Starting phenix.real_space_refine
on Tue Feb  3 21:56:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mxq_48718/02_2026/9mxq_48718.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mxq_48718/02_2026/9mxq_48718.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mxq_48718/02_2026/9mxq_48718.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mxq_48718/02_2026/9mxq_48718.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mxq_48718/02_2026/9mxq_48718.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mxq_48718/02_2026/9mxq_48718.map"
  }
  resolution = 3.85
  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=   0.014
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      14      5.16       5
     C    4639      2.51       5
     N    1174      2.21       5
     O    1311      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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7138
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4101
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 501, 4101
          Classifications: {'peptide': 501}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 34, 'TRANS': 466}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 20
          Unresolved non-hydrogen angles: 23
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3037
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 370, 3037
          Classifications: {'peptide': 370}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 25, 'TRANS': 344}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 27
          Unresolved non-hydrogen angles: 29
          Unresolved non-hydrogen dihedrals: 27
          Planarities with less than four sites: {'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 6
  Time building chain proxies: 1.13, per 1000 atoms: 0.16
  Number of scatterers: 7138
  At special positions: 0
  Unit cell: (77.04, 101.65, 124.12, 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      14     16.00
     O    1311      8.00
     N    1174      7.00
     C    4639      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: 0.46
  Conformation dependent library (CDL) restraints added in 261.3 milliseconds
  

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1648

  Finding SS restraints...
    Secondary structure from input PDB file:
      25 helices and 8 sheets defined
      35.7% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 44
      removed outlier: 3.804A  pdb=" N   LYS A  32 " --> pdb=" O   GLU A  28 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   MET A  41 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 83
      removed outlier: 3.567A  pdb=" N   LYS A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG A  83 " --> pdb=" O   GLU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 121 through 126
      removed outlier: 3.914A  pdb=" N   LYS A 126 " --> pdb=" O   GLU A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 155 through 175
      Proline residue:  A 170  - end of helix
      removed outlier: 3.775A  pdb=" N   ASN A 175 " --> pdb=" O   PHE A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 212
      removed outlier: 4.113A  pdb=" N   THR A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TRP A 212 " --> pdb=" O   HIS A 208 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 269
    Processing helix  chain 'A' and resid 277 through 283
      removed outlier: 3.576A  pdb=" N   LEU A 283 " --> pdb=" O   LEU A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 310
    Processing helix  chain 'A' and resid 365 through 383
      removed outlier: 4.208A  pdb=" N   GLU A 378 " --> pdb=" O   LYS A 374 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 401
      removed outlier: 3.856A  pdb=" N   TRP A 398 " --> pdb=" O   GLN A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 485
      removed outlier: 4.721A  pdb=" N   ALA A 481 " --> pdb=" O   THR A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 502 through 508
    Processing helix  chain 'A' and resid 515 through 526
      removed outlier: 3.590A  pdb=" N   ASN A 519 " --> pdb=" O   SER A 515 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ILE A 526 " --> pdb=" O   ILE A 522 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 27 through 45
    Processing helix  chain 'B' and resid 78 through 84
    Processing helix  chain 'B' and resid 84 through 92
      removed outlier: 4.223A  pdb=" N   VAL B  90 " --> pdb=" O   ASP B  86 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 155 through 168
      removed outlier: 3.560A  pdb=" N   ILE B 159 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
      removed outlier: 4.789A  pdb=" N   SER B 162 " --> pdb=" O   ALA B 158 " (cutoff:3.500A)
      removed outlier: 4.805A  pdb=" N   SER B 163 " --> pdb=" O   ILE B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 175
    Processing helix  chain 'B' and resid 194 through 212
    Processing helix  chain 'B' and resid 257 through 267
      removed outlier: 3.918A  pdb=" N   VAL B 261 " --> pdb=" O   ILE B 257 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   GLY B 262 " --> pdb=" O   GLN B 258 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LYS B 263 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 276 through 281
      removed outlier: 3.669A  pdb=" N   LEU B 279 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   CYS B 280 " --> pdb=" O   ARG B 277 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LYS B 281 " --> pdb=" O   GLN B 278 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 276 through 281'
    Processing helix  chain 'B' and resid 296 through 311
      removed outlier: 3.610A  pdb=" N   GLU B 302 " --> pdb=" O   GLU B 298 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   LEU B 310 " --> pdb=" O   ASN B 306 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LYS B 311 " --> pdb=" O   ARG B 307 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 363 through 384
      removed outlier: 3.516A  pdb=" N   GLN B 367 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   VAL B 381 " --> pdb=" O   THR B 377 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   ILE B 382 " --> pdb=" O   GLU B 378 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   TRP B 383 " --> pdb=" O   SER B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 394 through 402
      removed outlier: 4.161A  pdb=" N   TRP B 401 " --> pdb=" O   THR B 397 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 49
      removed outlier: 4.107A  pdb=" N   SER A  48 " --> pdb=" O   GLN A 145 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLN A 145 " --> pdb=" O   SER A  48 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 105 through 110
      removed outlier: 3.826A  pdb=" N   VAL A 179 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 252 through 253
      removed outlier: 4.010A  pdb=" N   TRP A 252 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 326 through 333
      removed outlier: 6.427A  pdb=" N   GLN A 336 " --> pdb=" O   GLN A 332 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 48
    Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 64
    Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 180
      removed outlier: 3.675A  pdb=" N   VAL B 179 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 355
      removed outlier: 3.691A  pdb=" N   LYS B 350 " --> pdb=" O   ILE B 341 " (cutoff:3.500A)

    232 hydrogen bonds defined for protein.
    672 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: 0.83

  Time building geometry restraints manager: 0.62 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: 2220
        1.34 -     1.46: 1491
        1.46 -     1.58: 3591
        1.58 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 7326
  Sorted by residual:
  bond pdb=" N   ILE B  94 "
       pdb=" CA  ILE B  94 "
    ideal  model  delta    sigma   weight residual
    1.462  1.495 -0.034 1.01e-02 9.80e+03 1.11e+01
  bond pdb=" N   HIS B  96 "
       pdb=" CA  HIS B  96 "
    ideal  model  delta    sigma   weight residual
    1.453  1.489 -0.036 1.32e-02 5.74e+03 7.50e+00
  bond pdb=" N   GLY B  93 "
       pdb=" CA  GLY B  93 "
    ideal  model  delta    sigma   weight residual
    1.446  1.477 -0.030 1.32e-02 5.74e+03 5.27e+00
  bond pdb=" N   GLN B  91 "
       pdb=" CA  GLN B  91 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.029 1.29e-02 6.01e+03 5.16e+00
  bond pdb=" CA  ILE B  94 "
       pdb=" C   ILE B  94 "
    ideal  model  delta    sigma   weight residual
    1.523  1.540 -0.017 8.80e-03 1.29e+04 3.75e+00
  ... (remaining 7321 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 9700
        1.70 -     3.40: 212
        3.40 -     5.11: 26
        5.11 -     6.81: 8
        6.81 -     8.51: 3
  Bond angle restraints: 9949
  Sorted by residual:
  angle pdb=" C   ASP A 364 "
        pdb=" CA  ASP A 364 "
        pdb=" CB  ASP A 364 "
      ideal   model   delta    sigma   weight residual
     115.79  109.78    6.01 1.19e+00 7.06e-01 2.55e+01
  angle pdb=" C   LYS A 390 "
        pdb=" N   LEU A 391 "
        pdb=" CA  LEU A 391 "
      ideal   model   delta    sigma   weight residual
     120.49  124.94   -4.45 1.42e+00 4.96e-01 9.80e+00
  angle pdb=" CA  GLY B  93 "
        pdb=" C   GLY B  93 "
        pdb=" O   GLY B  93 "
      ideal   model   delta    sigma   weight residual
     122.31  118.14    4.17 1.34e+00 5.57e-01 9.70e+00
  angle pdb=" C   PRO B 236 "
        pdb=" N   ASP B 237 "
        pdb=" CA  ASP B 237 "
      ideal   model   delta    sigma   weight residual
     121.54  126.63   -5.09 1.91e+00 2.74e-01 7.09e+00
  angle pdb=" C   HIS B 198 "
        pdb=" N   ARG B 199 "
        pdb=" CA  ARG B 199 "
      ideal   model   delta    sigma   weight residual
     121.14  116.82    4.32 1.75e+00 3.27e-01 6.10e+00
  ... (remaining 9944 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.72: 4049
       17.72 -    35.44: 298
       35.44 -    53.16: 35
       53.16 -    70.88: 18
       70.88 -    88.60: 10
  Dihedral angle restraints: 4410
    sinusoidal: 1864
      harmonic: 2546
  Sorted by residual:
  dihedral pdb=" CA  PRO A 392 "
           pdb=" C   PRO A 392 "
           pdb=" N   ILE A 393 "
           pdb=" CA  ILE A 393 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.66  -21.34     0      5.00e+00 4.00e-02 1.82e+01
  dihedral pdb=" CA  TYR B 342 "
           pdb=" C   TYR B 342 "
           pdb=" N   GLN B 343 "
           pdb=" CA  GLN B 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.16   17.84     0      5.00e+00 4.00e-02 1.27e+01
  dihedral pdb=" CA  VAL B 381 "
           pdb=" C   VAL B 381 "
           pdb=" N   ILE B 382 "
           pdb=" CA  ILE B 382 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.74  -17.26     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 4407 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 644
       0.032 -    0.064: 290
       0.064 -    0.096: 97
       0.096 -    0.128: 43
       0.128 -    0.160: 9
  Chirality restraints: 1083
  Sorted by residual:
  chirality pdb=" CA  PRO A 392 "
            pdb=" N   PRO A 392 "
            pdb=" C   PRO A 392 "
            pdb=" CB  PRO A 392 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.56    0.16 2.00e-01 2.50e+01 6.41e-01
  chirality pdb=" CB  THR A 286 "
            pdb=" CA  THR A 286 "
            pdb=" OG1 THR A 286 "
            pdb=" CG2 THR A 286 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.97e-01
  chirality pdb=" CA  ILE B  94 "
            pdb=" N   ILE B  94 "
            pdb=" C   ILE B  94 "
            pdb=" CB  ILE B  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.44e-01
  ... (remaining 1080 not shown)

  Planarity restraints: 1248
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 149 "   -0.029 5.00e-02 4.00e+02   4.37e-02 3.05e+00
        pdb=" N   PRO B 150 "    0.076 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "   -0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 419 "   -0.027 5.00e-02 4.00e+02   4.04e-02 2.61e+00
        pdb=" N   PRO A 420 "    0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A 420 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 420 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 411 "    0.024 5.00e-02 4.00e+02   3.73e-02 2.23e+00
        pdb=" N   PRO A 412 "   -0.065 5.00e-02 4.00e+02
        pdb=" CA  PRO A 412 "    0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO A 412 "    0.021 5.00e-02 4.00e+02
  ... (remaining 1245 not shown)

  Histogram of nonbonded interaction distances:
        2.55 -     3.02: 4080
        3.02 -     3.49: 7528
        3.49 -     3.96: 11199
        3.96 -     4.43: 12977
        4.43 -     4.90: 19943
  Nonbonded interactions: 55727
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 254 "
            pdb=" OE1 GLN A 258 "
     model   vdw
     2.551 3.040
  nonbonded pdb=" O   VAL A  35 "
            pdb=" OG1 THR A  39 "
     model   vdw
     2.605 3.040
  nonbonded pdb=" N   VAL B 148 "
            pdb=" O   VAL B 148 "
     model   vdw
     2.615 2.496
  nonbonded pdb=" N   ASP B 320 "
            pdb=" OD1 ASP B 320 "
     model   vdw
     2.615 3.120
  nonbonded pdb=" O   ASN B 175 "
            pdb=" OD1 ASN B 175 "
     model   vdw
     2.617 3.040
  ... (remaining 55722 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.930
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.090
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6366
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   0.036   7326  Z= 0.157
  Angle     :  0.628   8.509   9949  Z= 0.340
  Chirality :  0.044   0.160   1083
  Planarity :  0.005   0.044   1248
  Dihedral  : 13.241  88.600   2762
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 10.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.39 %
    Favored  : 99.61 %
  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: -1.38 (0.28), residues: 853
  helix: -0.14 (0.33), residues: 276
  sheet: -1.29 (0.50), residues: 103
  loop : -1.29 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  78 
 TYR   0.017   0.001   TYR A 483 
 PHE   0.015   0.002   PHE B  77 
 TRP   0.021   0.002   TRP A 153 
 HIS   0.002   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 7326)
  covalent geometry    : angle       0.62784 ( 9949)
  hydrogen bonds       : bond        0.17852 (  232)
  hydrogen bonds       : angle       7.62130 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  533 LEU cc_start: 0.8470 (tp) cc_final: 0.7369 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0908
  time to fit residues: 21.1507
Evaluate side-chains
  96 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0170
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    1.3422

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

Flipped N/Q/H residues before XYZ refinement:
A 269 GLN
** A 330 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 474 ASN
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.099404 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.083929 restraints weight = 32398.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.086170 restraints weight = 18745.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.087593 restraints weight = 12817.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.088622 restraints weight = 9791.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.089294 restraints weight = 8089.619|
|-----------------------------------------------------------------------------|
r_work (final): 0.4047
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6934
moved from start:          0.3225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7326  Z= 0.169
  Angle     :  0.709  10.804   9949  Z= 0.354
  Chirality :  0.045   0.146   1083
  Planarity :  0.005   0.041   1248
  Dihedral  :  4.797  22.168    922
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 16.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 11.94 %
    Favored  : 86.01 %
  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: -1.51 (0.28), residues: 853
  helix: -0.32 (0.30), residues: 302
  sheet: -1.47 (0.50), residues: 103
  loop : -1.32 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 307 
 TYR   0.016   0.002   TYR B 342 
 PHE   0.012   0.002   PHE B  77 
 TRP   0.022   0.002   TRP A 229 
 HIS   0.007   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 7326)
  covalent geometry    : angle       0.70950 ( 9949)
  hydrogen bonds       : bond        0.04309 (  232)
  hydrogen bonds       : angle       5.86897 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  373 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7941 (mm-40)
REVERT: B  302 GLU cc_start: 0.8091 (mp0) cc_final: 0.7724 (mp0)
REVERT: B  331 LYS cc_start: 0.4582 (tttt) cc_final: 0.4271 (ttmm)
REVERT: B  338 THR cc_start: 0.7277 (p) cc_final: 0.6968 (p)
  outliers start: 16
  outliers final: 9
  residues processed: 101
  average time/residue: 0.0764
  time to fit residues: 10.2045
Evaluate side-chains
  85 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.202 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue  120 LEU
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0870
   chunk 1 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 79 optimal weight:    5.9990
   chunk 7 optimal weight:    0.0870
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.9940

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 ASN
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 373 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.099004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.083660 restraints weight = 32128.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.085816 restraints weight = 18587.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.087341 restraints weight = 12704.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.088302 restraints weight = 9682.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.4051 r_free = 0.4051 target = 0.088856 restraints weight = 7995.392|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6981
moved from start:          0.3763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7326  Z= 0.134
  Angle     :  0.634  10.433   9949  Z= 0.313
  Chirality :  0.044   0.168   1083
  Planarity :  0.004   0.041   1248
  Dihedral  :  4.515  20.964    922
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.54 %
    Allowed  : 14.63 %
    Favored  : 83.83 %
  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: -1.31 (0.28), residues: 853
  helix: -0.15 (0.31), residues: 301
  sheet: -1.08 (0.48), residues: 114
  loop : -1.28 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 143 
 TYR   0.012   0.001   TYR A 339 
 PHE   0.011   0.001   PHE A 227 
 TRP   0.041   0.002   TRP B 401 
 HIS   0.006   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 7326)
  covalent geometry    : angle       0.63435 ( 9949)
  hydrogen bonds       : bond        0.03824 (  232)
  hydrogen bonds       : angle       5.45242 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 80
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  331 LYS cc_start: 0.4926 (tttt) cc_final: 0.4598 (ttmm)
REVERT: B  338 THR cc_start: 0.7305 (p) cc_final: 0.6979 (p)
  outliers start: 12
  outliers final: 5
  residues processed: 88
  average time/residue: 0.0719
  time to fit residues: 8.4738
Evaluate side-chains
  78 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    0.0050
   chunk 3 optimal weight:    3.9990
   chunk 32 optimal weight:    0.3980
   chunk 20 optimal weight:    4.9990
   chunk 52 optimal weight:    0.9990
   chunk 69 optimal weight:   10.0000
   chunk 61 optimal weight:    6.9990
   chunk 22 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 64 optimal weight:    0.5980
   overall best weight:    1.1998

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

Flipped N/Q/H residues before XYZ refinement:
A 161 GLN
A 175 ASN
A 474 ASN
** B  54 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.097816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.082091 restraints weight = 32935.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.084346 restraints weight = 18743.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.085814 restraints weight = 12759.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.086827 restraints weight = 9695.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.087495 restraints weight = 7997.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.4150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7326  Z= 0.137
  Angle     :  0.618  10.809   9949  Z= 0.308
  Chirality :  0.043   0.142   1083
  Planarity :  0.004   0.044   1248
  Dihedral  :  4.489  20.774    922
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 15.66 %
    Favored  : 82.16 %
  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: -1.25 (0.28), residues: 853
  helix: -0.09 (0.31), residues: 298
  sheet: -0.97 (0.48), residues: 114
  loop : -1.27 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 307 
 TYR   0.011   0.001   TYR A 339 
 PHE   0.013   0.001   PHE B 160 
 TRP   0.032   0.002   TRP B 401 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7326)
  covalent geometry    : angle       0.61772 ( 9949)
  hydrogen bonds       : bond        0.03657 (  232)
  hydrogen bonds       : angle       5.29215 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  331 LYS cc_start: 0.4696 (tttt) cc_final: 0.4161 (ttmm)
REVERT: B  338 THR cc_start: 0.7337 (p) cc_final: 0.7080 (p)
  outliers start: 17
  outliers final: 10
  residues processed: 85
  average time/residue: 0.0859
  time to fit residues: 9.7001
Evaluate side-chains
  79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue   22 LYS
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  409 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 10 optimal weight:    8.9990
   chunk 85 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 23 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0980
   chunk 74 optimal weight:    7.9990
   chunk 72 optimal weight:    0.0270
   chunk 27 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 71 optimal weight:    8.9990
   overall best weight:    1.8244

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

Flipped N/Q/H residues before XYZ refinement:
A 175 ASN
A 428 GLN
B 137 ASN
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.096721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.080731 restraints weight = 32989.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.082828 restraints weight = 19590.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.084248 restraints weight = 13653.211|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.085206 restraints weight = 10574.002|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.085756 restraints weight = 8796.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   7326  Z= 0.177
  Angle     :  0.661  13.003   9949  Z= 0.325
  Chirality :  0.044   0.147   1083
  Planarity :  0.004   0.049   1248
  Dihedral  :  4.612  21.210    922
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 17.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 19.26 %
    Favored  : 78.56 %
  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: -1.43 (0.28), residues: 853
  helix: -0.24 (0.30), residues: 300
  sheet: -1.06 (0.47), residues: 116
  loop : -1.39 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 307 
 TYR   0.015   0.002   TYR A 115 
 PHE   0.012   0.002   PHE A 227 
 TRP   0.022   0.002   TRP B 401 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00399 ( 7326)
  covalent geometry    : angle       0.66104 ( 9949)
  hydrogen bonds       : bond        0.03819 (  232)
  hydrogen bonds       : angle       5.36594 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 69
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  300 GLU cc_start: 0.9358 (tp30) cc_final: 0.9023 (mm-30)
REVERT: B  338 THR cc_start: 0.7676 (p) cc_final: 0.7459 (p)
  outliers start: 17
  outliers final: 11
  residues processed: 82
  average time/residue: 0.0827
  time to fit residues: 9.0575
Evaluate side-chains
  79 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  409 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 0 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 60 optimal weight:    8.9990
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    0.8980
   chunk 79 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 48 optimal weight:    8.9990
   chunk 75 optimal weight:    9.9990
   overall best weight:    1.7386

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

Flipped N/Q/H residues before XYZ refinement:
** A 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.096083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.080032 restraints weight = 32578.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.082156 restraints weight = 18875.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3933 r_free = 0.3933 target = 0.083587 restraints weight = 13044.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.084540 restraints weight = 10067.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.085011 restraints weight = 8389.588|
|-----------------------------------------------------------------------------|
r_work (final): 0.3964
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7155
moved from start:          0.4987

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7326  Z= 0.168
  Angle     :  0.650  12.674   9949  Z= 0.320
  Chirality :  0.044   0.131   1083
  Planarity :  0.004   0.049   1248
  Dihedral  :  4.665  21.027    922
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 17.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 20.15 %
    Favored  : 77.28 %
  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: -1.35 (0.28), residues: 853
  helix: -0.16 (0.30), residues: 293
  sheet: -1.00 (0.47), residues: 115
  loop : -1.35 (0.28), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 199 
 TYR   0.014   0.002   TYR A 115 
 PHE   0.017   0.002   PHE A 346 
 TRP   0.023   0.002   TRP B 401 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 7326)
  covalent geometry    : angle       0.65012 ( 9949)
  hydrogen bonds       : bond        0.03672 (  232)
  hydrogen bonds       : angle       5.34135 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 ILE cc_start: 0.9054 (tp) cc_final: 0.8581 (tp)
REVERT: B  145 GLN cc_start: 0.8311 (OUTLIER) cc_final: 0.7797 (tp40)
REVERT: B  300 GLU cc_start: 0.9377 (tp30) cc_final: 0.9030 (mm-30)
REVERT: B  338 THR cc_start: 0.7629 (p) cc_final: 0.7396 (p)
  outliers start: 20
  outliers final: 15
  residues processed: 89
  average time/residue: 0.0803
  time to fit residues: 9.7844
Evaluate side-chains
  86 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.282 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 THR
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  376 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 83 optimal weight:    0.9980
   chunk 74 optimal weight:   20.0000
   chunk 82 optimal weight:    0.9990
   chunk 78 optimal weight:    0.9980
   chunk 45 optimal weight:    7.9990
   chunk 67 optimal weight:    0.0060
   chunk 56 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 86 optimal weight:    0.6980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.7196

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.098798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.083739 restraints weight = 33687.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.085703 restraints weight = 20537.033|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.087036 restraints weight = 14511.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.087887 restraints weight = 11396.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.088482 restraints weight = 9620.253|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7047
moved from start:          0.5127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7326  Z= 0.114
  Angle     :  0.649  16.348   9949  Z= 0.309
  Chirality :  0.043   0.132   1083
  Planarity :  0.004   0.045   1248
  Dihedral  :  4.389  19.433    922
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 14.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 20.28 %
    Favored  : 77.41 %
  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 are not related in a simple way.
  whole: -1.04 (0.28), residues: 853
  helix:  0.03 (0.30), residues: 298
  sheet: -0.56 (0.49), residues: 114
  loop : -1.19 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 307 
 TYR   0.009   0.001   TYR A 405 
 PHE   0.012   0.001   PHE A 346 
 TRP   0.025   0.001   TRP B 401 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7326)
  covalent geometry    : angle       0.64908 ( 9949)
  hydrogen bonds       : bond        0.03329 (  232)
  hydrogen bonds       : angle       5.12928 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  380 ILE cc_start: 0.8865 (tp) cc_final: 0.8320 (tp)
REVERT: A  413 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7750 (tm-30)
REVERT: B  145 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7898 (tp40)
REVERT: B  300 GLU cc_start: 0.9350 (tp30) cc_final: 0.8997 (mm-30)
REVERT: B  301 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8794 (mt)
REVERT: B  338 THR cc_start: 0.7581 (p) cc_final: 0.7066 (p)
  outliers start: 18
  outliers final: 11
  residues processed: 88
  average time/residue: 0.0762
  time to fit residues: 9.1044
Evaluate side-chains
  82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  386 THR
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  160 PHE
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  301 LEU
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 6 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 8 optimal weight:    6.9990
   chunk 35 optimal weight:    6.9990
   chunk 36 optimal weight:    2.9990
   chunk 46 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 29 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   chunk 64 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 235 HIS
B  96 HIS
** B 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.091296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.075917 restraints weight = 33846.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.078320 restraints weight = 20173.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.079048 restraints weight = 13405.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.079267 restraints weight = 10881.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.079432 restraints weight = 10264.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3840
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.5855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.065   7326  Z= 0.345
  Angle     :  0.818  13.500   9949  Z= 0.423
  Chirality :  0.049   0.161   1083
  Planarity :  0.006   0.059   1248
  Dihedral  :  5.446  25.654    922
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 25.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.11 %
    Allowed  : 19.90 %
    Favored  : 75.99 %
  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: -1.82 (0.27), residues: 853
  helix: -0.40 (0.30), residues: 290
  sheet: -1.30 (0.48), residues: 116
  loop : -1.73 (0.27), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 307 
 TYR   0.030   0.003   TYR A 115 
 PHE   0.022   0.003   PHE B  77 
 TRP   0.030   0.003   TRP A 229 
 HIS   0.009   0.003   HIS A 235 

Details of bonding type rmsd
  covalent geometry    : bond        0.00767 ( 7326)
  covalent geometry    : angle       0.81825 ( 9949)
  hydrogen bonds       : bond        0.04888 (  232)
  hydrogen bonds       : angle       5.93173 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 60
  time to evaluate  : 0.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 MET cc_start: 0.8593 (mtt) cc_final: 0.8258 (mtt)
REVERT: A  334 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8386 (pp30)
REVERT: B  145 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8199 (tp40)
REVERT: B  331 LYS cc_start: 0.4230 (tttt) cc_final: 0.3874 (ttmm)
  outliers start: 32
  outliers final: 21
  residues processed: 86
  average time/residue: 0.0676
  time to fit residues: 8.0505
Evaluate side-chains
  82 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 59
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   47 ILE
Chi-restraints excluded: chain A residue  124 PHE
Chi-restraints excluded: chain A residue  159 ILE
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  334 GLN
Chi-restraints excluded: chain A residue  346 PHE
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain B residue    7 THR
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  135 ILE
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  403 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.3980
   chunk 53 optimal weight:    0.9980
   chunk 71 optimal weight:    0.0570
   chunk 12 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0050
   chunk 18 optimal weight:    5.9990
   chunk 28 optimal weight:    9.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.4712

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4239 r_free = 0.4239 target = 0.097227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.082176 restraints weight = 33678.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.084116 restraints weight = 20106.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.085500 restraints weight = 14104.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.086339 restraints weight = 10947.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.086840 restraints weight = 9196.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3985
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7094
moved from start:          0.5751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7326  Z= 0.122
  Angle     :  0.680  12.573   9949  Z= 0.330
  Chirality :  0.044   0.143   1083
  Planarity :  0.004   0.044   1248
  Dihedral  :  4.584  20.131    922
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 22.98 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.28), residues: 853
  helix: -0.07 (0.30), residues: 301
  sheet: -0.76 (0.49), residues: 114
  loop : -1.43 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  78 
 TYR   0.037   0.002   TYR A 181 
 PHE   0.011   0.002   PHE B 160 
 TRP   0.026   0.002   TRP B 401 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 7326)
  covalent geometry    : angle       0.67987 ( 9949)
  hydrogen bonds       : bond        0.03566 (  232)
  hydrogen bonds       : angle       5.31531 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.6286 (t80)
REVERT: A  380 ILE cc_start: 0.8851 (tp) cc_final: 0.8398 (tp)
REVERT: A  413 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7662 (tm-30)
REVERT: B   26 LEU cc_start: 0.8661 (tp) cc_final: 0.8075 (mp)
REVERT: B  145 GLN cc_start: 0.8231 (OUTLIER) cc_final: 0.8010 (tp40)
REVERT: B  300 GLU cc_start: 0.9348 (tp30) cc_final: 0.9030 (mm-30)
REVERT: B  338 THR cc_start: 0.7623 (p) cc_final: 0.7212 (p)
  outliers start: 15
  outliers final: 11
  residues processed: 79
  average time/residue: 0.0958
  time to fit residues: 10.2222
Evaluate side-chains
  81 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  375 ILE
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 13 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 75 optimal weight:   10.0000
   chunk 81 optimal weight:    5.9990
   chunk 56 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.096897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.082263 restraints weight = 33901.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.084828 restraints weight = 20497.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.085289 restraints weight = 13815.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.085467 restraints weight = 11646.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.085518 restraints weight = 10798.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3950
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.5854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7326  Z= 0.127
  Angle     :  0.668  12.666   9949  Z= 0.325
  Chirality :  0.043   0.142   1083
  Planarity :  0.004   0.045   1248
  Dihedral  :  4.451  20.157    922
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 15.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.69 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 23.36 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.28), residues: 853
  helix: -0.06 (0.30), residues: 307
  sheet: -0.61 (0.49), residues: 114
  loop : -1.38 (0.29), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 125 
 TYR   0.024   0.001   TYR A 181 
 PHE   0.012   0.002   PHE A 346 
 TRP   0.026   0.002   TRP B 401 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 7326)
  covalent geometry    : angle       0.66790 ( 9949)
  hydrogen bonds       : bond        0.03529 (  232)
  hydrogen bonds       : angle       5.20119 (  672)

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

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

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1706 Ramachandran restraints generated.
    853 Oldfield, 0 Emsley, 853 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 63
  time to evaluate  : 0.201 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  146 TYR cc_start: 0.7298 (OUTLIER) cc_final: 0.6282 (t80)
REVERT: A  380 ILE cc_start: 0.8929 (tp) cc_final: 0.8433 (tp)
REVERT: A  413 GLU cc_start: 0.8263 (OUTLIER) cc_final: 0.7893 (tm-30)
REVERT: B   26 LEU cc_start: 0.8732 (tp) cc_final: 0.8152 (mp)
REVERT: B  145 GLN cc_start: 0.8224 (OUTLIER) cc_final: 0.7656 (tp40)
REVERT: B  300 GLU cc_start: 0.9318 (tp30) cc_final: 0.9032 (mm-30)
REVERT: B  338 THR cc_start: 0.7579 (p) cc_final: 0.7084 (p)
  outliers start: 14
  outliers final: 10
  residues processed: 74
  average time/residue: 0.0777
  time to fit residues: 8.0092
Evaluate side-chains
  75 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 62
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 TYR
Chi-restraints excluded: chain A residue  187 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  413 GLU
Chi-restraints excluded: chain A residue  525 LEU
Chi-restraints excluded: chain B residue   58 THR
Chi-restraints excluded: chain B residue   75 VAL
Chi-restraints excluded: chain B residue  124 PHE
Chi-restraints excluded: chain B residue  145 GLN
Chi-restraints excluded: chain B residue  173 LYS
Chi-restraints excluded: chain B residue  184 MET
Chi-restraints excluded: chain B residue  376 THR
Chi-restraints excluded: chain B residue  417 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 67 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 41 optimal weight:    7.9990
   chunk 18 optimal weight:    9.9990
   chunk 51 optimal weight:    0.0070
   chunk 84 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 57 optimal weight:    1.9990
   overall best weight:    0.7200

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.097768 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.082744 restraints weight = 33854.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.084831 restraints weight = 20181.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.086139 restraints weight = 13982.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.087023 restraints weight = 10830.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.087514 restraints weight = 9084.079|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.5988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7326  Z= 0.119
  Angle     :  0.663  12.822   9949  Z= 0.323
  Chirality :  0.043   0.150   1083
  Planarity :  0.004   0.043   1248
  Dihedral  :  4.362  19.809    922
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 23.62 %
    Favored  : 74.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.28), residues: 853
  helix: -0.03 (0.30), residues: 309
  sheet: -0.45 (0.49), residues: 114
  loop : -1.33 (0.29), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 199 
 TYR   0.023   0.001   TYR A 181 
 PHE   0.011   0.001   PHE A 227 
 TRP   0.047   0.002   TRP B 410 
 HIS   0.005   0.001   HIS B 208 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7326)
  covalent geometry    : angle       0.66330 ( 9949)
  hydrogen bonds       : bond        0.03431 (  232)
  hydrogen bonds       : angle       5.06284 (  672)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1085.36 seconds
wall clock time: 19 minutes 27.20 seconds (1167.20 seconds total)