.227   1315
  Min Nonbonded Distance : 2.291

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 15.12 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.20 (0.31), residues: 651
  helix:  0.53 (0.31), residues: 261
  sheet: -1.23 (0.54), residues: 87
  loop : -1.86 (0.33), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 318 
 TYR   0.012   0.002   TYR A 123 
 PHE   0.014   0.002   PHE A 423 
 TRP   0.008   0.001   TRP A 322 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00377 ( 6220)
  covalent geometry    : angle       0.60510 ( 8611)
  hydrogen bonds       : bond        0.05345 (  236)
  hydrogen bonds       : angle       5.23679 (  664)
  metal coordination   : bond        0.00997 (    4)
  metal coordination   : angle       5.27524 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 122
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.7971 (t0) cc_final: 0.7689 (t0)
REVERT: A  240 ARG cc_start: 0.8556 (mtp-110) cc_final: 0.8261 (mtp-110)
REVERT: A  276 SER cc_start: 0.8634 (p) cc_final: 0.8245 (m)
REVERT: A  283 MET cc_start: 0.7618 (mmp) cc_final: 0.7376 (mmm)
REVERT: A  578 GLU cc_start: 0.8057 (tp30) cc_final: 0.7675 (tp30)
  outliers start: 11
  outliers final: 10
  residues processed: 128
  average time/residue: 0.1656
  time to fit residues: 27.6583
Evaluate side-chains
  125 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 115
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 21 optimal weight:    3.9990
   chunk 25 optimal weight:    0.7980
   chunk 54 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9980
   chunk 22 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 151 ASN
A 280 ASN
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** 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 = 0.3625 r_free = 0.3625 target = 0.102327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.086180 restraints weight = 42849.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.089728 restraints weight = 15682.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.091773 restraints weight = 7655.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.092979 restraints weight = 4659.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.093673 restraints weight = 3404.191|
|-----------------------------------------------------------------------------|
r_work (final): 0.3485
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1877

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6224  Z= 0.131
  Angle     :  0.585   9.653   8617  Z= 0.297
  Chirality :  0.038   0.129    980
  Planarity :  0.005   0.044    978
  Dihedral  : 18.806 130.483   1315
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 16.19 %
    Favored  : 81.32 %
  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: -0.65 (0.32), residues: 651
  helix:  1.08 (0.31), residues: 266
  sheet: -1.06 (0.56), residues: 82
  loop : -1.66 (0.34), residues: 303

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 582 
 TYR   0.013   0.002   TYR A 123 
 PHE   0.012   0.002   PHE A 423 
 TRP   0.007   0.001   TRP A 322 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6220)
  covalent geometry    : angle       0.56015 ( 8611)
  hydrogen bonds       : bond        0.04649 (  236)
  hydrogen bonds       : angle       4.79911 (  664)
  metal coordination   : bond        0.02129 (    4)
  metal coordination   : angle       6.37631 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 114
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.8018 (t0) cc_final: 0.7691 (t0)
REVERT: A  276 SER cc_start: 0.8672 (p) cc_final: 0.8228 (m)
REVERT: A  296 ASP cc_start: 0.7786 (t0) cc_final: 0.7488 (t0)
REVERT: A  394 ASP cc_start: 0.8271 (t0) cc_final: 0.8038 (t0)
REVERT: A  423 PHE cc_start: 0.8754 (p90) cc_final: 0.8342 (p90)
REVERT: A  578 GLU cc_start: 0.8089 (tp30) cc_final: 0.7733 (tp30)
  outliers start: 14
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1612
  time to fit residues: 25.5209
Evaluate side-chains
  122 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 111
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  393 ILE
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 43 optimal weight:    5.9990
   chunk 59 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 13 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   chunk 2 optimal weight:    1.9990
   chunk 44 optimal weight:    0.9990
   overall best weight:    1.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 280 ASN
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** 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 = 0.3599 r_free = 0.3599 target = 0.100869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.084759 restraints weight = 42836.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.088283 restraints weight = 15776.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.090327 restraints weight = 7771.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.091527 restraints weight = 4741.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.092208 restraints weight = 3453.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.2241

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6224  Z= 0.168
  Angle     :  0.603   8.317   8617  Z= 0.305
  Chirality :  0.038   0.127    980
  Planarity :  0.005   0.040    978
  Dihedral  : 18.775 131.568   1313
  Min Nonbonded Distance : 2.311

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 16.01 %
    Favored  : 80.78 %
  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: -0.33 (0.33), residues: 651
  helix:  1.44 (0.32), residues: 264
  sheet: -1.00 (0.61), residues: 70
  loop : -1.52 (0.34), residues: 317

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 240 
 TYR   0.008   0.002   TYR A 224 
 PHE   0.010   0.002   PHE A 423 
 TRP   0.008   0.001   TRP A 322 
 HIS   0.005   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 ( 6220)
  covalent geometry    : angle       0.58339 ( 8611)
  hydrogen bonds       : bond        0.04387 (  236)
  hydrogen bonds       : angle       4.58530 (  664)
  metal coordination   : bond        0.01405 (    4)
  metal coordination   : angle       5.78375 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 108
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 ASN cc_start: 0.7993 (t0) cc_final: 0.7741 (t0)
REVERT: A  394 ASP cc_start: 0.8263 (t0) cc_final: 0.8061 (t0)
REVERT: A  582 ARG cc_start: 0.8537 (mtt-85) cc_final: 0.8286 (mtt-85)
  outliers start: 18
  outliers final: 16
  residues processed: 120
  average time/residue: 0.1737
  time to fit residues: 27.0537
Evaluate side-chains
  123 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 107
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  424 THR
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 63 optimal weight:    5.9990
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 16 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 22 optimal weight:    0.7980
   chunk 14 optimal weight:    0.1980
   chunk 9 optimal weight:    0.6980
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
A 280 ASN
** A 386 GLN ** 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 = 0.3595 r_free = 0.3595 target = 0.100429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.084404 restraints weight = 43146.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.087908 restraints weight = 15726.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.089943 restraints weight = 7728.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.091075 restraints weight = 4686.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.091794 restraints weight = 3441.312|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.2497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6224  Z= 0.143
  Angle     :  0.571   6.801   8617  Z= 0.292
  Chirality :  0.037   0.127    980
  Planarity :  0.004   0.038    978
  Dihedral  : 18.744 129.580   1313
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 17.97 %
    Favored  : 78.65 %
  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: -0.19 (0.33), residues: 651
  helix:  1.58 (0.32), residues: 266
  sheet: -0.97 (0.62), residues: 70
  loop : -1.48 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 240 
 TYR   0.021   0.002   TYR A 224 
 PHE   0.008   0.001   PHE A 354 
 TRP   0.008   0.001   TRP A  76 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6220)
  covalent geometry    : angle       0.55747 ( 8611)
  hydrogen bonds       : bond        0.04150 (  236)
  hydrogen bonds       : angle       4.44262 (  664)
  metal coordination   : bond        0.01006 (    4)
  metal coordination   : angle       4.69195 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 112
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASP cc_start: 0.7933 (t0) cc_final: 0.7442 (t0)
REVERT: A  424 THR cc_start: 0.8582 (m) cc_final: 0.8382 (p)
REVERT: A  578 GLU cc_start: 0.8023 (tp30) cc_final: 0.7779 (tp30)
REVERT: A  606 GLU cc_start: 0.7882 (pt0) cc_final: 0.7672 (pt0)
  outliers start: 19
  outliers final: 17
  residues processed: 125
  average time/residue: 0.1711
  time to fit residues: 28.1358
Evaluate side-chains
  125 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  272 VAL
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 22 optimal weight:    0.2980
   chunk 30 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 37 optimal weight:    0.9990
   chunk 53 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 31 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0570
   overall best weight:    0.6300

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 GLN ** 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 = 0.3610 r_free = 0.3610 target = 0.101428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.085443 restraints weight = 42772.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.088947 restraints weight = 15565.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.090938 restraints weight = 7608.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.092136 restraints weight = 4636.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.092732 restraints weight = 3372.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7592
moved from start:          0.2671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6224  Z= 0.117
  Angle     :  0.556   6.178   8617  Z= 0.285
  Chirality :  0.037   0.126    980
  Planarity :  0.004   0.038    978
  Dihedral  : 18.664 127.664   1313
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 19.93 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.34), residues: 651
  helix:  1.83 (0.33), residues: 266
  sheet: -0.84 (0.63), residues: 70
  loop : -1.44 (0.34), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 240 
 TYR   0.015   0.002   TYR A 224 
 PHE   0.014   0.001   PHE A 423 
 TRP   0.008   0.001   TRP A  76 
 HIS   0.003   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 6220)
  covalent geometry    : angle       0.54586 ( 8611)
  hydrogen bonds       : bond        0.03858 (  236)
  hydrogen bonds       : angle       4.30298 (  664)
  metal coordination   : bond        0.00793 (    4)
  metal coordination   : angle       4.11489 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 113
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASP cc_start: 0.7862 (t0) cc_final: 0.7357 (t0)
REVERT: A  578 GLU cc_start: 0.8038 (tp30) cc_final: 0.7791 (tp30)
  outliers start: 17
  outliers final: 15
  residues processed: 123
  average time/residue: 0.1658
  time to fit residues: 26.9832
Evaluate side-chains
  126 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 111
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  589 ILE
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 58 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 45 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 13 optimal weight:    0.0870
   chunk 46 optimal weight:    0.0980
   chunk 2 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.5760

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 GLN ** 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 = 0.3615 r_free = 0.3615 target = 0.101717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.085876 restraints weight = 42772.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.089366 restraints weight = 15509.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.091365 restraints weight = 7537.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.092523 restraints weight = 4567.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.093094 restraints weight = 3330.083|
|-----------------------------------------------------------------------------|
r_work (final): 0.3476
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6224  Z= 0.110
  Angle     :  0.541   7.048   8617  Z= 0.276
  Chirality :  0.037   0.127    980
  Planarity :  0.004   0.037    978
  Dihedral  : 18.586 127.400   1313
  Min Nonbonded Distance : 2.148

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.99 %
    Favored  : 96.01 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 19.22 %
    Favored  : 77.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.23 (0.34), residues: 651
  helix:  2.05 (0.33), residues: 266
  sheet: -1.14 (0.61), residues: 78
  loop : -1.26 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 240 
 TYR   0.015   0.002   TYR A 364 
 PHE   0.009   0.001   PHE A 517 
 TRP   0.008   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6220)
  covalent geometry    : angle       0.53180 ( 8611)
  hydrogen bonds       : bond        0.03703 (  236)
  hydrogen bonds       : angle       4.17401 (  664)
  metal coordination   : bond        0.00692 (    4)
  metal coordination   : angle       3.73449 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.307 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASP cc_start: 0.7848 (t0) cc_final: 0.7353 (t0)
REVERT: A  419 PRO cc_start: 0.9117 (Cg_endo) cc_final: 0.8904 (Cg_exo)
REVERT: A  536 LYS cc_start: 0.2691 (OUTLIER) cc_final: 0.2476 (mttm)
REVERT: A  578 GLU cc_start: 0.8060 (tp30) cc_final: 0.7787 (tp30)
  outliers start: 18
  outliers final: 16
  residues processed: 127
  average time/residue: 0.1618
  time to fit residues: 26.9993
Evaluate side-chains
  129 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 112
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  585 ILE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 1 optimal weight:    2.9990
   chunk 49 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 33 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 386 GLN ** 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 = 0.3609 r_free = 0.3609 target = 0.101187 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.085328 restraints weight = 42897.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.088819 restraints weight = 15392.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.090829 restraints weight = 7449.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.091969 restraints weight = 4505.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.092672 restraints weight = 3305.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7577
moved from start:          0.2997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6224  Z= 0.124
  Angle     :  0.547   7.181   8617  Z= 0.279
  Chirality :  0.037   0.164    980
  Planarity :  0.004   0.040    978
  Dihedral  : 18.580 127.691   1313
  Min Nonbonded Distance : 2.207

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 19.40 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.34), residues: 651
  helix:  2.15 (0.33), residues: 266
  sheet: -1.30 (0.53), residues: 94
  loop : -1.29 (0.35), residues: 291

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 240 
 TYR   0.024   0.002   TYR A  90 
 PHE   0.018   0.001   PHE A 423 
 TRP   0.009   0.001   TRP A 322 
 HIS   0.003   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6220)
  covalent geometry    : angle       0.53748 ( 8611)
  hydrogen bonds       : bond        0.03731 (  236)
  hydrogen bonds       : angle       4.17925 (  664)
  metal coordination   : bond        0.00751 (    4)
  metal coordination   : angle       3.92646 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASP cc_start: 0.7943 (t0) cc_final: 0.7416 (t0)
REVERT: A  419 PRO cc_start: 0.9100 (Cg_endo) cc_final: 0.8891 (Cg_exo)
REVERT: A  578 GLU cc_start: 0.8097 (tp30) cc_final: 0.7815 (tp30)
  outliers start: 20
  outliers final: 16
  residues processed: 128
  average time/residue: 0.1634
  time to fit residues: 27.5378
Evaluate side-chains
  127 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 57 optimal weight:    0.0980
   chunk 2 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 19 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   chunk 41 optimal weight:    0.0370
   overall best weight:    0.4658

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 GLN ** 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 = 0.3627 r_free = 0.3627 target = 0.102254 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.086429 restraints weight = 42281.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.089939 restraints weight = 15180.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.091914 restraints weight = 7324.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.093093 restraints weight = 4455.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.093699 restraints weight = 3240.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.3127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6224  Z= 0.104
  Angle     :  0.539   7.758   8617  Z= 0.274
  Chirality :  0.036   0.133    980
  Planarity :  0.004   0.044    978
  Dihedral  : 18.490 126.508   1313
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 7.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.53 %
    Favored  : 96.47 %
  Rotamer:
    Outliers :  3.20 %
    Allowed  : 20.11 %
    Favored  : 76.69 %
  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:  0.34 (0.34), residues: 651
  helix:  2.26 (0.33), residues: 266
  sheet: -1.09 (0.54), residues: 86
  loop : -1.31 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 314 
 TYR   0.019   0.002   TYR A 224 
 PHE   0.018   0.001   PHE A 423 
 TRP   0.009   0.001   TRP A 322 
 HIS   0.002   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6220)
  covalent geometry    : angle       0.53131 ( 8611)
  hydrogen bonds       : bond        0.03569 (  236)
  hydrogen bonds       : angle       4.07036 (  664)
  metal coordination   : bond        0.00560 (    4)
  metal coordination   : angle       3.46496 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 118
  time to evaluate  : 0.314 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  296 ASP cc_start: 0.7849 (t0) cc_final: 0.7008 (t0)
REVERT: A  410 GLN cc_start: 0.8093 (tp40) cc_final: 0.7868 (tp-100)
REVERT: A  536 LYS cc_start: 0.2495 (OUTLIER) cc_final: 0.2172 (mttm)
REVERT: A  578 GLU cc_start: 0.8066 (tp30) cc_final: 0.7792 (tp30)
  outliers start: 18
  outliers final: 16
  residues processed: 129
  average time/residue: 0.1699
  time to fit residues: 28.6541
Evaluate side-chains
  132 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 115
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  608 LEU
Chi-restraints excluded: chain A residue  658 VAL
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 45 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 59 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   overall best weight:    1.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A 386 GLN ** 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 = 0.3551 r_free = 0.3551 target = 0.097582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.081983 restraints weight = 43599.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.085307 restraints weight = 15838.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.087220 restraints weight = 7759.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.088324 restraints weight = 4730.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.088780 restraints weight = 3480.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6224  Z= 0.216
  Angle     :  0.619   8.889   8617  Z= 0.319
  Chirality :  0.039   0.128    980
  Planarity :  0.006   0.051    978
  Dihedral  : 18.733 131.063   1313
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 12.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  3.02 %
    Allowed  : 21.53 %
    Favored  : 75.44 %
  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: -0.15 (0.33), residues: 651
  helix:  1.90 (0.32), residues: 267
  sheet: -1.49 (0.50), residues: 86
  loop : -1.59 (0.34), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 321 
 TYR   0.016   0.002   TYR A 224 
 PHE   0.038   0.002   PHE A 423 
 TRP   0.016   0.002   TRP A 322 
 HIS   0.004   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00466 ( 6220)
  covalent geometry    : angle       0.60464 ( 8611)
  hydrogen bonds       : bond        0.04074 (  236)
  hydrogen bonds       : angle       4.28512 (  664)
  metal coordination   : bond        0.01102 (    4)
  metal coordination   : angle       5.10899 (    6)

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

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

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1302 Ramachandran restraints generated.
    651 Oldfield, 0 Emsley, 651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 116
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  125 HIS cc_start: 0.7385 (t-90) cc_final: 0.7076 (t70)
REVERT: A  578 GLU cc_start: 0.8066 (tp30) cc_final: 0.7768 (tp30)
  outliers start: 17
  outliers final: 15
  residues processed: 126
  average time/residue: 0.1604
  time to fit residues: 26.8371
Evaluate side-chains
  127 residues out of total 562 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 112
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   92 LEU
Chi-restraints excluded: chain A residue  141 ASP
Chi-restraints excluded: chain A residue  148 GLN
Chi-restraints excluded: chain A residue  185 THR
Chi-restraints excluded: chain A residue  200 VAL
Chi-restraints excluded: chain A residue  201 TYR
Chi-restraints excluded: chain A residue  298 LEU
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  355 THR
Chi-restraints excluded: chain A residue  405 ILE
Chi-restraints excluded: chain A residue  516 PHE
Chi-restraints excluded: chain A residue  536 LYS
Chi-restraints excluded: chain A residue  606 GLU
Chi-restraints excluded: chain A residue  679 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 68
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 3 optimal weight:    2.9990
   chunk 56 optimal weight:    6.9990
   chunk 51 optimal weight:    2.9990
   chunk 42 optimal weight:    7.9990
   chunk 45 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 23 optimal weight:    1.9990
   chunk 47 optimal weight:    0.2980
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A  86 GLN
** A 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 477 GLN ** 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 = 0.3583 r_free = 0.3583 target = 0.099458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.083683 restraints weight = 43077.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.087091 restraints weight = 15519.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.089056 restraints weight = 7569.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.090228 restraints weight = 4613.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.090725 restraints weight = 3363.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.3362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6224  Z= 0.136
  Angle     :  0.570   8.340   8617  Z= 0.293
  Chirality :  0.037   0.130    980
  Planarity :  0.005   0.050    978
  Dihedral  : 18.660 129.480   1313
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.92 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 22.42 %
    Favored  : 74.73 %
  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:  0.04 (0.34), residues: 651
  helix:  2.09 (0.33), residues: 266
  sheet: -1.32 (0.51), residues: 86
  loop : -1.53 (0.35), residues: 299

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 314 
 TYR   0.017   0.002   TYR A 224 
 PHE   0.031   0.002   PHE A 423 
 TRP   0.024   0.001   TRP A 308 
 HIS   0.003   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6220)
  covalent geometry    : angle       0.55979 ( 8611)
  hydrogen bonds       : bond        0.03781 (  236)
  hydrogen bonds       : angle       4.14872 (  664)
  metal coordination   : bond        0.00709 (    4)
  metal coordination   : angle       4.14522 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2256.38 seconds
wall clock time: 39 minutes 3.18 seconds (2343.18 seconds total)