Starting phenix.real_space_refine
on Thu Sep 10 20:46:40 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6x12_21986/09_2026/6x12_21986.cif"
  }
  resolution = 3.52
  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=   0.003
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      18      5.16       5
     C    2019      2.51       5
     N     486      2.21       5
     O     535      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 3059
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3017
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 407, 3017
          Classifications: {'peptide': 407}
          Link IDs: {'PTRANS': 17, 'TRANS': 389}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'6OU': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 7
  Time building chain proxies: 0.75, per 1000 atoms: 0.25
  Number of scatterers: 3059
  At special positions: 0
  Unit cell: (67.6148, 79.4205, 69.7613, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P       1     15.00
     O     535      8.00
     N     486      7.00
     C    2019      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: 0.26
  Conformation dependent library (CDL) restraints added in 117.4 milliseconds
  

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  732

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 0 sheets defined
      86.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.08
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 10
    Processing helix  chain 'A' and resid 12 through 32
      removed outlier: 3.791A  pdb=" N   LEU A  17 " --> pdb=" O   LEU A  13 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE A  18 " --> pdb=" O   GLN A  14 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   VAL A  26 " --> pdb=" O   LEU A  22 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 43
      removed outlier: 3.518A  pdb=" N   THR A  41 " --> pdb=" O   HIS A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.535A  pdb=" N   LEU A  49 " --> pdb=" O   PRO A  45 " (cutoff:3.500A)
      removed outlier: 4.336A  pdb=" N   PHE A  50 " --> pdb=" O   PHE A  46 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   LEU A  57 " --> pdb=" O   LEU A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 71
      removed outlier: 3.784A  pdb=" N   ILE A  61 " --> pdb=" O   LEU A  57 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   LEU A  66 " --> pdb=" O   VAL A  62 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   VAL A  68 " --> pdb=" O   ALA A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 107
      removed outlier: 3.557A  pdb=" N   LEU A  90 " --> pdb=" O   VAL A  86 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ALA A  94 " --> pdb=" O   LEU A  90 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR A  98 " --> pdb=" O   ALA A  94 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   ILE A 102 " --> pdb=" O   THR A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 137
      removed outlier: 3.635A  pdb=" N   LEU A 134 " --> pdb=" O   LEU A 130 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LEU A 135 " --> pdb=" O   VAL A 131 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 141 through 148
    Processing helix  chain 'A' and resid 150 through 170
      removed outlier: 3.526A  pdb=" N   ILE A 165 " --> pdb=" O   LEU A 161 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR A 166 " --> pdb=" O   GLY A 162 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   TYR A 167 " --> pdb=" O   ILE A 163 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   LEU A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   ASN A 170 " --> pdb=" O   THR A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 174 through 220
      removed outlier: 3.631A  pdb=" N   VAL A 198 " --> pdb=" O   MET A 194 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   ASN A 199 " --> pdb=" O   TYR A 195 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY A 200 " --> pdb=" O   LYS A 196 " (cutoff:3.500A)
      Proline residue:  A 206  - end of helix
    Processing helix  chain 'A' and resid 222 through 254
      removed outlier: 3.827A  pdb=" N   LYS A 230 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   THR A 232 " --> pdb=" O   LEU A 228 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA A 233 " --> pdb=" O   ALA A 229 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   GLY A 238 " --> pdb=" O   ALA A 234 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU A 241 " --> pdb=" O   VAL A 237 " (cutoff:3.500A)
      removed outlier: 4.473A  pdb=" N   PHE A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   VAL A 249 " --> pdb=" O   LEU A 245 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   LYS A 252 " --> pdb=" O   PHE A 248 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   TYR A 254 " --> pdb=" O   LEU A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 257 through 276
      removed outlier: 3.617A  pdb=" N   PHE A 261 " --> pdb=" O   ASP A 257 " (cutoff:3.500A)
      removed outlier: 5.666A  pdb=" N   ASP A 267 " --> pdb=" O   LYS A 263 " (cutoff:3.500A)
      removed outlier: 5.231A  pdb=" N   ALA A 268 " --> pdb=" O   HIS A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 292
    Processing helix  chain 'A' and resid 295 through 309
      removed outlier: 3.523A  pdb=" N   TYR A 299 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      Proline residue:  A 304  - end of helix
      removed outlier: 3.725A  pdb=" N   THR A 308 " --> pdb=" O   PRO A 304 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 328
      removed outlier: 4.277A  pdb=" N   VAL A 320 " --> pdb=" O   LEU A 316 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   THR A 322 " --> pdb=" O   GLN A 318 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   PHE A 323 " --> pdb=" O   GLY A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 349
      removed outlier: 4.078A  pdb=" N   THR A 340 " --> pdb=" O   GLY A 336 " (cutoff:3.500A)
      removed outlier: 4.211A  pdb=" N   ILE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   THR A 344 " --> pdb=" O   THR A 340 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 347 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 371
      removed outlier: 3.708A  pdb=" N   ILE A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.228A  pdb=" N   VAL A 366 " --> pdb=" O   MET A 362 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   HIS A 368 " --> pdb=" O   CYS A 364 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER A 369 " --> pdb=" O   MET A 365 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 381
    Processing helix  chain 'A' and resid 382 through 389
      removed outlier: 3.850A  pdb=" N   ILE A 386 " --> pdb=" O   ALA A 382 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   ILE A 389 " --> pdb=" O   MET A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 417
      removed outlier: 4.021A  pdb=" N   GLY A 396 " --> pdb=" O   ILE A 392 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   VAL A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)

    211 hydrogen bonds defined for protein.
    633 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: 0.40

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 469
        1.31 -     1.43: 763
        1.43 -     1.56: 1835
        1.56 -     1.68: 14
        1.68 -     1.81: 34
  Bond restraints: 3115
  Sorted by residual:
  bond pdb=" C16 6OU A 501 "
       pdb=" O18 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.327  1.415 -0.088 2.00e-02 2.50e+03 1.93e+01
  bond pdb=" C31 6OU A 501 "
       pdb=" O30 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.331  1.409 -0.078 2.00e-02 2.50e+03 1.51e+01
  bond pdb=" C39 6OU A 501 "
       pdb=" C40 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.497  1.569 -0.072 2.00e-02 2.50e+03 1.31e+01
  bond pdb=" C15 6OU A 501 "
       pdb=" C16 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.501  1.563 -0.062 2.00e-02 2.50e+03 9.64e+00
  bond pdb=" C38 6OU A 501 "
       pdb=" C39 6OU A 501 "
    ideal  model  delta    sigma   weight residual
    1.530  1.582 -0.052 2.00e-02 2.50e+03 6.85e+00
  ... (remaining 3110 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.96: 4145
        2.96 -     5.93: 75
        5.93 -     8.89: 11
        8.89 -    11.86: 5
       11.86 -    14.82: 1
  Bond angle restraints: 4237
  Sorted by residual:
  angle pdb=" O22 6OU A 501 "
        pdb=" P23 6OU A 501 "
        pdb=" O26 6OU A 501 "
      ideal   model   delta    sigma   weight residual
      93.95  108.77  -14.82 3.00e+00 1.11e-01 2.44e+01
  angle pdb=" N   THR A 375 "
        pdb=" CA  THR A 375 "
        pdb=" C   THR A 375 "
      ideal   model   delta    sigma   weight residual
     114.04  108.42    5.62 1.24e+00 6.50e-01 2.05e+01
  angle pdb=" N   ALA A 205 "
        pdb=" CA  ALA A 205 "
        pdb=" C   ALA A 205 "
      ideal   model   delta    sigma   weight residual
     109.81  119.02   -9.21 2.21e+00 2.05e-01 1.74e+01
  angle pdb=" C   THR A 308 "
        pdb=" N   ILE A 309 "
        pdb=" CA  ILE A 309 "
      ideal   model   delta    sigma   weight residual
     122.95  118.55    4.40 1.24e+00 6.50e-01 1.26e+01
  angle pdb=" C   THR A 281 "
        pdb=" N   LEU A 282 "
        pdb=" CA  LEU A 282 "
      ideal   model   delta    sigma   weight residual
     120.09  124.47   -4.38 1.25e+00 6.40e-01 1.23e+01
  ... (remaining 4232 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.79: 1743
       27.79 -    55.58: 80
       55.58 -    83.38: 8
       83.38 -   111.17: 1
      111.17 -   138.96: 1
  Dihedral angle restraints: 1833
    sinusoidal: 678
      harmonic: 1155
  Sorted by residual:
  dihedral pdb=" C43 6OU A 501 "
           pdb=" C44 6OU A 501 "
           pdb=" C45 6OU A 501 "
           pdb=" C46 6OU A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -178.62  -39.66 -138.96     1      3.00e+01 1.11e-03 1.87e+01
  dihedral pdb=" CA  THR A 154 "
           pdb=" C   THR A 154 "
           pdb=" N   ILE A 155 "
           pdb=" CA  ILE A 155 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.30   16.70     0      5.00e+00 4.00e-02 1.12e+01
  dihedral pdb=" CA  VAL A 235 "
           pdb=" C   VAL A 235 "
           pdb=" N   TYR A 236 "
           pdb=" CA  TYR A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -164.40  -15.60     0      5.00e+00 4.00e-02 9.74e+00
  ... (remaining 1830 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.061: 413
       0.061 -    0.121: 96
       0.121 -    0.182: 17
       0.182 -    0.242: 2
       0.242 -    0.302: 2
  Chirality restraints: 530
  Sorted by residual:
  chirality pdb=" CB  ILE A 113 "
            pdb=" CA  ILE A 113 "
            pdb=" CG1 ILE A 113 "
            pdb=" CG2 ILE A 113 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.34    0.30 2.00e-01 2.50e+01 2.29e+00
  chirality pdb=" CB  ILE A 309 "
            pdb=" CA  ILE A 309 "
            pdb=" CG1 ILE A 309 "
            pdb=" CG2 ILE A 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.35    0.30 2.00e-01 2.50e+01 2.22e+00
  chirality pdb=" C20 6OU A 501 "
            pdb=" C19 6OU A 501 "
            pdb=" C21 6OU A 501 "
            pdb=" O30 6OU A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.35    2.55   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 527 not shown)

  Planarity restraints: 516
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 355 "    0.042 5.00e-02 4.00e+02   6.31e-02 6.37e+00
        pdb=" N   PRO A 356 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A 356 "    0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A 356 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 152 "    0.041 5.00e-02 4.00e+02   6.17e-02 6.09e+00
        pdb=" N   PRO A 153 "   -0.107 5.00e-02 4.00e+02
        pdb=" CA  PRO A 153 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 153 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 205 "    0.040 5.00e-02 4.00e+02   6.05e-02 5.86e+00
        pdb=" N   PRO A 206 "   -0.105 5.00e-02 4.00e+02
        pdb=" CA  PRO A 206 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 206 "    0.034 5.00e-02 4.00e+02
  ... (remaining 513 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 966
        2.84 -     3.35: 2885
        3.35 -     3.87: 4958
        3.87 -     4.38: 5530
        4.38 -     4.90: 9590
  Nonbonded interactions: 23929
  Sorted by model distance:
  nonbonded pdb=" O   SER A 349 "
            pdb=" OG  SER A 349 "
     model   vdw
     2.322 3.040
  nonbonded pdb=" OH  TYR A 236 "
            pdb=" O   ILE A 392 "
     model   vdw
     2.387 3.040
  nonbonded pdb=" NZ  LYS A  84 "
            pdb=" OE2 GLU A 416 "
     model   vdw
     2.398 3.120
  nonbonded pdb=" OE1 GLU A 296 "
            pdb=" OH  TYR A 299 "
     model   vdw
     2.423 3.040
  nonbonded pdb=" OD2 ASP A 267 "
            pdb=" NH2 ARG A 287 "
     model   vdw
     2.424 3.120
  ... (remaining 23924 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             1.360
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     4.130
  Find NCS groups from input model:        0.010
  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:0.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    6.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8421
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      :  0.008   0.088   3115  Z= 0.355
  Angle     :  1.079  14.824   4237  Z= 0.580
  Chirality :  0.056   0.302    530
  Planarity :  0.008   0.063    516
  Dihedral  : 15.873 138.961   1101
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  8.20 %
    Favored  : 91.80 %
  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: -5.29 (0.27), residues: 403
  helix: -3.21 (0.17), residues: 348
  sheet:  None (None), residues: 0
  loop : -3.27 (0.66), residues: 55

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.026   0.002   TYR A 299 
 PHE   0.010   0.002   PHE A 210 
 HIS   0.005   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00799 /  0.35 ( 3115)
  covalent geometry    : angle       1.07876 /  0.58 ( 4237)
  hydrogen bonds       : bond        0.18326 / 11.68 (  211)
  hydrogen bonds       : angle       6.52977 /  4.43 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7844 (mtt90) cc_final: 0.7616 (mtt-85)
REVERT: A   37 HIS cc_start: 0.7841 (t70) cc_final: 0.7585 (p90)
REVERT: A  136 ASP cc_start: 0.8232 (m-30) cc_final: 0.7670 (m-30)
REVERT: A  316 LEU cc_start: 0.9196 (mt) cc_final: 0.8985 (mm)
REVERT: A  347 LEU cc_start: 0.9059 (tp) cc_final: 0.8818 (tt)
  outliers start: 0
  outliers final: 0
  residues processed: 60
  average time/residue: 0.0689
  time to fit residues: 5.0168
Evaluate side-chains
  51 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 51
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.5980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    0.5980
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.8980
   chunk 37 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 338 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.107564 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.084848 restraints weight = 4622.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2932 r_free = 0.2932 target = 0.087721 restraints weight = 2361.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.089579 restraints weight = 1588.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.090854 restraints weight = 1256.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.091572 restraints weight = 1078.208|
|-----------------------------------------------------------------------------|
r_work (final): 0.3040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3115  Z= 0.176
  Angle     :  0.603   6.330   4237  Z= 0.311
  Chirality :  0.041   0.118    530
  Planarity :  0.005   0.039    516
  Dihedral  : 10.489  96.164    459
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 11.99 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.37), residues: 403
  helix: -1.39 (0.25), residues: 350
  sheet:  None (None), residues: 0
  loop : -2.29 (0.79), residues: 53

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 397 
 TYR   0.022   0.001   TYR A 299 
 PHE   0.009   0.001   PHE A 324 
 HIS   0.002   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.18 ( 3115)
  covalent geometry    : angle       0.60281 /  0.31 ( 4237)
  hydrogen bonds       : bond        0.04758 /  3.17 (  211)
  hydrogen bonds       : angle       4.28563 /  3.00 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.077 
Fit side-chains
REVERT: A    5 ARG cc_start: 0.7653 (mtt90) cc_final: 0.7448 (mtp-110)
REVERT: A  136 ASP cc_start: 0.8240 (m-30) cc_final: 0.7720 (m-30)
REVERT: A  251 LEU cc_start: 0.7287 (OUTLIER) cc_final: 0.7036 (mm)
REVERT: A  269 MET cc_start: 0.8280 (ttm) cc_final: 0.7809 (ttp)
  outliers start: 10
  outliers final: 6
  residues processed: 60
  average time/residue: 0.0605
  time to fit residues: 4.5241
Evaluate side-chains
  50 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  259 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 17 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0980
   chunk 32 optimal weight:    0.0570
   chunk 34 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 8 optimal weight:    0.4980
   chunk 26 optimal weight:    0.1980
   overall best weight:    0.3098

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.115890 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.093196 restraints weight = 4435.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.096244 restraints weight = 2262.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.098235 restraints weight = 1516.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.099546 restraints weight = 1189.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.099827 restraints weight = 1017.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3115  Z= 0.116
  Angle     :  0.558   6.161   4237  Z= 0.282
  Chirality :  0.040   0.132    530
  Planarity :  0.004   0.033    516
  Dihedral  :  8.309  50.798    459
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 14.83 %
    Favored  : 80.76 %
  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: -1.16 (0.41), residues: 403
  helix: -0.43 (0.27), residues: 353
  sheet:  None (None), residues: 0
  loop : -2.08 (0.85), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 276 
 TYR   0.022   0.001   TYR A 299 
 PHE   0.004   0.001   PHE A 273 
 HIS   0.003   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00258 /  0.12 ( 3115)
  covalent geometry    : angle       0.55776 /  0.28 ( 4237)
  hydrogen bonds       : bond        0.03774 /  2.55 (  211)
  hydrogen bonds       : angle       3.86215 /  2.73 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.134 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8197 (m-30) cc_final: 0.7663 (m-30)
REVERT: A  251 LEU cc_start: 0.7409 (OUTLIER) cc_final: 0.7093 (mm)
REVERT: A  269 MET cc_start: 0.8187 (ttm) cc_final: 0.7882 (ttp)
  outliers start: 14
  outliers final: 9
  residues processed: 53
  average time/residue: 0.0472
  time to fit residues: 3.3557
Evaluate side-chains
  48 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 38
  time to evaluate  : 0.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  259 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 36 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 26 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 5 optimal weight:    0.8980
   chunk 6 optimal weight:    0.6980
   chunk 8 optimal weight:    0.5980
   chunk 17 optimal weight:    0.9980
   chunk 15 optimal weight:    0.5980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2957 r_free = 0.2957 target = 0.089644 restraints weight = 4498.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.092583 restraints weight = 2305.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.094531 restraints weight = 1552.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3047 r_free = 0.3047 target = 0.095712 restraints weight = 1219.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.096020 restraints weight = 1054.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.2171

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3115  Z= 0.173
  Angle     :  0.593   6.146   4237  Z= 0.297
  Chirality :  0.042   0.133    530
  Planarity :  0.004   0.031    516
  Dihedral  :  8.314  53.647    459
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 16.72 %
    Favored  : 77.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.61 (0.42), residues: 403
  helix: -0.06 (0.28), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.87 (0.88), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 276 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 324 
 HIS   0.003   0.001   HIS A  37 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00420 /  0.17 ( 3115)
  covalent geometry    : angle       0.59340 /  0.30 ( 4237)
  hydrogen bonds       : bond        0.04321 /  2.91 (  211)
  hydrogen bonds       : angle       4.00824 /  2.84 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.124 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8207 (m-30) cc_final: 0.7702 (m-30)
REVERT: A  251 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7234 (mm)
REVERT: A  269 MET cc_start: 0.8251 (ttm) cc_final: 0.7787 (ttp)
  outliers start: 17
  outliers final: 13
  residues processed: 53
  average time/residue: 0.0428
  time to fit residues: 3.0072
Evaluate side-chains
  52 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 38
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  316 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 26 optimal weight:    0.4980
   chunk 23 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9980
   chunk 13 optimal weight:    0.0370
   chunk 25 optimal weight:    0.6980
   chunk 37 optimal weight:    0.8980
   chunk 32 optimal weight:    0.3980
   overall best weight:    0.4458

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.113894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2985 r_free = 0.2985 target = 0.091371 restraints weight = 4426.996|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.094363 restraints weight = 2271.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.096333 restraints weight = 1535.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.097511 restraints weight = 1209.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.098317 restraints weight = 1048.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3081
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8404
moved from start:          0.2330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   3115  Z= 0.129
  Angle     :  0.557   6.163   4237  Z= 0.276
  Chirality :  0.040   0.128    530
  Planarity :  0.004   0.030    516
  Dihedral  :  7.711  55.897    459
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  5.99 %
    Allowed  : 17.67 %
    Favored  : 76.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.18 (0.43), residues: 403
  helix:  0.22 (0.28), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.73 (0.89), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 276 
 TYR   0.022   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 273 
 HIS   0.002   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 ( 3115)
  covalent geometry    : angle       0.55676 /  0.28 ( 4237)
  hydrogen bonds       : bond        0.03848 /  2.60 (  211)
  hydrogen bonds       : angle       3.82415 /  2.71 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 41
  time to evaluate  : 0.111 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8180 (m-30) cc_final: 0.7662 (m-30)
REVERT: A  251 LEU cc_start: 0.7478 (OUTLIER) cc_final: 0.7156 (mm)
REVERT: A  269 MET cc_start: 0.8248 (ttm) cc_final: 0.7775 (ttp)
  outliers start: 19
  outliers final: 14
  residues processed: 58
  average time/residue: 0.0435
  time to fit residues: 3.4115
Evaluate side-chains
  53 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 38
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  316 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 2 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 22 optimal weight:    0.0980
   chunk 21 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   chunk 37 optimal weight:    0.3980
   chunk 26 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.113763 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.091298 restraints weight = 4460.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3028 r_free = 0.3028 target = 0.094229 restraints weight = 2306.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.096217 restraints weight = 1554.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.097462 restraints weight = 1220.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.097973 restraints weight = 1048.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8414
moved from start:          0.2454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3115  Z= 0.133
  Angle     :  0.567   6.166   4237  Z= 0.278
  Chirality :  0.041   0.143    530
  Planarity :  0.004   0.030    516
  Dihedral  :  7.443  56.504    459
  Min Nonbonded Distance : 2.638

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  5.68 %
    Allowed  : 18.93 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.04 (0.43), residues: 403
  helix:  0.35 (0.28), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.51 (0.92), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  80 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.006   0.001   PHE A 273 
 HIS   0.002   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00316 /  0.13 ( 3115)
  covalent geometry    : angle       0.56705 /  0.28 ( 4237)
  hydrogen bonds       : bond        0.03893 /  2.63 (  211)
  hydrogen bonds       : angle       3.82923 /  2.71 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 39
  time to evaluate  : 0.105 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8192 (m-30) cc_final: 0.7647 (m-30)
REVERT: A  220 GLN cc_start: 0.8148 (mm-40) cc_final: 0.7477 (mt0)
REVERT: A  251 LEU cc_start: 0.7486 (OUTLIER) cc_final: 0.7135 (mm)
REVERT: A  269 MET cc_start: 0.8279 (ttm) cc_final: 0.7789 (ttp)
  outliers start: 18
  outliers final: 15
  residues processed: 55
  average time/residue: 0.0456
  time to fit residues: 3.3282
Evaluate side-chains
  52 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 36
  time to evaluate  : 0.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue   98 THR
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  251 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  378 ASN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 24 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0870
   chunk 25 optimal weight:    0.6980
   chunk 33 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0030
   chunk 19 optimal weight:    0.2980
   chunk 1 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0770
   chunk 10 optimal weight:    1.9990
   chunk 29 optimal weight:    0.6980
   chunk 22 optimal weight:    0.0970
   overall best weight:    0.1124

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3031 r_free = 0.3031 target = 0.094024 restraints weight = 4448.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.097184 restraints weight = 2252.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.099338 restraints weight = 1506.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.100566 restraints weight = 1173.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.101235 restraints weight = 1016.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2758

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3115  Z= 0.099
  Angle     :  0.542   6.206   4237  Z= 0.265
  Chirality :  0.039   0.118    530
  Planarity :  0.004   0.029    516
  Dihedral  :  6.959  58.759    459
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 20.50 %
    Favored  : 75.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.44), residues: 403
  helix:  0.61 (0.29), residues: 352
  sheet:  None (None), residues: 0
  loop : -1.38 (0.92), residues: 51

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  80 
 TYR   0.020   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 273 
 HIS   0.002   0.001   HIS A 114 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00202 /  0.10 ( 3115)
  covalent geometry    : angle       0.54169 /  0.27 ( 4237)
  hydrogen bonds       : bond        0.03189 /  2.16 (  211)
  hydrogen bonds       : angle       3.59218 /  2.54 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 53
  time to evaluate  : 0.068 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8131 (m-30) cc_final: 0.7832 (m-30)
REVERT: A  220 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7444 (mt0)
REVERT: A  269 MET cc_start: 0.8234 (ttm) cc_final: 0.7752 (ttp)
REVERT: A  365 MET cc_start: 0.8027 (mmm) cc_final: 0.7564 (mmm)
REVERT: A  400 VAL cc_start: 0.8769 (p) cc_final: 0.8541 (p)
  outliers start: 14
  outliers final: 9
  residues processed: 64
  average time/residue: 0.0496
  time to fit residues: 4.0559
Evaluate side-chains
  60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 51
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  259 ILE
Chi-restraints excluded: chain A residue  378 ASN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 6 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 5 optimal weight:    0.1980
   chunk 12 optimal weight:    0.0670
   chunk 16 optimal weight:    0.1980
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 37 optimal weight:    0.5980
   chunk 18 optimal weight:    0.6980
   chunk 13 optimal weight:    0.1980
   overall best weight:    0.2518

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.116622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.093346 restraints weight = 4542.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.096399 restraints weight = 2302.509|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.098518 restraints weight = 1548.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.099690 restraints weight = 1215.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.100562 restraints weight = 1055.936|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.2859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   3115  Z= 0.107
  Angle     :  0.565   8.830   4237  Z= 0.274
  Chirality :  0.040   0.126    530
  Planarity :  0.005   0.065    516
  Dihedral  :  6.828  58.440    459
  Min Nonbonded Distance : 2.649

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 21.77 %
    Favored  : 74.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.44), residues: 403
  helix:  0.69 (0.29), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.45 (0.91), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 105 
 TYR   0.021   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 273 
 HIS   0.001   0.001   HIS A 223 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.11 ( 3115)
  covalent geometry    : angle       0.56457 /  0.27 ( 4237)
  hydrogen bonds       : bond        0.03378 /  2.28 (  211)
  hydrogen bonds       : angle       3.61305 /  2.56 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 49
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8016 (m-30) cc_final: 0.7715 (m-30)
REVERT: A  220 GLN cc_start: 0.8147 (mm-40) cc_final: 0.7489 (mt0)
REVERT: A  269 MET cc_start: 0.8255 (ttm) cc_final: 0.7767 (ttp)
  outliers start: 12
  outliers final: 11
  residues processed: 59
  average time/residue: 0.0374
  time to fit residues: 2.9480
Evaluate side-chains
  60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  378 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 33 optimal weight:    0.7980
   chunk 32 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 14 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 310 ASN
A 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.106871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.083990 restraints weight = 4645.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.086976 restraints weight = 2347.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.088932 restraints weight = 1567.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.090117 restraints weight = 1228.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.090924 restraints weight = 1061.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8430
moved from start:          0.2672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3115  Z= 0.171
  Angle     :  0.632  10.325   4237  Z= 0.306
  Chirality :  0.042   0.140    530
  Planarity :  0.004   0.043    516
  Dihedral  :  7.207  55.957    459
  Min Nonbonded Distance : 2.641

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 21.77 %
    Favored  : 73.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.47 (0.44), residues: 403
  helix:  0.62 (0.29), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.25 (0.93), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 105 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 324 
 HIS   0.002   0.001   HIS A 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00418 /  0.17 ( 3115)
  covalent geometry    : angle       0.63200 /  0.31 ( 4237)
  hydrogen bonds       : bond        0.04252 /  2.85 (  211)
  hydrogen bonds       : angle       3.88816 /  2.76 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.108 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8145 (m-30) cc_final: 0.7832 (m-30)
REVERT: A  220 GLN cc_start: 0.8284 (mm-40) cc_final: 0.7543 (mt0)
REVERT: A  269 MET cc_start: 0.8326 (ttm) cc_final: 0.7805 (ttp)
REVERT: A  310 ASN cc_start: 0.9165 (t0) cc_final: 0.8877 (t0)
  outliers start: 14
  outliers final: 12
  residues processed: 58
  average time/residue: 0.0444
  time to fit residues: 3.4719
Evaluate side-chains
  56 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 44
  time to evaluate  : 0.074 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  378 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 0 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 33 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 26 optimal weight:    0.5980
   chunk 9 optimal weight:    0.7980
   chunk 13 optimal weight:    0.0970
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.4778

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 378 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.108059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.084950 restraints weight = 4561.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.087948 restraints weight = 2279.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.089901 restraints weight = 1522.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.091189 restraints weight = 1198.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.091787 restraints weight = 1029.972|
|-----------------------------------------------------------------------------|
r_work (final): 0.2988
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8315
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3115  Z= 0.137
  Angle     :  0.620  10.418   4237  Z= 0.297
  Chirality :  0.041   0.136    530
  Planarity :  0.004   0.033    516
  Dihedral  :  7.104  56.351    459
  Min Nonbonded Distance : 2.639

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  5.05 %
    Allowed  : 21.45 %
    Favored  : 73.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.54 (0.44), residues: 403
  helix:  0.67 (0.29), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.20 (0.94), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 105 
 TYR   0.022   0.001   TYR A 299 
 PHE   0.008   0.001   PHE A 273 
 HIS   0.001   0.001   HIS A  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 ( 3115)
  covalent geometry    : angle       0.61964 /  0.30 ( 4237)
  hydrogen bonds       : bond        0.03950 /  2.65 (  211)
  hydrogen bonds       : angle       3.82768 /  2.72 (  633)

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

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

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  806 Ramachandran restraints generated.
    403 Oldfield, 0 Emsley, 403 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 47
  time to evaluate  : 0.152 
Fit side-chains
REVERT: A  136 ASP cc_start: 0.8038 (m-30) cc_final: 0.7705 (m-30)
REVERT: A  220 GLN cc_start: 0.8302 (mm-40) cc_final: 0.7542 (mt0)
REVERT: A  269 MET cc_start: 0.8301 (ttm) cc_final: 0.7774 (ttp)
REVERT: A  310 ASN cc_start: 0.9136 (t0) cc_final: 0.8788 (t0)
REVERT: A  405 ASP cc_start: 0.8489 (m-30) cc_final: 0.8284 (m-30)
  outliers start: 16
  outliers final: 14
  residues processed: 61
  average time/residue: 0.0456
  time to fit residues: 3.6742
Evaluate side-chains
  60 residues out of total 317 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   54 LEU
Chi-restraints excluded: chain A residue   58 VAL
Chi-restraints excluded: chain A residue   62 VAL
Chi-restraints excluded: chain A residue  102 ILE
Chi-restraints excluded: chain A residue  106 LEU
Chi-restraints excluded: chain A residue  169 MET
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  215 TYR
Chi-restraints excluded: chain A residue  225 VAL
Chi-restraints excluded: chain A residue  244 LEU
Chi-restraints excluded: chain A residue  256 ILE
Chi-restraints excluded: chain A residue  303 LEU
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  378 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 40
   random chunks:
   chunk 35 optimal weight:    0.6980
   chunk 32 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   chunk 24 optimal weight:    0.8980
   chunk 19 optimal weight:    0.1980
   chunk 1 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.5780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 203 GLN
A 318 GLN
A 378 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.111528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2937 r_free = 0.2937 target = 0.088459 restraints weight = 4593.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.091606 restraints weight = 2262.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.093686 restraints weight = 1494.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.094979 restraints weight = 1163.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.095718 restraints weight = 996.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.2952
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   3115  Z= 0.154
  Angle     :  0.637  10.166   4237  Z= 0.306
  Chirality :  0.042   0.141    530
  Planarity :  0.004   0.029    516
  Dihedral  :  7.174  55.971    459
  Min Nonbonded Distance : 2.637

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 21.14 %
    Favored  : 74.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.52 (0.44), residues: 403
  helix:  0.65 (0.29), residues: 353
  sheet:  None (None), residues: 0
  loop : -1.24 (0.93), residues: 50

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 105 
 TYR   0.023   0.001   TYR A 299 
 PHE   0.007   0.001   PHE A 273 
 HIS   0.002   0.001   HIS A 368 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00369 /  0.15 ( 3115)
  covalent geometry    : angle       0.63708 /  0.31 ( 4237)
  hydrogen bonds       : bond        0.04084 /  2.75 (  211)
  hydrogen bonds       : angle       3.87817 /  2.76 (  633)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 676.06 seconds
wall clock time: 12 minutes 19.42 seconds (739.42 seconds total)