Starting phenix.real_space_refine
on Tue Feb  3 19:11:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rp5_24612/02_2026/7rp5_24612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rp5_24612/02_2026/7rp5_24612.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.72
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rp5_24612/02_2026/7rp5_24612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rp5_24612/02_2026/7rp5_24612.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rp5_24612/02_2026/7rp5_24612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rp5_24612/02_2026/7rp5_24612.map"
  }
  resolution = 3.72
  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=   0.005 sd=   0.034
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      40      5.16       5
     C    4333      2.51       5
     N    1085      2.21       5
     O    1120      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6578
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3303
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 443, 3303
          Classifications: {'peptide': 443}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 423}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 3275
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 440, 3275
          Classifications: {'peptide': 440}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 420}
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 1.12, per 1000 atoms: 0.17
  Number of scatterers: 6578
  At special positions: 0
  Unit cell: (72.312, 86.984, 115.28, 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      40     16.00
     O    1120      8.00
     N    1085      7.00
     C    4333      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: 0.50
  Conformation dependent library (CDL) restraints added in 214.8 milliseconds
  

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1538

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 0 sheets defined
      76.2% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 29
      removed outlier: 3.708A  pdb=" N   ASP A  29 " --> pdb=" O   LEU A  25 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 71
      removed outlier: 3.545A  pdb=" N   LEU A  33 " --> pdb=" O   ASP A  29 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A  35 " --> pdb=" O   THR A  31 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 85
    Processing helix  chain 'A' and resid 87 through 99
      removed outlier: 3.727A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   VAL A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 109 through 114
    Processing helix  chain 'A' and resid 127 through 132
    Processing helix  chain 'A' and resid 133 through 141
      removed outlier: 4.044A  pdb=" N   LEU A 139 " --> pdb=" O   GLY A 135 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   GLY A 141 " --> pdb=" O   GLY A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 147 through 164
      removed outlier: 3.937A  pdb=" N   THR A 151 " --> pdb=" O   ARG A 147 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   VAL A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   GLN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   ARG A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   MET A 161 " --> pdb=" O   ASN A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 178
      removed outlier: 3.549A  pdb=" N   ARG A 174 " --> pdb=" O   GLY A 170 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   HIS A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   THR A 176 " --> pdb=" O   GLU A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 179 through 191
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 3.924A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 233
      removed outlier: 3.802A  pdb=" N   PHE A 219 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 269
      removed outlier: 3.701A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ILE A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   LEU A 258 " --> pdb=" O   LEU A 254 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 4.174A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
      removed outlier: 3.711A  pdb=" N   TRP A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 326
      removed outlier: 3.556A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 349
      removed outlier: 3.960A  pdb=" N   THR A 343 " --> pdb=" O   ALA A 339 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   LEU A 345 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 379
      removed outlier: 3.606A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLU A 377 " --> pdb=" O   MET A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 385 through 387
      No H-bonds generated for 'chain 'A' and resid 385 through 387'
    Processing helix  chain 'A' and resid 388 through 402
      removed outlier: 4.003A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ALA A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 417
      removed outlier: 3.899A  pdb=" N   ILE A 410 " --> pdb=" O   LEU A 406 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   VAL A 412 " --> pdb=" O   GLY A 408 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   MET A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 439
      removed outlier: 3.775A  pdb=" N   THR A 439 " --> pdb=" O   LEU A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 461
      removed outlier: 4.058A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   GLN A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   LEU A 461 " --> pdb=" O   GLU A 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 22 through 27
      removed outlier: 4.101A  pdb=" N   GLU B  27 " --> pdb=" O   ARG B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 29 through 49
      removed outlier: 4.108A  pdb=" N   LEU B  33 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B  44 " --> pdb=" O   ALA B  40 " (cutoff:3.500A)
      removed outlier: 4.775A  pdb=" N   GLY B  47 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 59
    Processing helix  chain 'B' and resid 61 through 67
    Processing helix  chain 'B' and resid 68 through 72
      removed outlier: 3.818A  pdb=" N   THR B  71 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   ALA B  72 " --> pdb=" O   VAL B  69 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 68 through 72'
    Processing helix  chain 'B' and resid 74 through 99
    Processing helix  chain 'B' and resid 108 through 114
    Processing helix  chain 'B' and resid 127 through 140
      removed outlier: 3.900A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 166
      removed outlier: 4.057A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 172 through 190
      removed outlier: 3.533A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   ALA B 188 " --> pdb=" O   ALA B 184 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   PHE B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 203
      removed outlier: 4.322A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   ILE B 201 " --> pdb=" O   ILE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 204 through 208
      removed outlier: 3.882A  pdb=" N   PHE B 208 " --> pdb=" O   ARG B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 231
    Processing helix  chain 'B' and resid 251 through 266
      removed outlier: 4.099A  pdb=" N   TYR B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   PHE B 265 " --> pdb=" O   ILE B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 267 through 281
      removed outlier: 5.523A  pdb=" N   VAL B 273 " --> pdb=" O   PHE B 269 " (cutoff:3.500A)
      removed outlier: 3.966A  pdb=" N   LEU B 274 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 309
      removed outlier: 4.208A  pdb=" N   LEU B 293 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 326
      removed outlier: 3.890A  pdb=" N   GLY B 326 " --> pdb=" O   ILE B 322 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 347
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 3.811A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 402
      removed outlier: 4.305A  pdb=" N   MET B 394 " --> pdb=" O   ALA B 390 " (cutoff:3.500A)
      removed outlier: 4.207A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ALA B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 418 through 420
      No H-bonds generated for 'chain 'B' and resid 418 through 420'
    Processing helix  chain 'B' and resid 421 through 439
      removed outlier: 3.684A  pdb=" N   MET B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ILE B 426 " --> pdb=" O   ILE B 422 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   LEU B 435 " --> pdb=" O   GLY B 431 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLN B 437 " --> pdb=" O   THR B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 4.351A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)

    413 hydrogen bonds defined for protein.
    1236 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: 0.64

  Time building geometry restraints manager: 0.62 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2056
        1.34 -     1.46: 1186
        1.46 -     1.57: 3406
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6722
  Sorted by residual:
  bond pdb=" CA  ARG B 147 "
       pdb=" CB  ARG B 147 "
    ideal  model  delta    sigma   weight residual
    1.524  1.550 -0.026 1.27e-02 6.20e+03 4.11e+00
  bond pdb=" N   ASN A 270 "
       pdb=" CA  ASN A 270 "
    ideal  model  delta    sigma   weight residual
    1.457  1.481 -0.024 1.29e-02 6.01e+03 3.45e+00
  bond pdb=" C   ILE A 109 "
       pdb=" N   PRO A 110 "
    ideal  model  delta    sigma   weight residual
    1.336  1.357 -0.021 1.25e-02 6.40e+03 2.84e+00
  bond pdb=" C   LEU A 423 "
       pdb=" N   PRO A 424 "
    ideal  model  delta    sigma   weight residual
    1.336  1.354 -0.019 1.23e-02 6.61e+03 2.28e+00
  bond pdb=" CG1 ILE A 200 "
       pdb=" CD1 ILE A 200 "
    ideal  model  delta    sigma   weight residual
    1.513  1.456  0.057 3.90e-02 6.57e+02 2.12e+00
  ... (remaining 6717 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.80: 8913
        2.80 -     5.60: 176
        5.60 -     8.40: 36
        8.40 -    11.20: 8
       11.20 -    13.99: 2
  Bond angle restraints: 9135
  Sorted by residual:
  angle pdb=" N   GLU B 148 "
        pdb=" CA  GLU B 148 "
        pdb=" C   GLU B 148 "
      ideal   model   delta    sigma   weight residual
     114.75  106.91    7.84 1.26e+00 6.30e-01 3.87e+01
  angle pdb=" N   ASN B 270 "
        pdb=" CA  ASN B 270 "
        pdb=" C   ASN B 270 "
      ideal   model   delta    sigma   weight residual
     114.75  107.14    7.61 1.26e+00 6.30e-01 3.65e+01
  angle pdb=" CA  ARG B 147 "
        pdb=" CB  ARG B 147 "
        pdb=" CG  ARG B 147 "
      ideal   model   delta    sigma   weight residual
     114.10  122.43   -8.33 2.00e+00 2.50e-01 1.73e+01
  angle pdb=" CA  LEU B  60 "
        pdb=" CB  LEU B  60 "
        pdb=" CG  LEU B  60 "
      ideal   model   delta    sigma   weight residual
     116.30  130.29  -13.99 3.50e+00 8.16e-02 1.60e+01
  angle pdb=" C   PHE A 166 "
        pdb=" N   ARG A 167 "
        pdb=" CA  ARG A 167 "
      ideal   model   delta    sigma   weight residual
     122.82  128.39   -5.57 1.42e+00 4.96e-01 1.54e+01
  ... (remaining 9130 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 3435
       17.87 -    35.74: 368
       35.74 -    53.62: 73
       53.62 -    71.49: 5
       71.49 -    89.36: 2
  Dihedral angle restraints: 3883
    sinusoidal: 1446
      harmonic: 2437
  Sorted by residual:
  dihedral pdb=" CA  ARG B 147 "
           pdb=" C   ARG B 147 "
           pdb=" N   GLU B 148 "
           pdb=" CA  GLU B 148 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.21   29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  ASN A 270 "
           pdb=" C   ASN A 270 "
           pdb=" N   LYS A 271 "
           pdb=" CA  LYS A 271 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.33   24.67     0      5.00e+00 4.00e-02 2.43e+01
  dihedral pdb=" CA  GLY B  47 "
           pdb=" C   GLY B  47 "
           pdb=" N   LEU B  48 "
           pdb=" CA  LEU B  48 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.58   22.42     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 3880 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 722
       0.050 -    0.100: 286
       0.100 -    0.149: 62
       0.149 -    0.199: 6
       0.199 -    0.249: 6
  Chirality restraints: 1082
  Sorted by residual:
  chirality pdb=" CA  THR B  31 "
            pdb=" N   THR B  31 "
            pdb=" C   THR B  31 "
            pdb=" CB  THR B  31 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.28    0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CB  ILE A 109 "
            pdb=" CA  ILE A 109 "
            pdb=" CG1 ILE A 109 "
            pdb=" CG2 ILE A 109 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CG  LEU A 145 "
            pdb=" CB  LEU A 145 "
            pdb=" CD1 LEU A 145 "
            pdb=" CD2 LEU A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.37e+00
  ... (remaining 1079 not shown)

  Planarity restraints: 1145
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG B 147 "    0.015 2.00e-02 2.50e+03   2.95e-02 8.69e+00
        pdb=" C   ARG B 147 "   -0.051 2.00e-02 2.50e+03
        pdb=" O   ARG B 147 "    0.019 2.00e-02 2.50e+03
        pdb=" N   GLU B 148 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "    0.045 5.00e-02 4.00e+02   6.71e-02 7.21e+00
        pdb=" N   PRO A 150 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 149 "   -0.037 5.00e-02 4.00e+02   5.62e-02 5.05e+00
        pdb=" N   PRO B 150 "    0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO B 150 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 150 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1142 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 2265
        2.86 -     3.37: 6278
        3.37 -     3.88: 10998
        3.88 -     4.39: 12097
        4.39 -     4.90: 21118
  Nonbonded interactions: 52756
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B  94 "
            pdb=" OG  SER B 350 "
     model   vdw
     2.346 3.040
  nonbonded pdb=" OD2 ASP B  54 "
            pdb=" NH2 ARG B 147 "
     model   vdw
     2.361 3.120
  nonbonded pdb=" OE1 GLU A 111 "
            pdb=" NH1 ARG A 120 "
     model   vdw
     2.386 3.120
  nonbonded pdb=" O   ALA B  58 "
            pdb=" ND2 ASN B  62 "
     model   vdw
     2.394 3.120
  nonbonded pdb=" O   THR A 312 "
            pdb=" NE  ARG A 340 "
     model   vdw
     2.400 3.120
  ... (remaining 52751 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
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 21 through 27 or (resid 28 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 29 through 460))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.500
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.160
  Find NCS groups from input model:        0.090
  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:0.890
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.800
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
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   0.063   6722  Z= 0.222
  Angle     :  1.009  13.994   9135  Z= 0.524
  Chirality :  0.055   0.249   1082
  Planarity :  0.007   0.067   1145
  Dihedral  : 14.743  89.359   2345
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 4.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 10.77 %
    Favored  : 88.77 %
  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: -4.74 (0.20), residues: 879
  helix: -2.76 (0.14), residues: 645
  sheet:  None (None), residues: 0
  loop : -3.67 (0.29), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  98 
 TYR   0.016   0.002   TYR A  94 
 PHE   0.014   0.002   PHE A 348 
 TRP   0.011   0.001   TRP B 125 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 6722)
  covalent geometry    : angle       1.00901 ( 9135)
  hydrogen bonds       : bond        0.11296 (  413)
  hydrogen bonds       : angle       6.03898 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 158
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8225 (mmtt) cc_final: 0.6778 (tptp)
REVERT: A  126 ARG cc_start: 0.7443 (mtm-85) cc_final: 0.7173 (ptp-170)
REVERT: A  171 ASP cc_start: 0.7933 (t0) cc_final: 0.7676 (t0)
REVERT: A  245 SER cc_start: 0.9066 (t) cc_final: 0.8655 (p)
REVERT: A  246 ASP cc_start: 0.8251 (p0) cc_final: 0.8002 (p0)
REVERT: A  291 TRP cc_start: 0.8347 (t60) cc_final: 0.7902 (t60)
REVERT: A  342 ILE cc_start: 0.9090 (tt) cc_final: 0.8722 (tp)
REVERT: B   38 MET cc_start: 0.7855 (mmt) cc_final: 0.7548 (mmt)
REVERT: B   85 CYS cc_start: 0.7598 (p) cc_final: 0.6972 (t)
REVERT: B  164 ASP cc_start: 0.7632 (t0) cc_final: 0.6717 (t0)
REVERT: B  205 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7176 (ttp80)
REVERT: B  224 MET cc_start: 0.8569 (tpp) cc_final: 0.7978 (mmt)
REVERT: B  373 MET cc_start: 0.7622 (mmm) cc_final: 0.7408 (mtp)
  outliers start: 3
  outliers final: 1
  residues processed: 161
  average time/residue: 0.0676
  time to fit residues: 14.5455
Evaluate side-chains
  118 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  145 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.0060
   chunk 33 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   overall best weight:    1.4002

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

Flipped N/Q/H residues before XYZ refinement:
A 287 ASN
B 250 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.130523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.113120 restraints weight = 11141.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116111 restraints weight = 6175.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.118130 restraints weight = 4136.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.119432 restraints weight = 3146.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.120393 restraints weight = 2614.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.1500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6722  Z= 0.164
  Angle     :  0.668   8.336   9135  Z= 0.326
  Chirality :  0.041   0.159   1082
  Planarity :  0.005   0.044   1145
  Dihedral  :  5.514  42.438    934
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 16.24 %
    Favored  : 80.58 %
  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: -2.16 (0.26), residues: 879
  helix: -0.74 (0.20), residues: 639
  sheet:  None (None), residues: 0
  loop : -3.12 (0.33), residues: 240

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 403 
 TYR   0.011   0.002   TYR B 382 
 PHE   0.012   0.001   PHE B 307 
 TRP   0.009   0.001   TRP B 125 
 HIS   0.002   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 ( 6722)
  covalent geometry    : angle       0.66791 ( 9135)
  hydrogen bonds       : bond        0.03465 (  413)
  hydrogen bonds       : angle       4.17968 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 124
  time to evaluate  : 0.275 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8281 (mmtt) cc_final: 0.7018 (tptp)
REVERT: A   91 MET cc_start: 0.6594 (mtm) cc_final: 0.6305 (tmm)
REVERT: A  126 ARG cc_start: 0.7744 (mtm-85) cc_final: 0.7460 (ptp-170)
REVERT: A  164 ASP cc_start: 0.8024 (t0) cc_final: 0.7545 (t0)
REVERT: A  171 ASP cc_start: 0.7936 (t0) cc_final: 0.7712 (t0)
REVERT: A  202 GLU cc_start: 0.8766 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: A  271 LYS cc_start: 0.8236 (tttt) cc_final: 0.7718 (ttmt)
REVERT: A  290 LYS cc_start: 0.8208 (mtmm) cc_final: 0.7766 (mttm)
REVERT: A  342 ILE cc_start: 0.9134 (tt) cc_final: 0.8851 (tt)
REVERT: A  360 MET cc_start: 0.7640 (mtt) cc_final: 0.7340 (mtt)
REVERT: A  394 MET cc_start: 0.8798 (mtm) cc_final: 0.8594 (mtp)
REVERT: B   38 MET cc_start: 0.8045 (mmt) cc_final: 0.7790 (mmt)
REVERT: B  164 ASP cc_start: 0.7826 (t0) cc_final: 0.7106 (t0)
REVERT: B  205 ARG cc_start: 0.7501 (ttp-110) cc_final: 0.7148 (ttp80)
REVERT: B  210 TYR cc_start: 0.8310 (t80) cc_final: 0.8090 (t80)
REVERT: B  224 MET cc_start: 0.8703 (tpp) cc_final: 0.8459 (mmt)
REVERT: B  305 LEU cc_start: 0.8594 (tp) cc_final: 0.8323 (tp)
  outliers start: 21
  outliers final: 11
  residues processed: 142
  average time/residue: 0.0723
  time to fit residues: 14.3825
Evaluate side-chains
  125 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 114
  time to evaluate  : 0.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  212 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  319 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 27 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 66 optimal weight:    7.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
B 157 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.132502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.114970 restraints weight = 10976.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.118046 restraints weight = 6021.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.120121 restraints weight = 4030.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.121278 restraints weight = 3052.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.122275 restraints weight = 2568.819|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7930
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6722  Z= 0.132
  Angle     :  0.629   9.022   9135  Z= 0.304
  Chirality :  0.041   0.150   1082
  Planarity :  0.004   0.043   1145
  Dihedral  :  5.154  44.487    934
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 8.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.03 %
    Favored  : 76.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -1.08 (0.29), residues: 879
  helix:  0.09 (0.21), residues: 641
  sheet:  None (None), residues: 0
  loop : -2.84 (0.36), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 403 
 TYR   0.008   0.001   TYR B 100 
 PHE   0.019   0.001   PHE A 166 
 TRP   0.007   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6722)
  covalent geometry    : angle       0.62860 ( 9135)
  hydrogen bonds       : bond        0.03257 (  413)
  hydrogen bonds       : angle       3.92815 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.168 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8206 (mmtt) cc_final: 0.7054 (tptp)
REVERT: A   91 MET cc_start: 0.6548 (mtm) cc_final: 0.6323 (tmm)
REVERT: A  126 ARG cc_start: 0.7679 (mtm-85) cc_final: 0.7378 (ptp-170)
REVERT: A  164 ASP cc_start: 0.7931 (t0) cc_final: 0.7524 (t0)
REVERT: A  171 ASP cc_start: 0.7897 (t0) cc_final: 0.7680 (t0)
REVERT: A  202 GLU cc_start: 0.8650 (tm-30) cc_final: 0.8318 (tm-30)
REVERT: A  204 MET cc_start: 0.8201 (mmm) cc_final: 0.7203 (mmm)
REVERT: A  271 LYS cc_start: 0.8028 (tttt) cc_final: 0.7620 (ttmt)
REVERT: A  290 LYS cc_start: 0.8116 (mtmm) cc_final: 0.7727 (mttm)
REVERT: A  342 ILE cc_start: 0.9186 (tt) cc_final: 0.8931 (tt)
REVERT: A  347 CYS cc_start: 0.8324 (t) cc_final: 0.7237 (m)
REVERT: A  360 MET cc_start: 0.7597 (mtt) cc_final: 0.7326 (mtt)
REVERT: B   38 MET cc_start: 0.7998 (mmt) cc_final: 0.7631 (mmt)
REVERT: B   77 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7817 (tt)
REVERT: B  164 ASP cc_start: 0.7809 (t0) cc_final: 0.7225 (t0)
REVERT: B  205 ARG cc_start: 0.7489 (ttp-110) cc_final: 0.7210 (ttp80)
REVERT: B  210 TYR cc_start: 0.8279 (t80) cc_final: 0.8064 (t80)
REVERT: B  224 MET cc_start: 0.8708 (tpp) cc_final: 0.8502 (mmt)
REVERT: B  305 LEU cc_start: 0.8572 (tp) cc_final: 0.8281 (tp)
  outliers start: 23
  outliers final: 18
  residues processed: 134
  average time/residue: 0.0683
  time to fit residues: 12.7889
Evaluate side-chains
  130 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 111
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue  133 PHE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  224 MET
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 35 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 73 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 13 optimal weight:    4.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    1.1184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.131662 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.114152 restraints weight = 11052.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.117178 restraints weight = 6087.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.119187 restraints weight = 4100.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.120388 restraints weight = 3124.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121341 restraints weight = 2624.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3460
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7951
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6722  Z= 0.145
  Angle     :  0.641   9.389   9135  Z= 0.308
  Chirality :  0.041   0.154   1082
  Planarity :  0.004   0.042   1145
  Dihedral  :  5.072  44.629    934
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.57 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 19.12 %
    Favored  : 76.63 %
  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 (0.29), residues: 879
  helix:  0.45 (0.22), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.73 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 403 
 TYR   0.009   0.001   TYR B 100 
 PHE   0.010   0.001   PHE B 307 
 TRP   0.008   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 6722)
  covalent geometry    : angle       0.64078 ( 9135)
  hydrogen bonds       : bond        0.03222 (  413)
  hydrogen bonds       : angle       3.88871 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 116
  time to evaluate  : 0.254 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8298 (mmtt) cc_final: 0.7082 (tptp)
REVERT: A   91 MET cc_start: 0.6534 (mtm) cc_final: 0.6277 (tmm)
REVERT: A  164 ASP cc_start: 0.8071 (t0) cc_final: 0.7515 (t0)
REVERT: A  171 ASP cc_start: 0.7902 (t0) cc_final: 0.7532 (t0)
REVERT: A  202 GLU cc_start: 0.8605 (tm-30) cc_final: 0.8366 (tm-30)
REVERT: A  204 MET cc_start: 0.8136 (mmm) cc_final: 0.7235 (mmm)
REVERT: A  271 LYS cc_start: 0.8023 (tttt) cc_final: 0.7623 (ttmt)
REVERT: A  290 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7783 (mttm)
REVERT: A  342 ILE cc_start: 0.9196 (tt) cc_final: 0.8929 (tt)
REVERT: A  347 CYS cc_start: 0.8400 (t) cc_final: 0.7329 (m)
REVERT: A  360 MET cc_start: 0.7706 (mtt) cc_final: 0.7465 (mtt)
REVERT: B   38 MET cc_start: 0.8026 (mmt) cc_final: 0.7665 (mmt)
REVERT: B   77 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7816 (tt)
REVERT: B  164 ASP cc_start: 0.7954 (t0) cc_final: 0.7328 (t0)
REVERT: B  205 ARG cc_start: 0.7496 (ttp-110) cc_final: 0.7162 (ttp80)
REVERT: B  224 MET cc_start: 0.8751 (tpp) cc_final: 0.8528 (mmt)
REVERT: B  305 LEU cc_start: 0.8525 (tp) cc_final: 0.8218 (tp)
  outliers start: 28
  outliers final: 16
  residues processed: 136
  average time/residue: 0.0721
  time to fit residues: 13.9474
Evaluate side-chains
  127 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 110
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  319 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    0.9980
   chunk 55 optimal weight:    0.4980
   chunk 75 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 52 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 6 optimal weight:   10.0000
   chunk 49 optimal weight:    0.0060
   chunk 81 optimal weight:    2.9990
   chunk 44 optimal weight:    0.1980
   chunk 8 optimal weight:    0.8980
   overall best weight:    0.4796

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.135696 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118280 restraints weight = 10965.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.121344 restraints weight = 6010.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.123429 restraints weight = 4022.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124436 restraints weight = 3053.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.125582 restraints weight = 2606.469|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.2211

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6722  Z= 0.114
  Angle     :  0.636  10.646   9135  Z= 0.300
  Chirality :  0.040   0.164   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.810  45.079    934
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 21.55 %
    Favored  : 74.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.21 (0.30), residues: 879
  helix:  0.74 (0.22), residues: 643
  sheet:  None (None), residues: 0
  loop : -2.57 (0.37), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  64 
 TYR   0.009   0.001   TYR B 210 
 PHE   0.022   0.001   PHE A 166 
 TRP   0.009   0.001   TRP A 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 6722)
  covalent geometry    : angle       0.63633 ( 9135)
  hydrogen bonds       : bond        0.03034 (  413)
  hydrogen bonds       : angle       3.74984 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 118
  time to evaluate  : 0.281 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8197 (mmtt) cc_final: 0.7066 (tptp)
REVERT: A  164 ASP cc_start: 0.8128 (t0) cc_final: 0.7504 (t0)
REVERT: A  171 ASP cc_start: 0.7716 (t0) cc_final: 0.7392 (t0)
REVERT: A  202 GLU cc_start: 0.8421 (tm-30) cc_final: 0.8186 (tm-30)
REVERT: A  204 MET cc_start: 0.8044 (mmm) cc_final: 0.7297 (mmm)
REVERT: A  271 LYS cc_start: 0.7885 (tttt) cc_final: 0.7559 (ttmt)
REVERT: A  290 LYS cc_start: 0.8157 (mtmm) cc_final: 0.7783 (mttm)
REVERT: A  291 TRP cc_start: 0.8556 (t60) cc_final: 0.8206 (t60)
REVERT: A  342 ILE cc_start: 0.9148 (tt) cc_final: 0.8891 (tt)
REVERT: A  347 CYS cc_start: 0.8300 (t) cc_final: 0.7037 (m)
REVERT: A  360 MET cc_start: 0.7651 (mtt) cc_final: 0.7358 (mtt)
REVERT: B   38 MET cc_start: 0.7867 (mmt) cc_final: 0.7508 (mmt)
REVERT: B   77 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7819 (tt)
REVERT: B   84 LEU cc_start: 0.8781 (mt) cc_final: 0.8560 (mt)
REVERT: B  164 ASP cc_start: 0.7963 (t0) cc_final: 0.7403 (t0)
REVERT: B  205 ARG cc_start: 0.7482 (ttp-110) cc_final: 0.7204 (ttp80)
REVERT: B  210 TYR cc_start: 0.8137 (t80) cc_final: 0.7920 (t80)
REVERT: B  224 MET cc_start: 0.8692 (tpp) cc_final: 0.8394 (mmt)
REVERT: B  301 LEU cc_start: 0.7955 (tt) cc_final: 0.6904 (mt)
REVERT: B  305 LEU cc_start: 0.8479 (tp) cc_final: 0.8156 (tp)
  outliers start: 23
  outliers final: 15
  residues processed: 134
  average time/residue: 0.0684
  time to fit residues: 13.1897
Evaluate side-chains
  127 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 111
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 1 optimal weight:    0.7980
   chunk 15 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   chunk 18 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.133769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.116919 restraints weight = 11088.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.119947 restraints weight = 5997.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.121902 restraints weight = 3954.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123262 restraints weight = 2987.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.124162 restraints weight = 2469.281|
|-----------------------------------------------------------------------------|
r_work (final): 0.3501
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6722  Z= 0.128
  Angle     :  0.645  10.160   9135  Z= 0.303
  Chirality :  0.041   0.168   1082
  Planarity :  0.004   0.042   1145
  Dihedral  :  4.776  44.743    934
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.23 %
    Favored  : 94.77 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 22.15 %
    Favored  : 73.75 %
  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: -0.07 (0.30), residues: 879
  helix:  0.83 (0.22), residues: 649
  sheet:  None (None), residues: 0
  loop : -2.59 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.007   0.001   TYR B 210 
 PHE   0.011   0.001   PHE B 307 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6722)
  covalent geometry    : angle       0.64489 ( 9135)
  hydrogen bonds       : bond        0.03060 (  413)
  hydrogen bonds       : angle       3.73537 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 113
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8250 (mmtt) cc_final: 0.7101 (tptp)
REVERT: A  164 ASP cc_start: 0.8107 (t0) cc_final: 0.7613 (t0)
REVERT: A  171 ASP cc_start: 0.7732 (t0) cc_final: 0.7451 (t0)
REVERT: A  204 MET cc_start: 0.7998 (mmm) cc_final: 0.7367 (mmm)
REVERT: A  271 LYS cc_start: 0.7903 (tttt) cc_final: 0.7543 (ttmt)
REVERT: A  290 LYS cc_start: 0.8222 (mtmm) cc_final: 0.7915 (mtmm)
REVERT: A  342 ILE cc_start: 0.9174 (tt) cc_final: 0.8925 (tt)
REVERT: A  347 CYS cc_start: 0.8308 (t) cc_final: 0.7052 (m)
REVERT: A  360 MET cc_start: 0.7677 (mtt) cc_final: 0.7392 (mtt)
REVERT: B   38 MET cc_start: 0.7916 (mmt) cc_final: 0.7545 (mmt)
REVERT: B   77 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7827 (tt)
REVERT: B  164 ASP cc_start: 0.8017 (t0) cc_final: 0.7478 (t0)
REVERT: B  205 ARG cc_start: 0.7502 (ttp-110) cc_final: 0.7159 (ttp80)
REVERT: B  224 MET cc_start: 0.8740 (tpp) cc_final: 0.8491 (mmt)
REVERT: B  274 LEU cc_start: 0.8290 (OUTLIER) cc_final: 0.7942 (mm)
REVERT: B  301 LEU cc_start: 0.7994 (tt) cc_final: 0.6980 (mt)
REVERT: B  305 LEU cc_start: 0.8582 (tp) cc_final: 0.8290 (tp)
  outliers start: 27
  outliers final: 17
  residues processed: 133
  average time/residue: 0.0632
  time to fit residues: 12.2756
Evaluate side-chains
  132 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 113
  time to evaluate  : 0.234 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 63 optimal weight:    0.0970
   chunk 55 optimal weight:    0.6980
   chunk 31 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9990
   chunk 75 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.135614 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118272 restraints weight = 10969.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121395 restraints weight = 6053.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.123403 restraints weight = 4043.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.124774 restraints weight = 3089.724|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.125603 restraints weight = 2555.207|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7882
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6722  Z= 0.121
  Angle     :  0.641  10.209   9135  Z= 0.302
  Chirality :  0.040   0.143   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.689  43.723    934
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 23.98 %
    Favored  : 72.53 %
  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 (0.30), residues: 879
  helix:  0.94 (0.22), residues: 645
  sheet:  None (None), residues: 0
  loop : -2.61 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.007   0.001   TYR B 210 
 PHE   0.010   0.001   PHE B 307 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 6722)
  covalent geometry    : angle       0.64128 ( 9135)
  hydrogen bonds       : bond        0.03007 (  413)
  hydrogen bonds       : angle       3.68340 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 117
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7189 (mp) cc_final: 0.6852 (pt)
REVERT: A   55 LYS cc_start: 0.8255 (mmtt) cc_final: 0.7073 (tptp)
REVERT: A  164 ASP cc_start: 0.8063 (t0) cc_final: 0.7548 (t0)
REVERT: A  171 ASP cc_start: 0.7689 (t0) cc_final: 0.7459 (t0)
REVERT: A  204 MET cc_start: 0.8033 (mmm) cc_final: 0.7473 (mmm)
REVERT: A  271 LYS cc_start: 0.7861 (tttt) cc_final: 0.7547 (ttmt)
REVERT: A  290 LYS cc_start: 0.8265 (mtmm) cc_final: 0.7951 (mtmm)
REVERT: A  342 ILE cc_start: 0.9163 (tt) cc_final: 0.8922 (tt)
REVERT: A  360 MET cc_start: 0.7649 (mtt) cc_final: 0.7346 (mtt)
REVERT: A  382 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.8123 (m-10)
REVERT: B   38 MET cc_start: 0.7885 (mmt) cc_final: 0.7531 (mmt)
REVERT: B   77 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7807 (tt)
REVERT: B  164 ASP cc_start: 0.8055 (t0) cc_final: 0.7482 (t0)
REVERT: B  205 ARG cc_start: 0.7505 (ttp-110) cc_final: 0.7167 (ttp80)
REVERT: B  224 MET cc_start: 0.8729 (tpp) cc_final: 0.8483 (mmt)
REVERT: B  274 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7870 (mm)
REVERT: B  301 LEU cc_start: 0.7965 (tt) cc_final: 0.6956 (mt)
REVERT: B  305 LEU cc_start: 0.8471 (tp) cc_final: 0.8158 (tp)
REVERT: B  367 LEU cc_start: 0.9019 (tt) cc_final: 0.8648 (tt)
REVERT: B  385 GLU cc_start: 0.7280 (tp30) cc_final: 0.6975 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 134
  average time/residue: 0.0657
  time to fit residues: 12.5287
Evaluate side-chains
  135 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  178 LEU
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  382 TYR
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 86 optimal weight:    5.9990
   chunk 18 optimal weight:    5.9990
   chunk 10 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9980
   chunk 44 optimal weight:    7.9990
   chunk 71 optimal weight:    7.9990
   chunk 38 optimal weight:    0.5980
   overall best weight:    1.0784

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.132725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.115225 restraints weight = 11098.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118260 restraints weight = 6158.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.120254 restraints weight = 4135.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121554 restraints weight = 3164.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.122170 restraints weight = 2635.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3470
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6722  Z= 0.145
  Angle     :  0.665  10.196   9135  Z= 0.314
  Chirality :  0.041   0.152   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.779  44.381    934
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.80 %
    Favored  : 94.20 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 23.98 %
    Favored  : 72.08 %
  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:  0.08 (0.30), residues: 879
  helix:  0.93 (0.22), residues: 649
  sheet:  None (None), residues: 0
  loop : -2.48 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.011   0.001   PHE B 307 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 6722)
  covalent geometry    : angle       0.66530 ( 9135)
  hydrogen bonds       : bond        0.03147 (  413)
  hydrogen bonds       : angle       3.72088 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 114
  time to evaluate  : 0.238 
Fit side-chains
REVERT: A   55 LYS cc_start: 0.8374 (mmtt) cc_final: 0.7108 (tptp)
REVERT: A  164 ASP cc_start: 0.8102 (t0) cc_final: 0.7604 (t0)
REVERT: A  171 ASP cc_start: 0.7721 (t0) cc_final: 0.7480 (t0)
REVERT: A  204 MET cc_start: 0.8012 (mmm) cc_final: 0.7147 (mtp)
REVERT: A  290 LYS cc_start: 0.8303 (mtmm) cc_final: 0.7988 (mtmm)
REVERT: A  342 ILE cc_start: 0.9205 (tt) cc_final: 0.8937 (tt)
REVERT: A  360 MET cc_start: 0.7687 (mtt) cc_final: 0.7388 (mtt)
REVERT: A  382 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8179 (m-10)
REVERT: B   38 MET cc_start: 0.7948 (mmt) cc_final: 0.7604 (mmt)
REVERT: B   65 MET cc_start: 0.7155 (mtm) cc_final: 0.6951 (mtp)
REVERT: B   77 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7822 (tt)
REVERT: B  164 ASP cc_start: 0.8088 (t0) cc_final: 0.7608 (t0)
REVERT: B  205 ARG cc_start: 0.7508 (ttp-110) cc_final: 0.7166 (ttp80)
REVERT: B  224 MET cc_start: 0.8769 (tpp) cc_final: 0.8510 (mmt)
REVERT: B  274 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.7845 (mm)
REVERT: B  301 LEU cc_start: 0.8011 (tt) cc_final: 0.7049 (mt)
REVERT: B  305 LEU cc_start: 0.8439 (tp) cc_final: 0.8095 (tp)
REVERT: B  367 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8649 (tt)
REVERT: B  385 GLU cc_start: 0.7421 (tp30) cc_final: 0.7061 (tt0)
  outliers start: 26
  outliers final: 18
  residues processed: 130
  average time/residue: 0.0592
  time to fit residues: 11.2921
Evaluate side-chains
  134 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 112
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  382 TYR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  367 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 26 optimal weight:    7.9990
   chunk 11 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.134191 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.116436 restraints weight = 11167.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.119479 restraints weight = 6196.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121519 restraints weight = 4178.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.122772 restraints weight = 3192.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.123457 restraints weight = 2675.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7916
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6722  Z= 0.134
  Angle     :  0.662  10.021   9135  Z= 0.312
  Chirality :  0.041   0.155   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.723  43.888    934
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.12 %
    Favored  : 94.88 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 24.28 %
    Favored  : 72.23 %
  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:  0.16 (0.30), residues: 879
  helix:  0.98 (0.22), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.42 (0.37), residues: 231

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.008   0.001   TYR B 419 
 PHE   0.016   0.001   PHE A 132 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 6722)
  covalent geometry    : angle       0.66161 ( 9135)
  hydrogen bonds       : bond        0.03107 (  413)
  hydrogen bonds       : angle       3.69652 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7267 (mp) cc_final: 0.6959 (pt)
REVERT: A   55 LYS cc_start: 0.8373 (mmtt) cc_final: 0.7073 (tptp)
REVERT: A  164 ASP cc_start: 0.8072 (t0) cc_final: 0.7574 (t0)
REVERT: A  171 ASP cc_start: 0.7737 (t0) cc_final: 0.7504 (t0)
REVERT: A  204 MET cc_start: 0.8037 (mmm) cc_final: 0.7224 (mtp)
REVERT: A  290 LYS cc_start: 0.8288 (mtmm) cc_final: 0.7965 (mtmm)
REVERT: A  342 ILE cc_start: 0.9180 (tt) cc_final: 0.8917 (tt)
REVERT: A  360 MET cc_start: 0.7692 (mtt) cc_final: 0.7362 (mtt)
REVERT: A  382 TYR cc_start: 0.8552 (OUTLIER) cc_final: 0.8094 (m-10)
REVERT: B   38 MET cc_start: 0.7923 (mmt) cc_final: 0.7585 (mmt)
REVERT: B   77 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7853 (tt)
REVERT: B  164 ASP cc_start: 0.8087 (t0) cc_final: 0.7628 (t0)
REVERT: B  205 ARG cc_start: 0.7551 (ttp-110) cc_final: 0.7270 (ttp80)
REVERT: B  274 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7796 (mm)
REVERT: B  301 LEU cc_start: 0.8050 (tt) cc_final: 0.7110 (mt)
REVERT: B  305 LEU cc_start: 0.8418 (tp) cc_final: 0.8057 (tp)
REVERT: B  367 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8653 (tt)
REVERT: B  385 GLU cc_start: 0.7331 (tp30) cc_final: 0.7002 (tt0)
  outliers start: 23
  outliers final: 19
  residues processed: 128
  average time/residue: 0.0592
  time to fit residues: 11.1331
Evaluate side-chains
  134 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  382 TYR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 87 optimal weight:    0.4980
   chunk 43 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 26 optimal weight:    9.9990
   chunk 20 optimal weight:    0.9990
   chunk 85 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.135669 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118284 restraints weight = 11031.716|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.121284 restraints weight = 6140.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123311 restraints weight = 4119.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124571 restraints weight = 3134.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3518 r_free = 0.3518 target = 0.125548 restraints weight = 2613.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3536
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6722  Z= 0.121
  Angle     :  0.657  13.232   9135  Z= 0.306
  Chirality :  0.040   0.152   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.579  41.679    934
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.01 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 24.58 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.32 (0.30), residues: 879
  helix:  1.12 (0.22), residues: 645
  sheet:  None (None), residues: 0
  loop : -2.39 (0.38), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 340 
 TYR   0.008   0.001   TYR B 210 
 PHE   0.018   0.001   PHE A 132 
 TRP   0.006   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6722)
  covalent geometry    : angle       0.65726 ( 9135)
  hydrogen bonds       : bond        0.02985 (  413)
  hydrogen bonds       : angle       3.61779 ( 1236)

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

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

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1758 Ramachandran restraints generated.
    879 Oldfield, 0 Emsley, 879 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 117
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7314 (mp) cc_final: 0.6973 (pt)
REVERT: A   55 LYS cc_start: 0.8383 (mmtt) cc_final: 0.7085 (tptp)
REVERT: A  164 ASP cc_start: 0.7982 (t0) cc_final: 0.7402 (t0)
REVERT: A  171 ASP cc_start: 0.7675 (t0) cc_final: 0.7458 (t0)
REVERT: A  204 MET cc_start: 0.8019 (mmm) cc_final: 0.7236 (mtp)
REVERT: A  245 SER cc_start: 0.8714 (t) cc_final: 0.8299 (p)
REVERT: A  290 LYS cc_start: 0.8283 (mtmm) cc_final: 0.7951 (mtmm)
REVERT: A  342 ILE cc_start: 0.9168 (tt) cc_final: 0.8930 (tt)
REVERT: A  360 MET cc_start: 0.7652 (mtt) cc_final: 0.7292 (mtt)
REVERT: A  382 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.8008 (m-10)
REVERT: A  401 SER cc_start: 0.9409 (t) cc_final: 0.9145 (t)
REVERT: B   38 MET cc_start: 0.7913 (mmt) cc_final: 0.7548 (mmt)
REVERT: B   77 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7737 (tt)
REVERT: B  164 ASP cc_start: 0.8056 (t0) cc_final: 0.7587 (t0)
REVERT: B  274 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7703 (mm)
REVERT: B  294 MET cc_start: 0.8036 (tmm) cc_final: 0.7830 (tmm)
REVERT: B  301 LEU cc_start: 0.7908 (tt) cc_final: 0.7059 (mt)
REVERT: B  305 LEU cc_start: 0.8436 (tp) cc_final: 0.8093 (tp)
REVERT: B  367 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8649 (tt)
REVERT: B  385 GLU cc_start: 0.7233 (tp30) cc_final: 0.6958 (tt0)
  outliers start: 24
  outliers final: 18
  residues processed: 135
  average time/residue: 0.0571
  time to fit residues: 11.3260
Evaluate side-chains
  135 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 113
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 THR
Chi-restraints excluded: chain A residue   60 LEU
Chi-restraints excluded: chain A residue   71 THR
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  260 ILE
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  382 TYR
Chi-restraints excluded: chain B residue   77 LEU
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  250 ASN
Chi-restraints excluded: chain B residue  262 PHE
Chi-restraints excluded: chain B residue  274 LEU
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  367 LEU
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 59 optimal weight:    0.0170
   chunk 29 optimal weight:    4.9990
   chunk 68 optimal weight:    0.7980
   chunk 15 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9990
   chunk 35 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 44 optimal weight:    0.7980
   chunk 82 optimal weight:    6.9990
   chunk 73 optimal weight:    5.9990
   overall best weight:    0.5620

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.136300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.118870 restraints weight = 11015.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.121901 restraints weight = 6102.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.123940 restraints weight = 4111.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.124952 restraints weight = 3131.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.126067 restraints weight = 2672.608|
|-----------------------------------------------------------------------------|
r_work (final): 0.3527
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.2768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6722  Z= 0.120
  Angle     :  0.661  12.837   9135  Z= 0.308
  Chirality :  0.040   0.145   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.529  40.175    934
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 24.73 %
    Favored  : 72.08 %
  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:  0.37 (0.30), residues: 879
  helix:  1.16 (0.22), residues: 645
  sheet:  None (None), residues: 0
  loop : -2.39 (0.37), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 205 
 TYR   0.012   0.001   TYR B 419 
 PHE   0.016   0.001   PHE A 132 
 TRP   0.006   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6722)
  covalent geometry    : angle       0.66099 ( 9135)
  hydrogen bonds       : bond        0.02959 (  413)
  hydrogen bonds       : angle       3.58500 ( 1236)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1047.98 seconds
wall clock time: 18 minutes 49.58 seconds (1129.58 seconds total)