Starting phenix.real_space_refine
on Thu Mar  6 04:20:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yr5_34046/03_2025/7yr5_34046.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yr5_34046/03_2025/7yr5_34046.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.63
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yr5_34046/03_2025/7yr5_34046.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yr5_34046/03_2025/7yr5_34046.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yr5_34046/03_2025/7yr5_34046.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yr5_34046/03_2025/7yr5_34046.cif"
  }
  resolution = 3.63
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.015
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      35      5.16       5
     C    3164      2.51       5
     N     775      2.21       5
     O     854      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4828
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "B"
      Number of atoms: 1899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 237, 1899
          Classifications: {'peptide': 237}
          Link IDs: {'PTRANS': 8, 'TRANS': 228}
    Chain: "A"
      Number of atoms: 2929
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 2929
          Classifications: {'peptide': 385}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 367}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 4.46, per 1000 atoms: 0.92
  Number of scatterers: 4828
  At special positions: 0
  Unit cell: (73.08, 103.32, 123.48, 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      35     16.00
     O     854      8.00
     N     775      7.00
     C    3164      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS B  88 " - pdb=" SG  CYS B 142 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 180 " - pdb=" SG  CYS B 237 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.20
  Conformation dependent library (CDL) restraints added in 609.2 milliseconds
  

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1126

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 5 sheets defined
      61.7% alpha, 7.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'B' and resid 257 through 290
      removed outlier: 4.103A  pdb=" N   LYS B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      Proline residue:  B 263  - end of helix
    Processing helix  chain 'A' and resid 19 through 40
      removed outlier: 4.237A  pdb=" N   PHE A  36 " --> pdb=" O   PHE A  32 " (cutoff:3.500A)
      Proline residue:  A  37  - end of helix
    Processing helix  chain 'A' and resid 40 through 51
      removed outlier: 4.150A  pdb=" N   LYS A  45 " --> pdb=" O   THR A  41 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   GLU A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
      removed outlier: 4.322A  pdb=" N   GLY A  49 " --> pdb=" O   LYS A  45 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ILE A  50 " --> pdb=" O   GLU A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 54 through 72
      removed outlier: 5.085A  pdb=" N   ILE A  61 " --> pdb=" O   GLU A  57 " (cutoff:3.500A)
      removed outlier: 4.715A  pdb=" N   SER A  62 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 83
    Processing helix  chain 'A' and resid 84 through 104
    Processing helix  chain 'A' and resid 111 through 139
      removed outlier: 3.690A  pdb=" N   CYS A 115 " --> pdb=" O   GLN A 111 " (cutoff:3.500A)
      Proline residue:  A 130  - end of helix
    Processing helix  chain 'A' and resid 142 through 152
    Processing helix  chain 'A' and resid 152 through 162
      removed outlier: 4.313A  pdb=" N   VAL A 156 " --> pdb=" O   ALA A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 172
      removed outlier: 5.924A  pdb=" N   PHE A 169 " --> pdb=" O   ASN A 165 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   GLY A 170 " --> pdb=" O   GLN A 166 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 175 through 188
      removed outlier: 3.519A  pdb=" N   ILE A 180 " --> pdb=" O   GLY A 176 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 194
    Processing helix  chain 'A' and resid 254 through 259
      removed outlier: 3.551A  pdb=" N   LEU A 257 " --> pdb=" O   ASP A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 291
      removed outlier: 4.491A  pdb=" N   PHE A 275 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   GLY A 276 " --> pdb=" O   ILE A 272 " (cutoff:3.500A)
      Proline residue:  A 280  - end of helix
      removed outlier: 5.279A  pdb=" N   SER A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   SER A 286 " --> pdb=" O   VAL A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 294 through 322
      removed outlier: 3.590A  pdb=" N   LEU A 302 " --> pdb=" O   SER A 298 " (cutoff:3.500A)
      Proline residue:  A 314  - end of helix
    Processing helix  chain 'A' and resid 323 through 326
    Processing helix  chain 'A' and resid 328 through 347
      removed outlier: 3.607A  pdb=" N   VAL A 338 " --> pdb=" O   ALA A 334 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   ALA A 339 " --> pdb=" O   ALA A 335 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ASN A 340 " --> pdb=" O   SER A 336 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 374
      removed outlier: 3.859A  pdb=" N   TRP A 369 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
      removed outlier: 4.302A  pdb=" N   LEU A 370 " --> pdb=" O   ALA A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 382
    Processing helix  chain 'A' and resid 383 through 412
      removed outlier: 3.983A  pdb=" N   SER A 388 " --> pdb=" O   PRO A 384 " (cutoff:3.500A)
      removed outlier: 5.138A  pdb=" N   SER A 389 " --> pdb=" O   GLN A 385 " (cutoff:3.500A)
      removed outlier: 4.108A  pdb=" N   GLY A 392 " --> pdb=" O   SER A 388 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   LEU A 393 " --> pdb=" O   SER A 389 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ILE A 396 " --> pdb=" O   GLY A 392 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   CYS A 400 " --> pdb=" O   ILE A 396 " (cutoff:3.500A)
      Proline residue:  A 401  - end of helix
      Proline residue:  A 406  - end of helix
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 448
      removed outlier: 3.934A  pdb=" N   ALA A 425 " --> pdb=" O   TYR A 421 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   CYS A 426 " --> pdb=" O   THR A 422 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 61 through 64
      removed outlier: 5.621A  pdb=" N   ILE B  62 " --> pdb=" O   GLN B  89 " (cutoff:3.500A)
      removed outlier: 7.364A  pdb=" N   THR B  91 " --> pdb=" O   ILE B  62 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   LEU B  64 " --> pdb=" O   THR B  91 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 72 through 74
      removed outlier: 3.715A  pdb=" N   GLN B 150 " --> pdb=" O   PHE B 144 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B 110 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 169 through 171
    Processing sheet with id=AA4, first strand: chain 'B' and resid 191 through 194
    Processing sheet with id=AA5, first strand: chain 'B' and resid 210 through 213

    278 hydrogen bonds defined for protein.
    798 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.35

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1472
        1.34 -     1.46: 1090
        1.46 -     1.58: 2336
        1.58 -     1.70: 0
        1.70 -     1.81: 51
  Bond restraints: 4949
  Sorted by residual:
  bond pdb=" N   VAL B  84 "
       pdb=" CA  VAL B  84 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.038 1.11e-02 8.12e+03 1.16e+01
  bond pdb=" N   ILE B  76 "
       pdb=" CA  ILE B  76 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.19e-02 7.06e+03 9.69e+00
  bond pdb=" N   VAL B 116 "
       pdb=" CA  VAL B 116 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.22e-02 6.72e+03 8.68e+00
  bond pdb=" N   VAL B  72 "
       pdb=" CA  VAL B  72 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.036 1.24e-02 6.50e+03 8.36e+00
  bond pdb=" N   LYS B 104 "
       pdb=" CA  LYS B 104 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.27e-02 6.20e+03 7.61e+00
  ... (remaining 4944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.38: 6220
        1.38 -     2.75: 367
        2.75 -     4.13: 89
        4.13 -     5.51: 33
        5.51 -     6.88: 6
  Bond angle restraints: 6715
  Sorted by residual:
  angle pdb=" C   ARG B 128 "
        pdb=" N   PHE B 129 "
        pdb=" CA  PHE B 129 "
      ideal   model   delta    sigma   weight residual
     122.77  117.48    5.29 1.33e+00 5.65e-01 1.58e+01
  angle pdb=" CA  PHE B 129 "
        pdb=" CB  PHE B 129 "
        pdb=" CG  PHE B 129 "
      ideal   model   delta    sigma   weight residual
     113.80  117.77   -3.97 1.00e+00 1.00e+00 1.58e+01
  angle pdb=" N   PHE B 154 "
        pdb=" CA  PHE B 154 "
        pdb=" C   PHE B 154 "
      ideal   model   delta    sigma   weight residual
     109.46  103.18    6.28 1.66e+00 3.63e-01 1.43e+01
  angle pdb=" C   CYS A 106 "
        pdb=" N   ASN A 107 "
        pdb=" CA  ASN A 107 "
      ideal   model   delta    sigma   weight residual
     122.61  128.02   -5.41 1.56e+00 4.11e-01 1.20e+01
  angle pdb=" C   CYS B  88 "
        pdb=" N   GLN B  89 "
        pdb=" CA  GLN B  89 "
      ideal   model   delta    sigma   weight residual
     123.05  118.23    4.82 1.40e+00 5.10e-01 1.18e+01
  ... (remaining 6710 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.54: 2481
       14.54 -    29.07: 292
       29.07 -    43.61: 82
       43.61 -    58.14: 13
       58.14 -    72.68: 7
  Dihedral angle restraints: 2875
    sinusoidal: 1101
      harmonic: 1774
  Sorted by residual:
  dihedral pdb=" CA  GLN A 166 "
           pdb=" C   GLN A 166 "
           pdb=" N   VAL A 167 "
           pdb=" CA  VAL A 167 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.92   26.08     0      5.00e+00 4.00e-02 2.72e+01
  dihedral pdb=" CA  LEU A 164 "
           pdb=" C   LEU A 164 "
           pdb=" N   ASN A 165 "
           pdb=" CA  ASN A 165 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.35   21.65     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  GLN A 110 "
           pdb=" C   GLN A 110 "
           pdb=" N   GLN A 111 "
           pdb=" CA  GLN A 111 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.98   20.02     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 2872 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 571
       0.052 -    0.104: 141
       0.104 -    0.156: 34
       0.156 -    0.208: 12
       0.208 -    0.261: 4
  Chirality restraints: 762
  Sorted by residual:
  chirality pdb=" CA  PHE B 154 "
            pdb=" N   PHE B 154 "
            pdb=" C   PHE B 154 "
            pdb=" CB  PHE B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.77   -0.26 2.00e-01 2.50e+01 1.70e+00
  chirality pdb=" CA  CYS B  88 "
            pdb=" N   CYS B  88 "
            pdb=" C   CYS B  88 "
            pdb=" CB  CYS B  88 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.75   -0.24 2.00e-01 2.50e+01 1.39e+00
  chirality pdb=" CA  ILE B  62 "
            pdb=" N   ILE B  62 "
            pdb=" C   ILE B  62 "
            pdb=" CB  ILE B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.66   -0.22 2.00e-01 2.50e+01 1.26e+00
  ... (remaining 759 not shown)

  Planarity restraints: 834
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 253 "    0.021 2.00e-02 2.50e+03   4.20e-02 1.76e+01
        pdb=" C   VAL B 253 "   -0.073 2.00e-02 2.50e+03
        pdb=" O   VAL B 253 "    0.027 2.00e-02 2.50e+03
        pdb=" N   VAL B 254 "    0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B  99 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.15e+00
        pdb=" C   VAL B  99 "    0.043 2.00e-02 2.50e+03
        pdb=" O   VAL B  99 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   ASN B 100 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 114 "   -0.009 2.00e-02 2.50e+03   1.85e-02 3.42e+00
        pdb=" C   VAL A 114 "    0.032 2.00e-02 2.50e+03
        pdb=" O   VAL A 114 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   CYS A 115 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 831 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1062
        2.78 -     3.31: 4795
        3.31 -     3.84: 7906
        3.84 -     4.37: 9100
        4.37 -     4.90: 15390
  Nonbonded interactions: 38253
  Sorted by model distance:
  nonbonded pdb=" OG  SER A  63 "
            pdb=" O   LEU A 403 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG  SER A  29 "
            pdb=" O   ASN A 127 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" OH  TYR A 138 "
            pdb=" O   ARG A 196 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" OH  TYR B 210 "
            pdb=" OH  TYR B 235 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" OG  SER B 134 "
            pdb=" O   GLU B 160 "
     model   vdw
     2.318 3.040
  ... (remaining 38248 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:             3.450
  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:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     17.180
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
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      :  0.005   0.042   4949  Z= 0.326
  Angle     :  0.808   6.881   6715  Z= 0.501
  Chirality :  0.054   0.261    762
  Planarity :  0.005   0.042    834
  Dihedral  : 13.919  72.678   1743
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.52 %
    Favored  : 98.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.05 (0.34), residues: 616
  helix:  0.65 (0.29), residues: 362
  sheet:  0.32 (0.53), residues: 102
  loop : -1.81 (0.42), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 
 PHE   0.017   0.001   PHE B 129 
 TYR   0.013   0.001   TYR A 445 
 ARG   0.003   0.000   ARG B 128 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.551 
Fit side-chains
REVERT: A  151 MET cc_start: 0.8056 (ttm) cc_final: 0.7434 (ttp)
REVERT: A  416 TYR cc_start: 0.7273 (t80) cc_final: 0.6929 (t80)
REVERT: A  418 ASP cc_start: 0.7536 (t70) cc_final: 0.7060 (p0)
REVERT: A  446 ARG cc_start: 0.8201 (mmp80) cc_final: 0.7579 (mtp180)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.1540
  time to fit residues: 22.7162
Evaluate side-chains
  84 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 15 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 18 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 55 optimal weight:    0.9990
   overall best weight:    1.7988

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
A 165 ASN
A 260 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.163099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.118414 restraints weight = 7838.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.121749 restraints weight = 3786.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.123822 restraints weight = 2334.674|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.043   4949  Z= 0.380
  Angle     :  0.724  10.886   6715  Z= 0.383
  Chirality :  0.046   0.165    762
  Planarity :  0.005   0.048    834
  Dihedral  :  5.235  26.691    665
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 11.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 14.04 %
    Favored  : 82.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.34), residues: 616
  helix:  0.60 (0.28), residues: 365
  sheet: -0.06 (0.52), residues: 104
  loop : -1.44 (0.45), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 369 
 HIS   0.006   0.001   HIS A 260 
 PHE   0.024   0.002   PHE B 129 
 TYR   0.012   0.002   TYR A 140 
 ARG   0.002   0.000   ARG A  86 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.541 
Fit side-chains
REVERT: A   48 GLU cc_start: 0.7936 (mm-30) cc_final: 0.7394 (mm-30)
REVERT: A   83 TYR cc_start: 0.6993 (m-10) cc_final: 0.6780 (m-10)
REVERT: A  416 TYR cc_start: 0.7570 (t80) cc_final: 0.7223 (t80)
REVERT: A  418 ASP cc_start: 0.7713 (t70) cc_final: 0.7341 (p0)
  outliers start: 16
  outliers final: 10
  residues processed: 96
  average time/residue: 0.1234
  time to fit residues: 16.4757
Evaluate side-chains
  92 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.544 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  179 THR
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain A residue  133 THR
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 46 optimal weight:    1.9990
   chunk 59 optimal weight:    0.7980
   chunk 1 optimal weight:    0.1980
   chunk 56 optimal weight:    0.2980
   chunk 44 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 14 optimal weight:    7.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.169961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.125100 restraints weight = 7852.055|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.128696 restraints weight = 3754.897|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.130964 restraints weight = 2277.651|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7735
moved from start:          0.1866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4949  Z= 0.202
  Angle     :  0.621   8.703   6715  Z= 0.324
  Chirality :  0.042   0.151    762
  Planarity :  0.005   0.043    834
  Dihedral  :  4.916  21.893    665
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 19.92 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.35), residues: 616
  helix:  0.87 (0.29), residues: 362
  sheet:  0.07 (0.53), residues: 104
  loop : -1.53 (0.46), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.001   HIS B 249 
 PHE   0.017   0.001   PHE B 129 
 TYR   0.008   0.001   TYR A 353 
 ARG   0.002   0.000   ARG B 238 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.497 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.8258 (ttpp) cc_final: 0.7478 (tmmt)
REVERT: A  418 ASP cc_start: 0.7505 (t70) cc_final: 0.7304 (p0)
REVERT: A  420 LYS cc_start: 0.9036 (tmmt) cc_final: 0.8696 (tmmt)
REVERT: A  438 PHE cc_start: 0.8035 (OUTLIER) cc_final: 0.7675 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 100
  average time/residue: 0.1320
  time to fit residues: 17.9402
Evaluate side-chains
  99 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.552 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 1 optimal weight:    6.9990
   chunk 5 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 38 optimal weight:    0.6980
   chunk 24 optimal weight:    2.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
A 129 ASN
A 291 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.166145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.121480 restraints weight = 7913.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.124932 restraints weight = 3841.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.127068 restraints weight = 2349.934|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.2198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4949  Z= 0.288
  Angle     :  0.663   8.422   6715  Z= 0.344
  Chirality :  0.043   0.153    762
  Planarity :  0.005   0.042    834
  Dihedral  :  5.016  24.734    665
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 11.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 21.44 %
    Favored  : 75.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.19 (0.35), residues: 616
  helix:  0.84 (0.29), residues: 365
  sheet: -0.01 (0.53), residues: 104
  loop : -1.37 (0.48), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 369 
 HIS   0.002   0.001   HIS B 249 
 PHE   0.022   0.002   PHE B 129 
 TYR   0.010   0.001   TYR B 210 
 ARG   0.002   0.000   ARG B 238 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.575 
Fit side-chains
REVERT: A   48 GLU cc_start: 0.7865 (mm-30) cc_final: 0.7326 (mm-30)
REVERT: A   82 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8356 (ttpp)
REVERT: A  418 ASP cc_start: 0.7509 (t70) cc_final: 0.7281 (p0)
REVERT: A  420 LYS cc_start: 0.9067 (tmmt) cc_final: 0.8339 (ttpp)
REVERT: A  438 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7698 (t80)
  outliers start: 18
  outliers final: 12
  residues processed: 97
  average time/residue: 0.1372
  time to fit residues: 18.1546
Evaluate side-chains
  94 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 81
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  143 PHE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  256 THR
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 56 optimal weight:    0.9990
   chunk 49 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 8 optimal weight:    9.9990
   chunk 55 optimal weight:    0.2980
   chunk 21 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 47 optimal weight:    0.5980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.168327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.123443 restraints weight = 7944.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.127000 restraints weight = 3815.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.129290 restraints weight = 2320.337|
|-----------------------------------------------------------------------------|
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4949  Z= 0.239
  Angle     :  0.633   8.214   6715  Z= 0.329
  Chirality :  0.042   0.146    762
  Planarity :  0.005   0.042    834
  Dihedral  :  4.990  23.019    665
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.42 %
    Allowed  : 24.48 %
    Favored  : 72.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.23 (0.35), residues: 616
  helix:  0.89 (0.29), residues: 365
  sheet: -0.08 (0.54), residues: 105
  loop : -1.32 (0.48), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 236 
 HIS   0.002   0.001   HIS B 249 
 PHE   0.018   0.002   PHE B 129 
 TYR   0.017   0.001   TYR A 287 
 ARG   0.001   0.000   ARG B 238 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.521 
Fit side-chains
REVERT: A  404 LEU cc_start: 0.8311 (pp) cc_final: 0.8085 (mt)
REVERT: A  420 LYS cc_start: 0.9051 (tmmt) cc_final: 0.8319 (ttpp)
REVERT: A  438 PHE cc_start: 0.8136 (OUTLIER) cc_final: 0.7699 (t80)
  outliers start: 18
  outliers final: 14
  residues processed: 98
  average time/residue: 0.1481
  time to fit residues: 19.8479
Evaluate side-chains
  99 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.546 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  264 LEU
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   chunk 1 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   chunk 23 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
B  89 GLN
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.167968 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.122673 restraints weight = 7933.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.126239 restraints weight = 3825.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.128449 restraints weight = 2332.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   4949  Z= 0.266
  Angle     :  0.649   8.517   6715  Z= 0.340
  Chirality :  0.043   0.149    762
  Planarity :  0.005   0.041    834
  Dihedral  :  5.019  24.186    665
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 24.67 %
    Favored  : 71.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.35), residues: 616
  helix:  0.88 (0.29), residues: 365
  sheet: -0.16 (0.53), residues: 105
  loop : -1.36 (0.47), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 236 
 HIS   0.003   0.001   HIS B 249 
 PHE   0.019   0.002   PHE B 129 
 TYR   0.021   0.001   TYR A 287 
 ARG   0.003   0.000   ARG B 238 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.563 
Fit side-chains
REVERT: A   48 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7220 (mm-30)
REVERT: A   65 MET cc_start: 0.8525 (tpp) cc_final: 0.8197 (ttm)
REVERT: A  438 PHE cc_start: 0.8155 (OUTLIER) cc_final: 0.7672 (t80)
  outliers start: 22
  outliers final: 17
  residues processed: 98
  average time/residue: 0.2039
  time to fit residues: 27.6086
Evaluate side-chains
  96 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 78
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  349 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  371 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 5 optimal weight:    8.9990
   chunk 59 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    0.0970
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 127 ASN
A 129 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.169701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.124910 restraints weight = 7760.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.128466 restraints weight = 3724.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.130728 restraints weight = 2261.807|
|-----------------------------------------------------------------------------|
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.2504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4949  Z= 0.223
  Angle     :  0.634   9.141   6715  Z= 0.331
  Chirality :  0.042   0.142    762
  Planarity :  0.005   0.042    834
  Dihedral  :  4.930  22.227    665
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 25.81 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.35), residues: 616
  helix:  0.96 (0.29), residues: 362
  sheet: -0.19 (0.53), residues: 105
  loop : -1.51 (0.47), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 
 PHE   0.016   0.001   PHE B 129 
 TYR   0.015   0.001   TYR A 287 
 ARG   0.002   0.000   ARG B 238 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 1.185 
Fit side-chains
REVERT: A  416 TYR cc_start: 0.7580 (t80) cc_final: 0.7057 (t80)
REVERT: A  438 PHE cc_start: 0.8161 (OUTLIER) cc_final: 0.7696 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 102
  average time/residue: 0.1760
  time to fit residues: 25.4167
Evaluate side-chains
  97 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.699 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  346 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9980
   chunk 38 optimal weight:    0.4980
   chunk 32 optimal weight:    0.1980
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0570
   chunk 22 optimal weight:    3.9990
   chunk 49 optimal weight:    0.4980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.3698

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.172277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.127347 restraints weight = 7855.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.131054 restraints weight = 3729.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.133358 restraints weight = 2245.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7668
moved from start:          0.2551

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4949  Z= 0.188
  Angle     :  0.613   9.075   6715  Z= 0.318
  Chirality :  0.041   0.137    762
  Planarity :  0.005   0.040    834
  Dihedral  :  4.791  22.443    665
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.19 %
    Favored  : 94.81 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 26.57 %
    Favored  : 70.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.36), residues: 616
  helix:  1.00 (0.29), residues: 362
  sheet: -0.16 (0.53), residues: 104
  loop : -1.44 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 
 PHE   0.022   0.001   PHE A 307 
 TYR   0.012   0.001   TYR A 287 
 ARG   0.001   0.000   ARG A  86 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 1.180 
Fit side-chains
REVERT: B  193 TYR cc_start: 0.7336 (m-80) cc_final: 0.7005 (m-10)
REVERT: A  134 MET cc_start: 0.8968 (mmm) cc_final: 0.8715 (mmt)
REVERT: A  416 TYR cc_start: 0.7457 (t80) cc_final: 0.6867 (t80)
REVERT: A  438 PHE cc_start: 0.8146 (OUTLIER) cc_final: 0.7716 (t80)
  outliers start: 16
  outliers final: 10
  residues processed: 94
  average time/residue: 0.1922
  time to fit residues: 25.2227
Evaluate side-chains
  91 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 80
  time to evaluate  : 0.535 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  169 ILE
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 2 optimal weight:    2.9990
   chunk 1 optimal weight:    8.9990
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:   20.0000
   chunk 38 optimal weight:    0.5980
   chunk 50 optimal weight:    5.9990
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.167872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.122465 restraints weight = 7848.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.126020 restraints weight = 3830.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.128228 restraints weight = 2326.829|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7756
moved from start:          0.2624

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4949  Z= 0.254
  Angle     :  0.649   8.212   6715  Z= 0.339
  Chirality :  0.042   0.145    762
  Planarity :  0.005   0.040    834
  Dihedral  :  4.886  23.380    665
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 25.43 %
    Favored  : 70.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.35), residues: 616
  helix:  0.94 (0.29), residues: 362
  sheet: -0.05 (0.54), residues: 101
  loop : -1.55 (0.47), residues: 153

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B 236 
 HIS   0.002   0.000   HIS A  52 
 PHE   0.019   0.002   PHE B 129 
 TYR   0.018   0.001   TYR A 287 
 ARG   0.002   0.000   ARG B 238 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.609 
Fit side-chains
REVERT: A   65 MET cc_start: 0.8583 (tpp) cc_final: 0.8245 (ttm)
REVERT: A  416 TYR cc_start: 0.7543 (t80) cc_final: 0.6970 (t80)
REVERT: A  438 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7711 (t80)
  outliers start: 20
  outliers final: 16
  residues processed: 93
  average time/residue: 0.2145
  time to fit residues: 27.5961
Evaluate side-chains
  97 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 80
  time to evaluate  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  278 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 36 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 2 optimal weight:    0.4980
   chunk 23 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 113 ASN
** A 166 GLN ** 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 = 0.4178 r_free = 0.4178 target = 0.167264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.121964 restraints weight = 8027.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.125559 restraints weight = 3885.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.127782 restraints weight = 2368.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4949  Z= 0.255
  Angle     :  0.653   7.992   6715  Z= 0.340
  Chirality :  0.042   0.148    762
  Planarity :  0.005   0.041    834
  Dihedral  :  4.950  25.719    665
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.57 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.35), residues: 616
  helix:  0.89 (0.29), residues: 365
  sheet: -0.10 (0.54), residues: 101
  loop : -1.41 (0.48), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 
 PHE   0.023   0.002   PHE A 307 
 TYR   0.017   0.001   TYR A 287 
 ARG   0.002   0.000   ARG B 238 

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

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

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1232 Ramachandran restraints generated.
    616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.813 
Fit side-chains
REVERT: B  193 TYR cc_start: 0.7372 (m-80) cc_final: 0.7005 (m-10)
REVERT: A   65 MET cc_start: 0.8561 (tpp) cc_final: 0.8264 (ttm)
REVERT: A  416 TYR cc_start: 0.7585 (t80) cc_final: 0.7030 (t80)
REVERT: A  438 PHE cc_start: 0.8221 (OUTLIER) cc_final: 0.7709 (t80)
  outliers start: 17
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1395
  time to fit residues: 19.0819
Evaluate side-chains
  98 residues out of total 528 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 82
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  116 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  201 VAL
Chi-restraints excluded: chain B residue  212 ILE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain A residue   81 ASN
Chi-restraints excluded: chain A residue  156 VAL
Chi-restraints excluded: chain A residue  189 CYS
Chi-restraints excluded: chain A residue  281 LEU
Chi-restraints excluded: chain A residue  315 SER
Chi-restraints excluded: chain A residue  329 ILE
Chi-restraints excluded: chain A residue  372 SER
Chi-restraints excluded: chain A residue  373 VAL
Chi-restraints excluded: chain A residue  374 LEU
Chi-restraints excluded: chain A residue  438 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 45 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 31 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 26 optimal weight:    0.4980
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B  89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 136 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 129 ASN
** A 166 GLN ** 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 = 0.4172 r_free = 0.4172 target = 0.167003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.121752 restraints weight = 7973.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.125300 restraints weight = 3836.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.127529 restraints weight = 2344.033|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.2753

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4949  Z= 0.260
  Angle     :  0.674   8.448   6715  Z= 0.352
  Chirality :  0.043   0.147    762
  Planarity :  0.005   0.041    834
  Dihedral  :  4.996  25.024    665
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 26.57 %
    Favored  : 70.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.35), residues: 616
  helix:  0.85 (0.29), residues: 368
  sheet: -0.13 (0.54), residues: 101
  loop : -1.51 (0.48), residues: 147

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 236 
 HIS   0.002   0.000   HIS B 249 
 PHE   0.029   0.002   PHE B 129 
 TYR   0.017   0.001   TYR A 287 
 ARG   0.003   0.000   ARG B 238 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2134.20 seconds
wall clock time: 39 minutes 18.22 seconds (2358.22 seconds total)