Starting phenix.real_space_refine
on Tue Mar 11 18:12:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rp5_24612/03_2025/7rp5_24612.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rp5_24612/03_2025/7rp5_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rp5_24612/03_2025/7rp5_24612.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rp5_24612/03_2025/7rp5_24612.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rp5_24612/03_2025/7rp5_24612.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rp5_24612/03_2025/7rp5_24612.cif"
  }
  resolution = 3.72
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.33, per 1000 atoms: 0.66
  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: 1.49
  Conformation dependent library (CDL) restraints added in 914.9 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: 0.60
  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: 1.72

  Time building geometry restraints manager: 1.80 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:                  0.010
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     18.590
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.710
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.430
-------------------------------------------------------------------------------
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= 0.313
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.011   0.001   TRP B 125 
 HIS   0.004   0.001   HIS A 284 
 PHE   0.014   0.002   PHE A 348 
 TYR   0.016   0.002   TYR A  94 
 ARG   0.002   0.000   ARG B  98 

*********************** 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  : 0.667 
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: 0.6716 (t0)
REVERT: B  205 ARG cc_start: 0.7425 (ttp-110) cc_final: 0.7176 (ttp80)
REVERT: B  224 MET cc_start: 0.8570 (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: 0.1901
  time to fit residues: 40.3843
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  : 0.702 
-------------------------------------------------------------------------------
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 74 optimal weight:    7.9990
   chunk 66 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    2.7788

-------------------------------------------------------------------------------
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 = 0.3514 r_free = 0.3514 target = 0.124850 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.107251 restraints weight = 11160.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.110105 restraints weight = 6259.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.112030 restraints weight = 4257.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8091
moved from start:          0.1837

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.055   6722  Z= 0.421
  Angle     :  0.780   8.709   9135  Z= 0.382
  Chirality :  0.045   0.167   1082
  Planarity :  0.006   0.047   1145
  Dihedral  :  5.964  47.119    934
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.48 %
    Favored  : 93.52 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 17.45 %
    Favored  : 78.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.26), residues: 879
  helix: -0.99 (0.19), residues: 655
  sheet:  None (None), residues: 0
  loop : -3.44 (0.32), residues: 224

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 125 
 HIS   0.003   0.001   HIS B 284 
 PHE   0.017   0.002   PHE B 328 
 TYR   0.014   0.002   TYR B 100 
 ARG   0.005   0.001   ARG B 403 

*********************** 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
  146 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 121
  time to evaluate  : 0.763 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8323 (m-30) cc_final: 0.8042 (m-30)
REVERT: A   55 LYS cc_start: 0.8337 (mmtt) cc_final: 0.7027 (tptp)
REVERT: A   91 MET cc_start: 0.6769 (mtm) cc_final: 0.6424 (tmm)
REVERT: A  164 ASP cc_start: 0.8071 (t0) cc_final: 0.7601 (t0)
REVERT: A  171 ASP cc_start: 0.8095 (t0) cc_final: 0.7876 (t0)
REVERT: A  271 LYS cc_start: 0.8279 (tttt) cc_final: 0.7699 (ttmt)
REVERT: A  290 LYS cc_start: 0.8240 (mtmm) cc_final: 0.7806 (mttm)
REVERT: A  360 MET cc_start: 0.7781 (mtt) cc_final: 0.7496 (mtt)
REVERT: A  456 GLN cc_start: 0.7630 (tt0) cc_final: 0.7388 (tt0)
REVERT: B   38 MET cc_start: 0.8170 (mmt) cc_final: 0.7963 (mmt)
REVERT: B  164 ASP cc_start: 0.7952 (t0) cc_final: 0.7340 (t0)
REVERT: B  205 ARG cc_start: 0.7585 (ttp-110) cc_final: 0.7190 (ttp80)
REVERT: B  305 LEU cc_start: 0.8648 (tp) cc_final: 0.8416 (tp)
  outliers start: 25
  outliers final: 16
  residues processed: 142
  average time/residue: 0.1548
  time to fit residues: 30.6226
Evaluate side-chains
  125 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 109
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
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  178 LEU
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  327 ASN
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  435 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  319 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 87 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 44 optimal weight:   20.0000
   chunk 86 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 14 optimal weight:    0.0970
   chunk 62 optimal weight:    0.4980
   chunk 27 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
B 157 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 = 0.3608 r_free = 0.3608 target = 0.131849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.114523 restraints weight = 11034.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.117616 restraints weight = 5990.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.119676 restraints weight = 3975.460|
|-----------------------------------------------------------------------------|
r_work (final): 0.3441
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6722  Z= 0.170
  Angle     :  0.639   9.076   9135  Z= 0.307
  Chirality :  0.040   0.161   1082
  Planarity :  0.004   0.043   1145
  Dihedral  :  5.314  45.546    934
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 21.85 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.29), residues: 879
  helix: -0.01 (0.21), residues: 643
  sheet:  None (None), residues: 0
  loop : -2.99 (0.35), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 125 
 HIS   0.001   0.000   HIS A 284 
 PHE   0.022   0.001   PHE A 166 
 TYR   0.008   0.001   TYR B 229 
 ARG   0.002   0.000   ARG B 403 

*********************** 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
  138 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 121
  time to evaluate  : 0.710 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8377 (m-30) cc_final: 0.8157 (m-30)
REVERT: A   55 LYS cc_start: 0.8251 (mmtt) cc_final: 0.7006 (tptp)
REVERT: A   91 MET cc_start: 0.6615 (mtm) cc_final: 0.6368 (tmm)
REVERT: A  164 ASP cc_start: 0.7974 (t0) cc_final: 0.7614 (t0)
REVERT: A  171 ASP cc_start: 0.7956 (t0) cc_final: 0.7595 (t0)
REVERT: A  271 LYS cc_start: 0.8140 (tttt) cc_final: 0.7582 (ttmt)
REVERT: A  290 LYS cc_start: 0.8124 (mtmm) cc_final: 0.7724 (mttm)
REVERT: A  342 ILE cc_start: 0.9183 (tt) cc_final: 0.8903 (tt)
REVERT: A  360 MET cc_start: 0.7640 (mtt) cc_final: 0.7296 (mtt)
REVERT: A  401 SER cc_start: 0.9452 (t) cc_final: 0.9221 (t)
REVERT: B   38 MET cc_start: 0.7990 (mmt) cc_final: 0.7674 (mmt)
REVERT: B  164 ASP cc_start: 0.7864 (t0) cc_final: 0.7290 (t0)
REVERT: B  205 ARG cc_start: 0.7504 (ttp-110) cc_final: 0.7208 (ttp80)
REVERT: B  250 ASN cc_start: 0.8676 (OUTLIER) cc_final: 0.8465 (p0)
  outliers start: 17
  outliers final: 12
  residues processed: 131
  average time/residue: 0.1553
  time to fit residues: 28.4998
Evaluate side-chains
  121 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  224 MET
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 1 optimal weight:    3.9990
   chunk 41 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9980
   chunk 21 optimal weight:    5.9990
   chunk 67 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.132514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114937 restraints weight = 11277.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.118054 restraints weight = 6181.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.120119 restraints weight = 4110.744|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2064

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6722  Z= 0.192
  Angle     :  0.638   9.398   9135  Z= 0.305
  Chirality :  0.041   0.154   1082
  Planarity :  0.004   0.042   1145
  Dihedral  :  5.047  43.113    934
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 22.46 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.29), residues: 879
  helix:  0.42 (0.22), residues: 640
  sheet:  None (None), residues: 0
  loop : -2.67 (0.37), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 125 
 HIS   0.002   0.000   HIS A 284 
 PHE   0.009   0.001   PHE B 317 
 TYR   0.007   0.001   TYR B 229 
 ARG   0.002   0.000   ARG A  64 

*********************** 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
  141 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 116
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8345 (m-30) cc_final: 0.8095 (m-30)
REVERT: A   55 LYS cc_start: 0.8289 (mmtt) cc_final: 0.7053 (tptp)
REVERT: A   91 MET cc_start: 0.6628 (mtm) cc_final: 0.6364 (tmm)
REVERT: A  164 ASP cc_start: 0.7969 (t0) cc_final: 0.7519 (t0)
REVERT: A  171 ASP cc_start: 0.7962 (t0) cc_final: 0.7610 (t0)
REVERT: A  271 LYS cc_start: 0.8021 (tttt) cc_final: 0.7634 (ttmt)
REVERT: A  290 LYS cc_start: 0.8132 (mtmm) cc_final: 0.7748 (mttm)
REVERT: A  342 ILE cc_start: 0.9188 (tt) cc_final: 0.8913 (tt)
REVERT: A  360 MET cc_start: 0.7728 (mtt) cc_final: 0.7444 (mtt)
REVERT: B   38 MET cc_start: 0.8003 (mmt) cc_final: 0.7628 (mmt)
REVERT: B  164 ASP cc_start: 0.7924 (t0) cc_final: 0.7321 (t0)
REVERT: B  205 ARG cc_start: 0.7529 (ttp-110) cc_final: 0.7177 (ttp80)
REVERT: B  274 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7973 (mm)
REVERT: B  305 LEU cc_start: 0.8471 (tp) cc_final: 0.8192 (tp)
  outliers start: 25
  outliers final: 16
  residues processed: 132
  average time/residue: 0.1581
  time to fit residues: 29.1417
Evaluate side-chains
  125 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
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  133 PHE
Chi-restraints excluded: chain A residue  136 LEU
Chi-restraints excluded: chain A residue  145 LEU
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  224 MET
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  383 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.8980
   chunk 75 optimal weight:    0.6980
   chunk 62 optimal weight:    0.4980
   chunk 52 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 79 optimal weight:    0.7980
   chunk 39 optimal weight:    0.6980
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.133077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3387 r_free = 0.3387 target = 0.115931 restraints weight = 10963.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.118988 restraints weight = 6011.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.121067 restraints weight = 4007.463|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6722  Z= 0.185
  Angle     :  0.629   9.599   9135  Z= 0.299
  Chirality :  0.040   0.153   1082
  Planarity :  0.004   0.042   1145
  Dihedral  :  4.875  39.227    934
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 22.76 %
    Favored  : 73.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.30), residues: 879
  helix:  0.62 (0.22), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.52 (0.37), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 125 
 HIS   0.001   0.000   HIS A 284 
 PHE   0.008   0.001   PHE B 307 
 TYR   0.008   0.001   TYR B 210 
 ARG   0.002   0.000   ARG A 340 

*********************** 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: 26
    poor density    : 115
  time to evaluate  : 0.733 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8407 (m-30) cc_final: 0.8165 (m-30)
REVERT: A   55 LYS cc_start: 0.8284 (mmtt) cc_final: 0.7070 (tptp)
REVERT: A   91 MET cc_start: 0.6603 (mtm) cc_final: 0.6364 (tmm)
REVERT: A  143 MET cc_start: 0.7449 (tpp) cc_final: 0.7232 (tpp)
REVERT: A  164 ASP cc_start: 0.8051 (t0) cc_final: 0.7447 (t0)
REVERT: A  171 ASP cc_start: 0.7840 (t0) cc_final: 0.7500 (t0)
REVERT: A  271 LYS cc_start: 0.7981 (tttt) cc_final: 0.7628 (ttmt)
REVERT: A  290 LYS cc_start: 0.8133 (mtmm) cc_final: 0.7746 (mttm)
REVERT: A  342 ILE cc_start: 0.9164 (tt) cc_final: 0.8880 (tt)
REVERT: A  360 MET cc_start: 0.7714 (mtt) cc_final: 0.7444 (mtt)
REVERT: B   38 MET cc_start: 0.7950 (mmt) cc_final: 0.7579 (mmt)
REVERT: B  164 ASP cc_start: 0.8027 (t0) cc_final: 0.7493 (t0)
REVERT: B  205 ARG cc_start: 0.7531 (ttp-110) cc_final: 0.7183 (ttp80)
REVERT: B  274 LEU cc_start: 0.8309 (OUTLIER) cc_final: 0.7974 (mm)
REVERT: B  305 LEU cc_start: 0.8501 (tp) cc_final: 0.8234 (tp)
  outliers start: 26
  outliers final: 19
  residues processed: 134
  average time/residue: 0.1514
  time to fit residues: 28.6512
Evaluate side-chains
  133 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 113
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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  293 LEU
Chi-restraints excluded: chain A residue  435 LEU
Chi-restraints excluded: chain B residue  130 VAL
Chi-restraints excluded: chain B residue  162 VAL
Chi-restraints excluded: chain B residue  224 MET
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  382 TYR
Chi-restraints excluded: chain B residue  383 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 77 optimal weight:    0.2980
   chunk 64 optimal weight:    0.5980
   chunk 80 optimal weight:    0.0970
   chunk 85 optimal weight:    0.6980
   overall best weight:    0.4578

-------------------------------------------------------------------------------
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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.135399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.118209 restraints weight = 10880.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.121311 restraints weight = 5994.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123360 restraints weight = 4001.787|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6722  Z= 0.171
  Angle     :  0.629   9.410   9135  Z= 0.297
  Chirality :  0.040   0.157   1082
  Planarity :  0.003   0.042   1145
  Dihedral  :  4.684  35.674    934
  Min Nonbonded Distance : 2.309

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 23.98 %
    Favored  : 72.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.30), residues: 879
  helix:  0.80 (0.22), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.55 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 125 
 HIS   0.001   0.000   HIS B  70 
 PHE   0.010   0.001   PHE B 307 
 TYR   0.007   0.001   TYR B 229 
 ARG   0.002   0.000   ARG B 403 

*********************** 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
  143 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 119
  time to evaluate  : 0.688 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8422 (m-30) cc_final: 0.8164 (m-30)
REVERT: A   55 LYS cc_start: 0.8239 (mmtt) cc_final: 0.7073 (tptp)
REVERT: A   91 MET cc_start: 0.6624 (mtm) cc_final: 0.6346 (tmm)
REVERT: A  164 ASP cc_start: 0.8094 (t0) cc_final: 0.7531 (t0)
REVERT: A  171 ASP cc_start: 0.7762 (t0) cc_final: 0.7474 (t0)
REVERT: A  202 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8172 (tm-30)
REVERT: A  271 LYS cc_start: 0.7893 (tttt) cc_final: 0.7532 (ttmt)
REVERT: A  290 LYS cc_start: 0.8119 (mtmm) cc_final: 0.7753 (mttm)
REVERT: A  342 ILE cc_start: 0.9156 (tt) cc_final: 0.8892 (tt)
REVERT: A  360 MET cc_start: 0.7643 (mtt) cc_final: 0.7332 (mtt)
REVERT: B   38 MET cc_start: 0.7912 (mmt) cc_final: 0.7551 (mmt)
REVERT: B  164 ASP cc_start: 0.7985 (t0) cc_final: 0.7428 (t0)
REVERT: B  205 ARG cc_start: 0.7517 (ttp-110) cc_final: 0.7173 (ttp80)
REVERT: B  274 LEU cc_start: 0.8242 (OUTLIER) cc_final: 0.7848 (mm)
REVERT: B  301 LEU cc_start: 0.7913 (tt) cc_final: 0.6844 (mt)
REVERT: B  305 LEU cc_start: 0.8547 (tp) cc_final: 0.8208 (tp)
  outliers start: 24
  outliers final: 18
  residues processed: 137
  average time/residue: 0.1490
  time to fit residues: 28.6678
Evaluate side-chains
  128 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.677 
-------------------------------------------------------------------------------
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  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  293 LEU
Chi-restraints excluded: chain A residue  376 VAL
Chi-restraints excluded: chain A residue  435 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  382 TYR
Chi-restraints excluded: chain B residue  383 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 59 optimal weight:    0.8980
   chunk 62 optimal weight:    0.5980
   chunk 0 optimal weight:   20.0000
   chunk 72 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 53 optimal weight:    0.9980
   chunk 75 optimal weight:    0.9980
   chunk 33 optimal weight:    4.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.134057 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.116700 restraints weight = 10933.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.119744 restraints weight = 6115.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121529 restraints weight = 4106.839|
|-----------------------------------------------------------------------------|
r_work (final): 0.3459
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7939
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6722  Z= 0.200
  Angle     :  0.650  11.153   9135  Z= 0.304
  Chirality :  0.041   0.164   1082
  Planarity :  0.004   0.042   1145
  Dihedral  :  4.680  34.918    934
  Min Nonbonded Distance : 2.318

Molprobity Statistics.
  All-atom Clashscore : 10.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 24.43 %
    Favored  : 71.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.30), residues: 879
  helix:  0.86 (0.22), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.42 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 125 
 HIS   0.001   0.000   HIS B 284 
 PHE   0.010   0.001   PHE B 307 
 TYR   0.006   0.001   TYR B 229 
 ARG   0.002   0.000   ARG A 340 

*********************** 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
  137 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 110
  time to evaluate  : 0.742 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8430 (m-30) cc_final: 0.8190 (m-30)
REVERT: A   55 LYS cc_start: 0.8260 (mmtt) cc_final: 0.7092 (tptp)
REVERT: A   91 MET cc_start: 0.6629 (mtm) cc_final: 0.6390 (tmm)
REVERT: A  164 ASP cc_start: 0.8080 (t0) cc_final: 0.7581 (t0)
REVERT: A  171 ASP cc_start: 0.7757 (t0) cc_final: 0.7474 (t0)
REVERT: A  202 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8194 (tm-30)
REVERT: A  271 LYS cc_start: 0.7868 (tttt) cc_final: 0.7520 (ttmt)
REVERT: A  290 LYS cc_start: 0.8158 (mtmm) cc_final: 0.7774 (mttm)
REVERT: A  342 ILE cc_start: 0.9179 (tt) cc_final: 0.8937 (tt)
REVERT: A  360 MET cc_start: 0.7645 (mtt) cc_final: 0.7364 (mtt)
REVERT: A  382 TYR cc_start: 0.8550 (OUTLIER) cc_final: 0.8157 (m-10)
REVERT: B   38 MET cc_start: 0.7964 (mmt) cc_final: 0.7596 (mmt)
REVERT: B  164 ASP cc_start: 0.8050 (t0) cc_final: 0.7510 (t0)
REVERT: B  205 ARG cc_start: 0.7525 (ttp-110) cc_final: 0.7180 (ttp80)
REVERT: B  274 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7854 (mm)
REVERT: B  301 LEU cc_start: 0.7923 (tt) cc_final: 0.6856 (mt)
REVERT: B  305 LEU cc_start: 0.8511 (tp) cc_final: 0.8158 (tp)
  outliers start: 27
  outliers final: 19
  residues processed: 129
  average time/residue: 0.1425
  time to fit residues: 26.3655
Evaluate side-chains
  128 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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  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  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  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  382 TYR
Chi-restraints excluded: chain B residue  383 HIS
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 49 optimal weight:    2.9990
   chunk 4 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 46 optimal weight:    0.5980
   chunk 76 optimal weight:    0.7980
   chunk 82 optimal weight:    5.9990
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.134938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117527 restraints weight = 10987.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.120523 restraints weight = 6136.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.122538 restraints weight = 4146.676|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7922
moved from start:          0.2503

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6722  Z= 0.186
  Angle     :  0.653  12.487   9135  Z= 0.303
  Chirality :  0.041   0.164   1082
  Planarity :  0.003   0.042   1145
  Dihedral  :  4.622  33.007    934
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.66 %
    Favored  : 95.34 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 25.80 %
    Favored  : 70.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.11 (0.30), residues: 879
  helix:  0.93 (0.22), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.34 (0.38), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 125 
 HIS   0.001   0.000   HIS B 284 
 PHE   0.012   0.001   PHE A 132 
 TYR   0.007   0.001   TYR B 419 
 ARG   0.002   0.000   ARG A 340 

*********************** 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
  138 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.919 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7231 (mp) cc_final: 0.6805 (pt)
REVERT: A   29 ASP cc_start: 0.8425 (m-30) cc_final: 0.8181 (m-30)
REVERT: A   55 LYS cc_start: 0.8275 (mmtt) cc_final: 0.7089 (tptp)
REVERT: A   91 MET cc_start: 0.6614 (mtm) cc_final: 0.6393 (tmm)
REVERT: A  164 ASP cc_start: 0.8051 (t0) cc_final: 0.7554 (t0)
REVERT: A  171 ASP cc_start: 0.7713 (t0) cc_final: 0.7491 (t0)
REVERT: A  202 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: A  271 LYS cc_start: 0.7804 (tttt) cc_final: 0.7443 (ttmt)
REVERT: A  290 LYS cc_start: 0.8150 (mtmm) cc_final: 0.7767 (mttm)
REVERT: A  342 ILE cc_start: 0.9174 (tt) cc_final: 0.8938 (tt)
REVERT: A  360 MET cc_start: 0.7639 (mtt) cc_final: 0.7365 (mtt)
REVERT: A  382 TYR cc_start: 0.8553 (OUTLIER) cc_final: 0.8163 (m-10)
REVERT: B   38 MET cc_start: 0.7936 (mmt) cc_final: 0.7582 (mmt)
REVERT: B  164 ASP cc_start: 0.8052 (t0) cc_final: 0.7529 (t0)
REVERT: B  205 ARG cc_start: 0.7513 (ttp-110) cc_final: 0.7169 (ttp80)
REVERT: B  274 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7783 (mm)
REVERT: B  301 LEU cc_start: 0.7925 (tt) cc_final: 0.6864 (mt)
REVERT: B  305 LEU cc_start: 0.8451 (tp) cc_final: 0.8087 (tp)
  outliers start: 23
  outliers final: 18
  residues processed: 133
  average time/residue: 0.1519
  time to fit residues: 29.0442
Evaluate side-chains
  129 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 109
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
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  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  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  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  382 TYR
Chi-restraints excluded: chain B residue  383 HIS
Chi-restraints excluded: chain B residue  435 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 57 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 83 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 21 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 71 optimal weight:    3.9990
   chunk 12 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.134438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.116927 restraints weight = 11046.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.119914 restraints weight = 6187.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.121937 restraints weight = 4192.068|
|-----------------------------------------------------------------------------|
r_work (final): 0.3465
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7932
moved from start:          0.2555

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= 0.199
  Angle     :  0.665  12.310   9135  Z= 0.307
  Chirality :  0.041   0.165   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.607  31.222    934
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.64 %
    Allowed  : 25.34 %
    Favored  : 71.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.30), residues: 879
  helix:  0.97 (0.22), residues: 649
  sheet:  None (None), residues: 0
  loop : -2.38 (0.38), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 125 
 HIS   0.001   0.000   HIS B 284 
 PHE   0.015   0.001   PHE A 132 
 TYR   0.007   0.001   TYR B 229 
 ARG   0.002   0.000   ARG A 340 

*********************** 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
  136 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 112
  time to evaluate  : 0.788 
Fit side-chains
REVERT: A   29 ASP cc_start: 0.8426 (m-30) cc_final: 0.8171 (m-30)
REVERT: A   55 LYS cc_start: 0.8359 (mmtt) cc_final: 0.7082 (tptp)
REVERT: A   91 MET cc_start: 0.6664 (mtm) cc_final: 0.6425 (tmm)
REVERT: A  143 MET cc_start: 0.7056 (tpp) cc_final: 0.6853 (tpp)
REVERT: A  164 ASP cc_start: 0.8059 (t0) cc_final: 0.7570 (t0)
REVERT: A  171 ASP cc_start: 0.7724 (t0) cc_final: 0.7515 (t0)
REVERT: A  202 GLU cc_start: 0.8428 (tm-30) cc_final: 0.8201 (tm-30)
REVERT: A  271 LYS cc_start: 0.7810 (tttt) cc_final: 0.7403 (ttmt)
REVERT: A  290 LYS cc_start: 0.8155 (mtmm) cc_final: 0.7772 (mttm)
REVERT: A  342 ILE cc_start: 0.9178 (tt) cc_final: 0.8930 (tt)
REVERT: A  360 MET cc_start: 0.7620 (mtt) cc_final: 0.7354 (mtt)
REVERT: A  382 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.8183 (m-10)
REVERT: B   38 MET cc_start: 0.7965 (mmt) cc_final: 0.7601 (mmt)
REVERT: B  164 ASP cc_start: 0.8059 (t0) cc_final: 0.7567 (t0)
REVERT: B  205 ARG cc_start: 0.7522 (ttp-110) cc_final: 0.7168 (ttp80)
REVERT: B  274 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7774 (mm)
REVERT: B  301 LEU cc_start: 0.8005 (tt) cc_final: 0.6964 (mt)
REVERT: B  305 LEU cc_start: 0.8430 (tp) cc_final: 0.8076 (tp)
REVERT: B  367 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8656 (tt)
  outliers start: 24
  outliers final: 17
  residues processed: 131
  average time/residue: 0.1634
  time to fit residues: 30.6840
Evaluate side-chains
  130 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 110
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
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  162 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 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  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  382 TYR
Chi-restraints excluded: chain B residue  383 HIS
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 81 optimal weight:    5.9990
   chunk 71 optimal weight:    6.9990
   chunk 68 optimal weight:    0.8980
   chunk 69 optimal weight:    0.0870
   chunk 57 optimal weight:    0.9990
   chunk 20 optimal weight:    0.6980
   chunk 78 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   chunk 61 optimal weight:    0.8980
   chunk 5 optimal weight:   10.0000
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.6358

-------------------------------------------------------------------------------
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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.135488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.118068 restraints weight = 11187.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.121162 restraints weight = 6204.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.123119 restraints weight = 4155.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3480
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6722  Z= 0.188
  Angle     :  0.664  12.122   9135  Z= 0.308
  Chirality :  0.041   0.146   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.376  19.005    932
  Min Nonbonded Distance : 2.321

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.89 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 25.95 %
    Favored  : 70.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.30), residues: 879
  helix:  1.03 (0.22), residues: 649
  sheet:  None (None), residues: 0
  loop : -2.37 (0.37), residues: 230

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 125 
 HIS   0.001   0.000   HIS B 284 
 PHE   0.017   0.001   PHE A 132 
 TYR   0.007   0.001   TYR B 229 
 ARG   0.002   0.000   ARG A 340 

********************** 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
  135 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 114
  time to evaluate  : 0.794 
Fit side-chains
REVERT: A   25 LEU cc_start: 0.7343 (mp) cc_final: 0.6925 (pt)
REVERT: A   29 ASP cc_start: 0.8416 (m-30) cc_final: 0.8183 (m-30)
REVERT: A   55 LYS cc_start: 0.8363 (mmtt) cc_final: 0.7065 (tptp)
REVERT: A   91 MET cc_start: 0.6617 (mtm) cc_final: 0.6401 (tmm)
REVERT: A  164 ASP cc_start: 0.8017 (t0) cc_final: 0.7408 (t0)
REVERT: A  171 ASP cc_start: 0.7722 (t0) cc_final: 0.7513 (t0)
REVERT: A  202 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8154 (tm-30)
REVERT: A  271 LYS cc_start: 0.7769 (tttt) cc_final: 0.7349 (ttmt)
REVERT: A  290 LYS cc_start: 0.8154 (mtmm) cc_final: 0.7770 (mttm)
REVERT: A  342 ILE cc_start: 0.9176 (tt) cc_final: 0.8913 (tt)
REVERT: A  360 MET cc_start: 0.7650 (mtt) cc_final: 0.7385 (mtt)
REVERT: A  382 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.8089 (m-10)
REVERT: B   38 MET cc_start: 0.7942 (mmt) cc_final: 0.7582 (mmt)
REVERT: B  164 ASP cc_start: 0.8042 (t0) cc_final: 0.7555 (t0)
REVERT: B  205 ARG cc_start: 0.7522 (ttp-110) cc_final: 0.7164 (ttp80)
REVERT: B  274 LEU cc_start: 0.8140 (OUTLIER) cc_final: 0.7727 (mm)
REVERT: B  301 LEU cc_start: 0.7874 (tt) cc_final: 0.6930 (mt)
REVERT: B  305 LEU cc_start: 0.8427 (tp) cc_final: 0.8072 (tp)
REVERT: B  367 LEU cc_start: 0.9051 (OUTLIER) cc_final: 0.8655 (tt)
REVERT: B  383 HIS cc_start: 0.7672 (OUTLIER) cc_final: 0.7329 (t-90)
  outliers start: 21
  outliers final: 16
  residues processed: 130
  average time/residue: 0.1465
  time to fit residues: 27.2122
Evaluate side-chains
  134 residues out of total 665 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 114
  time to evaluate  : 0.651 
-------------------------------------------------------------------------------
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  162 VAL
Chi-restraints excluded: chain A residue  194 LEU
Chi-restraints excluded: chain A residue  236 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  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  382 TYR
Chi-restraints excluded: chain B residue  383 HIS
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 20 optimal weight:    0.8980
   chunk 58 optimal weight:    0.6980
   chunk 67 optimal weight:    0.0980
   chunk 55 optimal weight:    0.2980
   chunk 78 optimal weight:    0.8980
   chunk 28 optimal weight:    0.1980
   chunk 7 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 60 optimal weight:    7.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.3980

-------------------------------------------------------------------------------
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**
B 250 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.137499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.120098 restraints weight = 11162.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123236 restraints weight = 6198.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125250 restraints weight = 4140.862|
|-----------------------------------------------------------------------------|
r_work (final): 0.3511
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6722  Z= 0.168
  Angle     :  0.655  11.926   9135  Z= 0.303
  Chirality :  0.040   0.150   1082
  Planarity :  0.004   0.041   1145
  Dihedral  :  4.275  19.084    932
  Min Nonbonded Distance : 2.307

Molprobity Statistics.
  All-atom Clashscore : 10.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 26.56 %
    Favored  : 70.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.30), residues: 879
  helix:  1.16 (0.22), residues: 641
  sheet:  None (None), residues: 0
  loop : -2.26 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 253 
 HIS   0.001   0.000   HIS B 284 
 PHE   0.015   0.001   PHE A 132 
 TYR   0.007   0.001   TYR B 229 
 ARG   0.002   0.000   ARG A  64 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2009.85 seconds
wall clock time: 35 minutes 31.46 seconds (2131.46 seconds total)