Starting phenix.real_space_refine
on Tue Feb 11 13:31:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8tgh_41236/02_2025/8tgh_41236_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8tgh_41236/02_2025/8tgh_41236.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8tgh_41236/02_2025/8tgh_41236.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8tgh_41236/02_2025/8tgh_41236.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8tgh_41236/02_2025/8tgh_41236_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8tgh_41236/02_2025/8tgh_41236_trim.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      57      5.16       5
     C    3843      2.51       5
     N     900      2.21       5
     O     978      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 5778
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2860
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 384, 2860
          Classifications: {'peptide': 384}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 23, 'TRANS': 360}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 2864
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 383, 2864
          Classifications: {'peptide': 383}
          Link IDs: {'PTRANS': 21, 'TRANS': 361}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 10
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 10
          Unusual residues: {'1WE': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 44
          Unusual residues: {'YHR': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.09, per 1000 atoms: 0.88
  Number of scatterers: 5778
  At special positions: 0
  Unit cell: (77.688, 62.416, 114.872, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      57     16.00
     O     978      8.00
     N     900      7.00
     C    3843      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.51
  Conformation dependent library (CDL) restraints added in 874.5 milliseconds
  

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  1WE A 601 "
  Number of C-beta restraints generated:  1370

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 0 sheets defined
      90.7% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.64
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 51
      removed outlier: 3.868A  pdb=" N   VAL A  23 " --> pdb=" O   SER A  19 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   LEU A  24 " --> pdb=" O   ARG A  20 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   PHE A  38 " --> pdb=" O   ASP A  34 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL A  41 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   VAL A  42 " --> pdb=" O   PHE A  38 " (cutoff:3.500A)
      Proline residue:  A  43  - end of helix
      Proline residue:  A  46  - end of helix
      removed outlier: 3.828A  pdb=" N   TYR A  50 " --> pdb=" O   PRO A  46 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ASP A  51 " --> pdb=" O   THR A  47 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 144
      removed outlier: 3.506A  pdb=" N   LEU A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 154
    Processing helix  chain 'A' and resid 157 through 165
      removed outlier: 4.041A  pdb=" N   ASN A 162 " --> pdb=" O   GLY A 158 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ARG A 163 " --> pdb=" O   PRO A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 187
    Processing helix  chain 'A' and resid 189 through 219
      removed outlier: 3.766A  pdb=" N   VAL A 195 " --> pdb=" O   THR A 191 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   ALA A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 221 through 254
      removed outlier: 4.524A  pdb=" N   ALA A 244 " --> pdb=" O   LEU A 240 " (cutoff:3.500A)
      Proline residue:  A 245  - end of helix
    Processing helix  chain 'A' and resid 257 through 278
    Processing helix  chain 'A' and resid 292 through 297
      removed outlier: 3.793A  pdb=" N   LEU A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 299 through 331
      removed outlier: 3.715A  pdb=" N   LEU A 319 " --> pdb=" O   GLY A 315 " (cutoff:3.500A)
      Proline residue:  A 321  - end of helix
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 336 through 342
      removed outlier: 4.162A  pdb=" N   LEU A 340 " --> pdb=" O   TRP A 336 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   PHE A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 342 through 364
      removed outlier: 3.540A  pdb=" N   SER A 346 " --> pdb=" O   PHE A 342 " (cutoff:3.500A)
      removed outlier: 4.367A  pdb=" N   GLY A 357 " --> pdb=" O   THR A 353 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   VAL A 358 " --> pdb=" O   ASN A 354 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   LEU A 359 " --> pdb=" O   LEU A 355 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   ASN A 361 " --> pdb=" O   GLY A 357 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   LYS A 362 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 383
    Processing helix  chain 'A' and resid 384 through 386
      No H-bonds generated for 'chain 'A' and resid 384 through 386'
    Processing helix  chain 'A' and resid 388 through 391
    Processing helix  chain 'A' and resid 392 through 421
      Proline residue:  A 412  - end of helix
      removed outlier: 4.107A  pdb=" N   GLY A 415 " --> pdb=" O   MET A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 456
      removed outlier: 3.622A  pdb=" N   TYR A 430 " --> pdb=" O   TYR A 426 " (cutoff:3.500A)
      removed outlier: 4.321A  pdb=" N   GLY A 440 " --> pdb=" O   ALA A 436 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   PHE A 441 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
      Proline residue:  A 445  - end of helix
      removed outlier: 4.941A  pdb=" N   GLY A 449 " --> pdb=" O   PRO A 445 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 472
    Processing helix  chain 'A' and resid 473 through 479
      removed outlier: 3.524A  pdb=" N   TYR A 477 " --> pdb=" O   LEU A 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 40
      removed outlier: 4.098A  pdb=" N   VAL B  23 " --> pdb=" O   SER B  19 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU B  24 " --> pdb=" O   ARG B  20 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 44 through 54
      removed outlier: 3.768A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 131 through 165
      removed outlier: 4.120A  pdb=" N   GLU B 135 " --> pdb=" O   PHE B 131 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   THR B 137 " --> pdb=" O   GLU B 133 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   ARG B 138 " --> pdb=" O   GLU B 134 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   PHE B 143 " --> pdb=" O   VAL B 139 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   ALA B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   SER B 145 " --> pdb=" O   VAL B 141 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   LYS B 146 " --> pdb=" O   LEU B 142 " (cutoff:3.500A)
      removed outlier: 4.693A  pdb=" N   ALA B 147 " --> pdb=" O   PHE B 143 " (cutoff:3.500A)
      Proline residue:  B 155  - end of helix
      removed outlier: 4.407A  pdb=" N   GLY B 158 " --> pdb=" O   ASN B 154 " (cutoff:3.500A)
      Proline residue:  B 159  - end of helix
    Processing helix  chain 'B' and resid 166 through 187
      removed outlier: 3.540A  pdb=" N   GLY B 173 " --> pdb=" O   PRO B 169 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   PHE B 174 " --> pdb=" O   MET B 170 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ALA B 185 " --> pdb=" O   THR B 181 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 189 through 219
      removed outlier: 3.864A  pdb=" N   LEU B 193 " --> pdb=" O   THR B 189 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   PHE B 194 " --> pdb=" O   TYR B 190 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   VAL B 195 " --> pdb=" O   THR B 191 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 242
      removed outlier: 3.882A  pdb=" N   ARG B 227 " --> pdb=" O   HIS B 223 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   LEU B 236 " --> pdb=" O   ALA B 232 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   ALA B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   VAL B 242 " --> pdb=" O   LEU B 238 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 254
      removed outlier: 3.838A  pdb=" N   GLY B 247 " --> pdb=" O   GLY B 243 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   SER B 248 " --> pdb=" O   ALA B 244 " (cutoff:3.500A)
      removed outlier: 4.893A  pdb=" N   VAL B 249 " --> pdb=" O   PRO B 245 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLU B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   PHE B 253 " --> pdb=" O   VAL B 249 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 257 through 276
      removed outlier: 3.825A  pdb=" N   CYS B 276 " --> pdb=" O   ALA B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 297
    Processing helix  chain 'B' and resid 299 through 318
      removed outlier: 3.797A  pdb=" N   ALA B 305 " --> pdb=" O   TYR B 301 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   GLY B 315 " --> pdb=" O   PHE B 311 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   VAL B 316 " --> pdb=" O   ALA B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 322 through 331
    Processing helix  chain 'B' and resid 339 through 341
      No H-bonds generated for 'chain 'B' and resid 339 through 341'
    Processing helix  chain 'B' and resid 342 through 364
      removed outlier: 3.514A  pdb=" N   SER B 346 " --> pdb=" O   PHE B 342 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   TYR B 349 " --> pdb=" O   ALA B 345 " (cutoff:3.500A)
      removed outlier: 5.485A  pdb=" N   ASN B 361 " --> pdb=" O   GLY B 357 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   LYS B 362 " --> pdb=" O   VAL B 358 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   MET B 363 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 383
      removed outlier: 3.542A  pdb=" N   CYS B 368 " --> pdb=" O   GLY B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 386
      No H-bonds generated for 'chain 'B' and resid 384 through 386'
    Processing helix  chain 'B' and resid 388 through 391
    Processing helix  chain 'B' and resid 392 through 422
      removed outlier: 3.617A  pdb=" N   ALA B 397 " --> pdb=" O   ILE B 393 " (cutoff:3.500A)
      removed outlier: 4.114A  pdb=" N   MET B 411 " --> pdb=" O   ASP B 407 " (cutoff:3.500A)
      Proline residue:  B 412  - end of helix
    Processing helix  chain 'B' and resid 427 through 455
      removed outlier: 3.552A  pdb=" N   ILE B 432 " --> pdb=" O   SER B 428 " (cutoff:3.500A)
      Proline residue:  B 445  - end of helix
      removed outlier: 3.879A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 472
      removed outlier: 3.692A  pdb=" N   LEU B 460 " --> pdb=" O   GLY B 456 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   MET B 461 " --> pdb=" O   PHE B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 479

    441 hydrogen bonds defined for protein.
    1296 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.73

  Time building geometry restraints manager: 1.73 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 861
        1.28 -     1.41: 1471
        1.41 -     1.54: 3480
        1.54 -     1.68: 10
        1.68 -     1.81: 100
  Bond restraints: 5922
  Sorted by residual:
  bond pdb=" C   ALA B 244 "
       pdb=" O   ALA B 244 "
    ideal  model  delta    sigma   weight residual
    1.244  1.157  0.087 1.00e-02 1.00e+04 7.62e+01
  bond pdb=" C   LEU B 238 "
       pdb=" O   LEU B 238 "
    ideal  model  delta    sigma   weight residual
    1.237  1.161  0.075 1.17e-02 7.31e+03 4.13e+01
  bond pdb=" C   PRO B 245 "
       pdb=" O   PRO B 245 "
    ideal  model  delta    sigma   weight residual
    1.236  1.144  0.092 1.76e-02 3.23e+03 2.71e+01
  bond pdb=" C   GLY B 243 "
       pdb=" O   GLY B 243 "
    ideal  model  delta    sigma   weight residual
    1.235  1.166  0.069 1.35e-02 5.49e+03 2.62e+01
  bond pdb=" C   VAL B 242 "
       pdb=" O   VAL B 242 "
    ideal  model  delta    sigma   weight residual
    1.230  1.161  0.069 1.57e-02 4.06e+03 1.92e+01
  ... (remaining 5917 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.69: 7998
        3.69 -     7.37: 61
        7.37 -    11.06: 6
       11.06 -    14.74: 0
       14.74 -    18.43: 1
  Bond angle restraints: 8066
  Sorted by residual:
  angle pdb=" CA  ALA B 244 "
        pdb=" C   ALA B 244 "
        pdb=" O   ALA B 244 "
      ideal   model   delta    sigma   weight residual
     118.79  110.51    8.28 9.60e-01 1.09e+00 7.45e+01
  angle pdb=" C7  YHR B 601 "
        pdb=" N8  YHR B 601 "
        pdb=" C9  YHR B 601 "
      ideal   model   delta    sigma   weight residual
     111.89  130.32  -18.43 3.00e+00 1.11e-01 3.77e+01
  angle pdb=" N   GLY A 243 "
        pdb=" CA  GLY A 243 "
        pdb=" C   GLY A 243 "
      ideal   model   delta    sigma   weight residual
     112.50  119.23   -6.73 1.16e+00 7.43e-01 3.36e+01
  angle pdb=" C   VAL B 242 "
        pdb=" CA  VAL B 242 "
        pdb=" CB  VAL B 242 "
      ideal   model   delta    sigma   weight residual
     112.19  106.43    5.76 1.15e+00 7.56e-01 2.51e+01
  angle pdb=" CA  LEU B 241 "
        pdb=" C   LEU B 241 "
        pdb=" O   LEU B 241 "
      ideal   model   delta    sigma   weight residual
     120.82  116.34    4.48 1.05e+00 9.07e-01 1.82e+01
  ... (remaining 8061 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.14: 3124
       23.14 -    46.28: 314
       46.28 -    69.42: 28
       69.42 -    92.56: 9
       92.56 -   115.70: 1
  Dihedral angle restraints: 3476
    sinusoidal: 1320
      harmonic: 2156
  Sorted by residual:
  dihedral pdb=" CA  VAL B 358 "
           pdb=" C   VAL B 358 "
           pdb=" N   LEU B 359 "
           pdb=" CA  LEU B 359 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.14  -19.86     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  PRO A  43 "
           pdb=" C   PRO A  43 "
           pdb=" N   ILE A  44 "
           pdb=" CA  ILE A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.18  -19.82     0      5.00e+00 4.00e-02 1.57e+01
  dihedral pdb=" C13 YHR B 601 "
           pdb=" C7  YHR B 601 "
           pdb=" N8  YHR B 601 "
           pdb=" C6  YHR B 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.66  -58.04  115.70     1      3.00e+01 1.11e-03 1.53e+01
  ... (remaining 3473 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 877
       0.078 -    0.156: 85
       0.156 -    0.234: 5
       0.234 -    0.312: 0
       0.312 -    0.389: 2
  Chirality restraints: 969
  Sorted by residual:
  chirality pdb=" C13 YHR B 601 "
            pdb=" C12 YHR B 601 "
            pdb=" C14 YHR B 601 "
            pdb=" N8  YHR B 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.68    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CG  LEU A 381 "
            pdb=" CB  LEU A 381 "
            pdb=" CD1 LEU A 381 "
            pdb=" CD2 LEU A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.23   -0.36 2.00e-01 2.50e+01 3.21e+00
  chirality pdb=" CA  VAL B 242 "
            pdb=" N   VAL B 242 "
            pdb=" C   VAL B 242 "
            pdb=" CB  VAL B 242 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.24e+00
  ... (remaining 966 not shown)

  Planarity restraints: 983
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  42 "    0.088 5.00e-02 4.00e+02   1.31e-01 2.76e+01
        pdb=" N   PRO A  43 "   -0.227 5.00e-02 4.00e+02
        pdb=" CA  PRO A  43 "    0.070 5.00e-02 4.00e+02
        pdb=" CD  PRO A  43 "    0.069 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 244 "   -0.022 2.00e-02 2.50e+03   4.53e-02 2.05e+01
        pdb=" C   ALA B 244 "    0.078 2.00e-02 2.50e+03
        pdb=" O   ALA B 244 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   PRO B 245 "   -0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 472 "   -0.056 5.00e-02 4.00e+02   8.48e-02 1.15e+01
        pdb=" N   PRO A 473 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO A 473 "   -0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 473 "   -0.047 5.00e-02 4.00e+02
  ... (remaining 980 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1562
        2.80 -     3.32: 5507
        3.32 -     3.85: 9391
        3.85 -     4.37: 10124
        4.37 -     4.90: 18688
  Nonbonded interactions: 45272
  Sorted by model distance:
  nonbonded pdb=" O   MET A 183 "
            pdb=" OG  SER A 187 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" OE1 GLU B 135 "
            pdb=" NH1 ARG B 138 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OD1 ASP A 299 "
            pdb=" NH1 ARG A 421 "
     model   vdw
     2.291 3.120
  nonbonded pdb=" OD2 ASP A 299 "
            pdb=" NE2 HIS A 422 "
     model   vdw
     2.299 3.120
  nonbonded pdb=" OD1 ASN A 313 "
            pdb=" N   1WE A 601 "
     model   vdw
     2.309 3.120
  ... (remaining 45267 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 19 through 278 or resid 289 through 482))
  selection = (chain 'B' and (resid 19 through 51 or resid 136 through 482))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.600
  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:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.500
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.690
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
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      :  0.007   0.092   5922  Z= 0.439
  Angle     :  0.812  18.427   8066  Z= 0.452
  Chirality :  0.049   0.389    969
  Planarity :  0.010   0.131    983
  Dihedral  : 17.208 115.698   2106
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 29.92 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.29), residues: 757
  helix:  0.97 (0.21), residues: 577
  sheet:  None (None), residues: 0
  loop : -1.28 (0.40), residues: 180

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 336 
 HIS   0.001   0.001   HIS A 167 
 PHE   0.033   0.002   PHE B 131 
 TYR   0.029   0.002   TYR B 190 
 ARG   0.006   0.001   ARG B 479 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 123
  time to evaluate  : 0.588 
Fit side-chains
  outliers start: 6
  outliers final: 1
  residues processed: 128
  average time/residue: 0.1202
  time to fit residues: 22.4286
Evaluate side-chains
  124 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  241 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 31 optimal weight:    0.5980
   chunk 19 optimal weight:    0.0020
   chunk 38 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9980
   chunk 69 optimal weight:    0.6980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 274 GLN
B 313 ASN
B 329 GLN
B 468 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.099691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.090484 restraints weight = 8201.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.093376 restraints weight = 3754.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.095188 restraints weight = 2073.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.1043

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   5922  Z= 0.245
  Angle     :  0.647   8.784   8066  Z= 0.322
  Chirality :  0.043   0.146    969
  Planarity :  0.007   0.077    983
  Dihedral  :  6.465  67.088    874
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 4.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  3.90 %
    Allowed  : 26.18 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.30), residues: 757
  helix:  1.71 (0.22), residues: 595
  sheet:  None (None), residues: 0
  loop : -1.17 (0.41), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 336 
 HIS   0.001   0.000   HIS A 223 
 PHE   0.017   0.001   PHE B 356 
 TYR   0.013   0.001   TYR A 430 
 ARG   0.003   0.000   ARG B 479 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 139
  time to evaluate  : 0.569 
Fit side-chains
REVERT: A  200 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7465 (tm-30)
REVERT: B  149 MET cc_start: 0.7088 (tpp) cc_final: 0.6643 (tpp)
REVERT: B  153 VAL cc_start: 0.7822 (p) cc_final: 0.7563 (t)
REVERT: B  168 ILE cc_start: 0.8421 (mp) cc_final: 0.8162 (mt)
  outliers start: 24
  outliers final: 8
  residues processed: 157
  average time/residue: 0.1196
  time to fit residues: 27.4640
Evaluate side-chains
  144 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 135
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 GLN
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  387 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 54 optimal weight:    0.7980
   chunk 47 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 67 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 51 optimal weight:    0.9990
   chunk 0 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 41 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN
B 200 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.098644 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.089372 restraints weight = 8265.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.092217 restraints weight = 3783.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.094052 restraints weight = 2115.385|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1237

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046   5922  Z= 0.297
  Angle     :  0.645   8.417   8066  Z= 0.318
  Chirality :  0.044   0.160    969
  Planarity :  0.006   0.061    983
  Dihedral  :  5.693  58.119    872
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 26.99 %
    Favored  : 70.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.31), residues: 757
  helix:  1.81 (0.22), residues: 591
  sheet:  None (None), residues: 0
  loop : -1.40 (0.41), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 223 
 PHE   0.020   0.002   PHE A 184 
 TYR   0.014   0.002   TYR A 476 
 ARG   0.003   0.000   ARG B 479 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A   38 PHE cc_start: 0.8452 (t80) cc_final: 0.8233 (t80)
REVERT: B  149 MET cc_start: 0.7091 (tpp) cc_final: 0.6720 (tpp)
REVERT: B  153 VAL cc_start: 0.7822 (p) cc_final: 0.7559 (t)
REVERT: B  168 ILE cc_start: 0.8403 (mp) cc_final: 0.8145 (mt)
  outliers start: 17
  outliers final: 15
  residues processed: 146
  average time/residue: 0.1189
  time to fit residues: 25.1931
Evaluate side-chains
  152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 137
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 13 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 44 optimal weight:    0.0270
   chunk 53 optimal weight:    0.0050
   chunk 34 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 38 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   overall best weight:    0.4252

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.100009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.090616 restraints weight = 8359.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.093507 restraints weight = 3802.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.095349 restraints weight = 2111.023|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7597
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5922  Z= 0.220
  Angle     :  0.615   7.585   8066  Z= 0.303
  Chirality :  0.042   0.147    969
  Planarity :  0.006   0.055    983
  Dihedral  :  5.309  50.044    872
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 3.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 26.99 %
    Favored  : 69.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.90 (0.31), residues: 757
  helix:  1.97 (0.22), residues: 591
  sheet:  None (None), residues: 0
  loop : -1.40 (0.41), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 336 
 HIS   0.001   0.000   HIS B 416 
 PHE   0.021   0.001   PHE B 356 
 TYR   0.013   0.001   TYR B 349 
 ARG   0.002   0.000   ARG B 479 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 133
  time to evaluate  : 0.577 
Fit side-chains
REVERT: A   38 PHE cc_start: 0.8455 (t80) cc_final: 0.8220 (t80)
REVERT: B  149 MET cc_start: 0.7112 (tpp) cc_final: 0.6724 (tpp)
REVERT: B  153 VAL cc_start: 0.7765 (p) cc_final: 0.7501 (t)
REVERT: B  168 ILE cc_start: 0.8296 (mp) cc_final: 0.8046 (mt)
  outliers start: 19
  outliers final: 16
  residues processed: 144
  average time/residue: 0.1149
  time to fit residues: 24.2606
Evaluate side-chains
  147 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 11 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9990
   chunk 9 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 73 optimal weight:    0.9980
   chunk 70 optimal weight:    3.9990
   chunk 55 optimal weight:    0.5980
   chunk 21 optimal weight:    0.6980
   chunk 46 optimal weight:    0.5980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.098177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.088883 restraints weight = 8263.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.091714 restraints weight = 3775.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.093526 restraints weight = 2111.453|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   5922  Z= 0.318
  Angle     :  0.642   7.827   8066  Z= 0.317
  Chirality :  0.044   0.161    969
  Planarity :  0.006   0.056    983
  Dihedral  :  5.047  45.756    872
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 26.83 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.31), residues: 757
  helix:  1.93 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.39 (0.41), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 223 
 PHE   0.023   0.002   PHE B 356 
 TYR   0.014   0.002   TYR B 471 
 ARG   0.003   0.000   ARG B 479 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A   38 PHE cc_start: 0.8434 (t80) cc_final: 0.8202 (t80)
REVERT: A  177 MET cc_start: 0.7601 (ttp) cc_final: 0.7337 (ttp)
REVERT: A  240 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8271 (mp)
REVERT: B   40 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7393 (t)
REVERT: B  149 MET cc_start: 0.7066 (tpp) cc_final: 0.6696 (tpp)
REVERT: B  153 VAL cc_start: 0.7809 (p) cc_final: 0.7545 (t)
REVERT: B  168 ILE cc_start: 0.8351 (mp) cc_final: 0.8086 (mt)
  outliers start: 25
  outliers final: 18
  residues processed: 150
  average time/residue: 0.1267
  time to fit residues: 27.3415
Evaluate side-chains
  150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 130
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  368 CYS
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 0 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0470
   chunk 36 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 1 optimal weight:    0.5980
   chunk 68 optimal weight:    0.8980
   chunk 61 optimal weight:    0.7980
   chunk 6 optimal weight:    0.4980
   chunk 12 optimal weight:    0.7980
   chunk 3 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.099136 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.089567 restraints weight = 8301.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.092487 restraints weight = 3724.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.094363 restraints weight = 2053.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   5922  Z= 0.244
  Angle     :  0.616   7.335   8066  Z= 0.305
  Chirality :  0.043   0.152    969
  Planarity :  0.006   0.055    983
  Dihedral  :  4.949  44.241    872
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.83 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.31), residues: 757
  helix:  2.03 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.39 (0.42), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 336 
 HIS   0.001   0.000   HIS B 416 
 PHE   0.020   0.001   PHE B 356 
 TYR   0.011   0.001   TYR A 476 
 ARG   0.001   0.000   ARG B 421 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 128
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A   38 PHE cc_start: 0.8431 (t80) cc_final: 0.8193 (t80)
REVERT: A  240 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8269 (mp)
REVERT: B   40 VAL cc_start: 0.7745 (OUTLIER) cc_final: 0.7377 (t)
REVERT: B  149 MET cc_start: 0.7035 (tpp) cc_final: 0.6658 (tpp)
REVERT: B  153 VAL cc_start: 0.7846 (p) cc_final: 0.7569 (t)
REVERT: B  168 ILE cc_start: 0.8322 (mp) cc_final: 0.8049 (mt)
  outliers start: 28
  outliers final: 21
  residues processed: 148
  average time/residue: 0.1211
  time to fit residues: 26.0044
Evaluate side-chains
  149 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 126
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  368 CYS
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 70 optimal weight:    0.1980
   chunk 5 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 2 optimal weight:    0.7980
   chunk 8 optimal weight:    0.4980
   chunk 3 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.099075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.089303 restraints weight = 8382.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.092260 restraints weight = 3747.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.094172 restraints weight = 2069.318|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7625
moved from start:          0.1553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   5922  Z= 0.257
  Angle     :  0.618   7.196   8066  Z= 0.306
  Chirality :  0.043   0.155    969
  Planarity :  0.006   0.055    983
  Dihedral  :  4.857  44.504    872
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  4.55 %
    Allowed  : 26.99 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.31), residues: 757
  helix:  2.03 (0.22), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.34 (0.44), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 336 
 HIS   0.001   0.000   HIS B 223 
 PHE   0.021   0.001   PHE B 356 
 TYR   0.015   0.001   TYR B 471 
 ARG   0.001   0.000   ARG B 421 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 130
  time to evaluate  : 0.560 
Fit side-chains
REVERT: A  177 MET cc_start: 0.7547 (ttp) cc_final: 0.7314 (ttp)
REVERT: A  240 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8292 (mp)
REVERT: B   40 VAL cc_start: 0.7782 (OUTLIER) cc_final: 0.7427 (t)
REVERT: B  149 MET cc_start: 0.7014 (tpp) cc_final: 0.6642 (tpp)
REVERT: B  153 VAL cc_start: 0.7854 (p) cc_final: 0.7577 (t)
REVERT: B  168 ILE cc_start: 0.8325 (mp) cc_final: 0.8050 (mt)
REVERT: B  479 ARG cc_start: 0.6857 (OUTLIER) cc_final: 0.6580 (ptt-90)
  outliers start: 28
  outliers final: 20
  residues processed: 151
  average time/residue: 0.1170
  time to fit residues: 25.6036
Evaluate side-chains
  148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 125
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  423 THR
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  316 VAL
Chi-restraints excluded: chain B residue  368 CYS
Chi-restraints excluded: chain B residue  474 LEU
Chi-restraints excluded: chain B residue  479 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 58 optimal weight:    0.6980
   chunk 23 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9990
   chunk 66 optimal weight:    0.0670
   chunk 52 optimal weight:    0.5980
   chunk 35 optimal weight:    0.0670
   chunk 53 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0980
   chunk 36 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   overall best weight:    0.2056

-------------------------------------------------------------------------------
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 = 0.3249 r_free = 0.3249 target = 0.101651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.092202 restraints weight = 8274.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.095063 restraints weight = 3755.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.096882 restraints weight = 2084.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.1703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5922  Z= 0.170
  Angle     :  0.602   6.534   8066  Z= 0.295
  Chirality :  0.041   0.150    969
  Planarity :  0.005   0.054    983
  Dihedral  :  4.816  42.755    872
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.15 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.31), residues: 757
  helix:  2.19 (0.22), residues: 593
  sheet:  None (None), residues: 0
  loop : -1.30 (0.44), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 336 
 HIS   0.001   0.000   HIS A 422 
 PHE   0.020   0.001   PHE B 131 
 TYR   0.009   0.001   TYR A 430 
 ARG   0.001   0.000   ARG B 421 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.640 
Fit side-chains
REVERT: A  177 MET cc_start: 0.7524 (ttp) cc_final: 0.7307 (ttp)
REVERT: A  240 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8305 (mp)
REVERT: A  359 LEU cc_start: 0.8361 (mt) cc_final: 0.8157 (mp)
REVERT: B   40 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7393 (t)
REVERT: B  149 MET cc_start: 0.6994 (tpp) cc_final: 0.6629 (tpp)
REVERT: B  153 VAL cc_start: 0.7895 (p) cc_final: 0.7636 (t)
REVERT: B  168 ILE cc_start: 0.8255 (mp) cc_final: 0.7997 (mt)
REVERT: B  331 MET cc_start: 0.8087 (mtm) cc_final: 0.7869 (mtm)
  outliers start: 26
  outliers final: 19
  residues processed: 142
  average time/residue: 0.1199
  time to fit residues: 24.6067
Evaluate side-chains
  148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 127
  time to evaluate  : 0.623 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  368 CYS
Chi-restraints excluded: chain B residue  387 HIS
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 7 optimal weight:    0.8980
   chunk 35 optimal weight:    0.0870
   chunk 22 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0970
   chunk 70 optimal weight:    0.2980
   chunk 3 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.3956

-------------------------------------------------------------------------------
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 = 0.3237 r_free = 0.3237 target = 0.100952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.091427 restraints weight = 8322.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.094405 restraints weight = 3719.653|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.096290 restraints weight = 2032.009|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7593
moved from start:          0.1773

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   5922  Z= 0.212
  Angle     :  0.611   6.613   8066  Z= 0.299
  Chirality :  0.042   0.153    969
  Planarity :  0.006   0.053    983
  Dihedral  :  4.744  44.396    872
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 27.97 %
    Favored  : 68.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.23 (0.31), residues: 757
  helix:  2.20 (0.22), residues: 593
  sheet:  None (None), residues: 0
  loop : -1.31 (0.44), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B 336 
 HIS   0.001   0.000   HIS A 422 
 PHE   0.021   0.001   PHE B 356 
 TYR   0.015   0.001   TYR B 471 
 ARG   0.002   0.000   ARG A 197 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 131
  time to evaluate  : 0.590 
Fit side-chains
REVERT: A  240 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8270 (mp)
REVERT: A  359 LEU cc_start: 0.8352 (mt) cc_final: 0.8146 (mp)
REVERT: B   40 VAL cc_start: 0.7719 (OUTLIER) cc_final: 0.7378 (t)
REVERT: B  149 MET cc_start: 0.7020 (tpp) cc_final: 0.6634 (tpp)
REVERT: B  153 VAL cc_start: 0.7880 (p) cc_final: 0.7618 (t)
REVERT: B  168 ILE cc_start: 0.8256 (mp) cc_final: 0.7986 (mt)
  outliers start: 23
  outliers final: 19
  residues processed: 144
  average time/residue: 0.1202
  time to fit residues: 24.9525
Evaluate side-chains
  150 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 129
  time to evaluate  : 0.620 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  179 LEU
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  368 CYS
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 10 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 4 optimal weight:    0.5980
   chunk 72 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 71 optimal weight:    0.6980
   chunk 16 optimal weight:    0.4980
   chunk 73 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.099561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.090038 restraints weight = 8366.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.092964 restraints weight = 3788.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.094817 restraints weight = 2093.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   5922  Z= 0.279
  Angle     :  0.635   6.893   8066  Z= 0.311
  Chirality :  0.044   0.165    969
  Planarity :  0.006   0.053    983
  Dihedral  :  4.767  44.491    872
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 27.80 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.31), residues: 757
  helix:  2.10 (0.22), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.40 (0.44), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 387 
 PHE   0.023   0.002   PHE B 356 
 TYR   0.014   0.002   TYR B 166 
 ARG   0.001   0.000   ARG B 421 

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

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

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1514 Ramachandran restraints generated.
    757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 129
  time to evaluate  : 0.650 
Fit side-chains
REVERT: A  240 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8248 (mp)
REVERT: B   40 VAL cc_start: 0.7747 (OUTLIER) cc_final: 0.7413 (t)
REVERT: B  149 MET cc_start: 0.7011 (tpp) cc_final: 0.6648 (tpp)
REVERT: B  153 VAL cc_start: 0.7889 (p) cc_final: 0.7617 (t)
REVERT: B  168 ILE cc_start: 0.8295 (mp) cc_final: 0.8010 (mt)
  outliers start: 22
  outliers final: 20
  residues processed: 143
  average time/residue: 0.1168
  time to fit residues: 24.8610
Evaluate side-chains
  148 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.564 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 SER
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  269 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  284 SER
Chi-restraints excluded: chain A residue  291 THR
Chi-restraints excluded: chain A residue  318 ILE
Chi-restraints excluded: chain A residue  381 LEU
Chi-restraints excluded: chain A residue  408 SER
Chi-restraints excluded: chain A residue  435 VAL
Chi-restraints excluded: chain A residue  437 PHE
Chi-restraints excluded: chain A residue  474 LEU
Chi-restraints excluded: chain A residue  477 TYR
Chi-restraints excluded: chain B residue   25 VAL
Chi-restraints excluded: chain B residue   35 ASN
Chi-restraints excluded: chain B residue   40 VAL
Chi-restraints excluded: chain B residue  132 LEU
Chi-restraints excluded: chain B residue  137 THR
Chi-restraints excluded: chain B residue  171 PHE
Chi-restraints excluded: chain B residue  268 LEU
Chi-restraints excluded: chain B residue  368 CYS
Chi-restraints excluded: chain B residue  474 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 60 optimal weight:    0.3980
   chunk 47 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 8 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 31 optimal weight:    0.3980
   chunk 24 optimal weight:    0.9990
   chunk 62 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
B  35 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.099371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.089836 restraints weight = 8464.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.092780 restraints weight = 3812.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.094549 restraints weight = 2100.066|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7620
moved from start:          0.1746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.126   5922  Z= 0.303
  Angle     :  1.112  59.146   8066  Z= 0.655
  Chirality :  0.043   0.176    969
  Planarity :  0.006   0.053    983
  Dihedral  :  4.808  44.595    872
  Min Nonbonded Distance : 1.843

Molprobity Statistics.
  All-atom Clashscore : 5.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  4.23 %
    Allowed  : 27.15 %
    Favored  : 68.62 %
  Cbeta Deviations :  0.15 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.31), residues: 757
  helix:  2.10 (0.22), residues: 590
  sheet:  None (None), residues: 0
  loop : -1.43 (0.43), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 366 
 HIS   0.001   0.000   HIS B 387 
 PHE   0.022   0.001   PHE B 356 
 TYR   0.012   0.002   TYR B 166 
 ARG   0.002   0.000   ARG B 479 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1994.74 seconds
wall clock time: 36 minutes 38.17 seconds (2198.17 seconds total)