Starting phenix.real_space_refine
on Tue Feb  3 16:00:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kze_62661/02_2026/9kze_62661.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kze_62661/02_2026/9kze_62661.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kze_62661/02_2026/9kze_62661.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kze_62661/02_2026/9kze_62661.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kze_62661/02_2026/9kze_62661.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kze_62661/02_2026/9kze_62661.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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      17      5.16       5
     C    2915      2.51       5
     N     770      2.21       5
     O     884      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4586
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 1417
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1417
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 9, 'TRANS': 176}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 1588
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 211, 1588
          Classifications: {'peptide': 211}
          Link IDs: {'PTRANS': 18, 'TRANS': 192}
    Chain: "A"
      Number of atoms: 1553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 196, 1553
          Classifications: {'peptide': 196}
          Link IDs: {'PTRANS': 14, 'TRANS': 181}
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 1.30, per 1000 atoms: 0.28
  Number of scatterers: 4586
  At special positions: 0
  Unit cell: (68.036, 87.608, 106.248, 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      17     16.00
     O     884      8.00
     N     770      7.00
     C    2915      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  23 " - pdb=" SG  CYS H 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H 155 " - pdb=" SG  CYS H 211 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L 104 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L 155 " - pdb=" SG  CYS L 214 " distance=2.03
    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

  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
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A 343 "
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 421.7 milliseconds
  

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1090

  Finding SS restraints...
    Secondary structure from input PDB file:
      9 helices and 10 sheets defined
      8.9% alpha, 22.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'H' and resid 95 through 99
      removed outlier: 3.746A  pdb=" N   THR H  99 " --> pdb=" O   PRO H  96 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 27 through 37
    Processing helix  chain 'L' and resid 95 through 99
      removed outlier: 4.021A  pdb=" N   GLU L  99 " --> pdb=" O   ALA L  96 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 142 through 148
      removed outlier: 3.813A  pdb=" N   GLU L 145 " --> pdb=" O   SER L 142 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLN L 147 " --> pdb=" O   GLU L 144 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA L 148 " --> pdb=" O   GLU L 145 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 202 through 206
      removed outlier: 4.124A  pdb=" N   GLN L 205 " --> pdb=" O   THR L 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 364 through 368
      removed outlier: 3.514A  pdb=" N   VAL A 367 " --> pdb=" O   ASP A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 410
      removed outlier: 3.570A  pdb=" N   VAL A 407 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
      removed outlier: 4.878A  pdb=" N   SER A 408 " --> pdb=" O   ASN A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
      removed outlier: 3.641A  pdb=" N   LEU H  89 " --> pdb=" O   LEU H  21 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 13
      removed outlier: 3.804A  pdb=" N   GLY H 124 " --> pdb=" O   ALA H 100 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ALA H 105 " --> pdb=" O   HIS H  40 " (cutoff:3.500A)
      removed outlier: 7.224A  pdb=" N   MET H  39 " --> pdb=" O   VAL H  55 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   VAL H  55 " --> pdb=" O   MET H  39 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   TRP H  41 " --> pdb=" O   VAL H  53 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 13
      removed outlier: 3.804A  pdb=" N   GLY H 124 " --> pdb=" O   ALA H 100 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   THR H 106 " --> pdb=" O   ARG H 116 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 13
      removed outlier: 3.545A  pdb=" N   ALA L 100 " --> pdb=" O   LEU L 124 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 24
      removed outlier: 3.525A  pdb=" N   CYS L  23 " --> pdb=" O   ALA L  87 " (cutoff:3.500A)
      removed outlier: 3.731A  pdb=" N   THR L  86 " --> pdb=" O   SER L  83 " (cutoff:3.500A)
      removed outlier: 4.095A  pdb=" N   SER L  83 " --> pdb=" O   THR L  86 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 105 through 106
      removed outlier: 3.509A  pdb=" N   VAL L 106 " --> pdb=" O   VAL L 117 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   VAL L 117 " --> pdb=" O   VAL L 106 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'L' and resid 135 through 137
      removed outlier: 4.906A  pdb=" N   SER L 158 " --> pdb=" O   ALA L 195 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   ALA L 195 " --> pdb=" O   SER L 158 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358
      removed outlier: 3.559A  pdb=" N   ASN A 354 " --> pdb=" O   SER A 399 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454

    103 hydrogen bonds defined for protein.
    225 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: 0.94

  Time building geometry restraints manager: 0.57 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: 1456
        1.34 -     1.46: 1163
        1.46 -     1.58: 2077
        1.58 -     1.70: 0
        1.70 -     1.81: 18
  Bond restraints: 4714
  Sorted by residual:
  bond pdb=" C1  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.77e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.32e+00
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.24e+00
  bond pdb=" C3  NAG B   2 "
       pdb=" O3  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.424 -0.021 2.00e-02 2.50e+03 1.08e+00
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.427 -0.021 2.00e-02 2.50e+03 1.07e+00
  ... (remaining 4709 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.22: 6260
        1.22 -     2.44: 128
        2.44 -     3.66: 38
        3.66 -     4.88: 6
        4.88 -     6.10: 2
  Bond angle restraints: 6434
  Sorted by residual:
  angle pdb=" C   PHE L 113 "
        pdb=" N   ASP L 114 "
        pdb=" CA  ASP L 114 "
      ideal   model   delta    sigma   weight residual
     121.80  127.90   -6.10 2.44e+00 1.68e-01 6.26e+00
  angle pdb=" N   PHE L 113 "
        pdb=" CA  PHE L 113 "
        pdb=" C   PHE L 113 "
      ideal   model   delta    sigma   weight residual
     113.37  110.35    3.02 1.38e+00 5.25e-01 4.78e+00
  angle pdb=" N   ASP L 114 "
        pdb=" CA  ASP L 114 "
        pdb=" C   ASP L 114 "
      ideal   model   delta    sigma   weight residual
     109.81  114.34   -4.53 2.21e+00 2.05e-01 4.21e+00
  angle pdb=" N   VAL H 165 "
        pdb=" CA  VAL H 165 "
        pdb=" C   VAL H 165 "
      ideal   model   delta    sigma   weight residual
     109.34  113.35   -4.01 2.08e+00 2.31e-01 3.71e+00
  angle pdb=" N   SER L  65 "
        pdb=" CA  SER L  65 "
        pdb=" C   SER L  65 "
      ideal   model   delta    sigma   weight residual
     110.80  114.77   -3.97 2.13e+00 2.20e-01 3.47e+00
  ... (remaining 6429 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    10.16: 2617
       10.16 -    20.33: 114
       20.33 -    30.49: 57
       30.49 -    40.66: 14
       40.66 -    50.82: 8
  Dihedral angle restraints: 2810
    sinusoidal: 1096
      harmonic: 1714
  Sorted by residual:
  dihedral pdb=" CA  ASP L 114 "
           pdb=" C   ASP L 114 "
           pdb=" N   PRO L 115 "
           pdb=" CA  PRO L 115 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.43   21.57     0      5.00e+00 4.00e-02 1.86e+01
  dihedral pdb=" SG  CYS A 391 "
           pdb=" CB  CYS A 525 "
           pdb=" SG  CYS A 525 "
           pdb=" CA  CYS A 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      79.00   28.18   50.82     1      2.00e+01 2.50e-03 8.84e+00
  dihedral pdb=" N   PHE H 137 "
           pdb=" CA  PHE H 137 "
           pdb=" CB  PHE H 137 "
           pdb=" CG  PHE H 137 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -107.99   47.99     3      1.50e+01 4.44e-03 8.57e+00
  ... (remaining 2807 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 524
       0.041 -    0.082: 126
       0.082 -    0.122: 56
       0.122 -    0.163: 1
       0.163 -    0.204: 1
  Chirality restraints: 708
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 343 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.20   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  ILE L  71 "
            pdb=" N   ILE L  71 "
            pdb=" C   ILE L  71 "
            pdb=" CB  ILE L  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.28e-01
  chirality pdb=" CA  VAL L  54 "
            pdb=" N   VAL L  54 "
            pdb=" C   VAL L  54 "
            pdb=" CB  VAL L  54 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.74e-01
  ... (remaining 705 not shown)

  Planarity restraints: 829
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP L 114 "   -0.025 5.00e-02 4.00e+02   3.75e-02 2.25e+00
        pdb=" N   PRO L 115 "    0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO L 115 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO L 115 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU H 163 "   -0.024 5.00e-02 4.00e+02   3.70e-02 2.19e+00
        pdb=" N   PRO H 164 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO H 164 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO H 164 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 520 "    0.021 5.00e-02 4.00e+02   3.17e-02 1.61e+00
        pdb=" N   PRO A 521 "   -0.055 5.00e-02 4.00e+02
        pdb=" CA  PRO A 521 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO A 521 "    0.018 5.00e-02 4.00e+02
  ... (remaining 826 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 728
        2.77 -     3.30: 4220
        3.30 -     3.83: 7415
        3.83 -     4.37: 8417
        4.37 -     4.90: 14642
  Nonbonded interactions: 35422
  Sorted by model distance:
  nonbonded pdb=" O   LYS L 170 "
            pdb=" OG  SER L 213 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   SER H 192 "
            pdb=" OH  TYR L 198 "
     model   vdw
     2.264 3.040
  nonbonded pdb=" O   ALA L 171 "
            pdb=" OG  SER L 174 "
     model   vdw
     2.270 3.040
  nonbonded pdb=" OG  SER L 142 "
            pdb=" OE1 GLU L 144 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OD1 ASN L  27 "
            pdb=" OG1 THR A 345 "
     model   vdw
     2.336 3.040
  ... (remaining 35417 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.150
  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:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     6.850
  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:1.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6524
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   4724  Z= 0.093
  Angle     :  0.479   6.103   6456  Z= 0.256
  Chirality :  0.042   0.204    708
  Planarity :  0.004   0.038    828
  Dihedral  :  7.633  48.651   1696
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  :  5.37 %
    Favored  : 92.05 %
  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: -2.84 (0.32), residues: 583
  helix: -4.34 (0.54), residues: 32
  sheet: -1.24 (0.41), residues: 142
  loop : -2.04 (0.29), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG H  80 
 TYR   0.009   0.001   TYR L  55 
 PHE   0.005   0.001   PHE L 160 
 TRP   0.005   0.001   TRP L 169 
 HIS   0.001   0.000   HIS H  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00178 ( 4714)
  covalent geometry    : angle       0.47845 ( 6434)
  SS BOND              : bond        0.00124 (    8)
  SS BOND              : angle       0.47567 (   16)
  hydrogen bonds       : bond        0.30476 (   97)
  hydrogen bonds       : angle      11.81117 (  225)
  link_BETA1-4         : bond        0.00059 (    1)
  link_BETA1-4         : angle       1.43362 (    3)
  link_NAG-ASN         : bond        0.00273 (    1)
  link_NAG-ASN         : angle       0.67859 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 113
  time to evaluate  : 0.101 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H   39 MET cc_start: 0.7156 (mmm) cc_final: 0.6836 (mmm)
REVERT: H   85 ASN cc_start: 0.7567 (m-40) cc_final: 0.7365 (m-40)
REVERT: L    6 GLN cc_start: 0.7554 (mt0) cc_final: 0.7279 (mt0)
REVERT: L   28 ILE cc_start: 0.8373 (tt) cc_final: 0.8100 (tp)
REVERT: L   36 SER cc_start: 0.8374 (p) cc_final: 0.8118 (p)
REVERT: L   90 THR cc_start: 0.8170 (m) cc_final: 0.7733 (p)
REVERT: L  137 THR cc_start: 0.7621 (m) cc_final: 0.7203 (t)
REVERT: L  160 PHE cc_start: 0.5246 (p90) cc_final: 0.4428 (p90)
REVERT: L  212 TYR cc_start: 0.5222 (OUTLIER) cc_final: 0.4899 (t80)
REVERT: A  430 THR cc_start: 0.8293 (m) cc_final: 0.7991 (p)
REVERT: A  450 ASN cc_start: 0.7400 (m110) cc_final: 0.7028 (t0)
  outliers start: 13
  outliers final: 6
  residues processed: 123
  average time/residue: 0.0469
  time to fit residues: 7.4239
Evaluate side-chains
  113 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 106
  time to evaluate  : 0.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 54 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 25 optimal weight:    0.4980
   chunk 50 optimal weight:    0.0060
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
H 179 HIS
H 186 GLN
H 214 ASN
L 205 GLN
** L 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** L 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 439 ASN
A 450 ASN
A 505 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.175180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.147791 restraints weight = 7609.883|
|-----------------------------------------------------------------------------|
r_work (start): 0.3903 rms_B_bonded: 3.26
r_work: 0.3785 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6837
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4724  Z= 0.149
  Angle     :  0.600   7.172   6456  Z= 0.313
  Chirality :  0.046   0.289    708
  Planarity :  0.005   0.037    828
  Dihedral  :  5.646  49.915    701
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 11.13 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.33), residues: 583
  helix: -3.95 (0.57), residues: 35
  sheet: -1.11 (0.39), residues: 155
  loop : -1.65 (0.31), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  20 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.012   0.001   PHE A 429 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.008   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 4714)
  covalent geometry    : angle       0.59896 ( 6434)
  SS BOND              : bond        0.00250 (    8)
  SS BOND              : angle       0.73142 (   16)
  hydrogen bonds       : bond        0.04033 (   97)
  hydrogen bonds       : angle       8.11521 (  225)
  link_BETA1-4         : bond        0.00092 (    1)
  link_BETA1-4         : angle       1.46958 (    3)
  link_NAG-ASN         : bond        0.00316 (    1)
  link_NAG-ASN         : angle       0.20293 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.104 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 MET cc_start: 0.7935 (mmm) cc_final: 0.7490 (mmm)
REVERT: H   57 SER cc_start: 0.8424 (t) cc_final: 0.7952 (p)
REVERT: H   84 GLN cc_start: 0.8412 (mp10) cc_final: 0.8186 (mp10)
REVERT: L   27 ASN cc_start: 0.7819 (t0) cc_final: 0.7617 (t0)
REVERT: L   90 THR cc_start: 0.8180 (m) cc_final: 0.7921 (p)
REVERT: L  137 THR cc_start: 0.7680 (m) cc_final: 0.7265 (t)
REVERT: L  160 PHE cc_start: 0.4894 (p90) cc_final: 0.4289 (p90)
REVERT: L  212 TYR cc_start: 0.5814 (OUTLIER) cc_final: 0.5385 (t80)
REVERT: A  369 TYR cc_start: 0.8574 (m-80) cc_final: 0.8276 (m-80)
REVERT: A  430 THR cc_start: 0.8332 (m) cc_final: 0.7999 (p)
REVERT: A  468 ILE cc_start: 0.8228 (mm) cc_final: 0.8006 (mm)
  outliers start: 18
  outliers final: 11
  residues processed: 112
  average time/residue: 0.0759
  time to fit residues: 10.6719
Evaluate side-chains
  115 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue  158 SER
Chi-restraints excluded: chain L residue  209 HIS
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0770
   chunk 23 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0010
   chunk 28 optimal weight:    1.9990
   chunk 21 optimal weight:    0.1980
   chunk 15 optimal weight:    7.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.4344

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
** L 209 HIS ** 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 = 0.4243 r_free = 0.4243 target = 0.174062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3910 r_free = 0.3910 target = 0.147270 restraints weight = 7565.643|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 3.21
r_work: 0.3779 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6848
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   4724  Z= 0.120
  Angle     :  0.552   6.864   6456  Z= 0.287
  Chirality :  0.044   0.177    708
  Planarity :  0.004   0.038    828
  Dihedral  :  5.454  50.050    701
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 13.32 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.17 (0.34), residues: 583
  helix: -3.63 (0.76), residues: 28
  sheet: -0.91 (0.40), residues: 151
  loop : -1.56 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  20 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.009   0.001   PHE A 429 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.008   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 4714)
  covalent geometry    : angle       0.55078 ( 6434)
  SS BOND              : bond        0.00149 (    8)
  SS BOND              : angle       0.66796 (   16)
  hydrogen bonds       : bond        0.03886 (   97)
  hydrogen bonds       : angle       7.61625 (  225)
  link_BETA1-4         : bond        0.00012 (    1)
  link_BETA1-4         : angle       1.48423 (    3)
  link_NAG-ASN         : bond        0.00281 (    1)
  link_NAG-ASN         : angle       0.34665 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 94
  time to evaluate  : 0.218 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 MET cc_start: 0.7880 (mmm) cc_final: 0.7482 (mmm)
REVERT: H   48 LYS cc_start: 0.8113 (mmtp) cc_final: 0.7695 (mmtp)
REVERT: H   80 ARG cc_start: 0.8165 (ptp-170) cc_final: 0.7915 (ttm170)
REVERT: L   27 ASN cc_start: 0.7784 (t0) cc_final: 0.7422 (t0)
REVERT: L   90 THR cc_start: 0.8184 (m) cc_final: 0.7913 (p)
REVERT: L  137 THR cc_start: 0.7656 (m) cc_final: 0.7259 (t)
REVERT: L  160 PHE cc_start: 0.5049 (p90) cc_final: 0.4437 (p90)
REVERT: L  212 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.5470 (t80)
REVERT: A  369 TYR cc_start: 0.8662 (m-80) cc_final: 0.8381 (m-80)
REVERT: A  430 THR cc_start: 0.8370 (m) cc_final: 0.8006 (p)
REVERT: A  468 ILE cc_start: 0.8456 (mm) cc_final: 0.8148 (mm)
  outliers start: 15
  outliers final: 11
  residues processed: 103
  average time/residue: 0.0892
  time to fit residues: 11.4608
Evaluate side-chains
  106 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue    9 SER
Chi-restraints excluded: chain L residue   45 LYS
Chi-restraints excluded: chain L residue   57 ASP
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 27 optimal weight:    0.6980
   chunk 10 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 57 optimal weight:    0.8980
   chunk 45 optimal weight:    0.5980
   chunk 32 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 35 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0770
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
L   6 GLN
** L 209 HIS ** 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 = 0.4221 r_free = 0.4221 target = 0.172186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.145588 restraints weight = 7478.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 3.20
r_work: 0.3754 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.3754
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6887
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   4724  Z= 0.138
  Angle     :  0.574   7.412   6456  Z= 0.294
  Chirality :  0.044   0.134    708
  Planarity :  0.004   0.037    828
  Dihedral  :  5.488  49.645    701
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 13.12 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.05 (0.34), residues: 583
  helix: -3.45 (0.78), residues: 28
  sheet: -0.75 (0.40), residues: 148
  loop : -1.51 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  20 
 TYR   0.020   0.001   TYR L  55 
 PHE   0.012   0.002   PHE A 429 
 TRP   0.011   0.001   TRP A 436 
 HIS   0.003   0.001   HIS L 209 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 4714)
  covalent geometry    : angle       0.57311 ( 6434)
  SS BOND              : bond        0.00173 (    8)
  SS BOND              : angle       0.68641 (   16)
  hydrogen bonds       : bond        0.03513 (   97)
  hydrogen bonds       : angle       7.13830 (  225)
  link_BETA1-4         : bond        0.00098 (    1)
  link_BETA1-4         : angle       1.47836 (    3)
  link_NAG-ASN         : bond        0.00145 (    1)
  link_NAG-ASN         : angle       0.42550 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 93
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 MET cc_start: 0.7877 (mmm) cc_final: 0.7467 (mmm)
REVERT: H   48 LYS cc_start: 0.8132 (mmtp) cc_final: 0.7696 (mmtp)
REVERT: H   51 GLU cc_start: 0.7550 (tt0) cc_final: 0.7263 (tt0)
REVERT: H   80 ARG cc_start: 0.8162 (ptp-170) cc_final: 0.7944 (ttm170)
REVERT: H  137 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.4849 (t80)
REVERT: H  186 GLN cc_start: 0.5653 (tt0) cc_final: 0.5422 (tt0)
REVERT: L   27 ASN cc_start: 0.7853 (t0) cc_final: 0.7376 (t0)
REVERT: L   90 THR cc_start: 0.8249 (m) cc_final: 0.7999 (p)
REVERT: L  137 THR cc_start: 0.7661 (m) cc_final: 0.7253 (t)
REVERT: L  160 PHE cc_start: 0.5022 (p90) cc_final: 0.4407 (p90)
REVERT: L  212 TYR cc_start: 0.5965 (OUTLIER) cc_final: 0.5450 (t80)
REVERT: A  430 THR cc_start: 0.8411 (m) cc_final: 0.8070 (p)
REVERT: A  468 ILE cc_start: 0.8498 (mm) cc_final: 0.8136 (mm)
  outliers start: 18
  outliers final: 13
  residues processed: 102
  average time/residue: 0.0704
  time to fit residues: 9.0701
Evaluate side-chains
  105 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  137 PHE
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue    9 SER
Chi-restraints excluded: chain L residue   51 VAL
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  399 SER
Chi-restraints excluded: chain A residue  456 LEU
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 32 optimal weight:    0.6980
   chunk 1 optimal weight:    3.9990
   chunk 5 optimal weight:    0.5980
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    0.0570
   chunk 35 optimal weight:    5.9990
   chunk 39 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9990
   chunk 45 optimal weight:    0.3980
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
H  44 GLN
L   6 GLN
** L 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 519 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.172437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.145891 restraints weight = 7551.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3872 rms_B_bonded: 3.15
r_work: 0.3758 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.2675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4724  Z= 0.120
  Angle     :  0.552   7.053   6456  Z= 0.283
  Chirality :  0.043   0.134    708
  Planarity :  0.004   0.039    828
  Dihedral  :  5.401  49.206    701
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 13.52 %
    Favored  : 82.31 %
  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: -1.92 (0.34), residues: 583
  helix: -3.24 (0.82), residues: 28
  sheet: -0.66 (0.40), residues: 148
  loop : -1.44 (0.31), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  75 
 TYR   0.017   0.001   TYR L  55 
 PHE   0.015   0.001   PHE H  76 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.005   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 4714)
  covalent geometry    : angle       0.55156 ( 6434)
  SS BOND              : bond        0.00166 (    8)
  SS BOND              : angle       0.61629 (   16)
  hydrogen bonds       : bond        0.03427 (   97)
  hydrogen bonds       : angle       6.86154 (  225)
  link_BETA1-4         : bond        0.00146 (    1)
  link_BETA1-4         : angle       1.39690 (    3)
  link_NAG-ASN         : bond        0.00186 (    1)
  link_NAG-ASN         : angle       0.49239 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 90
  time to evaluate  : 0.167 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 MET cc_start: 0.7820 (mmm) cc_final: 0.7472 (mmm)
REVERT: H   48 LYS cc_start: 0.8138 (mmtp) cc_final: 0.7758 (mmtp)
REVERT: H   51 GLU cc_start: 0.7537 (tt0) cc_final: 0.7295 (tt0)
REVERT: H   80 ARG cc_start: 0.8104 (ptp-170) cc_final: 0.7863 (ttm170)
REVERT: H  137 PHE cc_start: 0.5212 (OUTLIER) cc_final: 0.4867 (t80)
REVERT: L   27 ASN cc_start: 0.7820 (t0) cc_final: 0.7305 (t0)
REVERT: L  137 THR cc_start: 0.7624 (m) cc_final: 0.7234 (t)
REVERT: L  160 PHE cc_start: 0.5047 (p90) cc_final: 0.4456 (p90)
REVERT: L  212 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.5404 (t80)
REVERT: A  430 THR cc_start: 0.8454 (m) cc_final: 0.8143 (p)
REVERT: A  468 ILE cc_start: 0.8545 (mm) cc_final: 0.8190 (mm)
  outliers start: 21
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0777
  time to fit residues: 10.2529
Evaluate side-chains
  103 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 90
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  137 PHE
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 15 optimal weight:    0.0970
   chunk 26 optimal weight:    0.9990
   chunk 53 optimal weight:    0.0970
   chunk 13 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0040
   chunk 12 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.3590

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
** L 209 HIS ** 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 = 0.4205 r_free = 0.4205 target = 0.170611 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.143679 restraints weight = 7595.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3854 rms_B_bonded: 3.23
r_work: 0.3737 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6896
moved from start:          0.2799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4724  Z= 0.110
  Angle     :  0.551   6.804   6456  Z= 0.283
  Chirality :  0.043   0.135    708
  Planarity :  0.004   0.039    828
  Dihedral  :  5.187  48.436    699
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 13.72 %
    Favored  : 83.30 %
  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: -1.73 (0.35), residues: 583
  helix: -3.10 (0.86), residues: 28
  sheet: -0.51 (0.42), residues: 142
  loop : -1.30 (0.32), residues: 413

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  75 
 TYR   0.015   0.001   TYR L  55 
 PHE   0.008   0.001   PHE A 429 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 4714)
  covalent geometry    : angle       0.55017 ( 6434)
  SS BOND              : bond        0.00169 (    8)
  SS BOND              : angle       0.59162 (   16)
  hydrogen bonds       : bond        0.03222 (   97)
  hydrogen bonds       : angle       6.65303 (  225)
  link_BETA1-4         : bond        0.00105 (    1)
  link_BETA1-4         : angle       1.38477 (    3)
  link_NAG-ASN         : bond        0.00195 (    1)
  link_NAG-ASN         : angle       0.55338 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 89
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: H   39 MET cc_start: 0.7815 (mmm) cc_final: 0.7431 (mmm)
REVERT: H   48 LYS cc_start: 0.8084 (mmtp) cc_final: 0.7719 (mmtp)
REVERT: H   51 GLU cc_start: 0.7538 (tt0) cc_final: 0.7255 (tt0)
REVERT: H   80 ARG cc_start: 0.8091 (ptp-170) cc_final: 0.7873 (ttm170)
REVERT: H  137 PHE cc_start: 0.5276 (OUTLIER) cc_final: 0.4893 (t80)
REVERT: L   27 ASN cc_start: 0.7765 (t0) cc_final: 0.6878 (t0)
REVERT: L   36 SER cc_start: 0.8581 (p) cc_final: 0.8181 (p)
REVERT: L  129 GLN cc_start: 0.7530 (tm-30) cc_final: 0.7002 (tp-100)
REVERT: L  137 THR cc_start: 0.7589 (m) cc_final: 0.7195 (t)
REVERT: L  160 PHE cc_start: 0.5004 (p90) cc_final: 0.4437 (p90)
REVERT: L  212 TYR cc_start: 0.5924 (OUTLIER) cc_final: 0.5391 (t80)
REVERT: A  362 VAL cc_start: 0.8298 (t) cc_final: 0.8021 (m)
REVERT: A  430 THR cc_start: 0.8448 (m) cc_final: 0.8133 (p)
REVERT: A  468 ILE cc_start: 0.8543 (mm) cc_final: 0.8160 (mm)
  outliers start: 15
  outliers final: 10
  residues processed: 101
  average time/residue: 0.0704
  time to fit residues: 9.0706
Evaluate side-chains
  101 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 89
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  137 PHE
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue   39 VAL
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0050
   chunk 31 optimal weight:    7.9990
   chunk 19 optimal weight:    0.1980
   chunk 56 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 16 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
L   6 GLN
** L 209 HIS ** 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 = 0.4197 r_free = 0.4197 target = 0.169967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.143442 restraints weight = 7533.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3846 rms_B_bonded: 3.17
r_work: 0.3728 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.3728
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6918
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4724  Z= 0.132
  Angle     :  0.576   7.130   6456  Z= 0.297
  Chirality :  0.044   0.155    708
  Planarity :  0.004   0.040    828
  Dihedral  :  5.272  48.191    699
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 14.71 %
    Favored  : 82.50 %
  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: -1.75 (0.34), residues: 583
  helix: -3.18 (0.75), residues: 34
  sheet: -0.43 (0.43), residues: 129
  loop : -1.30 (0.31), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 116 
 TYR   0.018   0.001   TYR L  55 
 PHE   0.030   0.002   PHE H  76 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.004   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4714)
  covalent geometry    : angle       0.57464 ( 6434)
  SS BOND              : bond        0.00139 (    8)
  SS BOND              : angle       0.72044 (   16)
  hydrogen bonds       : bond        0.03365 (   97)
  hydrogen bonds       : angle       6.55920 (  225)
  link_BETA1-4         : bond        0.00138 (    1)
  link_BETA1-4         : angle       1.39914 (    3)
  link_NAG-ASN         : bond        0.00114 (    1)
  link_NAG-ASN         : angle       0.55394 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.164 
Fit side-chains
REVERT: H   39 MET cc_start: 0.7762 (mmm) cc_final: 0.7375 (mmm)
REVERT: H   48 LYS cc_start: 0.8130 (mmtp) cc_final: 0.7789 (mmtp)
REVERT: H   51 GLU cc_start: 0.7563 (tt0) cc_final: 0.7276 (tt0)
REVERT: H   80 ARG cc_start: 0.8101 (ptp-170) cc_final: 0.7890 (ttm170)
REVERT: H  137 PHE cc_start: 0.5365 (OUTLIER) cc_final: 0.5008 (t80)
REVERT: L   27 ASN cc_start: 0.7821 (t0) cc_final: 0.6853 (t0)
REVERT: L   36 SER cc_start: 0.8599 (p) cc_final: 0.8142 (p)
REVERT: L  137 THR cc_start: 0.7594 (m) cc_final: 0.7200 (t)
REVERT: L  160 PHE cc_start: 0.4992 (p90) cc_final: 0.4454 (p90)
REVERT: L  212 TYR cc_start: 0.5944 (OUTLIER) cc_final: 0.5417 (t80)
REVERT: A  430 THR cc_start: 0.8476 (m) cc_final: 0.8171 (p)
REVERT: A  468 ILE cc_start: 0.8558 (mm) cc_final: 0.8180 (mm)
REVERT: A  474 GLN cc_start: 0.6794 (tm-30) cc_final: 0.6581 (tm-30)
  outliers start: 14
  outliers final: 10
  residues processed: 98
  average time/residue: 0.0756
  time to fit residues: 9.5250
Evaluate side-chains
  98 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  137 PHE
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 39 optimal weight:    0.0010
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 47 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 12 optimal weight:    3.9990
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   overall best weight:    0.5986

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
** L 209 HIS ** 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 = 0.4179 r_free = 0.4179 target = 0.168279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.141665 restraints weight = 7610.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3831 rms_B_bonded: 3.18
r_work: 0.3712 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6940
moved from start:          0.3151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4724  Z= 0.144
  Angle     :  0.591   7.375   6456  Z= 0.303
  Chirality :  0.044   0.141    708
  Planarity :  0.004   0.039    828
  Dihedral  :  5.343  48.232    699
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.31 %
    Favored  : 81.91 %
  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: -1.72 (0.35), residues: 583
  helix: -3.13 (0.76), residues: 33
  sheet: -0.44 (0.41), residues: 148
  loop : -1.29 (0.32), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  20 
 TYR   0.014   0.001   TYR L  55 
 PHE   0.025   0.002   PHE H  76 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4714)
  covalent geometry    : angle       0.59021 ( 6434)
  SS BOND              : bond        0.00160 (    8)
  SS BOND              : angle       0.70033 (   16)
  hydrogen bonds       : bond        0.03416 (   97)
  hydrogen bonds       : angle       6.61195 (  225)
  link_BETA1-4         : bond        0.00179 (    1)
  link_BETA1-4         : angle       1.40424 (    3)
  link_NAG-ASN         : bond        0.00092 (    1)
  link_NAG-ASN         : angle       0.54228 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.142 
Fit side-chains
REVERT: H   39 MET cc_start: 0.7772 (mmm) cc_final: 0.7375 (mmm)
REVERT: H   48 LYS cc_start: 0.8163 (mmtp) cc_final: 0.7831 (mmtp)
REVERT: H   51 GLU cc_start: 0.7617 (tt0) cc_final: 0.7344 (tt0)
REVERT: H   80 ARG cc_start: 0.8109 (ptp-170) cc_final: 0.7887 (ttm170)
REVERT: H  137 PHE cc_start: 0.5623 (OUTLIER) cc_final: 0.5239 (t80)
REVERT: L   27 ASN cc_start: 0.7851 (t0) cc_final: 0.7268 (t0)
REVERT: L  137 THR cc_start: 0.7614 (m) cc_final: 0.7203 (t)
REVERT: L  158 SER cc_start: 0.6993 (p) cc_final: 0.6146 (t)
REVERT: L  160 PHE cc_start: 0.5042 (p90) cc_final: 0.4469 (p90)
REVERT: A  430 THR cc_start: 0.8496 (m) cc_final: 0.8184 (p)
REVERT: A  468 ILE cc_start: 0.8544 (mm) cc_final: 0.8128 (mm)
  outliers start: 14
  outliers final: 12
  residues processed: 92
  average time/residue: 0.0514
  time to fit residues: 6.2470
Evaluate side-chains
  94 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.124 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  110 LEU
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  137 PHE
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue   54 VAL
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9990
   chunk 43 optimal weight:    0.0050
   chunk 36 optimal weight:    0.2980
   chunk 45 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 6 optimal weight:    0.5980
   chunk 21 optimal weight:    0.3980
   chunk 29 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
** L 209 HIS ** 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 = 0.4188 r_free = 0.4188 target = 0.169178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.142663 restraints weight = 7484.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3849 rms_B_bonded: 3.17
r_work: 0.3731 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.3237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   4724  Z= 0.114
  Angle     :  0.594   7.472   6456  Z= 0.303
  Chirality :  0.044   0.137    708
  Planarity :  0.004   0.039    828
  Dihedral  :  5.306  48.539    699
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 15.51 %
    Favored  : 81.71 %
  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: -1.70 (0.35), residues: 583
  helix: -3.08 (0.77), residues: 33
  sheet: -0.43 (0.41), residues: 151
  loop : -1.29 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H  20 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.025   0.002   PHE H  76 
 TRP   0.011   0.001   TRP H  52 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 ( 4714)
  covalent geometry    : angle       0.59340 ( 6434)
  SS BOND              : bond        0.00159 (    8)
  SS BOND              : angle       0.69541 (   16)
  hydrogen bonds       : bond        0.03243 (   97)
  hydrogen bonds       : angle       6.48580 (  225)
  link_BETA1-4         : bond        0.00040 (    1)
  link_BETA1-4         : angle       1.33631 (    3)
  link_NAG-ASN         : bond        0.00215 (    1)
  link_NAG-ASN         : angle       0.57109 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.168 
Fit side-chains
REVERT: H   39 MET cc_start: 0.7744 (mmm) cc_final: 0.7367 (mmm)
REVERT: H   48 LYS cc_start: 0.8112 (mmtp) cc_final: 0.7819 (mmtp)
REVERT: H   51 GLU cc_start: 0.7544 (tt0) cc_final: 0.7274 (tt0)
REVERT: H  137 PHE cc_start: 0.5607 (OUTLIER) cc_final: 0.5221 (t80)
REVERT: L   27 ASN cc_start: 0.7834 (t0) cc_final: 0.7270 (t0)
REVERT: L  137 THR cc_start: 0.7585 (m) cc_final: 0.7181 (t)
REVERT: L  158 SER cc_start: 0.6975 (p) cc_final: 0.6130 (t)
REVERT: L  160 PHE cc_start: 0.5004 (p90) cc_final: 0.4506 (p90)
REVERT: L  221 SER cc_start: 0.6945 (p) cc_final: 0.6575 (p)
REVERT: A  430 THR cc_start: 0.8465 (m) cc_final: 0.8160 (p)
REVERT: A  468 ILE cc_start: 0.8519 (mm) cc_final: 0.8108 (mm)
  outliers start: 14
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0754
  time to fit residues: 8.5193
Evaluate side-chains
  89 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 77
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  137 PHE
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue   54 VAL
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 27 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0870
   chunk 12 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 55 optimal weight:    0.0670
   chunk 18 optimal weight:    0.9980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.4696

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
** L 209 HIS ** 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 = 0.4217 r_free = 0.4217 target = 0.171715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.145459 restraints weight = 7485.037|
|-----------------------------------------------------------------------------|
r_work (start): 0.3883 rms_B_bonded: 3.04
r_work: 0.3768 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.3341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4724  Z= 0.127
  Angle     :  0.599   8.378   6456  Z= 0.306
  Chirality :  0.044   0.146    708
  Planarity :  0.004   0.039    828
  Dihedral  :  5.331  48.587    699
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.90 %
    Favored  : 81.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.67 (0.35), residues: 583
  helix: -3.08 (0.77), residues: 33
  sheet: -0.36 (0.41), residues: 151
  loop : -1.29 (0.32), residues: 399

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG H  80 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.028   0.002   PHE H  76 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4714)
  covalent geometry    : angle       0.59830 ( 6434)
  SS BOND              : bond        0.00164 (    8)
  SS BOND              : angle       0.67778 (   16)
  hydrogen bonds       : bond        0.03262 (   97)
  hydrogen bonds       : angle       6.46980 (  225)
  link_BETA1-4         : bond        0.00043 (    1)
  link_BETA1-4         : angle       1.38127 (    3)
  link_NAG-ASN         : bond        0.00135 (    1)
  link_NAG-ASN         : angle       0.50253 (    3)

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

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

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1166 Ramachandran restraints generated.
    583 Oldfield, 0 Emsley, 583 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.166 
Fit side-chains
REVERT: H   39 MET cc_start: 0.7763 (mmm) cc_final: 0.7251 (mmm)
REVERT: H   48 LYS cc_start: 0.8104 (mmtp) cc_final: 0.7803 (mmtp)
REVERT: H   51 GLU cc_start: 0.7490 (tt0) cc_final: 0.7258 (tt0)
REVERT: H  137 PHE cc_start: 0.5757 (OUTLIER) cc_final: 0.5336 (t80)
REVERT: L   27 ASN cc_start: 0.7828 (t0) cc_final: 0.6762 (t0)
REVERT: L   36 SER cc_start: 0.8554 (p) cc_final: 0.8016 (p)
REVERT: L  137 THR cc_start: 0.7570 (m) cc_final: 0.7163 (t)
REVERT: L  160 PHE cc_start: 0.5007 (p90) cc_final: 0.4524 (p90)
REVERT: A  430 THR cc_start: 0.8484 (m) cc_final: 0.8182 (p)
REVERT: A  468 ILE cc_start: 0.8522 (mm) cc_final: 0.8093 (mm)
  outliers start: 13
  outliers final: 11
  residues processed: 98
  average time/residue: 0.0540
  time to fit residues: 6.9248
Evaluate side-chains
  96 residues out of total 503 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  120 GLN
Chi-restraints excluded: chain H residue  122 THR
Chi-restraints excluded: chain H residue  137 PHE
Chi-restraints excluded: chain H residue  157 VAL
Chi-restraints excluded: chain H residue  160 TYR
Chi-restraints excluded: chain H residue  165 VAL
Chi-restraints excluded: chain H residue  198 THR
Chi-restraints excluded: chain H residue  213 VAL
Chi-restraints excluded: chain L residue   54 VAL
Chi-restraints excluded: chain L residue   91 ILE
Chi-restraints excluded: chain L residue  212 TYR
Chi-restraints excluded: chain A residue  478 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 55 optimal weight:    0.5980
   chunk 53 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 41 optimal weight:    0.2980
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    0.0970
   chunk 47 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.4578

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

Flipped N/Q/H residues before XYZ refinement:
H 186 GLN
** L 209 HIS ** 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 = 0.4215 r_free = 0.4215 target = 0.171610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.145434 restraints weight = 7575.026|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 3.07
r_work: 0.3766 rms_B_bonded: 3.27 restraints_weight: 0.5000
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.3425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4724  Z= 0.122
  Angle     :  0.603   8.408   6456  Z= 0.307
  Chirality :  0.044   0.151    708
  Planarity :  0.004   0.039    828
  Dihedral  :  5.349  48.777    699
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.20 %
    Favored  : 92.80 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 16.30 %
    Favored  : 81.11 %
  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: -1.66 (0.35), residues: 583
  helix: -3.09 (0.76), residues: 33
  sheet: -0.38 (0.40), residues: 155
  loop : -1.28 (0.33), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  80 
 TYR   0.016   0.001   TYR L  55 
 PHE   0.026   0.002   PHE H  76 
 TRP   0.010   0.001   TRP A 436 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 4714)
  covalent geometry    : angle       0.60191 ( 6434)
  SS BOND              : bond        0.00184 (    8)
  SS BOND              : angle       0.67482 (   16)
  hydrogen bonds       : bond        0.03218 (   97)
  hydrogen bonds       : angle       6.47505 (  225)
  link_BETA1-4         : bond        0.00030 (    1)
  link_BETA1-4         : angle       1.37434 (    3)
  link_NAG-ASN         : bond        0.00159 (    1)
  link_NAG-ASN         : angle       0.54426 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1163.93 seconds
wall clock time: 20 minutes 45.74 seconds (1245.74 seconds total)