Starting phenix.real_space_refine
on Tue Mar  3 12:25:04 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/28qm_56750/03_2026/28qm_56750.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/28qm_56750/03_2026/28qm_56750.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/28qm_56750/03_2026/28qm_56750.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/28qm_56750/03_2026/28qm_56750.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/28qm_56750/03_2026/28qm_56750.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/28qm_56750/03_2026/28qm_56750.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.006
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       9      5.16       5
     C    2586      2.51       5
     N     673      2.21       5
     O     766      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 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: 4034
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2848
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 373, 2848
          Classifications: {'peptide': 373}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 21, 'TRANS': 351}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 21
          Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 16
    Chain: "B"
      Number of atoms: 1183
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 159, 1180
          Classifications: {'peptide': 159}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 154}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 28
      Conformer: "B"
        Number of residues, atoms: 159, 1180
          Classifications: {'peptide': 159}
          Incomplete info: {'truncation_to_alanine': 7}
          Link IDs: {'PTRANS': 4, 'TRANS': 154}
          Unresolved non-hydrogen bonds: 29
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 22
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 28
          bond proxies already assigned to first conformer: 1199
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 3
          Unusual residues: {'EOH': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.20, per 1000 atoms: 0.30
  Number of scatterers: 4034
  At special positions: 0
  Unit cell: (74.61, 105.283, 82.071, 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       9     16.00
     O     766      8.00
     N     673      7.00
     C    2586      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 178.5 milliseconds
  

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  976

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 4 sheets defined
      56.6% alpha, 10.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 17 through 32
    Processing helix  chain 'A' and resid 43 through 53
      Proline residue:  A  49  - end of helix
      removed outlier: 3.835A  pdb=" N   ALA A  53 " --> pdb=" O   PRO A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 74
      removed outlier: 3.641A  pdb=" N   GLY A  69 " --> pdb=" O   HIS A  65 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   GLY A  70 " --> pdb=" O   ASP A  66 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   GLN A  73 " --> pdb=" O   GLY A  69 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   SER A  74 " --> pdb=" O   GLY A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 88
    Processing helix  chain 'A' and resid 91 through 96
      removed outlier: 3.654A  pdb=" N   TRP A  95 " --> pdb=" O   TYR A  91 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ASP A  96 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 91 through 96'
    Processing helix  chain 'A' and resid 129 through 131
      No H-bonds generated for 'chain 'A' and resid 129 through 131'
    Processing helix  chain 'A' and resid 132 through 142
    Processing helix  chain 'A' and resid 154 through 165
      removed outlier: 3.756A  pdb=" N   THR A 158 " --> pdb=" O   GLU A 154 " (cutoff:3.500A)
      Proline residue:  A 160  - end of helix
      removed outlier: 4.561A  pdb=" N   ASP A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 202
    Processing helix  chain 'A' and resid 210 through 220
    Processing helix  chain 'A' and resid 229 through 231
      No H-bonds generated for 'chain 'A' and resid 229 through 231'
    Processing helix  chain 'A' and resid 232 through 240
    Processing helix  chain 'A' and resid 273 through 284
    Processing helix  chain 'A' and resid 287 through 298
    Processing helix  chain 'A' and resid 305 through 313
      removed outlier: 3.604A  pdb=" N   GLU A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 328
    Processing helix  chain 'A' and resid 336 through 354
    Processing helix  chain 'A' and resid 357 through 370
    Processing helix  chain 'B' and resid 14 through 25
    Processing helix  chain 'B' and resid 26 through 34
      removed outlier: 3.623A  pdb=" N   ILE B  32 " --> pdb=" O   ASP B  28 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   MET B  34 " --> pdb=" O   VAL B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 58
    Processing helix  chain 'B' and resid 59 through 69
    Processing helix  chain 'B' and resid 82 through 91
    Processing helix  chain 'B' and resid 92 through 102
    Processing helix  chain 'B' and resid 115 through 124
    Processing helix  chain 'B' and resid 125 through 135
    Processing helix  chain 'B' and resid 148 through 156
    Processing helix  chain 'B' and resid 158 through 165
      removed outlier: 3.542A  pdb=" N   TYR B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 170
    Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 39
      removed outlier: 6.525A  pdb=" N   VAL A   9 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   PHE A  62 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   TRP A  11 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 9.056A  pdb=" N   ALA A  64 " --> pdb=" O   TRP A  11 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ALA A 110 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 6.235A  pdb=" N   ALA A 265 " --> pdb=" O   PRO A 108 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   ILE A 267 " --> pdb=" O   ALA A 106 " (cutoff:3.500A)
      removed outlier: 7.476A  pdb=" N   ALA A 106 " --> pdb=" O   ILE A 267 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A 302 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 36 through 39
      removed outlier: 6.525A  pdb=" N   VAL A   9 " --> pdb=" O   ILE A  60 " (cutoff:3.500A)
      removed outlier: 8.073A  pdb=" N   PHE A  62 " --> pdb=" O   VAL A   9 " (cutoff:3.500A)
      removed outlier: 6.807A  pdb=" N   TRP A  11 " --> pdb=" O   PHE A  62 " (cutoff:3.500A)
      removed outlier: 9.056A  pdb=" N   ALA A  64 " --> pdb=" O   TRP A  11 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 99 through 100
    Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 228

    198 hydrogen bonds defined for protein.
    581 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: 0.59

  Time building geometry restraints manager: 0.34 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: 1323
        1.34 -     1.46: 639
        1.46 -     1.57: 2149
        1.57 -     1.69: 0
        1.69 -     1.80: 18
  Bond restraints: 4129
  Sorted by residual:
  bond pdb=" N   ASN A 174 "
       pdb=" CA  ASN A 174 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.35e-02 5.49e+03 5.68e+00
  bond pdb=" N   LEU B  66 "
       pdb=" CA  LEU B  66 "
    ideal  model  delta    sigma   weight residual
    1.459  1.486 -0.027 1.23e-02 6.61e+03 4.91e+00
  bond pdb=" N   GLY A 175 "
       pdb=" CA  GLY A 175 "
    ideal  model  delta    sigma   weight residual
    1.449  1.478 -0.029 1.45e-02 4.76e+03 3.93e+00
  bond pdb=" C   ILE A 133 "
       pdb=" N   PRO A 134 "
    ideal  model  delta    sigma   weight residual
    1.334  1.353 -0.019 2.34e-02 1.83e+03 6.42e-01
  bond pdb=" C   ASN A 174 "
       pdb=" O   ASN A 174 "
    ideal  model  delta    sigma   weight residual
    1.236  1.245 -0.009 1.28e-02 6.10e+03 5.04e-01
  ... (remaining 4124 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.00: 5417
        1.00 -     2.01: 151
        2.01 -     3.01: 34
        3.01 -     4.02: 16
        4.02 -     5.02: 3
  Bond angle restraints: 5621
  Sorted by residual:
  angle pdb=" CA  LEU B  66 "
        pdb=" C   LEU B  66 "
        pdb=" O   LEU B  66 "
      ideal   model   delta    sigma   weight residual
     120.42  118.03    2.39 1.06e+00 8.90e-01 5.08e+00
  angle pdb=" CA  TYR B  56 "
        pdb=" CB  TYR B  56 "
        pdb=" CG  TYR B  56 "
      ideal   model   delta    sigma   weight residual
     113.90  117.53   -3.63 1.80e+00 3.09e-01 4.07e+00
  angle pdb=" O   LEU B  66 "
        pdb=" C   LEU B  66 "
        pdb=" N   LEU B  67 "
      ideal   model   delta    sigma   weight residual
     122.15  124.08   -1.93 1.14e+00 7.69e-01 2.87e+00
  angle pdb=" O   ASN A 174 "
        pdb=" C   ASN A 174 "
        pdb=" N   GLY A 175 "
      ideal   model   delta    sigma   weight residual
     122.43  124.67   -2.24 1.33e+00 5.65e-01 2.84e+00
  angle pdb=" CA  GLU B  94 "
        pdb=" CB  GLU B  94 "
        pdb=" CG  GLU B  94 "
      ideal   model   delta    sigma   weight residual
     114.10  117.45   -3.35 2.00e+00 2.50e-01 2.80e+00
  ... (remaining 5616 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.00: 2106
       18.00 -    36.00: 244
       36.00 -    53.99: 70
       53.99 -    71.99: 6
       71.99 -    89.99: 7
  Dihedral angle restraints: 2433
    sinusoidal: 905
      harmonic: 1528
  Sorted by residual:
  dihedral pdb=" CB  GLU A 323 "
           pdb=" CG  GLU A 323 "
           pdb=" CD  GLU A 323 "
           pdb=" OE1 GLU A 323 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   89.99  -89.99     1      3.00e+01 1.11e-03 1.07e+01
  dihedral pdb=" CB  GLU B  64 "
           pdb=" CG  GLU B  64 "
           pdb=" CD  GLU B  64 "
           pdb=" OE1 GLU B  64 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -86.50   86.50     1      3.00e+01 1.11e-03 1.00e+01
  dihedral pdb=" N   LYS A 298 "
           pdb=" CA  LYS A 298 "
           pdb=" CB  LYS A 298 "
           pdb=" CG  LYS A 298 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.37   55.37     3      1.50e+01 4.44e-03 9.34e+00
  ... (remaining 2430 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 372
       0.027 -    0.053: 169
       0.053 -    0.080: 45
       0.080 -    0.106: 28
       0.106 -    0.133: 10
  Chirality restraints: 624
  Sorted by residual:
  chirality pdb=" CA  ILE A 117 "
            pdb=" N   ILE A 117 "
            pdb=" C   ILE A 117 "
            pdb=" CB  ILE A 117 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CA  LEU B  66 "
            pdb=" N   LEU B  66 "
            pdb=" C   LEU B  66 "
            pdb=" CB  LEU B  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.64   -0.13 2.00e-01 2.50e+01 4.41e-01
  chirality pdb=" CA  ILE A  60 "
            pdb=" N   ILE A  60 "
            pdb=" C   ILE A  60 "
            pdb=" CB  ILE A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.20e-01
  ... (remaining 621 not shown)

  Planarity restraints: 731
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 343 "    0.009 2.00e-02 2.50e+03   1.84e-02 3.39e+00
        pdb=" C   ALA A 343 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   ALA A 343 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A 344 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 347 "    0.009 2.00e-02 2.50e+03   1.80e-02 3.23e+00
        pdb=" C   ALA A 347 "   -0.031 2.00e-02 2.50e+03
        pdb=" O   ALA A 347 "    0.012 2.00e-02 2.50e+03
        pdb=" N   VAL A 348 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B 115 "    0.029 5.00e-02 4.00e+02   4.41e-02 3.11e+00
        pdb=" N   PRO B 116 "   -0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 116 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO B 116 "    0.025 5.00e-02 4.00e+02
  ... (remaining 728 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 271
        2.73 -     3.27: 4086
        3.27 -     3.82: 6692
        3.82 -     4.36: 7815
        4.36 -     4.90: 13911
  Nonbonded interactions: 32775
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A 350 "
            pdb=" OE1 GLN A 356 "
     model   vdw
     2.191 3.120
  nonbonded pdb=" OD2 ASP A  59 "
            pdb=" OG  SER A 271 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OD1 ASP A 165 "
            pdb=" NE2 GLN A 254 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   ASP A 198 "
            pdb=" ND2 ASN A 202 "
     model   vdw
     2.296 3.120
  nonbonded pdb=" O   GLU A 215 "
            pdb=" ND2 ASN A 219 "
     model   vdw
     2.299 3.120
  ... (remaining 32770 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=0.18 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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             7.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.050
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.710
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4129  Z= 0.148
  Angle     :  0.462   5.021   5621  Z= 0.245
  Chirality :  0.038   0.133    624
  Planarity :  0.004   0.044    731
  Dihedral  : 16.855  89.990   1457
  Min Nonbonded Distance : 2.191

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 22.94 %
    Favored  : 77.06 %
  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:  0.64 (0.36), residues: 529
  helix:  0.73 (0.31), residues: 264
  sheet: -0.59 (0.94), residues: 25
  loop :  0.38 (0.42), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  99 
 TYR   0.009   0.001   TYR A 107 
 PHE   0.008   0.001   PHE A  62 
 TRP   0.013   0.001   TRP B 123 
 HIS   0.004   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4129)
  covalent geometry    : angle       0.46228 ( 5621)
  hydrogen bonds       : bond        0.14267 (  191)
  hydrogen bonds       : angle       6.49296 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.1295
  time to fit residues: 7.8608
Evaluate side-chains
  48 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 26 optimal weight:    0.0870
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.8980
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 372 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.140624 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.109898 restraints weight = 8320.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3254 rms_B_bonded: 3.11
r_work: 0.3078 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3080
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.18   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3080 r_free = 0.3080    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3080
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.0729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4129  Z= 0.137
  Angle     :  0.480   6.613   5621  Z= 0.245
  Chirality :  0.039   0.134    624
  Planarity :  0.004   0.047    731
  Dihedral  :  3.557  15.586    560
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.79 %
    Favored  : 96.21 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 21.95 %
    Favored  : 76.56 %
  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:  1.26 (0.36), residues: 529
  helix:  1.45 (0.31), residues: 277
  sheet: -0.74 (0.95), residues: 25
  loop :  0.41 (0.42), residues: 227

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  99 
 TYR   0.010   0.001   TYR A 107 
 PHE   0.009   0.001   PHE A  62 
 TRP   0.012   0.001   TRP B 123 
 HIS   0.005   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 4129)
  covalent geometry    : angle       0.48009 ( 5621)
  hydrogen bonds       : bond        0.03836 (  191)
  hydrogen bonds       : angle       4.40724 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ASP cc_start: 0.8015 (t0) cc_final: 0.7699 (t0)
  outliers start: 6
  outliers final: 2
  residues processed: 60
  average time/residue: 0.1126
  time to fit residues: 7.9714
Evaluate side-chains
  52 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain B residue  160 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 46 optimal weight:    0.0470
   chunk 33 optimal weight:    0.6980
   chunk 44 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9980
   chunk 35 optimal weight:    2.9990
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:    0.0670
   chunk 17 optimal weight:    0.0020
   chunk 13 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.1624

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.144069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.112614 restraints weight = 7787.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3293 rms_B_bonded: 3.05
r_work: 0.3121 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3122
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3122 r_free = 0.3122    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3122
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   4129  Z= 0.083
  Angle     :  0.441   9.012   5621  Z= 0.220
  Chirality :  0.038   0.124    624
  Planarity :  0.004   0.049    731
  Dihedral  :  3.324  15.081    560
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 5.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 22.44 %
    Favored  : 76.31 %
  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:  1.69 (0.37), residues: 529
  helix:  1.94 (0.31), residues: 276
  sheet: -0.83 (0.95), residues: 25
  loop :  0.46 (0.42), residues: 228

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  99 
 TYR   0.007   0.001   TYR A  18 
 PHE   0.008   0.001   PHE A  93 
 TRP   0.008   0.001   TRP B 123 
 HIS   0.003   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00183 ( 4129)
  covalent geometry    : angle       0.44110 ( 5621)
  hydrogen bonds       : bond        0.03084 (  191)
  hydrogen bonds       : angle       4.09442 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.145 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ASP cc_start: 0.7997 (t0) cc_final: 0.7648 (t0)
REVERT: B  165 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8179 (mm)
  outliers start: 5
  outliers final: 1
  residues processed: 60
  average time/residue: 0.1012
  time to fit residues: 7.1773
Evaluate side-chains
  55 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 53
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 TYR
Chi-restraints excluded: chain B residue  165 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 44 optimal weight:    0.1980
   chunk 50 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9990
   chunk 41 optimal weight:    0.7980
   chunk 20 optimal weight:    0.9980
   chunk 32 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.140738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.109883 restraints weight = 8221.246|
|-----------------------------------------------------------------------------|
r_work (start): 0.3257 rms_B_bonded: 3.12
r_work: 0.3074 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3061
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.26   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3061 r_free = 0.3061    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3061
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1041

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   4129  Z= 0.142
  Angle     :  0.523  10.634   5621  Z= 0.251
  Chirality :  0.040   0.137    624
  Planarity :  0.004   0.049    731
  Dihedral  :  3.468  15.178    560
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 22.69 %
    Favored  : 75.31 %
  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:  1.59 (0.36), residues: 529
  helix:  1.89 (0.31), residues: 271
  sheet: -0.83 (0.94), residues: 25
  loop :  0.38 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  99 
 TYR   0.010   0.001   TYR A 107 
 PHE   0.010   0.001   PHE A  62 
 TRP   0.008   0.001   TRP B 123 
 HIS   0.004   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 4129)
  covalent geometry    : angle       0.52276 ( 5621)
  hydrogen bonds       : bond        0.03567 (  191)
  hydrogen bonds       : angle       4.14359 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 54
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  208 ASP cc_start: 0.8012 (t0) cc_final: 0.7694 (t0)
  outliers start: 8
  outliers final: 4
  residues processed: 61
  average time/residue: 0.0936
  time to fit residues: 6.8038
Evaluate side-chains
  57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 53
  time to evaluate  : 0.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain B residue  160 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 11 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9980
   chunk 47 optimal weight:    0.3980
   chunk 3 optimal weight:    5.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 10 optimal weight:    0.6980
   chunk 5 optimal weight:    0.2980
   chunk 34 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.140739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.110629 restraints weight = 12547.902|
|-----------------------------------------------------------------------------|
r_work (start): 0.3267 rms_B_bonded: 4.21
r_work: 0.3041 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8425
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4129  Z= 0.128
  Angle     :  0.523  12.556   5621  Z= 0.247
  Chirality :  0.039   0.133    624
  Planarity :  0.004   0.051    731
  Dihedral  :  3.493  17.970    560
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 24.19 %
    Favored  : 74.06 %
  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:  1.59 (0.36), residues: 529
  helix:  1.97 (0.31), residues: 270
  sheet: -0.89 (0.91), residues: 25
  loop :  0.30 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 170 
 TYR   0.009   0.001   TYR A 107 
 PHE   0.008   0.001   PHE A  62 
 TRP   0.008   0.001   TRP B 123 
 HIS   0.004   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 4129)
  covalent geometry    : angle       0.52311 ( 5621)
  hydrogen bonds       : bond        0.03364 (  191)
  hydrogen bonds       : angle       4.11449 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.138 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7930 (tt)
REVERT: A  208 ASP cc_start: 0.8057 (t0) cc_final: 0.7742 (t0)
  outliers start: 7
  outliers final: 4
  residues processed: 58
  average time/residue: 0.0988
  time to fit residues: 6.7913
Evaluate side-chains
  58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 53
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain B residue  160 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 33 optimal weight:    0.5980
   chunk 47 optimal weight:    0.4980
   chunk 42 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 35 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.139952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.109616 restraints weight = 12616.605|
|-----------------------------------------------------------------------------|
r_work (start): 0.3249 rms_B_bonded: 4.32
r_work: 0.3020 rms_B_bonded: 4.62 restraints_weight: 0.5000
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3002
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3002 r_free = 0.3002    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3002
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8439
moved from start:          0.1154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4129  Z= 0.147
  Angle     :  0.546  13.846   5621  Z= 0.258
  Chirality :  0.040   0.136    624
  Planarity :  0.004   0.051    731
  Dihedral  :  3.554  17.908    560
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 5.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 24.69 %
    Favored  : 73.57 %
  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:  1.55 (0.36), residues: 529
  helix:  1.95 (0.31), residues: 270
  sheet: -0.92 (0.90), residues: 25
  loop :  0.26 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 154 
 TYR   0.011   0.001   TYR A 107 
 PHE   0.010   0.001   PHE A  62 
 TRP   0.009   0.001   TRP B 123 
 HIS   0.005   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 4129)
  covalent geometry    : angle       0.54597 ( 5621)
  hydrogen bonds       : bond        0.03515 (  191)
  hydrogen bonds       : angle       4.14354 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.7930 (tt)
REVERT: A  208 ASP cc_start: 0.8078 (t0) cc_final: 0.7771 (t0)
REVERT: B  154 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7557 (mtm180)
  outliers start: 7
  outliers final: 5
  residues processed: 62
  average time/residue: 0.1078
  time to fit residues: 7.9008
Evaluate side-chains
  60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 54
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue   66 ASP
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain B residue  160 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 17 optimal weight:    0.0040
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   chunk 48 optimal weight:    0.3980
   chunk 29 optimal weight:    0.3980
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    0.9980
   chunk 31 optimal weight:    0.3980
   chunk 11 optimal weight:    0.3980
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.142468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.111040 restraints weight = 13843.888|
|-----------------------------------------------------------------------------|
r_work (start): 0.3275 rms_B_bonded: 4.64
r_work: 0.3041 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3041
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3032
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3032 r_free = 0.3032    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3032
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   4129  Z= 0.093
  Angle     :  0.514  14.526   5621  Z= 0.238
  Chirality :  0.038   0.127    624
  Planarity :  0.004   0.052    731
  Dihedral  :  3.393  15.617    560
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.69 %
    Favored  : 74.31 %
  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:  1.79 (0.37), residues: 529
  helix:  2.15 (0.31), residues: 270
  sheet: -0.88 (0.91), residues: 25
  loop :  0.38 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 154 
 TYR   0.007   0.001   TYR A  18 
 PHE   0.007   0.001   PHE A  93 
 TRP   0.008   0.001   TRP B  90 
 HIS   0.004   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 ( 4129)
  covalent geometry    : angle       0.51356 ( 5621)
  hydrogen bonds       : bond        0.02946 (  191)
  hydrogen bonds       : angle       4.01582 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7915 (tt)
REVERT: A  208 ASP cc_start: 0.8080 (t0) cc_final: 0.7759 (t0)
REVERT: B   34 MET cc_start: 0.5497 (tpp) cc_final: 0.4937 (mmt)
  outliers start: 4
  outliers final: 1
  residues processed: 60
  average time/residue: 0.1000
  time to fit residues: 7.1415
Evaluate side-chains
  57 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 55
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  136 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 20 optimal weight:    2.9990
   chunk 26 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 50 optimal weight:    0.1980
   chunk 3 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 14 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9990
   chunk 36 optimal weight:    3.9990
   chunk 47 optimal weight:    0.3980
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.5182

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.141852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.111563 restraints weight = 5644.516|
|-----------------------------------------------------------------------------|
r_work (start): 0.3258 rms_B_bonded: 2.56
r_work: 0.3124 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3135
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3135 r_free = 0.3135    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3135
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4129  Z= 0.120
  Angle     :  0.529  13.766   5621  Z= 0.249
  Chirality :  0.039   0.134    624
  Planarity :  0.004   0.052    731
  Dihedral  :  3.417  15.858    560
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.22 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 24.19 %
    Favored  : 74.56 %
  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:  1.76 (0.36), residues: 529
  helix:  2.13 (0.31), residues: 270
  sheet: -0.93 (0.90), residues: 25
  loop :  0.35 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 154 
 TYR   0.009   0.001   TYR A 107 
 PHE   0.008   0.001   PHE A  62 
 TRP   0.008   0.001   TRP B 123 
 HIS   0.004   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 4129)
  covalent geometry    : angle       0.52935 ( 5621)
  hydrogen bonds       : bond        0.03192 (  191)
  hydrogen bonds       : angle       4.02874 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 55
  time to evaluate  : 0.202 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.7868 (tt)
REVERT: A  208 ASP cc_start: 0.7941 (t0) cc_final: 0.7635 (t0)
REVERT: B   34 MET cc_start: 0.5455 (tpp) cc_final: 0.4895 (mmt)
REVERT: B  154 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7526 (mtm180)
  outliers start: 5
  outliers final: 3
  residues processed: 59
  average time/residue: 0.1066
  time to fit residues: 7.4779
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain B residue  160 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 12 optimal weight:    0.4980
   chunk 31 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN
B  41 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.139533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.108525 restraints weight = 13940.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.3227 rms_B_bonded: 4.77
r_work: 0.2985 rms_B_bonded: 4.89 restraints_weight: 0.5000
r_work (final): 0.2985
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2961
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.25   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2961 r_free = 0.2961    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2961
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1247

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   4129  Z= 0.162
  Angle     :  0.558  13.367   5621  Z= 0.266
  Chirality :  0.040   0.138    624
  Planarity :  0.004   0.052    731
  Dihedral  :  3.588  17.207    560
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 4.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.50 %
    Allowed  : 23.94 %
    Favored  : 74.56 %
  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:  1.58 (0.36), residues: 529
  helix:  1.99 (0.31), residues: 270
  sheet: -0.91 (0.89), residues: 25
  loop :  0.24 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 154 
 TYR   0.012   0.001   TYR A 107 
 PHE   0.011   0.001   PHE A  62 
 TRP   0.009   0.001   TRP B 123 
 HIS   0.006   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00405 ( 4129)
  covalent geometry    : angle       0.55771 ( 5621)
  hydrogen bonds       : bond        0.03589 (  191)
  hydrogen bonds       : angle       4.12653 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7851 (tt)
REVERT: A  208 ASP cc_start: 0.8090 (t0) cc_final: 0.7765 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 61
  average time/residue: 0.1047
  time to fit residues: 7.5804
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 54
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain B residue  160 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 35 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9980
   chunk 4 optimal weight:    0.2980
   chunk 2 optimal weight:    0.2980
   chunk 49 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 23 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.140337 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.110145 restraints weight = 8205.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 3.00
r_work: 0.3083 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3083
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3067
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3067 r_free = 0.3067    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3067
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4129  Z= 0.135
  Angle     :  0.561  15.664   5621  Z= 0.262
  Chirality :  0.039   0.134    624
  Planarity :  0.004   0.052    731
  Dihedral  :  3.553  16.550    560
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.69 %
    Favored  : 74.31 %
  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:  1.64 (0.36), residues: 529
  helix:  2.04 (0.30), residues: 271
  sheet: -0.90 (0.90), residues: 25
  loop :  0.27 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 154 
 TYR   0.010   0.001   TYR A 107 
 PHE   0.008   0.001   PHE A  62 
 TRP   0.008   0.001   TRP B 123 
 HIS   0.005   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4129)
  covalent geometry    : angle       0.56121 ( 5621)
  hydrogen bonds       : bond        0.03352 (  191)
  hydrogen bonds       : angle       4.08756 (  581)

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

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

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1058 Ramachandran restraints generated.
    529 Oldfield, 0 Emsley, 529 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 55
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A  136 LEU cc_start: 0.8312 (OUTLIER) cc_final: 0.7872 (tt)
REVERT: A  208 ASP cc_start: 0.8007 (t0) cc_final: 0.7718 (t0)
REVERT: B   34 MET cc_start: 0.5348 (tpp) cc_final: 0.5045 (mmt)
REVERT: B  154 ARG cc_start: 0.7991 (mtm110) cc_final: 0.7410 (mtm180)
  outliers start: 4
  outliers final: 3
  residues processed: 59
  average time/residue: 0.1121
  time to fit residues: 7.7636
Evaluate side-chains
  58 residues out of total 412 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 54
  time to evaluate  : 0.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  246 THR
Chi-restraints excluded: chain A residue  250 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 52
   random chunks:
   chunk 33 optimal weight:    0.4980
   chunk 30 optimal weight:    0.5980
   chunk 39 optimal weight:    2.9990
   chunk 37 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 23 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 356 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.140197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.108566 restraints weight = 16809.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3236 rms_B_bonded: 5.41
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3235
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3235 r_free = 0.3235    target_work(ls_wunit_k1) = 0.107         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3235
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.1286

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4129  Z= 0.139
  Angle     :  0.565  15.557   5621  Z= 0.263
  Chirality :  0.040   0.135    624
  Planarity :  0.004   0.052    731
  Dihedral  :  3.557  16.555    560
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 4.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 24.94 %
    Favored  : 74.06 %
  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:  1.64 (0.36), residues: 529
  helix:  2.04 (0.30), residues: 271
  sheet: -0.91 (0.90), residues: 25
  loop :  0.27 (0.41), residues: 233

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 154 
 TYR   0.010   0.001   TYR A 107 
 PHE   0.009   0.001   PHE A  62 
 TRP   0.009   0.001   TRP B 123 
 HIS   0.005   0.001   HIS B  85 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 4129)
  covalent geometry    : angle       0.56538 ( 5621)
  hydrogen bonds       : bond        0.03377 (  191)
  hydrogen bonds       : angle       4.08197 (  581)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1300.92 seconds
wall clock time: 22 minutes 58.65 seconds (1378.65 seconds total)