Starting phenix.real_space_refine
on Tue Mar  3 17:35:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7zth_14960/03_2026/7zth_14960.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7zth_14960/03_2026/7zth_14960.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7zth_14960/03_2026/7zth_14960.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7zth_14960/03_2026/7zth_14960.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7zth_14960/03_2026/7zth_14960.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7zth_14960/03_2026/7zth_14960.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   1.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      84      5.49       5
     S      18      5.16       5
     C    4622      2.51       5
     N    1325      2.21       5
     O    1571      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7620
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2962
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 360, 2962
          Classifications: {'peptide': 360}
          Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 343}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "B"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 362, 2977
          Classifications: {'peptide': 362}
          Link IDs: {'PCIS': 2, 'PTRANS': 14, 'TRANS': 345}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'LLP:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "C"
      Number of atoms: 834
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 834
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
    Chain: "D"
      Number of atoms: 847
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 847
          Classifications: {'DNA': 41}
          Link IDs: {'rna3p': 40}
  Time building chain proxies: 1.56, per 1000 atoms: 0.20
  Number of scatterers: 7620
  At special positions: 0
  Unit cell: (82.677, 90.678, 132.461, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P      84     15.00
     O    1571      8.00
     N    1325      7.00
     C    4622      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.64
  Conformation dependent library (CDL) restraints added in 204.5 milliseconds
  

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1368

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 6 sheets defined
      37.4% alpha, 8.6% beta
      12 base pairs and 56 stacking pairs defined.
    Time for finding SS restraints: 0.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 120 through 125
    Processing helix  chain 'A' and resid 126 through 129
    Processing helix  chain 'A' and resid 148 through 159
      removed outlier: 3.545A  pdb=" N   ARG A 152 " --> pdb=" O   GLU A 148 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   GLU A 154 " --> pdb=" O   SER A 150 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ILE A 155 " --> pdb=" O   PHE A 151 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   TYR A 157 " --> pdb=" O   ARG A 153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 190
      removed outlier: 4.151A  pdb=" N   GLN A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   LEU A 185 " --> pdb=" O   LEU A 181 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   LEU A 187 " --> pdb=" O   GLN A 183 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   LEU A 188 " --> pdb=" O   GLN A 184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 204 through 209
      removed outlier: 3.695A  pdb=" N   LEU A 209 " --> pdb=" O   MET A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 233
    Processing helix  chain 'A' and resid 255 through 267
      removed outlier: 3.554A  pdb=" N   LYS A 259 " --> pdb=" O   ILE A 255 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   GLN A 260 " --> pdb=" O   ASN A 256 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ALA A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLU A 266 " --> pdb=" O   LEU A 262 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   ALA A 267 " --> pdb=" O   HIS A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 316
      removed outlier: 4.130A  pdb=" N   VAL A 315 " --> pdb=" O   ILE A 312 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ARG A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 312 through 316'
    Processing helix  chain 'A' and resid 323 through 334
      removed outlier: 3.971A  pdb=" N   HIS A 328 " --> pdb=" O   ALA A 324 " (cutoff:3.500A)
      removed outlier: 4.651A  pdb=" N   LEU A 329 " --> pdb=" O   PRO A 325 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ASN A 332 " --> pdb=" O   HIS A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 346
      removed outlier: 3.537A  pdb=" N   GLN A 346 " --> pdb=" O   ARG A 343 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 352
      removed outlier: 3.879A  pdb=" N   ALA A 351 " --> pdb=" O   GLN A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 381
      removed outlier: 4.161A  pdb=" N   LYS A 367 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   ILE A 368 " --> pdb=" O   ARG A 364 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LYS A 372 " --> pdb=" O   ILE A 368 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   LYS A 375 " --> pdb=" O   ARG A 371 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU A 379 " --> pdb=" O   LYS A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 407 through 416
      removed outlier: 3.895A  pdb=" N   GLU A 413 " --> pdb=" O   GLN A 409 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ALA A 415 " --> pdb=" O   LEU A 411 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU A 416 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 419
      No H-bonds generated for 'chain 'A' and resid 417 through 419'
    Processing helix  chain 'A' and resid 447 through 449
      No H-bonds generated for 'chain 'A' and resid 447 through 449'
    Processing helix  chain 'A' and resid 450 through 463
      removed outlier: 4.186A  pdb=" N   ALA A 456 " --> pdb=" O   GLU A 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 132
      removed outlier: 4.361A  pdb=" N   TYR B 127 " --> pdb=" O   GLN B 123 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN B 130 " --> pdb=" O   LYS B 126 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR B 131 " --> pdb=" O   TYR B 127 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   MET B 132 " --> pdb=" O   PHE B 128 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 150 through 156
      removed outlier: 3.715A  pdb=" N   ILE B 155 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ALA B 156 " --> pdb=" O   ARG B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 163
    Processing helix  chain 'B' and resid 178 through 183
    Processing helix  chain 'B' and resid 207 through 211
      removed outlier: 3.788A  pdb=" N   HIS B 211 " --> pdb=" O   LEU B 208 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 232
      removed outlier: 3.682A  pdb=" N   ILE B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL B 232 " --> pdb=" O   VAL B 228 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 227 through 232'
    Processing helix  chain 'B' and resid 254 through 266
      removed outlier: 3.852A  pdb=" N   HIS B 263 " --> pdb=" O   LYS B 259 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   ALA B 265 " --> pdb=" O   LEU B 261 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 296
      removed outlier: 3.588A  pdb=" N   MET B 295 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   ASP B 296 " --> pdb=" O   LEU B 292 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 291 through 296'
    Processing helix  chain 'B' and resid 323 through 334
      removed outlier: 3.843A  pdb=" N   HIS B 328 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   LEU B 329 " --> pdb=" O   PRO B 325 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LYS B 333 " --> pdb=" O   LEU B 329 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 350 through 355
      removed outlier: 3.566A  pdb=" N   GLN B 355 " --> pdb=" O   ALA B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 380
      removed outlier: 3.518A  pdb=" N   TYR B 369 " --> pdb=" O   MET B 365 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   ARG B 370 " --> pdb=" O   ARG B 366 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   LYS B 375 " --> pdb=" O   ARG B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 383
      No H-bonds generated for 'chain 'B' and resid 381 through 383'
    Processing helix  chain 'B' and resid 407 through 415
      removed outlier: 3.951A  pdb=" N   LEU B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL B 412 " --> pdb=" O   GLU B 408 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   GLU B 413 " --> pdb=" O   GLN B 409 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA B 415 " --> pdb=" O   LEU B 411 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 447 through 449
      No H-bonds generated for 'chain 'B' and resid 447 through 449'
    Processing helix  chain 'B' and resid 450 through 462
      removed outlier: 3.663A  pdb=" N   ALA B 456 " --> pdb=" O   GLU B 452 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 172 through 175
    Processing sheet with id=AA2, first strand: chain 'A' and resid 215 through 219
      removed outlier: 3.532A  pdb=" N   ILE A 197 " --> pdb=" O   VAL A 217 " (cutoff:3.500A)
      removed outlier: 6.496A  pdb=" N   VAL A 194 " --> pdb=" O   VAL A 238 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   TYR A 240 " --> pdb=" O   VAL A 194 " (cutoff:3.500A)
      removed outlier: 7.346A  pdb=" N   GLY A 196 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
      removed outlier: 6.663A  pdb=" N   VAL A 239 " --> pdb=" O   ILE A 274 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 387 through 390
      removed outlier: 3.544A  pdb=" N   ILE A 390 " --> pdb=" O   VAL A 399 " (cutoff:3.500A)
      removed outlier: 4.389A  pdb=" N   VAL A 399 " --> pdb=" O   ILE A 390 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 215 through 217
      removed outlier: 6.914A  pdb=" N   ILE B 273 " --> pdb=" O   ILE B 302 " (cutoff:3.500A)
      removed outlier: 8.261A  pdb=" N   LEU B 304 " --> pdb=" O   ILE B 273 " (cutoff:3.500A)
      removed outlier: 6.403A  pdb=" N   GLU B 275 " --> pdb=" O   LEU B 304 " (cutoff:3.500A)
      removed outlier: 8.725A  pdb=" N   ALA B 306 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   GLY B 305 " --> pdb=" O   TYR B 319 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 221 through 222
    Processing sheet with id=AA6, first strand: chain 'B' and resid 389 through 390
      removed outlier: 3.971A  pdb=" N   VAL B 399 " --> pdb=" O   ILE B 390 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   ILE B 439 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   TYR B 423 " --> pdb=" O   VAL B 440 " (cutoff:3.500A)

    134 hydrogen bonds defined for protein.
    381 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      27 hydrogen bonds
      54 hydrogen bond angles
      0 basepair planarities
      12 basepair parallelities
      56 stacking parallelities
  Total time for adding SS restraints: 1.05

  Time building geometry restraints manager: 0.82 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1671
        1.33 -     1.45: 2151
        1.45 -     1.57: 3955
        1.57 -     1.69: 164
        1.69 -     1.81: 32
  Bond restraints: 7973
  Sorted by residual:
  bond pdb=" OP4 LLP B 309 "
       pdb=" P   LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.536  0.190 2.00e-02 2.50e+03 9.02e+01
  bond pdb=" OP4 LLP A 309 "
       pdb=" P   LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.726  1.540  0.186 2.00e-02 2.50e+03 8.67e+01
  bond pdb=" NZ  LLP A 309 "
       pdb=" C4' LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.437 -0.164 2.00e-02 2.50e+03 6.73e+01
  bond pdb=" NZ  LLP B 309 "
       pdb=" C4' LLP B 309 "
    ideal  model  delta    sigma   weight residual
    1.273  1.432 -0.159 2.00e-02 2.50e+03 6.32e+01
  bond pdb=" C4  LLP A 309 "
       pdb=" C4' LLP A 309 "
    ideal  model  delta    sigma   weight residual
    1.464  1.618 -0.154 2.00e-02 2.50e+03 5.89e+01
  ... (remaining 7968 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 10570
        2.16 -     4.32: 499
        4.32 -     6.48: 59
        6.48 -     8.64: 14
        8.64 -    10.80: 10
  Bond angle restraints: 11152
  Sorted by residual:
  angle pdb=" N   ILE A 289 "
        pdb=" CA  ILE A 289 "
        pdb=" C   ILE A 289 "
      ideal   model   delta    sigma   weight residual
     109.01  100.06    8.95 1.13e+00 7.83e-01 6.28e+01
  angle pdb=" C   ASP A 277 "
        pdb=" N   TYR A 278 "
        pdb=" CA  TYR A 278 "
      ideal   model   delta    sigma   weight residual
     121.54  131.33   -9.79 1.91e+00 2.74e-01 2.62e+01
  angle pdb=" CA  ILE A 289 "
        pdb=" C   ILE A 289 "
        pdb=" N   PRO A 290 "
      ideal   model   delta    sigma   weight residual
     117.00  120.72   -3.72 9.50e-01 1.11e+00 1.54e+01
  angle pdb=" C   ILE A 105 "
        pdb=" N   ARG A 106 "
        pdb=" CA  ARG A 106 "
      ideal   model   delta    sigma   weight residual
     121.54  128.72   -7.18 1.91e+00 2.74e-01 1.42e+01
  angle pdb=" NZ  LLP B 309 "
        pdb=" C4' LLP B 309 "
        pdb=" C4  LLP B 309 "
      ideal   model   delta    sigma   weight residual
     120.09  109.29   10.80 3.00e+00 1.11e-01 1.30e+01
  ... (remaining 11147 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.96: 3953
       29.96 -    59.91: 576
       59.91 -    89.87: 27
       89.87 -   119.83: 0
      119.83 -   149.78: 3
  Dihedral angle restraints: 4559
    sinusoidal: 2427
      harmonic: 2132
  Sorted by residual:
  dihedral pdb=" CA  GLY B 286 "
           pdb=" C   GLY B 286 "
           pdb=" N   LYS B 287 "
           pdb=" CA  LYS B 287 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -136.34  -43.66     0      5.00e+00 4.00e-02 7.63e+01
  dihedral pdb=" CA  GLY B 177 "
           pdb=" C   GLY B 177 "
           pdb=" N   VAL B 178 "
           pdb=" CA  VAL B 178 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.51   28.49     0      5.00e+00 4.00e-02 3.25e+01
  dihedral pdb=" CA  ASN B 136 "
           pdb=" C   ASN B 136 "
           pdb=" N   HIS B 137 "
           pdb=" CA  HIS B 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.03   27.97     0      5.00e+00 4.00e-02 3.13e+01
  ... (remaining 4556 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.081: 1018
       0.081 -    0.161: 193
       0.161 -    0.241: 8
       0.241 -    0.322: 1
       0.322 -    0.402: 1
  Chirality restraints: 1221
  Sorted by residual:
  chirality pdb=" CB  ILE A 446 "
            pdb=" CA  ILE A 446 "
            pdb=" CG1 ILE A 446 "
            pdb=" CG2 ILE A 446 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.24    0.40 2.00e-01 2.50e+01 4.05e+00
  chirality pdb=" CA  ILE A 289 "
            pdb=" N   ILE A 289 "
            pdb=" C   ILE A 289 "
            pdb=" CB  ILE A 289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.26 2.00e-01 2.50e+01 1.72e+00
  chirality pdb=" CG  LEU B 187 "
            pdb=" CB  LEU B 187 "
            pdb=" CD1 LEU B 187 "
            pdb=" CD2 LEU B 187 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.40   -0.19 2.00e-01 2.50e+01 8.97e-01
  ... (remaining 1218 not shown)

  Planarity restraints: 1133
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP A 309 "    0.157 2.00e-02 2.50e+03   2.82e-01 7.96e+02
        pdb=" NZ  LLP A 309 "   -0.384 2.00e-02 2.50e+03
        pdb=" C4  LLP A 309 "   -0.132 2.00e-02 2.50e+03
        pdb=" C4' LLP A 309 "    0.359 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CE  LLP B 309 "   -0.297 2.00e-02 2.50e+03   2.77e-01 7.65e+02
        pdb=" NZ  LLP B 309 "    0.311 2.00e-02 2.50e+03
        pdb=" C4  LLP B 309 "   -0.253 2.00e-02 2.50e+03
        pdb=" C4' LLP B 309 "    0.240 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 289 "    0.048 5.00e-02 4.00e+02   7.24e-02 8.40e+00
        pdb=" N   PRO A 290 "   -0.125 5.00e-02 4.00e+02
        pdb=" CA  PRO A 290 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 290 "    0.040 5.00e-02 4.00e+02
  ... (remaining 1130 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.78: 1636
        2.78 -     3.31: 6210
        3.31 -     3.84: 12588
        3.84 -     4.37: 13923
        4.37 -     4.90: 22293
  Nonbonded interactions: 56650
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 240 "
            pdb=" OD2 ASP A 276 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   SER A 314 "
            pdb=" OG  SER A 314 "
     model   vdw
     2.261 3.040
  nonbonded pdb=" OE1 GLN A 184 "
            pdb=" OH  TYR A 330 "
     model   vdw
     2.268 3.040
  nonbonded pdb=" O   GLU B 453 "
            pdb=" OG1 THR B 457 "
     model   vdw
     2.290 3.040
  nonbonded pdb=" O   GLY B 177 "
            pdb=" OG  SER B 318 "
     model   vdw
     2.294 3.040
  ... (remaining 56645 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'
  selection = (chain 'B' and resid 105 through 464)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.080
  Find NCS groups from input model:        0.050
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.720
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7538
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      :  0.009   0.190   7973  Z= 0.420
  Angle     :  1.065  10.797  11152  Z= 0.585
  Chirality :  0.060   0.402   1221
  Planarity :  0.014   0.282   1133
  Dihedral  : 23.039 149.781   3191
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 6.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.97 %
    Favored  : 90.03 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 15.06 %
    Favored  : 83.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.31 (0.24), residues: 712
  helix: -4.33 (0.17), residues: 232
  sheet: -3.13 (0.41), residues: 112
  loop : -3.09 (0.28), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 316 
 TYR   0.028   0.003   TYR B 202 
 PHE   0.025   0.004   PHE A 307 
 TRP   0.026   0.003   TRP A 124 
 HIS   0.015   0.002   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00909 ( 7973)
  covalent geometry    : angle       1.06527 (11152)
  hydrogen bonds       : bond        0.23684 (  161)
  hydrogen bonds       : angle       8.19228 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.213 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7870 (mp0) cc_final: 0.6731 (pm20)
REVERT: A  138 ARG cc_start: 0.7915 (mtt-85) cc_final: 0.7291 (mtp180)
REVERT: A  353 MET cc_start: 0.7643 (mtm) cc_final: 0.7435 (mtm)
  outliers start: 8
  outliers final: 3
  residues processed: 91
  average time/residue: 0.1114
  time to fit residues: 12.9892
Evaluate side-chains
  58 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 55
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  402 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    5.9990
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A 142 ASN
A 146 GLN
A 211 HIS
B 211 HIS
B 328 HIS
B 332 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.168831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.132726 restraints weight = 14362.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.134456 restraints weight = 11016.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.135133 restraints weight = 7724.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.135451 restraints weight = 6320.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.135829 restraints weight = 5893.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.1619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7973  Z= 0.142
  Angle     :  0.644   7.904  11152  Z= 0.356
  Chirality :  0.043   0.208   1221
  Planarity :  0.006   0.060   1133
  Dihedral  : 24.697 145.551   1748
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 18.79 %
    Favored  : 78.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.30 (0.27), residues: 712
  helix: -3.15 (0.27), residues: 240
  sheet: -2.16 (0.49), residues: 106
  loop : -2.87 (0.28), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 283 
 TYR   0.019   0.001   TYR A 157 
 PHE   0.011   0.001   PHE B 109 
 TRP   0.015   0.002   TRP A 124 
 HIS   0.011   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 7973)
  covalent geometry    : angle       0.64352 (11152)
  hydrogen bonds       : bond        0.04569 (  161)
  hydrogen bonds       : angle       5.76526 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.313 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7680 (mp0) cc_final: 0.6674 (pm20)
REVERT: A  138 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7414 (mtp180)
REVERT: A  434 ILE cc_start: 0.7478 (pt) cc_final: 0.7218 (pt)
REVERT: B  370 ARG cc_start: 0.7613 (ttm-80) cc_final: 0.7353 (ttm110)
  outliers start: 16
  outliers final: 12
  residues processed: 85
  average time/residue: 0.0738
  time to fit residues: 8.9867
Evaluate side-chains
  74 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 77 optimal weight:    9.9990
   chunk 74 optimal weight:   10.0000
   chunk 65 optimal weight:    7.9990
   chunk 11 optimal weight:    0.0570
   chunk 73 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 59 optimal weight:    6.9990
   chunk 38 optimal weight:    4.9990
   chunk 3 optimal weight:   10.0000
   chunk 43 optimal weight:    1.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    3.8106

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
** B 110 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 123 GLN
** B 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 404 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.163311 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.126753 restraints weight = 14419.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.127986 restraints weight = 12986.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.128596 restraints weight = 9237.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.128943 restraints weight = 8357.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.129803 restraints weight = 7076.008|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   7973  Z= 0.253
  Angle     :  0.737   6.481  11152  Z= 0.400
  Chirality :  0.047   0.192   1221
  Planarity :  0.006   0.052   1133
  Dihedral  : 24.745 142.784   1748
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.96 %
    Favored  : 89.04 %
  Rotamer:
    Outliers :  5.59 %
    Allowed  : 19.41 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.15 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.03 (0.28), residues: 712
  helix: -2.81 (0.30), residues: 228
  sheet: -2.10 (0.48), residues: 106
  loop : -2.78 (0.28), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 163 
 TYR   0.018   0.002   TYR A 157 
 PHE   0.017   0.003   PHE A 307 
 TRP   0.013   0.002   TRP A 124 
 HIS   0.009   0.002   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00579 ( 7973)
  covalent geometry    : angle       0.73664 (11152)
  hydrogen bonds       : bond        0.05011 (  161)
  hydrogen bonds       : angle       5.94006 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 63
  time to evaluate  : 0.247 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7679 (mp0) cc_final: 0.6674 (pm20)
REVERT: A  138 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7341 (mtp180)
  outliers start: 36
  outliers final: 24
  residues processed: 93
  average time/residue: 0.0637
  time to fit residues: 8.7297
Evaluate side-chains
  78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 54
  time to evaluate  : 0.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  226 ILE
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  301 VAL
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 75 optimal weight:   10.0000
   chunk 32 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 46 optimal weight:    6.9990
   chunk 74 optimal weight:   10.0000
   chunk 65 optimal weight:    1.9990
   chunk 71 optimal weight:    0.8980
   chunk 22 optimal weight:    0.9980
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 123 GLN
B 145 HIS
B 438 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.168693 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.133127 restraints weight = 14559.264|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.134886 restraints weight = 10432.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.135112 restraints weight = 8070.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.135580 restraints weight = 6744.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3898 r_free = 0.3898 target = 0.135729 restraints weight = 5756.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3863
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.2362

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7973  Z= 0.136
  Angle     :  0.610   9.807  11152  Z= 0.329
  Chirality :  0.042   0.177   1221
  Planarity :  0.005   0.050   1133
  Dihedral  : 24.435 144.799   1748
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 20.96 %
    Favored  : 73.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.55 (0.29), residues: 712
  helix: -2.38 (0.32), residues: 229
  sheet: -1.80 (0.49), residues: 106
  loop : -2.52 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 316 
 TYR   0.016   0.001   TYR A 157 
 PHE   0.008   0.001   PHE A 307 
 TRP   0.011   0.001   TRP A 124 
 HIS   0.008   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 7973)
  covalent geometry    : angle       0.61021 (11152)
  hydrogen bonds       : bond        0.03680 (  161)
  hydrogen bonds       : angle       5.18281 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 67
  time to evaluate  : 0.248 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7592 (mp0) cc_final: 0.6648 (pm20)
REVERT: A  138 ARG cc_start: 0.7678 (mtt-85) cc_final: 0.7349 (mtp180)
REVERT: B  148 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6630 (tp30)
REVERT: B  281 GLU cc_start: 0.7099 (pm20) cc_final: 0.6830 (pm20)
  outliers start: 33
  outliers final: 20
  residues processed: 92
  average time/residue: 0.0634
  time to fit residues: 8.5664
Evaluate side-chains
  78 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 58
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  434 ILE
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  452 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 56 optimal weight:    7.9990
   chunk 49 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 59 optimal weight:    0.4980
   chunk 25 optimal weight:   10.0000
   chunk 74 optimal weight:   10.0000
   chunk 29 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   chunk 5 optimal weight:    2.9990
   chunk 43 optimal weight:    4.9990
   overall best weight:    3.8988

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

Flipped N/Q/H residues before XYZ refinement:
A 361 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.163330 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.126629 restraints weight = 14693.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.128176 restraints weight = 13220.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.128867 restraints weight = 9190.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.129189 restraints weight = 8263.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.129966 restraints weight = 6847.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7582
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041   7973  Z= 0.257
  Angle     :  0.743   9.532  11152  Z= 0.397
  Chirality :  0.048   0.218   1221
  Planarity :  0.006   0.052   1133
  Dihedral  : 24.623 143.867   1748
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 10.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.52 %
    Favored  : 88.48 %
  Rotamer:
    Outliers :  6.06 %
    Allowed  : 21.27 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.66 (0.29), residues: 712
  helix: -2.53 (0.31), residues: 239
  sheet: -1.87 (0.49), residues: 107
  loop : -2.52 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 393 
 TYR   0.019   0.002   TYR B 336 
 PHE   0.016   0.003   PHE A 307 
 TRP   0.015   0.002   TRP A 124 
 HIS   0.010   0.002   HIS B 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 ( 7973)
  covalent geometry    : angle       0.74278 (11152)
  hydrogen bonds       : bond        0.04726 (  161)
  hydrogen bonds       : angle       5.69864 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 57
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7627 (mp0) cc_final: 0.6687 (pm20)
REVERT: A  138 ARG cc_start: 0.7792 (mtt-85) cc_final: 0.7387 (mtp180)
REVERT: B  148 GLU cc_start: 0.7343 (mm-30) cc_final: 0.6738 (tp30)
  outliers start: 39
  outliers final: 32
  residues processed: 85
  average time/residue: 0.0639
  time to fit residues: 8.0155
Evaluate side-chains
  83 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 51
  time to evaluate  : 0.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  228 VAL
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain A residue  458 VAL
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  202 TYR
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Chi-restraints excluded: chain B residue  458 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 28 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 75 optimal weight:   10.0000
   chunk 15 optimal weight:    4.9990
   chunk 59 optimal weight:    0.0770
   chunk 77 optimal weight:   10.0000
   chunk 31 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 7 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   overall best weight:    1.1742

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.167735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.131879 restraints weight = 14442.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.133719 restraints weight = 11040.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.134194 restraints weight = 8176.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.134577 restraints weight = 6546.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.134895 restraints weight = 5913.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7475
moved from start:          0.2658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7973  Z= 0.138
  Angle     :  0.617   8.951  11152  Z= 0.333
  Chirality :  0.043   0.184   1221
  Planarity :  0.005   0.054   1133
  Dihedral  : 24.409 145.795   1748
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  5.43 %
    Allowed  : 22.05 %
    Favored  : 72.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.29 (0.29), residues: 712
  helix: -2.23 (0.32), residues: 238
  sheet: -1.69 (0.49), residues: 108
  loop : -2.28 (0.30), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 432 
 TYR   0.015   0.001   TYR B 336 
 PHE   0.009   0.001   PHE A 334 
 TRP   0.015   0.001   TRP A 124 
 HIS   0.009   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 7973)
  covalent geometry    : angle       0.61720 (11152)
  hydrogen bonds       : bond        0.03774 (  161)
  hydrogen bonds       : angle       5.09319 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 61
  time to evaluate  : 0.252 
Fit side-chains
REVERT: A  114 ILE cc_start: 0.6373 (tt) cc_final: 0.6035 (tt)
REVERT: A  122 GLU cc_start: 0.7547 (mp0) cc_final: 0.6652 (pm20)
REVERT: A  138 ARG cc_start: 0.7742 (mtt-85) cc_final: 0.7377 (mtp180)
REVERT: A  434 ILE cc_start: 0.7435 (pt) cc_final: 0.7202 (pt)
REVERT: B  148 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6522 (tp30)
REVERT: B  281 GLU cc_start: 0.6892 (pm20) cc_final: 0.6690 (pm20)
  outliers start: 35
  outliers final: 29
  residues processed: 87
  average time/residue: 0.0639
  time to fit residues: 8.3212
Evaluate side-chains
  87 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 58
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 61 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 73 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 78 optimal weight:    9.9990
   chunk 51 optimal weight:    7.9990
   chunk 7 optimal weight:    0.4980
   chunk 18 optimal weight:    0.0040
   overall best weight:    2.0998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.166383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.130607 restraints weight = 14452.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.130981 restraints weight = 14638.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.132061 restraints weight = 10135.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.132517 restraints weight = 8400.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.133200 restraints weight = 7023.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.2732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   7973  Z= 0.166
  Angle     :  0.645  10.272  11152  Z= 0.344
  Chirality :  0.044   0.197   1221
  Planarity :  0.005   0.053   1133
  Dihedral  : 24.396 146.060   1748
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.13 %
    Favored  : 90.87 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 22.05 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.14 (0.30), residues: 712
  helix: -2.11 (0.32), residues: 238
  sheet: -1.66 (0.48), residues: 108
  loop : -2.17 (0.31), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 245 
 TYR   0.015   0.002   TYR A 157 
 PHE   0.010   0.002   PHE A 307 
 TRP   0.017   0.001   TRP A 124 
 HIS   0.008   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 7973)
  covalent geometry    : angle       0.64461 (11152)
  hydrogen bonds       : bond        0.03926 (  161)
  hydrogen bonds       : angle       5.10197 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 58
  time to evaluate  : 0.242 
Fit side-chains
REVERT: A  122 GLU cc_start: 0.7615 (mp0) cc_final: 0.6686 (pm20)
REVERT: A  138 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7349 (mtp180)
REVERT: A  307 PHE cc_start: 0.8606 (OUTLIER) cc_final: 0.7469 (t80)
REVERT: B  148 GLU cc_start: 0.7253 (mm-30) cc_final: 0.6582 (tp30)
  outliers start: 37
  outliers final: 32
  residues processed: 88
  average time/residue: 0.0561
  time to fit residues: 7.6024
Evaluate side-chains
  91 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 58
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  178 VAL
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  310 SER
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Chi-restraints excluded: chain B residue  452 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 21 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 8 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 42 optimal weight:    0.1980
   chunk 2 optimal weight:   10.0000
   chunk 9 optimal weight:    6.9990
   chunk 10 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    1.1984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.168794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.132778 restraints weight = 14410.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.133728 restraints weight = 12852.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.134531 restraints weight = 9290.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.135013 restraints weight = 7729.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.135804 restraints weight = 6617.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7973  Z= 0.133
  Angle     :  0.616  13.050  11152  Z= 0.326
  Chirality :  0.042   0.187   1221
  Planarity :  0.005   0.053   1133
  Dihedral  : 24.246 147.871   1748
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 22.83 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.95 (0.30), residues: 712
  helix: -2.03 (0.32), residues: 246
  sheet: -1.43 (0.47), residues: 108
  loop : -2.03 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 370 
 TYR   0.014   0.001   TYR B 336 
 PHE   0.007   0.001   PHE B 128 
 TRP   0.017   0.001   TRP A 124 
 HIS   0.007   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7973)
  covalent geometry    : angle       0.61643 (11152)
  hydrogen bonds       : bond        0.03584 (  161)
  hydrogen bonds       : angle       4.95472 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 66
  time to evaluate  : 0.220 
Fit side-chains
REVERT: A  114 ILE cc_start: 0.6417 (tt) cc_final: 0.6073 (tt)
REVERT: A  122 GLU cc_start: 0.7514 (mp0) cc_final: 0.6715 (pm20)
REVERT: A  138 ARG cc_start: 0.7726 (mtt-85) cc_final: 0.7349 (mtp180)
REVERT: A  307 PHE cc_start: 0.8430 (OUTLIER) cc_final: 0.7131 (t80)
REVERT: B  148 GLU cc_start: 0.7185 (mm-30) cc_final: 0.6495 (tp30)
  outliers start: 34
  outliers final: 27
  residues processed: 92
  average time/residue: 0.0641
  time to fit residues: 8.6140
Evaluate side-chains
  88 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 60
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  202 TYR
Chi-restraints excluded: chain A residue  239 VAL
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  230 SER
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  383 TYR
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 8 optimal weight:    5.9990
   chunk 36 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 4 optimal weight:    6.9990
   chunk 24 optimal weight:    0.9990
   chunk 79 optimal weight:   10.0000
   chunk 44 optimal weight:    0.7980
   chunk 73 optimal weight:   10.0000
   chunk 68 optimal weight:    4.9990
   chunk 22 optimal weight:    0.3980
   overall best weight:    0.8382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.170468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.135170 restraints weight = 14208.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.136046 restraints weight = 13396.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.137140 restraints weight = 9440.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3921 r_free = 0.3921 target = 0.137541 restraints weight = 7572.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.138466 restraints weight = 6491.501|
|-----------------------------------------------------------------------------|
r_work (final): 0.3898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   7973  Z= 0.122
  Angle     :  0.594  12.544  11152  Z= 0.316
  Chirality :  0.041   0.182   1221
  Planarity :  0.005   0.052   1133
  Dihedral  : 24.109 149.366   1748
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  Rotamer:
    Outliers :  4.81 %
    Allowed  : 22.52 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.64 (0.30), residues: 712
  helix: -1.79 (0.32), residues: 249
  sheet: -1.18 (0.49), residues: 108
  loop : -1.84 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 370 
 TYR   0.014   0.001   TYR B 336 
 PHE   0.008   0.001   PHE B 307 
 TRP   0.032   0.002   TRP A 124 
 HIS   0.005   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 7973)
  covalent geometry    : angle       0.59404 (11152)
  hydrogen bonds       : bond        0.03330 (  161)
  hydrogen bonds       : angle       4.74535 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
REVERT: A  122 GLU cc_start: 0.7567 (mp0) cc_final: 0.6827 (pm20)
REVERT: A  138 ARG cc_start: 0.7687 (mtt-85) cc_final: 0.7394 (mtp180)
REVERT: A  307 PHE cc_start: 0.8375 (OUTLIER) cc_final: 0.7113 (t80)
REVERT: B  148 GLU cc_start: 0.7129 (mm-30) cc_final: 0.6450 (tp30)
  outliers start: 31
  outliers final: 27
  residues processed: 100
  average time/residue: 0.0682
  time to fit residues: 9.9964
Evaluate side-chains
  93 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 65
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 33 optimal weight:    0.9990
   chunk 59 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:   10.0000
   chunk 4 optimal weight:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 27 optimal weight:    5.9990
   chunk 56 optimal weight:    6.9990
   overall best weight:    1.5188

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.169164 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.133656 restraints weight = 14159.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.134624 restraints weight = 13831.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.135279 restraints weight = 9928.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.135904 restraints weight = 8788.129|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.136564 restraints weight = 7318.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.3366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7973  Z= 0.144
  Angle     :  0.637  12.268  11152  Z= 0.338
  Chirality :  0.043   0.189   1221
  Planarity :  0.005   0.053   1133
  Dihedral  : 24.096 149.795   1748
  Min Nonbonded Distance : 2.379

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.30 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 23.14 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.30), residues: 712
  helix: -1.73 (0.32), residues: 249
  sheet: -1.04 (0.50), residues: 105
  loop : -1.82 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 343 
 TYR   0.017   0.001   TYR A 157 
 PHE   0.011   0.001   PHE B 307 
 TRP   0.028   0.002   TRP A 124 
 HIS   0.006   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 7973)
  covalent geometry    : angle       0.63746 (11152)
  hydrogen bonds       : bond        0.03493 (  161)
  hydrogen bonds       : angle       4.82767 (  435)

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

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

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1424 Ramachandran restraints generated.
    712 Oldfield, 0 Emsley, 712 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 66
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  114 ILE cc_start: 0.6364 (tt) cc_final: 0.5958 (tt)
REVERT: A  122 GLU cc_start: 0.7593 (mp0) cc_final: 0.6851 (pm20)
REVERT: A  138 ARG cc_start: 0.7754 (mtt-85) cc_final: 0.7372 (mtp180)
REVERT: A  307 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.7267 (t80)
REVERT: B  148 GLU cc_start: 0.7177 (mm-30) cc_final: 0.6538 (tp30)
  outliers start: 32
  outliers final: 30
  residues processed: 93
  average time/residue: 0.0586
  time to fit residues: 8.2544
Evaluate side-chains
  94 residues out of total 644 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 63
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 LEU
Chi-restraints excluded: chain A residue  172 VAL
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  197 ILE
Chi-restraints excluded: chain A residue  244 SER
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  278 TYR
Chi-restraints excluded: chain A residue  307 PHE
Chi-restraints excluded: chain A residue  310 SER
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  320 MET
Chi-restraints excluded: chain A residue  329 LEU
Chi-restraints excluded: chain A residue  340 THR
Chi-restraints excluded: chain A residue  399 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  412 VAL
Chi-restraints excluded: chain B residue  112 THR
Chi-restraints excluded: chain B residue  141 LEU
Chi-restraints excluded: chain B residue  168 THR
Chi-restraints excluded: chain B residue  172 VAL
Chi-restraints excluded: chain B residue  234 THR
Chi-restraints excluded: chain B residue  247 PHE
Chi-restraints excluded: chain B residue  251 SER
Chi-restraints excluded: chain B residue  254 SER
Chi-restraints excluded: chain B residue  288 THR
Chi-restraints excluded: chain B residue  312 ILE
Chi-restraints excluded: chain B residue  326 LEU
Chi-restraints excluded: chain B residue  328 HIS
Chi-restraints excluded: chain B residue  401 VAL
Chi-restraints excluded: chain B residue  402 VAL
Chi-restraints excluded: chain B residue  439 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 80
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 21 optimal weight:    7.9990
   chunk 37 optimal weight:    0.5980
   chunk 69 optimal weight:    0.8980
   chunk 54 optimal weight:   10.0000
   chunk 11 optimal weight:    0.9980
   chunk 53 optimal weight:    9.9990
   chunk 63 optimal weight:    4.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.171205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.135566 restraints weight = 14288.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.137004 restraints weight = 11796.702|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.137840 restraints weight = 8657.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.138135 restraints weight = 6835.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.138703 restraints weight = 5940.081|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.3574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7973  Z= 0.125
  Angle     :  0.606  11.809  11152  Z= 0.322
  Chirality :  0.041   0.180   1221
  Planarity :  0.005   0.053   1133
  Dihedral  : 24.009 150.748   1748
  Min Nonbonded Distance : 2.366

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 23.14 %
    Favored  : 71.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.38 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.35 (0.31), residues: 712
  helix: -1.59 (0.32), residues: 249
  sheet: -0.90 (0.50), residues: 105
  loop : -1.68 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 370 
 TYR   0.027   0.001   TYR B 284 
 PHE   0.007   0.001   PHE B 352 
 TRP   0.019   0.002   TRP A 124 
 HIS   0.005   0.001   HIS B 110 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7973)
  covalent geometry    : angle       0.60606 (11152)
  hydrogen bonds       : bond        0.03248 (  161)
  hydrogen bonds       : angle       4.64156 (  435)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1024.12 seconds
wall clock time: 18 minutes 27.61 seconds (1107.61 seconds total)