Starting phenix.real_space_refine
on Wed Sep 17 14:25:58 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gbc_51210/09_2025/9gbc_51210.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gbc_51210/09_2025/9gbc_51210.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gbc_51210/09_2025/9gbc_51210.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gbc_51210/09_2025/9gbc_51210.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gbc_51210/09_2025/9gbc_51210.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gbc_51210/09_2025/9gbc_51210.map"
  }
  resolution = 2.7
  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=   0.004
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      21      5.16       5
     C    5461      2.51       5
     N    1468      2.21       5
     O    1792      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8742
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5335
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 668, 5335
          Classifications: {'peptide': 668}
          Link IDs: {'PTRANS': 14, 'TRANS': 653}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3287
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 425, 3287
          Classifications: {'peptide': 425}
          Link IDs: {'PTRANS': 14, 'TRANS': 410}
    Chain: "A"
      Number of atoms: 77
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 77, 77
          Classifications: {'water': 77}
          Link IDs: {None: 76}
    Chain: "B"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 43
          Classifications: {'water': 43}
          Link IDs: {None: 42}
  Time building chain proxies: 1.98, per 1000 atoms: 0.23
  Number of scatterers: 8742
  At special positions: 0
  Unit cell: (79.18, 82.14, 120.62, 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      21     16.00
     O    1792      8.00
     N    1468      7.00
     C    5461      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: 0.79
  Conformation dependent library (CDL) restraints added in 277.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1978

  Finding SS restraints...
    Secondary structure from input PDB file:
      12 helices and 18 sheets defined
      6.1% alpha, 47.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 125
    Processing helix  chain 'A' and resid 136 through 139
      removed outlier: 3.808A  pdb=" N   HIS A 139 " --> pdb=" O   LYS A 136 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 136 through 139'
    Processing helix  chain 'A' and resid 144 through 150
    Processing helix  chain 'A' and resid 201 through 205
    Processing helix  chain 'A' and resid 561 through 567
    Processing helix  chain 'A' and resid 570 through 575
      removed outlier: 3.534A  pdb=" N   LYS A 575 " --> pdb=" O   LEU A 571 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 736
    Processing helix  chain 'B' and resid 94 through 99
    Processing helix  chain 'B' and resid 108 through 112
    Processing helix  chain 'B' and resid 188 through 193
      removed outlier: 3.584A  pdb=" N   MET B 193 " --> pdb=" O   ALA B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 227
    Processing helix  chain 'B' and resid 284 through 286
      No H-bonds generated for 'chain 'B' and resid 284 through 286'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 130 through 134
      removed outlier: 6.397A  pdb=" N   LYS A 180 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 7.948A  pdb=" N   ILE A 230 " --> pdb=" O   LYS A 180 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   PHE A 182 " --> pdb=" O   ILE A 230 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 155 through 159
    Processing sheet with id=AA3, first strand: chain 'A' and resid 239 through 247
      removed outlier: 3.911A  pdb=" N   ASP A 432 " --> pdb=" O   HIS A 460 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   HIS A 448 " --> pdb=" O   ILE A 444 " (cutoff:3.500A)
      removed outlier: 9.831A  pdb=" N   VAL A 533 " --> pdb=" O   TYR A 557 " (cutoff:3.500A)
      removed outlier: 7.492A  pdb=" N   TYR A 557 " --> pdb=" O   VAL A 533 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   TYR A 535 " --> pdb=" O   LYS A 555 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   VAL A 654 " --> pdb=" O   TYR A 650 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 286
    Processing sheet with id=AA5, first strand: chain 'A' and resid 289 through 291
    Processing sheet with id=AA6, first strand: chain 'A' and resid 404 through 406
    Processing sheet with id=AA7, first strand: chain 'A' and resid 616 through 618
    Processing sheet with id=AA8, first strand: chain 'A' and resid 723 through 724
    Processing sheet with id=AA9, first strand: chain 'B' and resid 53 through 56
      removed outlier: 3.633A  pdb=" N   ILE B  53 " --> pdb=" O   HIS B  48 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 53 through 56
      removed outlier: 3.633A  pdb=" N   ILE B  53 " --> pdb=" O   HIS B  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 72 through 80
      removed outlier: 4.352A  pdb=" N   ILE B  77 " --> pdb=" O   TYR B  85 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   TYR B  85 " --> pdb=" O   ILE B  77 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   GLU B  79 " --> pdb=" O   LYS B  83 " (cutoff:3.500A)
      removed outlier: 6.449A  pdb=" N   LYS B  83 " --> pdb=" O   GLU B  79 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   TRP B 139 " --> pdb=" O   PRO B  88 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 164 through 166
    Processing sheet with id=AB4, first strand: chain 'B' and resid 174 through 176
      removed outlier: 4.087A  pdb=" N   ARG B 208 " --> pdb=" O   TYR B 219 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   TYR B 219 " --> pdb=" O   ARG B 208 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 232 through 239
      removed outlier: 6.738A  pdb=" N   GLN B 246 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   CYS B 235 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   LEU B 244 " --> pdb=" O   CYS B 235 " (cutoff:3.500A)
      removed outlier: 5.118A  pdb=" N   HIS B 237 " --> pdb=" O   TYR B 242 " (cutoff:3.500A)
      removed outlier: 7.664A  pdb=" N   TYR B 242 " --> pdb=" O   HIS B 237 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ARG B 261 " --> pdb=" O   MET B 247 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 288 through 291
      removed outlier: 7.131A  pdb=" N   ILE B 307 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   PHE B 291 " --> pdb=" O   GLY B 305 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   GLY B 305 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 288 through 291
      removed outlier: 7.131A  pdb=" N   ILE B 307 " --> pdb=" O   SER B 289 " (cutoff:3.500A)
      removed outlier: 4.568A  pdb=" N   PHE B 291 " --> pdb=" O   GLY B 305 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   GLY B 305 " --> pdb=" O   PHE B 291 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   ILE B 320 " --> pdb=" O   GLY B 333 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   VAL B 382 " --> pdb=" O   GLY B 333 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   THR B 335 " --> pdb=" O   VAL B 382 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 340 through 349
      removed outlier: 6.371A  pdb=" N   SER B 358 " --> pdb=" O   THR B 342 " (cutoff:3.500A)
      removed outlier: 4.282A  pdb=" N   ILE B 344 " --> pdb=" O   VAL B 356 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   VAL B 356 " --> pdb=" O   ILE B 344 " (cutoff:3.500A)
      removed outlier: 4.662A  pdb=" N   ARG B 346 " --> pdb=" O   THR B 354 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   THR B 354 " --> pdb=" O   ARG B 346 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ALA B 348 " --> pdb=" O   HIS B 352 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   HIS B 352 " --> pdb=" O   ALA B 348 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 397 through 401

    423 hydrogen bonds defined for protein.
    1128 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: 1.57

  Time building geometry restraints manager: 1.05 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2810
        1.34 -     1.46: 1867
        1.46 -     1.57: 4113
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 8826
  Sorted by residual:
  bond pdb=" CG  PRO B 308 "
       pdb=" CD  PRO B 308 "
    ideal  model  delta    sigma   weight residual
    1.503  1.539 -0.036 3.40e-02 8.65e+02 1.14e+00
  bond pdb=" CG  ARG B  57 "
       pdb=" CD  ARG B  57 "
    ideal  model  delta    sigma   weight residual
    1.520  1.551 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" N   LYS B 402 "
       pdb=" CA  LYS B 402 "
    ideal  model  delta    sigma   weight residual
    1.457  1.470 -0.013 1.29e-02 6.01e+03 9.58e-01
  bond pdb=" CG  PRO A 724 "
       pdb=" CD  PRO A 724 "
    ideal  model  delta    sigma   weight residual
    1.503  1.534 -0.031 3.40e-02 8.65e+02 8.49e-01
  bond pdb=" CG  ARG A 461 "
       pdb=" CD  ARG A 461 "
    ideal  model  delta    sigma   weight residual
    1.520  1.496  0.024 3.00e-02 1.11e+03 6.24e-01
  ... (remaining 8821 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.16: 11436
        1.16 -     2.32: 450
        2.32 -     3.49: 65
        3.49 -     4.65: 12
        4.65 -     5.81: 5
  Bond angle restraints: 11968
  Sorted by residual:
  angle pdb=" C   TYR B 411 "
        pdb=" N   ASN B 412 "
        pdb=" CA  ASN B 412 "
      ideal   model   delta    sigma   weight residual
     120.38  125.11   -4.73 1.46e+00 4.69e-01 1.05e+01
  angle pdb=" N   ASN B 412 "
        pdb=" CA  ASN B 412 "
        pdb=" C   ASN B 412 "
      ideal   model   delta    sigma   weight residual
     111.75  115.32   -3.57 1.28e+00 6.10e-01 7.78e+00
  angle pdb=" C   LYS B 402 "
        pdb=" CA  LYS B 402 "
        pdb=" CB  LYS B 402 "
      ideal   model   delta    sigma   weight residual
     110.42  115.71   -5.29 1.99e+00 2.53e-01 7.08e+00
  angle pdb=" C   LYS A 640 "
        pdb=" N   GLY A 641 "
        pdb=" CA  GLY A 641 "
      ideal   model   delta    sigma   weight residual
     121.22  116.12    5.10 2.07e+00 2.33e-01 6.07e+00
  angle pdb=" C   TYR B 401 "
        pdb=" N   LYS B 402 "
        pdb=" CA  LYS B 402 "
      ideal   model   delta    sigma   weight residual
     121.54  125.91   -4.37 1.91e+00 2.74e-01 5.24e+00
  ... (remaining 11963 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.81: 4763
       17.81 -    35.62: 287
       35.62 -    53.44: 49
       53.44 -    71.25: 11
       71.25 -    89.06: 5
  Dihedral angle restraints: 5115
    sinusoidal: 1969
      harmonic: 3146
  Sorted by residual:
  dihedral pdb=" CA  LEU B 129 "
           pdb=" C   LEU B 129 "
           pdb=" N   GLN B 130 "
           pdb=" CA  GLN B 130 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.98  -21.02     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  TRP A 705 "
           pdb=" C   TRP A 705 "
           pdb=" N   LYS A 706 "
           pdb=" CA  LYS A 706 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.92   17.08     0      5.00e+00 4.00e-02 1.17e+01
  dihedral pdb=" CB  GLU B 391 "
           pdb=" CG  GLU B 391 "
           pdb=" CD  GLU B 391 "
           pdb=" OE1 GLU B 391 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.06   89.06     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 5112 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 701
       0.030 -    0.059: 366
       0.059 -    0.089: 116
       0.089 -    0.119: 70
       0.119 -    0.149: 23
  Chirality restraints: 1276
  Sorted by residual:
  chirality pdb=" CA  ILE B 209 "
            pdb=" N   ILE B 209 "
            pdb=" C   ILE B 209 "
            pdb=" CB  ILE B 209 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" CA  ILE A 336 "
            pdb=" N   ILE A 336 "
            pdb=" C   ILE A 336 "
            pdb=" CB  ILE A 336 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.16e-01
  chirality pdb=" CA  ILE B  89 "
            pdb=" N   ILE B  89 "
            pdb=" C   ILE B  89 "
            pdb=" CB  ILE B  89 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.03e-01
  ... (remaining 1273 not shown)

  Planarity restraints: 1556
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 461 "    0.381 9.50e-02 1.11e+02   1.71e-01 1.80e+01
        pdb=" NE  ARG A 461 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 461 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 461 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 461 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 368 "   -0.039 5.00e-02 4.00e+02   5.95e-02 5.67e+00
        pdb=" N   PRO A 369 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 369 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 369 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER B 186 "    0.035 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO B 187 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 187 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 187 "    0.029 5.00e-02 4.00e+02
  ... (remaining 1553 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.66: 78
        2.66 -     3.22: 7444
        3.22 -     3.78: 13148
        3.78 -     4.34: 19914
        4.34 -     4.90: 33316
  Nonbonded interactions: 73900
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 674 "
            pdb=" OE1 GLN A 676 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" NZ  LYS A 671 "
            pdb=" OE2 GLU A 677 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" OE1 GLU A 621 "
            pdb=" NH1 ARG B 167 "
     model   vdw
     2.257 3.120
  nonbonded pdb=" OD1 ASP B 145 "
            pdb=" O   HOH B 501 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OG  SER B  98 "
            pdb=" O   GLY B 127 "
     model   vdw
     2.271 3.040
  ... (remaining 73895 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:             7.240
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.160
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  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:6.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.730
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8888
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8826  Z= 0.121
  Angle     :  0.543   5.809  11968  Z= 0.308
  Chirality :  0.045   0.149   1276
  Planarity :  0.006   0.171   1556
  Dihedral  : 12.207  89.060   3137
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 2.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  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 aren not related in a simple way.
  whole:  0.22 (0.24), residues: 1087
  helix: -1.35 (0.79), residues: 40
  sheet:  1.00 (0.22), residues: 520
  loop : -0.60 (0.26), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG B 255 
 TYR   0.016   0.001   TYR B  71 
 PHE   0.019   0.001   PHE A 767 
 TRP   0.028   0.002   TRP B 175 
 HIS   0.003   0.001   HIS B 237 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8826)
  covalent geometry    : angle       0.54327 (11968)
  hydrogen bonds       : bond        0.07894 (  419)
  hydrogen bonds       : angle       5.79386 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.256 
Fit side-chains
REVERT: A  705 TRP cc_start: 0.8367 (t60) cc_final: 0.8130 (t60)
  outliers start: 0
  outliers final: 1
  residues processed: 91
  average time/residue: 0.6732
  time to fit residues: 64.5953
Evaluate side-chains
  61 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 60
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  350 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 97 optimal weight:    0.0370
   chunk 53 optimal weight:    0.6980
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.2980
   chunk 106 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   overall best weight:    0.3456

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

Flipped N/Q/H residues before XYZ refinement:
A 392 ASN
A 453 ASN
A 460 HIS
A 528 ASN
A 589 ASN
A 742 GLN
A 775 ASN
B 130 GLN
B 136 ASN
B 147 ASN
B 169 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.086098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.071125 restraints weight = 12616.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.2804 rms_B_bonded: 2.07
r_work: 0.2681 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2554 rms_B_bonded: 3.79 restraints_weight: 0.2500
r_work (final): 0.2554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8890
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   8826  Z= 0.096
  Angle     :  0.474   7.266  11968  Z= 0.265
  Chirality :  0.044   0.147   1276
  Planarity :  0.003   0.050   1556
  Dihedral  :  4.832  85.881   1216
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 1.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  4.58 %
    Favored  : 94.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.40 (0.24), residues: 1087
  helix: -0.89 (0.86), residues: 40
  sheet:  1.04 (0.21), residues: 532
  loop : -0.44 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 381 
 TYR   0.015   0.001   TYR A 361 
 PHE   0.013   0.001   PHE A 767 
 TRP   0.011   0.001   TRP A 705 
 HIS   0.003   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00210 ( 8826)
  covalent geometry    : angle       0.47405 (11968)
  hydrogen bonds       : bond        0.03096 (  419)
  hydrogen bonds       : angle       5.07704 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 73
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  381 ARG cc_start: 0.8364 (mmm-85) cc_final: 0.8063 (mtp85)
REVERT: A  763 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8505 (mt-10)
REVERT: B  128 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8370 (pp20)
REVERT: B  314 GLU cc_start: 0.7726 (mt-10) cc_final: 0.6970 (mp0)
  outliers start: 7
  outliers final: 1
  residues processed: 75
  average time/residue: 0.7238
  time to fit residues: 57.5335
Evaluate side-chains
  66 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 64
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  426 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 94 optimal weight:    0.0870
   chunk 46 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 80 optimal weight:    3.9990
   chunk 83 optimal weight:    0.9980
   chunk 72 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   overall best weight:    1.6164

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

Flipped N/Q/H residues before XYZ refinement:
A 593 ASN
A 775 ASN
B 169 GLN
B 365 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.079626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2671 r_free = 0.2671 target = 0.064676 restraints weight = 12926.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.2666 rms_B_bonded: 2.07
r_work: 0.2542 rms_B_bonded: 2.24 restraints_weight: 0.5000
r_work: 0.2415 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9001
moved from start:          0.1571

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.033   8826  Z= 0.247
  Angle     :  0.571   6.706  11968  Z= 0.318
  Chirality :  0.047   0.151   1276
  Planarity :  0.004   0.055   1556
  Dihedral  :  4.731  18.927   1214
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  :  6.43 %
    Favored  : 92.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.32 (0.24), residues: 1087
  helix: -1.02 (0.82), residues: 46
  sheet:  1.02 (0.21), residues: 531
  loop : -0.52 (0.26), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 441 
 TYR   0.016   0.002   TYR A 634 
 PHE   0.022   0.002   PHE A 767 
 TRP   0.011   0.001   TRP A 653 
 HIS   0.007   0.002   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00597 ( 8826)
  covalent geometry    : angle       0.57086 (11968)
  hydrogen bonds       : bond        0.04294 (  419)
  hydrogen bonds       : angle       5.28033 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A  763 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8525 (mt-10)
REVERT: B  128 GLU cc_start: 0.8911 (OUTLIER) cc_final: 0.8393 (pp20)
REVERT: B  314 GLU cc_start: 0.7865 (mt-10) cc_final: 0.7245 (mp0)
  outliers start: 7
  outliers final: 2
  residues processed: 67
  average time/residue: 0.7713
  time to fit residues: 54.6710
Evaluate side-chains
  59 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 56
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  440 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 73 optimal weight:    0.0770
   chunk 17 optimal weight:    0.8980
   chunk 60 optimal weight:    0.2980
   chunk 64 optimal weight:    2.9990
   chunk 87 optimal weight:    0.0270
   chunk 103 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    0.7980
   chunk 77 optimal weight:    0.8980
   chunk 3 optimal weight:    0.0670
   overall best weight:    0.2534

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

Flipped N/Q/H residues before XYZ refinement:
A 425 GLN
A 775 ASN
B  48 HIS
B 169 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.083555 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.068818 restraints weight = 12959.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.2777 rms_B_bonded: 2.05
r_work: 0.2655 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2528 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8926
moved from start:          0.1706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8826  Z= 0.082
  Angle     :  0.444   6.550  11968  Z= 0.249
  Chirality :  0.043   0.140   1276
  Planarity :  0.003   0.047   1556
  Dihedral  :  4.023  15.198   1214
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  :  7.08 %
    Favored  : 91.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.45 (0.24), residues: 1087
  helix: -0.99 (0.80), residues: 46
  sheet:  1.06 (0.21), residues: 533
  loop : -0.38 (0.26), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 441 
 TYR   0.017   0.001   TYR A 634 
 PHE   0.012   0.001   PHE A 767 
 TRP   0.007   0.001   TRP A 653 
 HIS   0.002   0.001   HIS A 745 

Details of bonding type rmsd
  covalent geometry    : bond        0.00168 ( 8826)
  covalent geometry    : angle       0.44415 (11968)
  hydrogen bonds       : bond        0.02922 (  419)
  hydrogen bonds       : angle       4.88720 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 66
  time to evaluate  : 0.374 
Fit side-chains
   revert: symmetry clash
REVERT: A  381 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.8216 (mtp85)
REVERT: A  563 GLU cc_start: 0.8074 (mp0) cc_final: 0.7871 (mp0)
REVERT: A  763 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8453 (mt-10)
REVERT: B  128 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8444 (pp20)
REVERT: B  314 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7192 (mp0)
  outliers start: 9
  outliers final: 2
  residues processed: 70
  average time/residue: 0.6686
  time to fit residues: 49.8270
Evaluate side-chains
  66 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 63
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  426 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    3.9990
   chunk 73 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 96 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 62 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 50 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
A 425 GLN
A 593 ASN
B  48 HIS
B 169 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.080850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.065848 restraints weight = 12874.758|
|-----------------------------------------------------------------------------|
r_work (start): 0.2694 rms_B_bonded: 2.06
r_work: 0.2577 rms_B_bonded: 2.22 restraints_weight: 0.5000
r_work: 0.2453 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.2453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8984
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   8826  Z= 0.180
  Angle     :  0.502   6.335  11968  Z= 0.281
  Chirality :  0.045   0.143   1276
  Planarity :  0.003   0.051   1556
  Dihedral  :  4.396  15.388   1214
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 1.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.09 %
    Allowed  :  7.63 %
    Favored  : 91.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.42 (0.25), residues: 1087
  helix: -0.96 (0.82), residues: 46
  sheet:  0.99 (0.21), residues: 546
  loop : -0.37 (0.27), residues: 495

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 441 
 TYR   0.013   0.001   TYR B 161 
 PHE   0.018   0.001   PHE A 767 
 TRP   0.007   0.001   TRP B 236 
 HIS   0.006   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 8826)
  covalent geometry    : angle       0.50199 (11968)
  hydrogen bonds       : bond        0.03754 (  419)
  hydrogen bonds       : angle       5.01988 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A  563 GLU cc_start: 0.8072 (mp0) cc_final: 0.7863 (mp0)
REVERT: A  569 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8173 (tp30)
REVERT: A  670 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7721 (tp30)
REVERT: A  763 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8469 (mt-10)
REVERT: B  128 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8501 (pp20)
  outliers start: 10
  outliers final: 5
  residues processed: 72
  average time/residue: 0.7115
  time to fit residues: 54.2982
Evaluate side-chains
  69 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 61
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  569 GLU
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  426 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 100 optimal weight:    0.3980
   chunk 99 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 27 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 3 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 70 optimal weight:    0.5980
   chunk 85 optimal weight:    0.5980
   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 425 GLN
B  48 HIS
B 169 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.082491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.067443 restraints weight = 12877.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.2733 rms_B_bonded: 2.08
r_work: 0.2609 rms_B_bonded: 2.27 restraints_weight: 0.5000
r_work: 0.2482 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8963
moved from start:          0.1761

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8826  Z= 0.112
  Angle     :  0.457   6.340  11968  Z= 0.257
  Chirality :  0.044   0.141   1276
  Planarity :  0.003   0.050   1556
  Dihedral  :  4.156  14.411   1214
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.30 %
    Favored  : 97.70 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  7.63 %
    Favored  : 90.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.24), residues: 1087
  helix: -0.95 (0.82), residues: 46
  sheet:  1.07 (0.21), residues: 540
  loop : -0.36 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 381 
 TYR   0.011   0.001   TYR A 361 
 PHE   0.015   0.001   PHE A 767 
 TRP   0.007   0.001   TRP A 653 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 8826)
  covalent geometry    : angle       0.45689 (11968)
  hydrogen bonds       : bond        0.03233 (  419)
  hydrogen bonds       : angle       4.88428 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.351 
Fit side-chains
   revert: symmetry clash
REVERT: A  381 ARG cc_start: 0.8418 (mmm-85) cc_final: 0.8080 (mtp85)
REVERT: A  563 GLU cc_start: 0.8065 (mp0) cc_final: 0.7838 (mp0)
REVERT: A  569 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8123 (tp30)
REVERT: A  670 GLU cc_start: 0.8083 (OUTLIER) cc_final: 0.7732 (tp30)
REVERT: A  763 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8468 (mt-10)
REVERT: B  128 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8429 (pp20)
  outliers start: 13
  outliers final: 7
  residues processed: 71
  average time/residue: 0.6548
  time to fit residues: 49.3821
Evaluate side-chains
  72 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  569 GLU
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  426 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 104 optimal weight:    0.7980
   chunk 43 optimal weight:    0.8980
   chunk 90 optimal weight:    1.9990
   chunk 71 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
B 169 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.080589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2692 r_free = 0.2692 target = 0.065676 restraints weight = 12994.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.2699 rms_B_bonded: 2.06
r_work: 0.2574 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2447 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8992
moved from start:          0.1786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   8826  Z= 0.176
  Angle     :  0.499   6.357  11968  Z= 0.279
  Chirality :  0.045   0.142   1276
  Planarity :  0.003   0.052   1556
  Dihedral  :  4.408  15.401   1214
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 1.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  8.17 %
    Favored  : 90.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.24), residues: 1087
  helix: -0.74 (0.90), residues: 40
  sheet:  1.07 (0.21), residues: 540
  loop : -0.40 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 441 
 TYR   0.018   0.001   TYR A 634 
 PHE   0.018   0.001   PHE A 767 
 TRP   0.007   0.001   TRP B 175 
 HIS   0.006   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00420 ( 8826)
  covalent geometry    : angle       0.49871 (11968)
  hydrogen bonds       : bond        0.03712 (  419)
  hydrogen bonds       : angle       5.01767 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A  563 GLU cc_start: 0.8083 (mp0) cc_final: 0.7873 (mp0)
REVERT: A  670 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7577 (tp30)
REVERT: A  763 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8489 (mt-10)
REVERT: B  128 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8508 (pp20)
  outliers start: 13
  outliers final: 8
  residues processed: 70
  average time/residue: 0.6787
  time to fit residues: 50.5535
Evaluate side-chains
  67 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 57
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  446 THR
Chi-restraints excluded: chain A residue  545 SER
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain B residue   73 THR
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  129 LEU
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  440 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 78 optimal weight:    2.9990
   chunk 61 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 48 optimal weight:    2.9990
   chunk 56 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A 143 GLN
A 775 ASN
B  48 HIS
B 169 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2916 r_free = 0.2916 target = 0.078644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.063800 restraints weight = 12926.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.2660 rms_B_bonded: 2.04
r_work: 0.2536 rms_B_bonded: 2.23 restraints_weight: 0.5000
r_work: 0.2408 rms_B_bonded: 3.69 restraints_weight: 0.2500
r_work (final): 0.2408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9017
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.036   8826  Z= 0.266
  Angle     :  0.567   6.474  11968  Z= 0.316
  Chirality :  0.047   0.152   1276
  Planarity :  0.004   0.053   1556
  Dihedral  :  4.751  16.940   1214
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 1.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  8.39 %
    Favored  : 90.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.24), residues: 1087
  helix: -0.84 (0.89), residues: 40
  sheet:  1.10 (0.21), residues: 537
  loop : -0.49 (0.25), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 441 
 TYR   0.019   0.002   TYR A 634 
 PHE   0.022   0.002   PHE A 767 
 TRP   0.008   0.001   TRP A 496 
 HIS   0.006   0.002   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00644 ( 8826)
  covalent geometry    : angle       0.56668 (11968)
  hydrogen bonds       : bond        0.04259 (  419)
  hydrogen bonds       : angle       5.20472 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 59
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: A  563 GLU cc_start: 0.8067 (mp0) cc_final: 0.7814 (mp0)
REVERT: A  670 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7680 (tp30)
REVERT: B  128 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8515 (pp20)
  outliers start: 13
  outliers final: 4
  residues processed: 67
  average time/residue: 0.6951
  time to fit residues: 49.4668
Evaluate side-chains
  62 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  426 THR
Chi-restraints excluded: chain B residue  440 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 4 optimal weight:    0.0020
   chunk 40 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 86 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 68 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   overall best weight:    0.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 775 ASN
B  48 HIS
B 169 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2977 r_free = 0.2977 target = 0.082057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.067041 restraints weight = 12789.922|
|-----------------------------------------------------------------------------|
r_work (start): 0.2717 rms_B_bonded: 2.06
r_work: 0.2594 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2467 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.2467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8968
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8826  Z= 0.108
  Angle     :  0.466   6.364  11968  Z= 0.261
  Chirality :  0.044   0.140   1276
  Planarity :  0.003   0.049   1556
  Dihedral  :  4.219  15.063   1214
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  :  9.59 %
    Favored  : 89.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.24), residues: 1087
  helix: -0.98 (0.82), residues: 46
  sheet:  1.02 (0.21), residues: 540
  loop : -0.41 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 381 
 TYR   0.020   0.001   TYR A 634 
 PHE   0.015   0.001   PHE A 767 
 TRP   0.010   0.001   TRP A 653 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 8826)
  covalent geometry    : angle       0.46637 (11968)
  hydrogen bonds       : bond        0.03187 (  419)
  hydrogen bonds       : angle       4.92493 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 60
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
REVERT: A  563 GLU cc_start: 0.8080 (mp0) cc_final: 0.7846 (mp0)
REVERT: A  670 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7758 (tp30)
REVERT: A  763 GLU cc_start: 0.8730 (mt-10) cc_final: 0.8486 (mt-10)
REVERT: B  128 GLU cc_start: 0.8898 (OUTLIER) cc_final: 0.8415 (pp20)
  outliers start: 8
  outliers final: 3
  residues processed: 66
  average time/residue: 0.6531
  time to fit residues: 45.8602
Evaluate side-chains
  62 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  426 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 81 optimal weight:    0.0020
   chunk 62 optimal weight:    0.7980
   chunk 86 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
B 169 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.081464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.066586 restraints weight = 12835.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.2720 rms_B_bonded: 2.04
r_work: 0.2596 rms_B_bonded: 2.25 restraints_weight: 0.5000
r_work: 0.2469 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.2469
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8975
moved from start:          0.1860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8826  Z= 0.128
  Angle     :  0.479   6.331  11968  Z= 0.267
  Chirality :  0.044   0.142   1276
  Planarity :  0.003   0.050   1556
  Dihedral  :  4.237  15.482   1214
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 10.13 %
    Favored  : 89.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.24), residues: 1087
  helix: -0.93 (0.83), residues: 46
  sheet:  1.04 (0.21), residues: 540
  loop : -0.40 (0.26), residues: 501

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 381 
 TYR   0.019   0.001   TYR A 634 
 PHE   0.016   0.001   PHE A 767 
 TRP   0.008   0.001   TRP A 653 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 8826)
  covalent geometry    : angle       0.47858 (11968)
  hydrogen bonds       : bond        0.03329 (  419)
  hydrogen bonds       : angle       4.90158 ( 1128)

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

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

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2174 Ramachandran restraints generated.
    1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 60
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
REVERT: A  670 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7742 (tp30)
REVERT: A  763 GLU cc_start: 0.8721 (mt-10) cc_final: 0.8486 (mt-10)
REVERT: B  128 GLU cc_start: 0.8913 (OUTLIER) cc_final: 0.8546 (pp20)
  outliers start: 6
  outliers final: 3
  residues processed: 65
  average time/residue: 0.6848
  time to fit residues: 47.1772
Evaluate side-chains
  62 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 57
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  193 SER
Chi-restraints excluded: chain A residue  262 THR
Chi-restraints excluded: chain A residue  670 GLU
Chi-restraints excluded: chain B residue  128 GLU
Chi-restraints excluded: chain B residue  426 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.5980
   chunk 69 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 29 optimal weight:    0.3980
   chunk 63 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 169 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.081508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.066467 restraints weight = 12771.307|
|-----------------------------------------------------------------------------|
r_work (start): 0.2716 rms_B_bonded: 2.07
r_work: 0.2593 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2466 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8977
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   8826  Z= 0.130
  Angle     :  0.480   6.306  11968  Z= 0.268
  Chirality :  0.044   0.142   1276
  Planarity :  0.003   0.050   1556
  Dihedral  :  4.225  14.530   1214
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 2.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.76 %
    Allowed  : 10.13 %
    Favored  : 89.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.24), residues: 1087
  helix: -0.76 (0.90), residues: 40
  sheet:  1.05 (0.21), residues: 540
  loop : -0.39 (0.26), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 381 
 TYR   0.020   0.001   TYR A 634 
 PHE   0.016   0.001   PHE A 767 
 TRP   0.009   0.001   TRP A 653 
 HIS   0.004   0.001   HIS A 315 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8826)
  covalent geometry    : angle       0.47951 (11968)
  hydrogen bonds       : bond        0.03321 (  419)
  hydrogen bonds       : angle       4.88284 ( 1128)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2777.58 seconds
wall clock time: 48 minutes 18.24 seconds (2898.24 seconds total)