Starting phenix.real_space_refine
on Wed Sep 17 04:23:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9j66_61167/09_2025/9j66_61167.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9j66_61167/09_2025/9j66_61167.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9j66_61167/09_2025/9j66_61167.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9j66_61167/09_2025/9j66_61167.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9j66_61167/09_2025/9j66_61167.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9j66_61167/09_2025/9j66_61167.map"
  }
  resolution = 3.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    2580      2.51       5
     N     674      2.21       5
     O     771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4044
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 886
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 886
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 4, 'TRANS': 119}
          Unresolved non-hydrogen bonds: 61
          Unresolved non-hydrogen angles: 73
          Unresolved non-hydrogen dihedrals: 51
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'ARG:plan': 1, 'GLU:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 30
    Chain: "C"
      Number of atoms: 760
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 760
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 7, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 22
    Chain: "A"
      Number of atoms: 1484
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1484
          Classifications: {'peptide': 193}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 11, 'TRANS': 181}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 43
          Unresolved non-hydrogen angles: 53
          Unresolved non-hydrogen dihedrals: 36
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 25
    Chain: "D"
      Number of atoms: 914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 135, 914
          Classifications: {'peptide': 135}
          Incomplete info: {'truncation_to_alanine': 40}
          Link IDs: {'PTRANS': 7, 'TRANS': 127}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 172
          Unresolved non-hydrogen angles: 217
          Unresolved non-hydrogen dihedrals: 146
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 5, 'TYR:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 3}
          Unresolved non-hydrogen planarities: 125
  Time building chain proxies: 1.28, per 1000 atoms: 0.32
  Number of scatterers: 4044
  At special positions: 0
  Unit cell: (71.25, 118.75, 89.3, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O     771      8.00
     N     674      7.00
     C    2580      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  23 " - pdb=" SG  CYS C  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 336 " - pdb=" SG  CYS D 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 379 " - pdb=" SG  CYS D 432 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.32
  Conformation dependent library (CDL) restraints added in 195.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1028

  Finding SS restraints...
    Secondary structure from input PDB file:
      10 helices and 11 sheets defined
      10.2% alpha, 26.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 337 through 341
    Processing helix  chain 'A' and resid 349 through 353
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 383 through 390
      removed outlier: 3.672A  pdb=" N   LEU A 387 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 5.111A  pdb=" N   ASN A 388 " --> pdb=" O   THR A 385 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 390 " --> pdb=" O   LEU A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 4.398A  pdb=" N   ARG A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 404 through 408'
    Processing helix  chain 'A' and resid 417 through 422
    Processing helix  chain 'A' and resid 502 through 505
    Processing helix  chain 'D' and resid 337 through 342
      removed outlier: 3.669A  pdb=" N   PHE D 342 " --> pdb=" O   PHE D 338 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 405 through 410
      removed outlier: 3.573A  pdb=" N   ARG D 408 " --> pdb=" O   ASP D 405 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 416 through 421
    Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 6
      removed outlier: 5.382A  pdb=" N   SER B  84 " --> pdb=" O   VAL B  18 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   VAL B  18 " --> pdb=" O   SER B  84 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   SER B  16 " --> pdb=" O   LEU B  86 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6
      removed outlier: 3.661A  pdb=" N   ASP B  73 " --> pdb=" O   THR B  78 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 50
      removed outlier: 7.114A  pdb=" N   TRP B  36 " --> pdb=" O   MET B  48 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ARG B  50 " --> pdb=" O   ILE B  34 " (cutoff:3.500A)
      removed outlier: 6.868A  pdb=" N   ILE B  34 " --> pdb=" O   ARG B  50 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   TYR B 112 " --> pdb=" O   ARG B  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 106
    Processing sheet with id=AA5, first strand: chain 'C' and resid 19 through 24
      removed outlier: 3.855A  pdb=" N   VAL C  19 " --> pdb=" O   ILE C  75 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ASP C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   SER C  67 " --> pdb=" O   ASP C  70 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 54
    Processing sheet with id=AA7, first strand: chain 'C' and resid 85 through 86
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.607A  pdb=" N   ILE A 402 " --> pdb=" O   TYR A 508 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   TRP A 436 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AB2, first strand: chain 'D' and resid 395 through 403

    109 hydrogen bonds defined for protein.
    255 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.57

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1297
        1.34 -     1.46: 1097
        1.46 -     1.58: 1725
        1.58 -     1.70: 1
        1.70 -     1.82: 22
  Bond restraints: 4142
  Sorted by residual:
  bond pdb=" N   ILE D 410 "
       pdb=" CA  ILE D 410 "
    ideal  model  delta    sigma   weight residual
    1.474  1.458  0.016 1.57e-02 4.06e+03 1.04e+00
  bond pdb=" CA  ASP A 364 "
       pdb=" CB  ASP A 364 "
    ideal  model  delta    sigma   weight residual
    1.539  1.581 -0.042 4.88e-02 4.20e+02 7.42e-01
  bond pdb=" CA  VAL C  58 "
       pdb=" CB  VAL C  58 "
    ideal  model  delta    sigma   weight residual
    1.547  1.538  0.009 1.10e-02 8.26e+03 7.23e-01
  bond pdb=" CA  THR A 470 "
       pdb=" CB  THR A 470 "
    ideal  model  delta    sigma   weight residual
    1.528  1.550 -0.022 2.61e-02 1.47e+03 6.81e-01
  bond pdb=" CA  PRO A 479 "
       pdb=" C   PRO A 479 "
    ideal  model  delta    sigma   weight residual
    1.527  1.519  0.008 1.07e-02 8.73e+03 5.69e-01
  ... (remaining 4137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.98: 5280
        0.98 -     1.96: 310
        1.96 -     2.94: 50
        2.94 -     3.92: 20
        3.92 -     4.90: 5
  Bond angle restraints: 5665
  Sorted by residual:
  angle pdb=" N   ILE D 410 "
        pdb=" CA  ILE D 410 "
        pdb=" C   ILE D 410 "
      ideal   model   delta    sigma   weight residual
     106.21  108.82   -2.61 1.07e+00 8.73e-01 5.93e+00
  angle pdb=" C   SER D 359 "
        pdb=" N   ASN D 360 "
        pdb=" CA  ASN D 360 "
      ideal   model   delta    sigma   weight residual
     122.46  125.88   -3.42 1.41e+00 5.03e-01 5.89e+00
  angle pdb=" CA  TYR B 109 "
        pdb=" CB  TYR B 109 "
        pdb=" CG  TYR B 109 "
      ideal   model   delta    sigma   weight residual
     113.90  118.24   -4.34 1.80e+00 3.09e-01 5.81e+00
  angle pdb=" CA  ILE D 410 "
        pdb=" C   ILE D 410 "
        pdb=" O   ILE D 410 "
      ideal   model   delta    sigma   weight residual
     122.63  120.81    1.82 8.70e-01 1.32e+00 4.36e+00
  angle pdb=" N   ALA C  51 "
        pdb=" CA  ALA C  51 "
        pdb=" CB  ALA C  51 "
      ideal   model   delta    sigma   weight residual
     113.65  110.68    2.97 1.47e+00 4.63e-01 4.08e+00
  ... (remaining 5660 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 2213
       17.58 -    35.15: 153
       35.15 -    52.73: 30
       52.73 -    70.31: 4
       70.31 -    87.88: 4
  Dihedral angle restraints: 2404
    sinusoidal: 796
      harmonic: 1608
  Sorted by residual:
  dihedral pdb=" CB  CYS C  23 "
           pdb=" SG  CYS C  23 "
           pdb=" SG  CYS C  88 "
           pdb=" CB  CYS C  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  144.84  -51.84     1      1.00e+01 1.00e-02 3.67e+01
  dihedral pdb=" CB  CYS A 480 "
           pdb=" SG  CYS A 480 "
           pdb=" SG  CYS A 488 "
           pdb=" CB  CYS A 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -130.58   44.58     1      1.00e+01 1.00e-02 2.76e+01
  dihedral pdb=" CB  CYS D 379 "
           pdb=" SG  CYS D 379 "
           pdb=" SG  CYS D 432 "
           pdb=" CB  CYS D 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -44.66  -41.34     1      1.00e+01 1.00e-02 2.39e+01
  ... (remaining 2401 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.035: 424
       0.035 -    0.070: 139
       0.070 -    0.105: 53
       0.105 -    0.141: 23
       0.141 -    0.176: 2
  Chirality restraints: 641
  Sorted by residual:
  chirality pdb=" CB  THR A 470 "
            pdb=" CA  THR A 470 "
            pdb=" OG1 THR A 470 "
            pdb=" CG2 THR A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.38    0.18 2.00e-01 2.50e+01 7.72e-01
  chirality pdb=" CB  VAL A 524 "
            pdb=" CA  VAL A 524 "
            pdb=" CG1 VAL A 524 "
            pdb=" CG2 VAL A 524 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.47   -0.16 2.00e-01 2.50e+01 6.66e-01
  chirality pdb=" CA  ASN D 360 "
            pdb=" N   ASN D 360 "
            pdb=" C   ASN D 360 "
            pdb=" CB  ASN D 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.48e-01
  ... (remaining 638 not shown)

  Planarity restraints: 735
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C  79 "   -0.052 5.00e-02 4.00e+02   7.99e-02 1.02e+01
        pdb=" N   PRO C  80 "    0.138 5.00e-02 4.00e+02
        pdb=" CA  PRO C  80 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO C  80 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C   7 "   -0.025 5.00e-02 4.00e+02   3.84e-02 2.36e+00
        pdb=" N   PRO C   8 "    0.066 5.00e-02 4.00e+02
        pdb=" CA  PRO C   8 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C   8 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR D 376 "    0.007 2.00e-02 2.50e+03   1.45e-02 2.11e+00
        pdb=" C   THR D 376 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   THR D 376 "    0.010 2.00e-02 2.50e+03
        pdb=" N   PHE D 377 "    0.008 2.00e-02 2.50e+03
  ... (remaining 732 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1265
        2.82 -     3.34: 3534
        3.34 -     3.86: 6328
        3.86 -     4.38: 7162
        4.38 -     4.90: 12696
  Nonbonded interactions: 30985
  Sorted by model distance:
  nonbonded pdb=" O   ASP B  90 "
            pdb=" OH  TYR B  94 "
     model   vdw
     2.298 3.040
  nonbonded pdb=" O   ARG B  67 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.338 3.040
  nonbonded pdb=" ND2 ASN A 501 "
            pdb=" O   TYR A 505 "
     model   vdw
     2.372 3.120
  nonbonded pdb=" O   THR B  33 "
            pdb=" OG1 THR B  33 "
     model   vdw
     2.381 3.040
  nonbonded pdb=" N   GLY B  15 "
            pdb=" O   LEU B  86 "
     model   vdw
     2.392 3.120
  ... (remaining 30980 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:             8.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.270
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6997
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      :  0.003   0.042   4150  Z= 0.126
  Angle     :  0.553   4.902   5681  Z= 0.308
  Chirality :  0.044   0.176    641
  Planarity :  0.005   0.080    735
  Dihedral  : 12.697  87.884   1352
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.35), residues: 539
  helix: -3.38 (0.70), residues: 39
  sheet: -1.32 (0.47), residues: 127
  loop : -1.28 (0.31), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 355 
 TYR   0.017   0.001   TYR B 109 
 PHE   0.007   0.001   PHE C  94 
 TRP   0.011   0.002   TRP C  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4142)
  covalent geometry    : angle       0.55256 ( 5665)
  SS BOND              : bond        0.00265 (    8)
  SS BOND              : angle       0.72383 (   16)
  hydrogen bonds       : bond        0.25605 (  103)
  hydrogen bonds       : angle      11.35749 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8491 (m-10) cc_final: 0.8003 (m-10)
REVERT: A  424 LYS cc_start: 0.7974 (tttp) cc_final: 0.7647 (ttpt)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.0652
  time to fit residues: 6.9144
Evaluate side-chains
  68 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0010
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    4.9990
   chunk 53 optimal weight:    0.9990
   chunk 19 optimal weight:    3.9990
   overall best weight:    0.6990

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
C   6 GLN
C  92 ASN
D 439 ASN
D 506 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.185383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152527 restraints weight = 4990.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.152863 restraints weight = 4582.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.155716 restraints weight = 3816.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.156238 restraints weight = 2672.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.156618 restraints weight = 2423.883|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7089
moved from start:          0.1399

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4150  Z= 0.178
  Angle     :  0.584   6.334   5681  Z= 0.310
  Chirality :  0.047   0.143    641
  Planarity :  0.005   0.064    735
  Dihedral  :  4.835  63.167    598
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 11.96 %
    Favored  : 85.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.06 (0.35), residues: 539
  helix: -3.34 (0.78), residues: 33
  sheet: -1.31 (0.48), residues: 126
  loop : -1.24 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 457 
 TYR   0.040   0.002   TYR B 109 
 PHE   0.013   0.002   PHE C  94 
 TRP   0.015   0.002   TRP B  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 4142)
  covalent geometry    : angle       0.58284 ( 5665)
  SS BOND              : bond        0.00524 (    8)
  SS BOND              : angle       0.80248 (   16)
  hydrogen bonds       : bond        0.04064 (  103)
  hydrogen bonds       : angle       7.45687 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.151 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8775 (m-10) cc_final: 0.8181 (m-10)
  outliers start: 9
  outliers final: 6
  residues processed: 71
  average time/residue: 0.0610
  time to fit residues: 5.6878
Evaluate side-chains
  72 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  117 THR
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 5 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 1 optimal weight:    0.3980
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0470
   chunk 47 optimal weight:    2.9990
   chunk 21 optimal weight:    0.0870
   chunk 0 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.188100 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.154258 restraints weight = 4897.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.157342 restraints weight = 4461.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.160400 restraints weight = 3072.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.160705 restraints weight = 2277.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.161328 restraints weight = 2157.980|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7009
moved from start:          0.1687

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   4150  Z= 0.116
  Angle     :  0.522   5.885   5681  Z= 0.273
  Chirality :  0.045   0.157    641
  Planarity :  0.004   0.054    735
  Dihedral  :  4.530  61.450    598
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 14.25 %
    Favored  : 83.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.88 (0.35), residues: 539
  helix: -3.26 (0.81), residues: 33
  sheet: -1.06 (0.48), residues: 126
  loop : -1.16 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 457 
 TYR   0.031   0.001   TYR B 109 
 PHE   0.013   0.001   PHE C  94 
 TRP   0.010   0.002   TRP B  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4142)
  covalent geometry    : angle       0.52081 ( 5665)
  SS BOND              : bond        0.00328 (    8)
  SS BOND              : angle       0.76656 (   16)
  hydrogen bonds       : bond        0.03298 (  103)
  hydrogen bonds       : angle       6.61047 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 70
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8580 (m-10) cc_final: 0.8042 (m-10)
  outliers start: 9
  outliers final: 9
  residues processed: 75
  average time/residue: 0.0628
  time to fit residues: 6.0571
Evaluate side-chains
  73 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  478 THR
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0970
   chunk 8 optimal weight:    5.9990
   chunk 42 optimal weight:    5.9990
   chunk 34 optimal weight:    1.9990
   chunk 14 optimal weight:    3.9990
   chunk 40 optimal weight:    0.0030
   chunk 3 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.186353 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.153046 restraints weight = 4873.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.155656 restraints weight = 4442.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.157089 restraints weight = 3261.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.157671 restraints weight = 2581.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.159008 restraints weight = 2429.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7035
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   4150  Z= 0.125
  Angle     :  0.516   5.473   5681  Z= 0.270
  Chirality :  0.045   0.149    641
  Planarity :  0.004   0.050    735
  Dihedral  :  4.520  62.234    598
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  3.05 %
    Allowed  : 16.28 %
    Favored  : 80.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.74 (0.36), residues: 539
  helix: -3.28 (0.79), residues: 33
  sheet: -0.80 (0.46), residues: 146
  loop : -1.11 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 457 
 TYR   0.025   0.001   TYR B 109 
 PHE   0.012   0.001   PHE C  94 
 TRP   0.008   0.002   TRP B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4142)
  covalent geometry    : angle       0.51562 ( 5665)
  SS BOND              : bond        0.00377 (    8)
  SS BOND              : angle       0.73450 (   16)
  hydrogen bonds       : bond        0.03078 (  103)
  hydrogen bonds       : angle       6.29024 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8637 (m-10) cc_final: 0.8101 (m-10)
  outliers start: 12
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0488
  time to fit residues: 4.7916
Evaluate side-chains
  75 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 36 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 2 optimal weight:    5.9990
   chunk 15 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0970
   chunk 17 optimal weight:    4.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
B  59 ASN
D 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.178681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.146915 restraints weight = 4981.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147470 restraints weight = 4401.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149104 restraints weight = 3778.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.149519 restraints weight = 2890.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.150931 restraints weight = 2677.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2411

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.055   4150  Z= 0.265
  Angle     :  0.628   6.275   5681  Z= 0.334
  Chirality :  0.048   0.167    641
  Planarity :  0.005   0.053    735
  Dihedral  :  5.448  73.079    598
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 16.79 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.98 (0.36), residues: 539
  helix: -3.41 (0.79), residues: 33
  sheet: -1.07 (0.47), residues: 146
  loop : -1.23 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 457 
 TYR   0.025   0.002   TYR B 109 
 PHE   0.017   0.002   PHE C  94 
 TRP   0.012   0.002   TRP C  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00621 ( 4142)
  covalent geometry    : angle       0.62638 ( 5665)
  SS BOND              : bond        0.00659 (    8)
  SS BOND              : angle       0.94756 (   16)
  hydrogen bonds       : bond        0.03800 (  103)
  hydrogen bonds       : angle       7.05476 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.137 
Fit side-chains
REVERT: C   36 TYR cc_start: 0.8847 (m-10) cc_final: 0.8169 (m-10)
REVERT: A  392 PHE cc_start: 0.8068 (m-80) cc_final: 0.7831 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 73
  average time/residue: 0.0570
  time to fit residues: 5.5133
Evaluate side-chains
  74 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  470 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 50 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0020
   chunk 34 optimal weight:    1.9990
   chunk 4 optimal weight:    0.6980
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 360 ASN
D 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.180720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.149094 restraints weight = 5006.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149034 restraints weight = 4322.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.151132 restraints weight = 3899.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.151750 restraints weight = 2817.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.153753 restraints weight = 2659.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7123
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   4150  Z= 0.176
  Angle     :  0.563   6.348   5681  Z= 0.298
  Chirality :  0.046   0.150    641
  Planarity :  0.005   0.050    735
  Dihedral  :  5.133  70.182    598
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 18.58 %
    Favored  : 77.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.36), residues: 539
  helix: -3.35 (0.82), residues: 33
  sheet: -1.17 (0.46), residues: 141
  loop : -1.17 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  50 
 TYR   0.023   0.002   TYR B 109 
 PHE   0.016   0.001   PHE C  94 
 TRP   0.012   0.002   TRP B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 4142)
  covalent geometry    : angle       0.56227 ( 5665)
  SS BOND              : bond        0.00481 (    8)
  SS BOND              : angle       0.88907 (   16)
  hydrogen bonds       : bond        0.03228 (  103)
  hydrogen bonds       : angle       6.67578 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8737 (m-10) cc_final: 0.8105 (m-10)
REVERT: A  392 PHE cc_start: 0.7983 (m-80) cc_final: 0.7723 (m-80)
  outliers start: 17
  outliers final: 11
  residues processed: 72
  average time/residue: 0.0475
  time to fit residues: 4.6791
Evaluate side-chains
  74 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 21 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 52 optimal weight:    4.9990
   chunk 20 optimal weight:    0.7980
   chunk 44 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 45 optimal weight:    0.7980
   chunk 15 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.179141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.147698 restraints weight = 5051.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.148283 restraints weight = 4396.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.150287 restraints weight = 3813.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.150698 restraints weight = 2720.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.152353 restraints weight = 2579.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.3765
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.2682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   4150  Z= 0.190
  Angle     :  0.580   6.169   5681  Z= 0.307
  Chirality :  0.046   0.154    641
  Planarity :  0.005   0.050    735
  Dihedral  :  5.249  72.373    598
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 19.08 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.96 (0.36), residues: 539
  helix: -3.39 (0.81), residues: 33
  sheet: -1.19 (0.45), residues: 145
  loop : -1.15 (0.32), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  67 
 TYR   0.022   0.002   TYR B 109 
 PHE   0.016   0.001   PHE C  94 
 TRP   0.013   0.002   TRP B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00453 ( 4142)
  covalent geometry    : angle       0.57910 ( 5665)
  SS BOND              : bond        0.00418 (    8)
  SS BOND              : angle       0.90777 (   16)
  hydrogen bonds       : bond        0.03249 (  103)
  hydrogen bonds       : angle       6.72271 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 63
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8771 (m-10) cc_final: 0.8109 (m-10)
REVERT: A  392 PHE cc_start: 0.8027 (m-80) cc_final: 0.7747 (m-80)
  outliers start: 17
  outliers final: 12
  residues processed: 70
  average time/residue: 0.0563
  time to fit residues: 5.3338
Evaluate side-chains
  75 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  516 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0770
   chunk 10 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 42 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.180536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.149316 restraints weight = 4921.631|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.150014 restraints weight = 4126.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152050 restraints weight = 3769.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.152892 restraints weight = 2579.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153692 restraints weight = 2438.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4150  Z= 0.167
  Angle     :  0.567   5.806   5681  Z= 0.299
  Chirality :  0.046   0.153    641
  Planarity :  0.005   0.050    735
  Dihedral  :  5.131  70.782    598
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.34 %
    Favored  : 76.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.00 (0.36), residues: 539
  helix: -3.58 (0.69), residues: 39
  sheet: -1.20 (0.45), residues: 148
  loop : -1.10 (0.33), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  67 
 TYR   0.021   0.001   TYR B 109 
 PHE   0.015   0.001   PHE C  94 
 TRP   0.013   0.002   TRP B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4142)
  covalent geometry    : angle       0.56529 ( 5665)
  SS BOND              : bond        0.00464 (    8)
  SS BOND              : angle       1.04440 (   16)
  hydrogen bonds       : bond        0.03110 (  103)
  hydrogen bonds       : angle       6.59600 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.153 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8734 (m-10) cc_final: 0.8110 (m-10)
REVERT: A  392 PHE cc_start: 0.7996 (m-80) cc_final: 0.7693 (m-80)
  outliers start: 15
  outliers final: 13
  residues processed: 66
  average time/residue: 0.0579
  time to fit residues: 5.1446
Evaluate side-chains
  73 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 2 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 45 optimal weight:    0.0060
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0770
   chunk 14 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   overall best weight:    0.6956

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 439 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.180078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.148825 restraints weight = 5083.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.149526 restraints weight = 4409.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.151529 restraints weight = 3740.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.151962 restraints weight = 2704.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.153549 restraints weight = 2554.045|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7141
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4150  Z= 0.177
  Angle     :  0.575   5.835   5681  Z= 0.304
  Chirality :  0.046   0.153    641
  Planarity :  0.005   0.048    735
  Dihedral  :  5.181  71.757    598
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.24 %
    Favored  : 92.76 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.59 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.99 (0.36), residues: 539
  helix: -3.58 (0.69), residues: 39
  sheet: -1.11 (0.45), residues: 146
  loop : -1.14 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B  67 
 TYR   0.021   0.001   TYR B 109 
 PHE   0.016   0.001   PHE C  94 
 TRP   0.013   0.002   TRP B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 4142)
  covalent geometry    : angle       0.57319 ( 5665)
  SS BOND              : bond        0.00477 (    8)
  SS BOND              : angle       1.04521 (   16)
  hydrogen bonds       : bond        0.03174 (  103)
  hydrogen bonds       : angle       6.64308 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.164 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8777 (m-10) cc_final: 0.8151 (m-10)
REVERT: A  392 PHE cc_start: 0.8037 (m-80) cc_final: 0.7722 (m-80)
  outliers start: 15
  outliers final: 14
  residues processed: 68
  average time/residue: 0.0579
  time to fit residues: 5.2942
Evaluate side-chains
  74 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 60
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0060
   chunk 18 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 14 optimal weight:    8.9990
   chunk 27 optimal weight:    0.6980
   chunk 48 optimal weight:    0.7980
   overall best weight:    0.5196

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  92 ASN
D 439 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.182023 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150636 restraints weight = 4946.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.151273 restraints weight = 4200.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.153512 restraints weight = 3692.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.154361 restraints weight = 2563.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.154995 restraints weight = 2420.926|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.2921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4150  Z= 0.143
  Angle     :  0.551   5.581   5681  Z= 0.290
  Chirality :  0.045   0.148    641
  Planarity :  0.004   0.050    735
  Dihedral  :  4.946  68.847    598
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 8.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 19.59 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.36), residues: 539
  helix: -3.37 (0.82), residues: 33
  sheet: -1.10 (0.45), residues: 148
  loop : -1.09 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  67 
 TYR   0.020   0.001   TYR B  32 
 PHE   0.014   0.001   PHE C  94 
 TRP   0.012   0.002   TRP B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 4142)
  covalent geometry    : angle       0.54880 ( 5665)
  SS BOND              : bond        0.00418 (    8)
  SS BOND              : angle       0.98481 (   16)
  hydrogen bonds       : bond        0.02981 (  103)
  hydrogen bonds       : angle       6.40503 (  255)

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

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

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1078 Ramachandran restraints generated.
    539 Oldfield, 0 Emsley, 539 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 61
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: C   36 TYR cc_start: 0.8700 (m-10) cc_final: 0.8084 (m-10)
REVERT: A  392 PHE cc_start: 0.7918 (m-80) cc_final: 0.7638 (m-80)
  outliers start: 16
  outliers final: 15
  residues processed: 68
  average time/residue: 0.0588
  time to fit residues: 5.5111
Evaluate side-chains
  76 residues out of total 475 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 61
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue    2 VAL
Chi-restraints excluded: chain C residue    5 THR
Chi-restraints excluded: chain C residue    9 SER
Chi-restraints excluded: chain C residue   54 LEU
Chi-restraints excluded: chain C residue   73 LEU
Chi-restraints excluded: chain C residue   92 ASN
Chi-restraints excluded: chain C residue   97 THR
Chi-restraints excluded: chain A residue  350 VAL
Chi-restraints excluded: chain A residue  376 THR
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  390 LEU
Chi-restraints excluded: chain A residue  391 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  500 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 21 optimal weight:    0.0030
   chunk 23 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 4 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0070
   chunk 9 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.3808

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

Flipped N/Q/H residues before XYZ refinement:
** B   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 ASN
** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  92 ASN
D 439 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.181678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.150593 restraints weight = 4982.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.150921 restraints weight = 4206.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.152976 restraints weight = 3747.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.154000 restraints weight = 2692.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.154696 restraints weight = 2497.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7113
moved from start:          0.2883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.077   4150  Z= 0.206
  Angle     :  1.161  59.200   5681  Z= 0.695
  Chirality :  0.085   1.821    641
  Planarity :  0.005   0.050    735
  Dihedral  :  4.946  68.843    598
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  3.82 %
    Allowed  : 19.59 %
    Favored  : 76.59 %
  Cbeta Deviations :  0.19 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.86 (0.36), residues: 539
  helix: -3.38 (0.81), residues: 33
  sheet: -1.10 (0.45), residues: 148
  loop : -1.08 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  67 
 TYR   0.020   0.001   TYR B  32 
 PHE   0.014   0.001   PHE C  94 
 TRP   0.012   0.002   TRP B  47 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 4142)
  covalent geometry    : angle       1.16138 ( 5665)
  SS BOND              : bond        0.00416 (    8)
  SS BOND              : angle       0.99592 (   16)
  hydrogen bonds       : bond        0.02970 (  103)
  hydrogen bonds       : angle       6.40593 (  255)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1001.92 seconds
wall clock time: 18 minutes 5.95 seconds (1085.95 seconds total)