Starting phenix.real_space_refine
on Tue Mar  3 11:11:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7lxx_23578/03_2026/7lxx_23578.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7lxx_23578/03_2026/7lxx_23578.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7lxx_23578/03_2026/7lxx_23578.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7lxx_23578/03_2026/7lxx_23578.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7lxx_23578/03_2026/7lxx_23578.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7lxx_23578/03_2026/7lxx_23578.map"
  }
  resolution = 3.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.029
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      10      5.16       5
     C    1724      2.51       5
     N     466      2.21       5
     O     540      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 2740
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "H"
      Number of atoms: 971
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 126, 971
          Classifications: {'peptide': 126}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 123}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 4
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "L"
      Number of atoms: 777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 777
          Classifications: {'peptide': 107}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 6, 'TRANS': 100}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 940
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 940
          Classifications: {'peptide': 119}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 114}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 21
          Unresolved non-hydrogen angles: 27
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 0.74, per 1000 atoms: 0.27
  Number of scatterers: 2740
  At special positions: 0
  Unit cell: (71.4, 86.1, 71.4, 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      10     16.00
     O     540      8.00
     N     466      7.00
     C    1724      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.07
    Simple disulfide: pdb=" SG  CYS L  22 " - pdb=" SG  CYS L  90 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  15 " - pdb=" SG  CYS A 136 " distance=2.02

  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 "
    BETA1-6
      " NAG B   1 " - " FUC B   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A1301 " - " ASN A 149 "
      " NAG B   1 " - " ASN A  17 "
  Time building additional restraints: 0.23
  Conformation dependent library (CDL) restraints added in 83.9 milliseconds
  

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  642

  Finding SS restraints...
    Secondary structure from input PDB file:
      3 helices and 9 sheets defined
      4.3% alpha, 50.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.09
  Creating SS restraints...
    Processing helix  chain 'H' and resid 28 through 32
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'L' and resid 81 through 85
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.847A  pdb=" N   ILE H  34 " --> pdb=" O   SER H  50 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   SER H  50 " --> pdb=" O   ILE H  34 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 3.669A  pdb=" N   TYR H 115 " --> pdb=" O   ARG H  98 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11
      removed outlier: 6.530A  pdb=" N   TRP L  37 " --> pdb=" O   MET L  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11
    Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23
    Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 66
    Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.464A  pdb=" N   ALA A 243 " --> pdb=" O   ILE A 101 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   ILE A 101 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 5.646A  pdb=" N   ARG A 102 " --> pdb=" O   ASN A 121 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 84
      removed outlier: 12.962A  pdb=" N   PHE A 238 " --> pdb=" O   PHE A 135 " (cutoff:3.500A)
      removed outlier: 12.148A  pdb=" N   ASN A 137 " --> pdb=" O   PHE A 238 " (cutoff:3.500A)
      removed outlier: 9.535A  pdb=" N   THR A 240 " --> pdb=" O   ASN A 137 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   LEU A 242 " --> pdb=" O   PRO A 139 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   GLN A 134 " --> pdb=" O   ALA A 163 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   ALA A 163 " --> pdb=" O   GLN A 134 " (cutoff:3.500A)
      removed outlier: 8.600A  pdb=" N   CYS A 136 " --> pdb=" O   SER A 161 " (cutoff:3.500A)
      removed outlier: 7.818A  pdb=" N   SER A 161 " --> pdb=" O   CYS A 136 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ASP A 138 " --> pdb=" O   VAL A 159 " (cutoff:3.500A)
      removed outlier: 6.741A  pdb=" N   VAL A 159 " --> pdb=" O   ASP A 138 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   PHE A 140 " --> pdb=" O   PHE A 157 " (cutoff:3.500A)
      removed outlier: 4.875A  pdb=" N   PHE A 157 " --> pdb=" O   PHE A 140 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   GLY A 142 " --> pdb=" O   SER A 155 " (cutoff:3.500A)

    120 hydrogen bonds defined for protein.
    276 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: 0.28

  Time building geometry restraints manager: 0.32 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 719
        1.33 -     1.45: 607
        1.45 -     1.57: 1465
        1.57 -     1.69: 0
        1.69 -     1.81: 13
  Bond restraints: 2804
  Sorted by residual:
  bond pdb=" C5  NAG B   2 "
       pdb=" O5  NAG B   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.464 -0.051 2.00e-02 2.50e+03 6.60e+00
  bond pdb=" C5  NAG A1301 "
       pdb=" O5  NAG A1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.463 -0.050 2.00e-02 2.50e+03 6.20e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.461 -0.048 2.00e-02 2.50e+03 5.70e+00
  bond pdb=" CD  GLU A 154 "
       pdb=" OE2 GLU A 154 "
    ideal  model  delta    sigma   weight residual
    1.249  1.204  0.045 1.90e-02 2.77e+03 5.54e+00
  bond pdb=" CG  ASP H 114 "
       pdb=" OD2 ASP H 114 "
    ideal  model  delta    sigma   weight residual
    1.249  1.204  0.045 1.90e-02 2.77e+03 5.51e+00
  ... (remaining 2799 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.40: 3138
        1.40 -     2.81: 545
        2.81 -     4.21: 89
        4.21 -     5.62: 26
        5.62 -     7.02: 12
  Bond angle restraints: 3810
  Sorted by residual:
  angle pdb=" C   ASN A  81 "
        pdb=" N   PRO A  82 "
        pdb=" CA  PRO A  82 "
      ideal   model   delta    sigma   weight residual
     120.03  127.05   -7.02 9.90e-01 1.02e+00 5.03e+01
  angle pdb=" C   ALA L  45 "
        pdb=" N   PRO L  46 "
        pdb=" CA  PRO L  46 "
      ideal   model   delta    sigma   weight residual
     119.85  126.55   -6.70 1.01e+00 9.80e-01 4.40e+01
  angle pdb=" C   ARG L  56 "
        pdb=" N   PRO L  57 "
        pdb=" CA  PRO L  57 "
      ideal   model   delta    sigma   weight residual
     119.78  126.60   -6.82 1.03e+00 9.43e-01 4.38e+01
  angle pdb=" C   ASP A 138 "
        pdb=" N   PRO A 139 "
        pdb=" CA  PRO A 139 "
      ideal   model   delta    sigma   weight residual
     120.14  126.93   -6.79 1.06e+00 8.90e-01 4.10e+01
  angle pdb=" C   THR A 250 "
        pdb=" N   PRO A 251 "
        pdb=" CA  PRO A 251 "
      ideal   model   delta    sigma   weight residual
     119.85  126.28   -6.43 1.01e+00 9.80e-01 4.05e+01
  ... (remaining 3805 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.98: 1585
       14.98 -    29.95: 61
       29.95 -    44.93: 11
       44.93 -    59.90: 5
       59.90 -    74.87: 4
  Dihedral angle restraints: 1666
    sinusoidal: 660
      harmonic: 1006
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  96 "
           pdb=" CB  CYS H  96 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  120.22  -27.22     1      1.00e+01 1.00e-02 1.06e+01
  dihedral pdb=" CG  ARG H  67 "
           pdb=" CD  ARG H  67 "
           pdb=" NE  ARG H  67 "
           pdb=" CZ  ARG H  67 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  141.04   38.96     2      1.50e+01 4.44e-03 8.43e+00
  dihedral pdb=" CB  GLU A 154 "
           pdb=" CG  GLU A 154 "
           pdb=" CD  GLU A 154 "
           pdb=" OE1 GLU A 154 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   74.87  -74.87     1      3.00e+01 1.11e-03 7.88e+00
  ... (remaining 1663 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 309
       0.061 -    0.121: 95
       0.121 -    0.181: 14
       0.181 -    0.241: 7
       0.241 -    0.302: 2
  Chirality restraints: 427
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.48    0.08 2.00e-02 2.50e+03 1.72e+01
  chirality pdb=" C1  FUC B   3 "
            pdb=" O6  NAG B   1 "
            pdb=" C2  FUC B   3 "
            pdb=" O5  FUC B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.47    0.07 2.00e-02 2.50e+03 1.06e+01
  chirality pdb=" C2  NAG A1301 "
            pdb=" C1  NAG A1301 "
            pdb=" C3  NAG A1301 "
            pdb=" N2  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.79    0.30 2.00e-01 2.50e+01 2.28e+00
  ... (remaining 424 not shown)

  Planarity restraints: 481
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "   -0.353 2.00e-02 2.50e+03   3.06e-01 1.17e+03
        pdb=" C7  NAG B   1 "    0.085 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "   -0.123 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "    0.544 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.154 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR H  95 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.17e+00
        pdb=" C   TYR H  95 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   TYR H  95 "    0.019 2.00e-02 2.50e+03
        pdb=" N   CYS H  96 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE H  29 "    0.025 2.00e-02 2.50e+03   1.52e-02 4.05e+00
        pdb=" CG  PHE H  29 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 PHE H  29 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 PHE H  29 "   -0.013 2.00e-02 2.50e+03
        pdb=" CE1 PHE H  29 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 PHE H  29 "    0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE H  29 "    0.014 2.00e-02 2.50e+03
  ... (remaining 478 not shown)

  Histogram of nonbonded interaction distances:
        2.52 -     3.00: 1519
        3.00 -     3.47: 2371
        3.47 -     3.95: 4484
        3.95 -     4.42: 5187
        4.42 -     4.90: 8533
  Nonbonded interactions: 22094
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP H  73 "
            pdb=" NZ  LYS H  76 "
     model   vdw
     2.519 3.120
  nonbonded pdb=" N   ASP H  62 "
            pdb=" OD1 ASP H  62 "
     model   vdw
     2.529 3.120
  nonbonded pdb=" O   THR A 250 "
            pdb=" OG1 THR A 250 "
     model   vdw
     2.573 3.040
  nonbonded pdb=" N   ASN L  33 "
            pdb=" OD1 ASN L  33 "
     model   vdw
     2.579 3.120
  nonbonded pdb=" N   LYS H 104 "
            pdb=" N   TRP H 105 "
     model   vdw
     2.582 2.560
  ... (remaining 22089 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:             2.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.050
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     4.510
  Find NCS groups from input model:        0.010
  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:5.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7476
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      :  0.012   0.056   2811  Z= 0.665
  Angle     :  1.200   7.023   3828  Z= 0.796
  Chirality :  0.064   0.302    427
  Planarity :  0.015   0.306    479
  Dihedral  :  9.984  74.874   1015
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 0.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.75 %
    Favored  : 98.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.69 (0.46), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.72 (0.40), residues: 154
  loop :  0.35 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  78 
 TYR   0.025   0.004   TYR H 103 
 PHE   0.025   0.004   PHE H  29 
 TRP   0.022   0.004   TRP L 101 
 HIS   0.002   0.001   HIS A  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.01211 ( 2804)
  covalent geometry    : angle       1.19329 ( 3810)
  SS BOND              : bond        0.02145 (    3)
  SS BOND              : angle       2.19574 (    6)
  hydrogen bonds       : bond        0.16936 (  105)
  hydrogen bonds       : angle       8.24625 (  276)
  link_BETA1-4         : bond        0.05409 (    1)
  link_BETA1-4         : angle       2.27361 (    3)
  link_BETA1-6         : bond        0.04677 (    1)
  link_BETA1-6         : angle       1.86634 (    3)
  link_NAG-ASN         : bond        0.05294 (    2)
  link_NAG-ASN         : angle       2.28691 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.078 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 86
  average time/residue: 0.3209
  time to fit residues: 28.6535
Evaluate side-chains
  61 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.121 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    0.0570
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0980
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    0.0970
   chunk 19 optimal weight:    0.1980
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.1296

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H 118 GLN
L  33 ASN
A  99 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.142674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.135049 restraints weight = 3618.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.3536 rms_B_bonded: 1.17
r_work: 0.3481 rms_B_bonded: 1.42 restraints_weight: 0.5000
r_work: 0.3394 rms_B_bonded: 2.68 restraints_weight: 0.2500
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.1966

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   2811  Z= 0.126
  Angle     :  0.621   6.454   3828  Z= 0.313
  Chirality :  0.044   0.172    427
  Planarity :  0.004   0.036    479
  Dihedral  :  6.267  56.728    459
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.79 %
    Favored  : 98.21 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 11.58 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.46), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.87 (0.40), residues: 152
  loop : -0.02 (0.48), residues: 184

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 102 
 TYR   0.019   0.002   TYR A 248 
 PHE   0.012   0.002   PHE A 238 
 TRP   0.008   0.001   TRP H 116 
 HIS   0.003   0.001   HIS L  41 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 ( 2804)
  covalent geometry    : angle       0.60878 ( 3810)
  SS BOND              : bond        0.00345 (    3)
  SS BOND              : angle       0.94829 (    6)
  hydrogen bonds       : bond        0.03894 (  105)
  hydrogen bonds       : angle       6.41292 (  276)
  link_BETA1-4         : bond        0.00797 (    1)
  link_BETA1-4         : angle       2.57799 (    3)
  link_BETA1-6         : bond        0.01141 (    1)
  link_BETA1-6         : angle       1.34771 (    3)
  link_NAG-ASN         : bond        0.00390 (    2)
  link_NAG-ASN         : angle       2.37579 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 67
  time to evaluate  : 0.077 
Fit side-chains
REVERT: L   84 ASP cc_start: 0.8064 (m-30) cc_final: 0.7822 (m-30)
REVERT: A  102 ARG cc_start: 0.8337 (mmt90) cc_final: 0.7987 (mmt90)
  outliers start: 9
  outliers final: 3
  residues processed: 70
  average time/residue: 0.3503
  time to fit residues: 25.4129
Evaluate side-chains
  66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue  118 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 16 optimal weight:    0.1980
   chunk 20 optimal weight:    0.5980
   chunk 31 optimal weight:    0.7980
   chunk 28 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0980
   chunk 3 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.4180

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
L  33 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.135769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.127952 restraints weight = 3622.062|
|-----------------------------------------------------------------------------|
r_work (start): 0.3455 rms_B_bonded: 1.16
r_work: 0.3401 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.3315 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.3315
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   2811  Z= 0.243
  Angle     :  0.673   7.666   3828  Z= 0.342
  Chirality :  0.046   0.220    427
  Planarity :  0.005   0.029    479
  Dihedral  :  6.227  48.129    459
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 11.23 %
    Favored  : 83.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.10 (0.46), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.53 (0.41), residues: 154
  loop : -0.28 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 102 
 TYR   0.018   0.002   TYR A 248 
 PHE   0.017   0.003   PHE H  29 
 TRP   0.013   0.002   TRP H  47 
 HIS   0.006   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 2804)
  covalent geometry    : angle       0.66059 ( 3810)
  SS BOND              : bond        0.00504 (    3)
  SS BOND              : angle       1.11798 (    6)
  hydrogen bonds       : bond        0.04123 (  105)
  hydrogen bonds       : angle       6.48278 (  276)
  link_BETA1-4         : bond        0.00749 (    1)
  link_BETA1-4         : angle       1.93786 (    3)
  link_BETA1-6         : bond        0.00278 (    1)
  link_BETA1-6         : angle       2.13223 (    3)
  link_NAG-ASN         : bond        0.00209 (    2)
  link_NAG-ASN         : angle       2.62063 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.088 
Fit side-chains
REVERT: L   84 ASP cc_start: 0.8295 (m-30) cc_final: 0.8078 (m-30)
REVERT: A  122 ASN cc_start: 0.7777 (p0) cc_final: 0.7561 (p0)
  outliers start: 14
  outliers final: 10
  residues processed: 78
  average time/residue: 0.3120
  time to fit residues: 25.2735
Evaluate side-chains
  77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue  110 THR
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  154 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 18 optimal weight:    0.9980
   chunk 12 optimal weight:    0.0000
   chunk 23 optimal weight:    0.5980
   chunk 15 optimal weight:    0.7980
   chunk 14 optimal weight:    0.4980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.4784

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.133592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.126239 restraints weight = 3574.344|
|-----------------------------------------------------------------------------|
r_work (start): 0.3426 rms_B_bonded: 1.08
r_work: 0.3371 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.3286 rms_B_bonded: 2.47 restraints_weight: 0.2500
r_work (final): 0.3286
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.073   2811  Z= 0.277
  Angle     :  0.690   8.045   3828  Z= 0.352
  Chirality :  0.049   0.284    427
  Planarity :  0.005   0.056    479
  Dihedral  :  6.540  40.024    459
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 13.33 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.47), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.28 (0.42), residues: 154
  loop : -0.39 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 102 
 TYR   0.020   0.002   TYR A 248 
 PHE   0.018   0.002   PHE H  29 
 TRP   0.012   0.002   TRP A  64 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00616 ( 2804)
  covalent geometry    : angle       0.67315 ( 3810)
  SS BOND              : bond        0.00538 (    3)
  SS BOND              : angle       1.14583 (    6)
  hydrogen bonds       : bond        0.04016 (  105)
  hydrogen bonds       : angle       6.77488 (  276)
  link_BETA1-4         : bond        0.00440 (    1)
  link_BETA1-4         : angle       1.63237 (    3)
  link_BETA1-6         : bond        0.00225 (    1)
  link_BETA1-6         : angle       2.21755 (    3)
  link_NAG-ASN         : bond        0.00089 (    2)
  link_NAG-ASN         : angle       3.28617 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.060 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8238 (mtt) cc_final: 0.8022 (mtt)
  outliers start: 16
  outliers final: 10
  residues processed: 76
  average time/residue: 0.3264
  time to fit residues: 25.7564
Evaluate side-chains
  73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 63
  time to evaluate  : 0.104 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   69 THR
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   94 THR
Chi-restraints excluded: chain L residue  110 THR
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 30 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    0.1980
   chunk 1 optimal weight:    0.9990
   chunk 0 optimal weight:    0.7980
   chunk 16 optimal weight:    0.1980
   chunk 4 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:    0.2980
   chunk 21 optimal weight:    0.1980
   overall best weight:    0.2980

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H  84 ASN
H 118 GLN
L  41 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.132065 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.123576 restraints weight = 3599.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3432 rms_B_bonded: 1.17
r_work: 0.3382 rms_B_bonded: 1.43 restraints_weight: 0.5000
r_work: 0.3293 rms_B_bonded: 2.66 restraints_weight: 0.2500
r_work (final): 0.3293
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   2811  Z= 0.190
  Angle     :  0.622   7.810   3828  Z= 0.320
  Chirality :  0.046   0.261    427
  Planarity :  0.004   0.041    479
  Dihedral  :  6.178  41.923    459
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 14.04 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.23 (0.47), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.13 (0.42), residues: 154
  loop : -0.32 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  19 
 TYR   0.019   0.002   TYR A 248 
 PHE   0.014   0.002   PHE H  29 
 TRP   0.008   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00428 ( 2804)
  covalent geometry    : angle       0.60705 ( 3810)
  SS BOND              : bond        0.00402 (    3)
  SS BOND              : angle       1.08484 (    6)
  hydrogen bonds       : bond        0.03528 (  105)
  hydrogen bonds       : angle       6.46800 (  276)
  link_BETA1-4         : bond        0.00489 (    1)
  link_BETA1-4         : angle       1.56850 (    3)
  link_BETA1-6         : bond        0.00223 (    1)
  link_BETA1-6         : angle       2.13374 (    3)
  link_NAG-ASN         : bond        0.00116 (    2)
  link_NAG-ASN         : angle       2.90380 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.070 
Fit side-chains
REVERT: A  153 MET cc_start: 0.8240 (mtt) cc_final: 0.8024 (mtt)
  outliers start: 14
  outliers final: 12
  residues processed: 76
  average time/residue: 0.3473
  time to fit residues: 27.3358
Evaluate side-chains
  78 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 66
  time to evaluate  : 0.098 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue   83 MET
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   94 THR
Chi-restraints excluded: chain L residue  110 THR
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Chi-restraints excluded: chain A residue  154 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 15 optimal weight:    0.0980
   chunk 10 optimal weight:    0.7980
   chunk 24 optimal weight:    0.7980
   chunk 32 optimal weight:    0.2980
   chunk 18 optimal weight:    0.9990
   chunk 17 optimal weight:    0.3980
   chunk 6 optimal weight:    0.0020
   chunk 22 optimal weight:    0.3980
   chunk 5 optimal weight:    0.3980
   chunk 16 optimal weight:    0.2980
   chunk 23 optimal weight:    0.0970
   overall best weight:    0.1586

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H  84 ASN
H 118 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.134160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.125636 restraints weight = 3659.301|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.18
r_work: 0.3408 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3319 rms_B_bonded: 2.71 restraints_weight: 0.2500
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   2811  Z= 0.128
  Angle     :  0.576   7.568   3828  Z= 0.298
  Chirality :  0.044   0.231    427
  Planarity :  0.004   0.026    479
  Dihedral  :  5.573  38.315    459
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 15.09 %
    Favored  : 80.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.47), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.13 (0.42), residues: 154
  loop : -0.25 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  19 
 TYR   0.017   0.001   TYR A 248 
 PHE   0.010   0.001   PHE A 238 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 2804)
  covalent geometry    : angle       0.56394 ( 3810)
  SS BOND              : bond        0.00345 (    3)
  SS BOND              : angle       0.95509 (    6)
  hydrogen bonds       : bond        0.03125 (  105)
  hydrogen bonds       : angle       6.06665 (  276)
  link_BETA1-4         : bond        0.00531 (    1)
  link_BETA1-4         : angle       1.40618 (    3)
  link_BETA1-6         : bond        0.00250 (    1)
  link_BETA1-6         : angle       1.89306 (    3)
  link_NAG-ASN         : bond        0.00178 (    2)
  link_NAG-ASN         : angle       2.51247 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.107 
Fit side-chains
REVERT: H   19 ARG cc_start: 0.8086 (ttt90) cc_final: 0.7882 (ttm170)
REVERT: A   20 THR cc_start: 0.8460 (p) cc_final: 0.8227 (p)
REVERT: A  153 MET cc_start: 0.8297 (mtt) cc_final: 0.8050 (mtt)
  outliers start: 14
  outliers final: 8
  residues processed: 75
  average time/residue: 0.3836
  time to fit residues: 29.7445
Evaluate side-chains
  72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 64
  time to evaluate  : 0.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue   73 ASP
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  110 THR
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 15 optimal weight:    0.1980
   chunk 32 optimal weight:    0.4980
   chunk 1 optimal weight:    0.8980
   chunk 5 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 17 optimal weight:    0.0020
   chunk 20 optimal weight:    0.6980
   chunk 2 optimal weight:    0.9980
   chunk 30 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.3188

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.136555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.129103 restraints weight = 3514.723|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 1.12
r_work: 0.3408 rms_B_bonded: 1.35 restraints_weight: 0.5000
r_work: 0.3321 rms_B_bonded: 2.50 restraints_weight: 0.2500
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   2811  Z= 0.195
  Angle     :  0.612   7.747   3828  Z= 0.316
  Chirality :  0.046   0.254    427
  Planarity :  0.004   0.028    479
  Dihedral  :  5.765  40.666    459
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 17.54 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.29 (0.46), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.05 (0.42), residues: 154
  loop : -0.32 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 102 
 TYR   0.015   0.002   TYR A 248 
 PHE   0.015   0.002   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00438 ( 2804)
  covalent geometry    : angle       0.59996 ( 3810)
  SS BOND              : bond        0.00449 (    3)
  SS BOND              : angle       0.95800 (    6)
  hydrogen bonds       : bond        0.03440 (  105)
  hydrogen bonds       : angle       6.20372 (  276)
  link_BETA1-4         : bond        0.00534 (    1)
  link_BETA1-4         : angle       1.36709 (    3)
  link_BETA1-6         : bond        0.00216 (    1)
  link_BETA1-6         : angle       1.99714 (    3)
  link_NAG-ASN         : bond        0.00167 (    2)
  link_NAG-ASN         : angle       2.55482 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A   20 THR cc_start: 0.8491 (p) cc_final: 0.8215 (p)
REVERT: A  102 ARG cc_start: 0.8510 (mmm-85) cc_final: 0.8290 (mmt90)
  outliers start: 10
  outliers final: 11
  residues processed: 73
  average time/residue: 0.3847
  time to fit residues: 28.9565
Evaluate side-chains
  77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   46 GLU
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue   85 SER
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  110 THR
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 3 optimal weight:    0.9990
   chunk 24 optimal weight:    0.7980
   chunk 29 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 15 optimal weight:    0.0980
   chunk 5 optimal weight:    0.7980
   chunk 22 optimal weight:    0.2980
   chunk 20 optimal weight:    0.5980
   chunk 12 optimal weight:    0.2980
   chunk 6 optimal weight:    0.1980
   chunk 10 optimal weight:    0.0980
   overall best weight:    0.1980

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.134726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.125747 restraints weight = 3625.233|
|-----------------------------------------------------------------------------|
r_work (start): 0.3464 rms_B_bonded: 1.22
r_work: 0.3410 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3314 rms_B_bonded: 2.79 restraints_weight: 0.2500
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.3696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   2811  Z= 0.146
  Angle     :  0.595   7.622   3828  Z= 0.308
  Chirality :  0.044   0.241    427
  Planarity :  0.004   0.028    479
  Dihedral  :  5.567  40.735    459
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  4.21 %
    Allowed  : 17.89 %
    Favored  : 77.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.47), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.05 (0.42), residues: 154
  loop : -0.30 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  19 
 TYR   0.017   0.001   TYR A 248 
 PHE   0.011   0.002   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 2804)
  covalent geometry    : angle       0.58167 ( 3810)
  SS BOND              : bond        0.00380 (    3)
  SS BOND              : angle       1.22125 (    6)
  hydrogen bonds       : bond        0.03173 (  105)
  hydrogen bonds       : angle       6.06928 (  276)
  link_BETA1-4         : bond        0.00585 (    1)
  link_BETA1-4         : angle       1.31542 (    3)
  link_BETA1-6         : bond        0.00238 (    1)
  link_BETA1-6         : angle       1.95410 (    3)
  link_NAG-ASN         : bond        0.00160 (    2)
  link_NAG-ASN         : angle       2.62539 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.105 
Fit side-chains
REVERT: L   84 ASP cc_start: 0.8177 (m-30) cc_final: 0.7893 (m-30)
REVERT: A   20 THR cc_start: 0.8483 (p) cc_final: 0.8242 (p)
REVERT: A  153 MET cc_start: 0.8253 (mtt) cc_final: 0.8031 (mtt)
  outliers start: 12
  outliers final: 10
  residues processed: 69
  average time/residue: 0.3790
  time to fit residues: 26.9538
Evaluate side-chains
  72 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.066 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  110 THR
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 12 optimal weight:    0.0070
   chunk 3 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    0.3980
   chunk 22 optimal weight:    0.0060
   chunk 16 optimal weight:    0.3980
   chunk 11 optimal weight:    0.5980
   chunk 4 optimal weight:    0.3980
   chunk 23 optimal weight:    0.4980
   overall best weight:    0.2414

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.137641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.129824 restraints weight = 3606.090|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.13
r_work: 0.3408 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.3323 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.3323
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   2811  Z= 0.164
  Angle     :  0.595   6.570   3828  Z= 0.312
  Chirality :  0.045   0.246    427
  Planarity :  0.004   0.031    479
  Dihedral  :  5.584  40.841    459
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.86 %
    Allowed  : 18.95 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.47), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.02 (0.42), residues: 154
  loop : -0.32 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG H  19 
 TYR   0.015   0.002   TYR A 248 
 PHE   0.012   0.002   PHE H  29 
 TRP   0.007   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 2804)
  covalent geometry    : angle       0.58257 ( 3810)
  SS BOND              : bond        0.00387 (    3)
  SS BOND              : angle       1.17649 (    6)
  hydrogen bonds       : bond        0.03245 (  105)
  hydrogen bonds       : angle       6.08369 (  276)
  link_BETA1-4         : bond        0.00543 (    1)
  link_BETA1-4         : angle       1.24450 (    3)
  link_BETA1-6         : bond        0.00234 (    1)
  link_BETA1-6         : angle       1.97171 (    3)
  link_NAG-ASN         : bond        0.00164 (    2)
  link_NAG-ASN         : angle       2.56687 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.060 
Fit side-chains
REVERT: L   84 ASP cc_start: 0.8165 (m-30) cc_final: 0.7902 (m-30)
REVERT: A   20 THR cc_start: 0.8491 (p) cc_final: 0.8206 (p)
REVERT: A  153 MET cc_start: 0.8200 (mtt) cc_final: 0.7987 (mtt)
  outliers start: 11
  outliers final: 10
  residues processed: 71
  average time/residue: 0.3436
  time to fit residues: 25.2066
Evaluate side-chains
  74 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain H residue  114 ASP
Chi-restraints excluded: chain H residue  124 VAL
Chi-restraints excluded: chain L residue   96 SER
Chi-restraints excluded: chain L residue  110 THR
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 28 optimal weight:    0.0970
   chunk 10 optimal weight:    0.0370
   chunk 25 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0770
   chunk 12 optimal weight:    0.0370
   chunk 29 optimal weight:    0.0370
   chunk 21 optimal weight:    0.0770
   chunk 13 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 27 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.0530

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.132278 restraints weight = 3569.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 1.16
r_work: 0.3455 rms_B_bonded: 1.38 restraints_weight: 0.5000
r_work: 0.3369 rms_B_bonded: 2.51 restraints_weight: 0.2500
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   2811  Z= 0.103
  Angle     :  0.574   7.433   3828  Z= 0.299
  Chirality :  0.043   0.219    427
  Planarity :  0.003   0.029    479
  Dihedral  :  5.138  36.115    459
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.27 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 21.40 %
    Favored  : 76.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.47), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.07 (0.42), residues: 154
  loop : -0.27 (0.48), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG H  19 
 TYR   0.013   0.001   TYR A 248 
 PHE   0.010   0.001   PHE A 238 
 TRP   0.007   0.001   TRP L 101 
 HIS   0.002   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 ( 2804)
  covalent geometry    : angle       0.56289 ( 3810)
  SS BOND              : bond        0.00300 (    3)
  SS BOND              : angle       1.08816 (    6)
  hydrogen bonds       : bond        0.02862 (  105)
  hydrogen bonds       : angle       5.75481 (  276)
  link_BETA1-4         : bond        0.00604 (    1)
  link_BETA1-4         : angle       1.15086 (    3)
  link_BETA1-6         : bond        0.00288 (    1)
  link_BETA1-6         : angle       1.77517 (    3)
  link_NAG-ASN         : bond        0.00165 (    2)
  link_NAG-ASN         : angle       2.43199 (    6)

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

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

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  672 Ramachandran restraints generated.
    336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 66
  time to evaluate  : 0.075 
Fit side-chains
REVERT: A   20 THR cc_start: 0.8427 (p) cc_final: 0.8158 (p)
REVERT: A  153 MET cc_start: 0.8223 (mtt) cc_final: 0.8013 (mtt)
  outliers start: 7
  outliers final: 6
  residues processed: 71
  average time/residue: 0.3958
  time to fit residues: 29.0125
Evaluate side-chains
  69 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 63
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 VAL
Chi-restraints excluded: chain H residue   65 LYS
Chi-restraints excluded: chain A residue   16 VAL
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue   83 VAL
Chi-restraints excluded: chain A residue  118 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 33
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 2 optimal weight:    0.2980
   chunk 21 optimal weight:    0.4980
   chunk 23 optimal weight:    0.6980
   chunk 0 optimal weight:    0.0870
   chunk 9 optimal weight:    0.0980
   chunk 5 optimal weight:    0.3980
   chunk 20 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0870
   chunk 4 optimal weight:    0.1980
   chunk 29 optimal weight:    0.4980
   overall best weight:    0.1536

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

Flipped N/Q/H residues before XYZ refinement:
H  56 ASN
H 118 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.131261 restraints weight = 3505.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 1.09
r_work: 0.3441 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.3355 rms_B_bonded: 2.53 restraints_weight: 0.2500
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   2811  Z= 0.128
  Angle     :  0.598   7.718   3828  Z= 0.310
  Chirality :  0.044   0.234    427
  Planarity :  0.004   0.029    479
  Dihedral  :  5.093  34.534    459
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 20.70 %
    Favored  : 76.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.47), residues: 336
  helix:  None (None), residues: 0
  sheet:  0.14 (0.43), residues: 154
  loop : -0.32 (0.47), residues: 182

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 102 
 TYR   0.013   0.001   TYR A 248 
 PHE   0.011   0.001   PHE A 238 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.003   0.001   HIS H  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 2804)
  covalent geometry    : angle       0.58786 ( 3810)
  SS BOND              : bond        0.00356 (    3)
  SS BOND              : angle       1.06355 (    6)
  hydrogen bonds       : bond        0.03070 (  105)
  hydrogen bonds       : angle       5.81831 (  276)
  link_BETA1-4         : bond        0.00575 (    1)
  link_BETA1-4         : angle       1.00981 (    3)
  link_BETA1-6         : bond        0.00266 (    1)
  link_BETA1-6         : angle       1.78650 (    3)
  link_NAG-ASN         : bond        0.00172 (    2)
  link_NAG-ASN         : angle       2.33054 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1265.34 seconds
wall clock time: 22 minutes 13.77 seconds (1333.77 seconds total)