Starting phenix.real_space_refine
on Wed Sep 17 08:59:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbj_61316/09_2025/9jbj_61316.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbj_61316/09_2025/9jbj_61316.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.73
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbj_61316/09_2025/9jbj_61316.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbj_61316/09_2025/9jbj_61316.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbj_61316/09_2025/9jbj_61316.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbj_61316/09_2025/9jbj_61316.map"
  }
  resolution = 3.73
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.009
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      45      5.16       5
     C    4795      2.51       5
     N    1096      2.21       5
     O    1257      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7193
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3578
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 477, 3578
          Classifications: {'peptide': 477}
          Incomplete info: {'truncation_to_alanine': 28}
          Link IDs: {'PTRANS': 17, 'TRANS': 459}
          Chain breaks: 9
          Unresolved non-hydrogen bonds: 156
          Unresolved non-hydrogen angles: 208
          Unresolved non-hydrogen dihedrals: 150
          Unresolved non-hydrogen chiralities: 12
          Planarities with less than four sites: {'PHE:plan': 6, 'ASP:plan': 1, 'TYR:plan': 2, 'TRP:plan': 4, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 94
    Chain: "B"
      Number of atoms: 3615
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 478, 3615
          Classifications: {'peptide': 478}
          Incomplete info: {'truncation_to_alanine': 21}
          Link IDs: {'PTRANS': 17, 'TRANS': 460}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 122
          Unresolved non-hydrogen angles: 164
          Unresolved non-hydrogen dihedrals: 118
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASP:plan': 1, 'TRP:plan': 3, 'ARG:plan': 1, 'PHE:plan': 4}
          Unresolved non-hydrogen planarities: 84
  Time building chain proxies: 1.94, per 1000 atoms: 0.27
  Number of scatterers: 7193
  At special positions: 0
  Unit cell: (99.9, 128.02, 70.3, 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      45     16.00
     O    1257      8.00
     N    1096      7.00
     C    4795      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 359.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1790

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 0 sheets defined
      79.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 61
    Processing helix  chain 'A' and resid 66 through 75
      removed outlier: 3.540A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 91
    Processing helix  chain 'A' and resid 99 through 124
      removed outlier: 3.513A  pdb=" N   LEU A 103 " --> pdb=" O   ASP A  99 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 143
      removed outlier: 3.565A  pdb=" N   LYS A 133 " --> pdb=" O   SER A 129 " (cutoff:3.500A)
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 158
      removed outlier: 4.017A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 196
      removed outlier: 3.510A  pdb=" N   TYR A 168 " --> pdb=" O   GLU A 164 " (cutoff:3.500A)
      removed outlier: 4.271A  pdb=" N   ALA A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
      removed outlier: 3.802A  pdb=" N   LEU A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   ASN A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      Proline residue:  A 182  - end of helix
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 220 through 233
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 4.122A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
    Processing helix  chain 'A' and resid 273 through 287
    Processing helix  chain 'A' and resid 288 through 302
      removed outlier: 3.670A  pdb=" N   LEU A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 320
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 3.989A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 367
      removed outlier: 3.603A  pdb=" N   THR A 351 " --> pdb=" O   MET A 347 " (cutoff:3.500A)
      Proline residue:  A 356  - end of helix
      removed outlier: 3.836A  pdb=" N   THR A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 398
    Processing helix  chain 'A' and resid 414 through 435
    Processing helix  chain 'A' and resid 449 through 461
      removed outlier: 3.737A  pdb=" N   SER A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LEU A 459 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   THR A 461 " --> pdb=" O   THR A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 490
    Processing helix  chain 'A' and resid 492 through 499
    Processing helix  chain 'A' and resid 518 through 532
    Processing helix  chain 'A' and resid 666 through 676
      removed outlier: 3.688A  pdb=" N   PHE A 670 " --> pdb=" O   ILE A 666 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   SER A 674 " --> pdb=" O   PHE A 670 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 691 through 702
      removed outlier: 4.037A  pdb=" N   VAL A 698 " --> pdb=" O   PHE A 694 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   PHE A 699 " --> pdb=" O   PHE A 695 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ASN A 700 " --> pdb=" O   CYS A 696 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 704 through 710
    Processing helix  chain 'B' and resid 41 through 63
      removed outlier: 3.755A  pdb=" N   LEU B  54 " --> pdb=" O   PHE B  50 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA B  59 " --> pdb=" O   CYS B  55 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 80
      removed outlier: 4.018A  pdb=" N   GLY B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 4.012A  pdb=" N   LEU B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 91
    Processing helix  chain 'B' and resid 99 through 124
      removed outlier: 3.610A  pdb=" N   LEU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 137
    Processing helix  chain 'B' and resid 138 through 143
    Processing helix  chain 'B' and resid 149 through 158
      removed outlier: 3.660A  pdb=" N   ILE B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 196
      removed outlier: 3.632A  pdb=" N   TYR B 168 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ALA B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      removed outlier: 3.902A  pdb=" N   LEU B 180 " --> pdb=" O   SER B 176 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ASN B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      Proline residue:  B 182  - end of helix
    Processing helix  chain 'B' and resid 209 through 216
      removed outlier: 4.064A  pdb=" N   VAL B 214 " --> pdb=" O   GLY B 210 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 220 through 233
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 4.024A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 5.112A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 264
    Processing helix  chain 'B' and resid 273 through 284
    Processing helix  chain 'B' and resid 288 through 302
      removed outlier: 4.094A  pdb=" N   LEU B 292 " --> pdb=" O   LEU B 288 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 320
    Processing helix  chain 'B' and resid 327 through 337
    Processing helix  chain 'B' and resid 340 through 367
      removed outlier: 3.876A  pdb=" N   THR B 351 " --> pdb=" O   MET B 347 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
      removed outlier: 3.559A  pdb=" N   THR B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 375 through 398
      removed outlier: 3.561A  pdb=" N   GLN B 380 " --> pdb=" O   ALA B 376 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL B 389 " --> pdb=" O   ASP B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 435
      removed outlier: 3.526A  pdb=" N   LEU B 419 " --> pdb=" O   THR B 415 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL B 425 " --> pdb=" O   ALA B 421 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   MET B 430 " --> pdb=" O   CYS B 426 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ILE B 431 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 449 through 461
      removed outlier: 3.711A  pdb=" N   SER B 453 " --> pdb=" O   LEU B 449 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   LEU B 459 " --> pdb=" O   TYR B 455 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   THR B 461 " --> pdb=" O   THR B 457 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 490
    Processing helix  chain 'B' and resid 492 through 499
    Processing helix  chain 'B' and resid 518 through 533
      removed outlier: 3.598A  pdb=" N   ILE B 522 " --> pdb=" O   LYS B 518 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   THR B 523 " --> pdb=" O   GLU B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 667 through 676
      removed outlier: 3.848A  pdb=" N   ALA B 671 " --> pdb=" O   ILE B 667 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   SER B 674 " --> pdb=" O   PHE B 670 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 691 through 701
      removed outlier: 3.777A  pdb=" N   VAL B 698 " --> pdb=" O   PHE B 694 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   PHE B 699 " --> pdb=" O   PHE B 695 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   ASN B 700 " --> pdb=" O   CYS B 696 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 704 through 710
      removed outlier: 3.765A  pdb=" N   PHE B 708 " --> pdb=" O   GLY B 704 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLY B 709 " --> pdb=" O   PHE B 705 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1428 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.81

  Time building geometry restraints manager: 0.85 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: 1314
        1.33 -     1.45: 1762
        1.45 -     1.57: 4191
        1.57 -     1.69: 0
        1.69 -     1.82: 72
  Bond restraints: 7339
  Sorted by residual:
  bond pdb=" N   VAL A  77 "
       pdb=" CA  VAL A  77 "
    ideal  model  delta    sigma   weight residual
    1.456  1.496 -0.039 1.08e-02 8.57e+03 1.34e+01
  bond pdb=" N   LEU A 677 "
       pdb=" CA  LEU A 677 "
    ideal  model  delta    sigma   weight residual
    1.458  1.488 -0.030 9.00e-03 1.23e+04 1.11e+01
  bond pdb=" N   VAL A  91 "
       pdb=" CA  VAL A  91 "
    ideal  model  delta    sigma   weight residual
    1.462  1.497 -0.034 1.06e-02 8.90e+03 1.05e+01
  bond pdb=" N   LEU A  82 "
       pdb=" CA  LEU A  82 "
    ideal  model  delta    sigma   weight residual
    1.462  1.489 -0.027 8.50e-03 1.38e+04 1.04e+01
  bond pdb=" N   VAL A 241 "
       pdb=" CA  VAL A 241 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.09e-02 8.42e+03 8.99e+00
  ... (remaining 7334 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.07: 9143
        2.07 -     4.13: 765
        4.13 -     6.20: 61
        6.20 -     8.26: 8
        8.26 -    10.33: 4
  Bond angle restraints: 9981
  Sorted by residual:
  angle pdb=" N   ILE A 190 "
        pdb=" CA  ILE A 190 "
        pdb=" C   ILE A 190 "
      ideal   model   delta    sigma   weight residual
     110.72  106.24    4.48 1.01e+00 9.80e-01 1.97e+01
  angle pdb=" N   THR B 284 "
        pdb=" CA  THR B 284 "
        pdb=" C   THR B 284 "
      ideal   model   delta    sigma   weight residual
     113.20  107.94    5.26 1.21e+00 6.83e-01 1.89e+01
  angle pdb=" C   ASN B 198 "
        pdb=" CA  ASN B 198 "
        pdb=" CB  ASN B 198 "
      ideal   model   delta    sigma   weight residual
     116.63  111.65    4.98 1.16e+00 7.43e-01 1.84e+01
  angle pdb=" N   TYR A 455 "
        pdb=" CA  TYR A 455 "
        pdb=" C   TYR A 455 "
      ideal   model   delta    sigma   weight residual
     111.82  107.19    4.63 1.16e+00 7.43e-01 1.59e+01
  angle pdb=" CA  THR B  66 "
        pdb=" C   THR B  66 "
        pdb=" O   THR B  66 "
      ideal   model   delta    sigma   weight residual
     121.98  117.52    4.46 1.13e+00 7.83e-01 1.56e+01
  ... (remaining 9976 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.69: 3621
       14.69 -    29.38: 436
       29.38 -    44.07: 164
       44.07 -    58.76: 35
       58.76 -    73.45: 17
  Dihedral angle restraints: 4273
    sinusoidal: 1518
      harmonic: 2755
  Sorted by residual:
  dihedral pdb=" CA  ASN A 337 "
           pdb=" CB  ASN A 337 "
           pdb=" CG  ASN A 337 "
           pdb=" OD1 ASN A 337 "
      ideal   model   delta sinusoidal    sigma   weight residual
     120.00 -175.37  -64.63     2      2.00e+01 2.50e-03 9.80e+00
  dihedral pdb=" N   ASN B 181 "
           pdb=" CA  ASN B 181 "
           pdb=" CB  ASN B 181 "
           pdb=" CG  ASN B 181 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -115.55   55.55     3      1.50e+01 4.44e-03 9.35e+00
  dihedral pdb=" CB  MET B 264 "
           pdb=" CG  MET B 264 "
           pdb=" SD  MET B 264 "
           pdb=" CE  MET B 264 "
      ideal   model   delta sinusoidal    sigma   weight residual
      60.00    6.74   53.26     3      1.50e+01 4.44e-03 9.19e+00
  ... (remaining 4270 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 729
       0.046 -    0.093: 313
       0.093 -    0.139: 123
       0.139 -    0.186: 58
       0.186 -    0.232: 19
  Chirality restraints: 1242
  Sorted by residual:
  chirality pdb=" CA  ILE A 485 "
            pdb=" N   ILE A 485 "
            pdb=" C   ILE A 485 "
            pdb=" CB  ILE A 485 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  ILE A 190 "
            pdb=" N   ILE A 190 "
            pdb=" C   ILE A 190 "
            pdb=" CB  ILE A 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CA  ILE A  65 "
            pdb=" N   ILE A  65 "
            pdb=" C   ILE A  65 "
            pdb=" CB  ILE A  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.02e+00
  ... (remaining 1239 not shown)

  Planarity restraints: 1203
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 451 "    0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   TYR A 451 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   TYR A 451 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER A 452 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 340 "   -0.015 2.00e-02 2.50e+03   3.09e-02 9.54e+00
        pdb=" C   VAL A 340 "    0.053 2.00e-02 2.50e+03
        pdb=" O   VAL A 340 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU A 341 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 164 "    0.012 2.00e-02 2.50e+03   2.40e-02 5.75e+00
        pdb=" C   GLU A 164 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   GLU A 164 "    0.016 2.00e-02 2.50e+03
        pdb=" N   TYR A 165 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1200 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1328
        2.77 -     3.30: 8229
        3.30 -     3.83: 12126
        3.83 -     4.37: 14830
        4.37 -     4.90: 23018
  Nonbonded interactions: 59531
  Sorted by model distance:
  nonbonded pdb=" O   GLN B 520 "
            pdb=" OG1 THR B 523 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   TYR B 377 "
            pdb=" NE2 GLN B 380 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" O   THR B 524 "
            pdb=" OG1 THR B 527 "
     model   vdw
     2.245 3.040
  nonbonded pdb=" O   MET B 521 "
            pdb=" OG1 THR B 524 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OD1 ASP A  99 "
            pdb=" OG  SER A 101 "
     model   vdw
     2.311 3.040
  ... (remaining 59526 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 35 through 68 or (resid 69 through 71 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 72 through 103 or (resid 104 and ( \ 
name N or name CA or name C or name O or name CB )) or resid 105 through 533 or  \ 
resid 666 through 710))
  selection = (chain 'B' and (resid 35 through 53 or (resid 54 and (name N or name CA or name  \ 
C or name O or name CB )) or resid 55 through 113 or (resid 114 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 115 through 191 or (resid 192  \ 
through 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 
4 through 196 or resid 200 through 296 or (resid 297 and (name N or name CA or n \ 
ame C or name O or name CB or name CG )) or resid 298 through 318 or (resid 319  \ 
and (name N or name CA or name C or name O or name CB )) or resid 320 through 52 \ 
7 or (resid 528 through 529 and (name N or name CA or name C or name O or name C \ 
B )) or resid 530 through 678 or (resid 679 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 680 through 710))
}

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:             5.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.150
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7051
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   0.042   7339  Z= 0.521
  Angle     :  1.092  10.331   9981  Z= 0.786
  Chirality :  0.067   0.232   1242
  Planarity :  0.005   0.041   1203
  Dihedral  : 15.717  73.447   2483
  Min Nonbonded Distance : 2.237

Molprobity Statistics.
  All-atom Clashscore : 13.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.22 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.28), residues: 917
  helix: -0.33 (0.19), residues: 703
  sheet:  None (None), residues: 0
  loop : -1.13 (0.45), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 130 
 TYR   0.016   0.002   TYR A 104 
 PHE   0.015   0.001   PHE A 336 
 TRP   0.017   0.002   TRP B 678 
 HIS   0.004   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00710 ( 7339)
  covalent geometry    : angle       1.09230 ( 9981)
  hydrogen bonds       : bond        0.21117 (  476)
  hydrogen bonds       : angle       8.25955 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 187
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  110 LYS cc_start: 0.7017 (mtpt) cc_final: 0.6782 (mtpt)
REVERT: A  429 MET cc_start: 0.8131 (tpt) cc_final: 0.7765 (tpt)
REVERT: B  290 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7737 (tt)
  outliers start: 19
  outliers final: 3
  residues processed: 197
  average time/residue: 0.0682
  time to fit residues: 19.0652
Evaluate side-chains
  164 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 160
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 TYR
Chi-restraints excluded: chain A residue  190 ILE
Chi-restraints excluded: chain A residue  485 ILE
Chi-restraints excluded: chain B residue  290 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A  89 ASN
A 143 GLN
A 216 GLN
A 230 ASN
A 310 HIS
A 337 ASN
A 433 ASN
B  63 ASN
B  89 ASN
B 191 GLN
B 198 ASN
B 216 GLN
B 230 ASN
B 243 ASN

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4346 r_free = 0.4346 target = 0.151670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.123179 restraints weight = 15499.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.126436 restraints weight = 9021.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.128496 restraints weight = 6344.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.129750 restraints weight = 5029.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.130716 restraints weight = 4359.582|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7339  Z= 0.159
  Angle     :  0.679   9.520   9981  Z= 0.334
  Chirality :  0.042   0.137   1242
  Planarity :  0.004   0.035   1203
  Dihedral  :  4.482  39.382    983
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 20.28 %
    Favored  : 75.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.01 (0.28), residues: 917
  helix:  0.33 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop : -0.79 (0.49), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  41 
 TYR   0.025   0.002   TYR A 165 
 PHE   0.027   0.002   PHE B 434 
 TRP   0.016   0.001   TRP A 678 
 HIS   0.002   0.001   HIS A 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 7339)
  covalent geometry    : angle       0.67853 ( 9981)
  hydrogen bonds       : bond        0.05198 (  476)
  hydrogen bonds       : angle       5.45354 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 174
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.7522 (m-80) cc_final: 0.7280 (m-80)
REVERT: A  185 PHE cc_start: 0.7680 (m-80) cc_final: 0.7415 (m-80)
REVERT: A  336 PHE cc_start: 0.6938 (m-80) cc_final: 0.6490 (m-80)
REVERT: A  429 MET cc_start: 0.8501 (tpt) cc_final: 0.8290 (tpt)
REVERT: B  170 TYR cc_start: 0.7277 (m-80) cc_final: 0.7046 (m-80)
REVERT: B  529 PHE cc_start: 0.8627 (t80) cc_final: 0.8333 (t80)
  outliers start: 34
  outliers final: 21
  residues processed: 194
  average time/residue: 0.0713
  time to fit residues: 19.6703
Evaluate side-chains
  179 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 158
  time to evaluate  : 0.273 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  176 SER
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  389 VAL
Chi-restraints excluded: chain A residue  396 TRP
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  179 MET
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  396 TRP
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    0.3980
   chunk 1 optimal weight:    0.9980
   chunk 64 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
A 191 GLN
B  63 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.150806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.123286 restraints weight = 16374.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.126610 restraints weight = 9332.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.128831 restraints weight = 6481.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.130153 restraints weight = 5075.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.131174 restraints weight = 4355.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7169
moved from start:          0.2620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7339  Z= 0.140
  Angle     :  0.657  11.237   9981  Z= 0.319
  Chirality :  0.042   0.195   1242
  Planarity :  0.004   0.037   1203
  Dihedral  :  3.969  14.410    975
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 11.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 21.71 %
    Favored  : 73.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.61 (0.29), residues: 917
  helix:  0.77 (0.20), residues: 714
  sheet:  None (None), residues: 0
  loop : -0.60 (0.50), residues: 203

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG B  41 
 TYR   0.039   0.002   TYR A 104 
 PHE   0.023   0.002   PHE B 434 
 TRP   0.012   0.001   TRP B 678 
 HIS   0.001   0.001   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 7339)
  covalent geometry    : angle       0.65668 ( 9981)
  hydrogen bonds       : bond        0.04657 (  476)
  hydrogen bonds       : angle       5.07242 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 179
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.7847 (m-10) cc_final: 0.7533 (m-80)
REVERT: A  170 TYR cc_start: 0.7311 (m-80) cc_final: 0.7049 (m-80)
REVERT: A  185 PHE cc_start: 0.7960 (m-80) cc_final: 0.7719 (m-80)
REVERT: A  296 GLU cc_start: 0.7993 (mm-30) cc_final: 0.7579 (mm-30)
REVERT: A  394 LEU cc_start: 0.9010 (pp) cc_final: 0.8420 (tp)
REVERT: A  396 TRP cc_start: 0.7174 (OUTLIER) cc_final: 0.6948 (t60)
REVERT: A  429 MET cc_start: 0.8478 (tpt) cc_final: 0.8236 (tpt)
REVERT: A  521 MET cc_start: 0.6314 (OUTLIER) cc_final: 0.6044 (tpt)
REVERT: B  170 TYR cc_start: 0.7232 (m-80) cc_final: 0.7005 (m-80)
REVERT: B  338 MET cc_start: 0.2125 (mmm) cc_final: 0.1889 (mmm)
REVERT: B  365 LEU cc_start: 0.9025 (OUTLIER) cc_final: 0.8768 (mm)
REVERT: B  392 ILE cc_start: 0.7080 (mm) cc_final: 0.6860 (mm)
REVERT: B  396 TRP cc_start: 0.7190 (OUTLIER) cc_final: 0.6953 (t60)
REVERT: B  529 PHE cc_start: 0.8724 (t80) cc_final: 0.8466 (t80)
REVERT: B  694 PHE cc_start: 0.7151 (OUTLIER) cc_final: 0.6852 (t80)
  outliers start: 39
  outliers final: 23
  residues processed: 203
  average time/residue: 0.0623
  time to fit residues: 18.1487
Evaluate side-chains
  186 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 158
  time to evaluate  : 0.264 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  131 PHE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  345 SER
Chi-restraints excluded: chain A residue  347 MET
Chi-restraints excluded: chain A residue  385 ASP
Chi-restraints excluded: chain A residue  396 TRP
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  681 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  396 TRP
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0060
   chunk 27 optimal weight:    0.9990
   chunk 80 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 74 optimal weight:    1.9990
   chunk 35 optimal weight:    9.9990
   chunk 23 optimal weight:    4.9990
   chunk 54 optimal weight:    4.9990
   chunk 92 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.7400

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
B 422 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.150554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.122189 restraints weight = 15904.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.125506 restraints weight = 9103.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.127673 restraints weight = 6350.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.128914 restraints weight = 5028.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.129889 restraints weight = 4358.156|
|-----------------------------------------------------------------------------|
r_work (final): 0.4055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7166
moved from start:          0.3016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7339  Z= 0.131
  Angle     :  0.640   9.239   9981  Z= 0.311
  Chirality :  0.042   0.179   1242
  Planarity :  0.004   0.037   1203
  Dihedral  :  3.879  13.388    975
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 23.51 %
    Favored  : 71.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.67 (0.29), residues: 917
  helix:  0.84 (0.20), residues: 722
  sheet:  None (None), residues: 0
  loop : -0.78 (0.50), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 130 
 TYR   0.015   0.001   TYR A 104 
 PHE   0.036   0.001   PHE A 434 
 TRP   0.014   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7339)
  covalent geometry    : angle       0.64005 ( 9981)
  hydrogen bonds       : bond        0.04339 (  476)
  hydrogen bonds       : angle       4.89902 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 170
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.7981 (m-10) cc_final: 0.7662 (m-80)
REVERT: A  170 TYR cc_start: 0.7212 (m-80) cc_final: 0.6932 (m-80)
REVERT: A  176 SER cc_start: 0.8897 (m) cc_final: 0.8529 (m)
REVERT: A  215 LEU cc_start: 0.7630 (OUTLIER) cc_final: 0.7339 (mm)
REVERT: A  329 VAL cc_start: 0.6946 (m) cc_final: 0.6587 (t)
REVERT: A  394 LEU cc_start: 0.8909 (pp) cc_final: 0.8385 (tp)
REVERT: A  413 MET cc_start: 0.4478 (mmt) cc_final: 0.3691 (pmm)
REVERT: A  521 MET cc_start: 0.6160 (OUTLIER) cc_final: 0.5920 (tpt)
REVERT: B  170 TYR cc_start: 0.7155 (m-80) cc_final: 0.6892 (m-80)
REVERT: B  365 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8722 (mm)
REVERT: B  392 ILE cc_start: 0.7110 (mm) cc_final: 0.6878 (mm)
REVERT: B  694 PHE cc_start: 0.7292 (OUTLIER) cc_final: 0.6995 (t80)
  outliers start: 36
  outliers final: 20
  residues processed: 192
  average time/residue: 0.0642
  time to fit residues: 17.6541
Evaluate side-chains
  180 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 156
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  396 TRP
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  681 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 78 optimal weight:    0.4980
   chunk 30 optimal weight:    1.9990
   chunk 67 optimal weight:    4.9990
   chunk 23 optimal weight:    5.9990
   chunk 91 optimal weight:   10.0000
   chunk 71 optimal weight:    0.9990
   chunk 25 optimal weight:    0.7980
   chunk 8 optimal weight:    0.3980
   chunk 69 optimal weight:    0.8980
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4332 r_free = 0.4332 target = 0.151003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.123116 restraints weight = 15712.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.126398 restraints weight = 8922.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.128410 restraints weight = 6195.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.129883 restraints weight = 4918.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.130714 restraints weight = 4203.947|
|-----------------------------------------------------------------------------|
r_work (final): 0.4068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7153
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7339  Z= 0.131
  Angle     :  0.656   9.907   9981  Z= 0.321
  Chirality :  0.042   0.208   1242
  Planarity :  0.004   0.039   1203
  Dihedral  :  3.850  12.988    975
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 12.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 24.55 %
    Favored  : 71.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.66 (0.29), residues: 917
  helix:  0.81 (0.19), residues: 726
  sheet:  None (None), residues: 0
  loop : -0.69 (0.52), residues: 191

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 130 
 TYR   0.017   0.001   TYR A 104 
 PHE   0.037   0.001   PHE A 336 
 TRP   0.013   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 7339)
  covalent geometry    : angle       0.65557 ( 9981)
  hydrogen bonds       : bond        0.04276 (  476)
  hydrogen bonds       : angle       4.84279 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 182
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.7997 (m-10) cc_final: 0.7618 (m-80)
REVERT: A  170 TYR cc_start: 0.7209 (m-80) cc_final: 0.6919 (m-80)
REVERT: A  176 SER cc_start: 0.8869 (m) cc_final: 0.8467 (m)
REVERT: A  179 MET cc_start: 0.7141 (mtm) cc_final: 0.6778 (ptt)
REVERT: A  185 PHE cc_start: 0.7675 (m-80) cc_final: 0.7387 (m-80)
REVERT: A  215 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7261 (mm)
REVERT: A  296 GLU cc_start: 0.7884 (mm-30) cc_final: 0.7632 (mm-30)
REVERT: A  329 VAL cc_start: 0.6975 (m) cc_final: 0.6621 (t)
REVERT: A  394 LEU cc_start: 0.9050 (pp) cc_final: 0.8528 (tp)
REVERT: A  413 MET cc_start: 0.4282 (mmt) cc_final: 0.3485 (pmm)
REVERT: A  521 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5906 (tpt)
REVERT: A  694 PHE cc_start: 0.7303 (OUTLIER) cc_final: 0.6857 (t80)
REVERT: B  170 TYR cc_start: 0.7168 (m-80) cc_final: 0.6864 (m-80)
REVERT: B  179 MET cc_start: 0.7319 (mtm) cc_final: 0.6889 (ptt)
REVERT: B  292 LEU cc_start: 0.7063 (OUTLIER) cc_final: 0.6816 (mm)
REVERT: B  338 MET cc_start: 0.2040 (mmm) cc_final: 0.1718 (mmm)
REVERT: B  365 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8735 (mm)
REVERT: B  413 MET cc_start: 0.3897 (mmt) cc_final: 0.3121 (ptt)
REVERT: B  694 PHE cc_start: 0.7329 (OUTLIER) cc_final: 0.7041 (t80)
  outliers start: 32
  outliers final: 21
  residues processed: 203
  average time/residue: 0.0693
  time to fit residues: 20.0047
Evaluate side-chains
  186 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 159
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  396 TRP
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  681 PHE
Chi-restraints excluded: chain A residue  694 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 90 optimal weight:    1.9990
   chunk 43 optimal weight:    6.9990
   chunk 26 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 67 optimal weight:    0.1980
   chunk 64 optimal weight:    5.9990
   chunk 41 optimal weight:   20.0000
   chunk 13 optimal weight:    0.5980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.150397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3941 r_free = 0.3941 target = 0.122311 restraints weight = 15745.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.125494 restraints weight = 9157.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.127498 restraints weight = 6465.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4035 r_free = 0.4035 target = 0.128874 restraints weight = 5157.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.129784 restraints weight = 4435.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7172
moved from start:          0.3508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7339  Z= 0.135
  Angle     :  0.671  10.388   9981  Z= 0.329
  Chirality :  0.042   0.181   1242
  Planarity :  0.004   0.040   1203
  Dihedral  :  3.817  11.929    975
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 24.81 %
    Favored  : 70.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.62 (0.29), residues: 917
  helix:  0.79 (0.20), residues: 724
  sheet:  None (None), residues: 0
  loop : -0.73 (0.52), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 130 
 TYR   0.018   0.001   TYR A 104 
 PHE   0.041   0.002   PHE B 336 
 TRP   0.014   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 7339)
  covalent geometry    : angle       0.67086 ( 9981)
  hydrogen bonds       : bond        0.04281 (  476)
  hydrogen bonds       : angle       4.87294 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 169
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.8082 (m-10) cc_final: 0.7621 (m-80)
REVERT: A  170 TYR cc_start: 0.7198 (m-80) cc_final: 0.6907 (m-80)
REVERT: A  176 SER cc_start: 0.8843 (m) cc_final: 0.8458 (m)
REVERT: A  179 MET cc_start: 0.7294 (mtm) cc_final: 0.6877 (mtp)
REVERT: A  185 PHE cc_start: 0.7721 (m-80) cc_final: 0.7427 (m-80)
REVERT: A  215 LEU cc_start: 0.7584 (OUTLIER) cc_final: 0.7277 (mm)
REVERT: A  282 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7879 (mm)
REVERT: A  336 PHE cc_start: 0.7029 (m-80) cc_final: 0.6607 (m-80)
REVERT: A  394 LEU cc_start: 0.9054 (pp) cc_final: 0.8540 (tp)
REVERT: A  413 MET cc_start: 0.4141 (mmt) cc_final: 0.3283 (pmm)
REVERT: A  429 MET cc_start: 0.8494 (tpt) cc_final: 0.7729 (tpp)
REVERT: A  521 MET cc_start: 0.6174 (OUTLIER) cc_final: 0.5941 (tpt)
REVERT: A  694 PHE cc_start: 0.7319 (OUTLIER) cc_final: 0.6787 (t80)
REVERT: B  170 TYR cc_start: 0.7188 (m-80) cc_final: 0.6932 (m-80)
REVERT: B  179 MET cc_start: 0.7352 (mtm) cc_final: 0.6929 (ptt)
REVERT: B  292 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6810 (mm)
REVERT: B  338 MET cc_start: 0.1832 (mmm) cc_final: 0.1545 (mmm)
REVERT: B  365 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8716 (mm)
REVERT: B  394 LEU cc_start: 0.9131 (pp) cc_final: 0.8740 (tp)
REVERT: B  413 MET cc_start: 0.3796 (mmt) cc_final: 0.3111 (ptt)
REVERT: B  694 PHE cc_start: 0.7390 (OUTLIER) cc_final: 0.7058 (t80)
  outliers start: 39
  outliers final: 26
  residues processed: 194
  average time/residue: 0.0683
  time to fit residues: 18.6442
Evaluate side-chains
  192 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 159
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  390 SER
Chi-restraints excluded: chain A residue  396 TRP
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  681 PHE
Chi-restraints excluded: chain A residue  694 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  331 ILE
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 71 optimal weight:    0.1980
   chunk 87 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9990
   chunk 75 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 24 optimal weight:    3.9990
   chunk 10 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 32 optimal weight:    0.6980
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.149980 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.121782 restraints weight = 15911.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.125051 restraints weight = 9095.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.127172 restraints weight = 6327.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.128542 restraints weight = 4980.793|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.129447 restraints weight = 4270.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.4045
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.3647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7339  Z= 0.143
  Angle     :  0.693  10.863   9981  Z= 0.336
  Chirality :  0.043   0.162   1242
  Planarity :  0.004   0.040   1203
  Dihedral  :  3.871  12.398    975
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 25.58 %
    Favored  : 69.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.29), residues: 917
  helix:  0.77 (0.19), residues: 725
  sheet:  None (None), residues: 0
  loop : -0.79 (0.51), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 130 
 TYR   0.019   0.001   TYR A 104 
 PHE   0.043   0.002   PHE B 434 
 TRP   0.014   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 7339)
  covalent geometry    : angle       0.69349 ( 9981)
  hydrogen bonds       : bond        0.04289 (  476)
  hydrogen bonds       : angle       4.94420 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  209 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 169
  time to evaluate  : 0.323 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.8134 (m-10) cc_final: 0.7605 (m-80)
REVERT: A  170 TYR cc_start: 0.7191 (m-80) cc_final: 0.6907 (m-80)
REVERT: A  176 SER cc_start: 0.8874 (m) cc_final: 0.8480 (m)
REVERT: A  179 MET cc_start: 0.7299 (mtm) cc_final: 0.6837 (mtt)
REVERT: A  185 PHE cc_start: 0.7807 (m-80) cc_final: 0.7580 (m-80)
REVERT: A  215 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7354 (mm)
REVERT: A  282 LEU cc_start: 0.8216 (OUTLIER) cc_final: 0.7922 (mm)
REVERT: A  394 LEU cc_start: 0.9078 (pp) cc_final: 0.8678 (tp)
REVERT: A  413 MET cc_start: 0.3974 (mmt) cc_final: 0.3101 (pmm)
REVERT: A  429 MET cc_start: 0.8498 (tpt) cc_final: 0.7781 (tpp)
REVERT: A  521 MET cc_start: 0.6176 (OUTLIER) cc_final: 0.5925 (tpt)
REVERT: A  694 PHE cc_start: 0.7343 (OUTLIER) cc_final: 0.6785 (t80)
REVERT: B  170 TYR cc_start: 0.7160 (m-80) cc_final: 0.6857 (m-80)
REVERT: B  179 MET cc_start: 0.7375 (mtm) cc_final: 0.6927 (ptt)
REVERT: B  292 LEU cc_start: 0.7115 (OUTLIER) cc_final: 0.6810 (mm)
REVERT: B  365 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8703 (mm)
REVERT: B  394 LEU cc_start: 0.9096 (pp) cc_final: 0.8751 (tp)
REVERT: B  413 MET cc_start: 0.3902 (mmt) cc_final: 0.3248 (ptt)
REVERT: B  694 PHE cc_start: 0.7415 (OUTLIER) cc_final: 0.7114 (t80)
  outliers start: 40
  outliers final: 24
  residues processed: 195
  average time/residue: 0.0638
  time to fit residues: 17.7579
Evaluate side-chains
  188 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 157
  time to evaluate  : 0.266 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  681 PHE
Chi-restraints excluded: chain A residue  694 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   93 LEU
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  217 ASN
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Chi-restraints excluded: chain B residue  695 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 24 optimal weight:    0.8980
   chunk 73 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 39 optimal weight:   10.0000
   chunk 26 optimal weight:    2.9990
   chunk 63 optimal weight:    0.3980
   chunk 87 optimal weight:    0.5980
   chunk 23 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4331 r_free = 0.4331 target = 0.150489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.122733 restraints weight = 15835.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.125985 restraints weight = 8943.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.128071 restraints weight = 6165.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.129357 restraints weight = 4850.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.130301 restraints weight = 4168.533|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7165
moved from start:          0.3802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   7339  Z= 0.133
  Angle     :  0.697  11.917   9981  Z= 0.337
  Chirality :  0.043   0.163   1242
  Planarity :  0.004   0.040   1203
  Dihedral  :  3.902  18.257    975
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 11.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  4.65 %
    Allowed  : 25.84 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.53 (0.28), residues: 917
  helix:  0.79 (0.19), residues: 722
  sheet:  None (None), residues: 0
  loop : -1.03 (0.48), residues: 195

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 130 
 TYR   0.016   0.001   TYR A 104 
 PHE   0.049   0.002   PHE B 336 
 TRP   0.013   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 7339)
  covalent geometry    : angle       0.69652 ( 9981)
  hydrogen bonds       : bond        0.04213 (  476)
  hydrogen bonds       : angle       4.89564 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 168
  time to evaluate  : 0.272 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.8119 (m-10) cc_final: 0.7672 (m-80)
REVERT: A  170 TYR cc_start: 0.7137 (m-80) cc_final: 0.6904 (m-80)
REVERT: A  176 SER cc_start: 0.8868 (m) cc_final: 0.8471 (m)
REVERT: A  179 MET cc_start: 0.7306 (mtm) cc_final: 0.6870 (mtt)
REVERT: A  215 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7367 (mm)
REVERT: A  282 LEU cc_start: 0.8161 (OUTLIER) cc_final: 0.7849 (mm)
REVERT: A  338 MET cc_start: 0.1911 (mmm) cc_final: 0.1586 (mmm)
REVERT: A  394 LEU cc_start: 0.9066 (pp) cc_final: 0.8722 (tp)
REVERT: A  413 MET cc_start: 0.3727 (mmt) cc_final: 0.3024 (pmm)
REVERT: A  429 MET cc_start: 0.8496 (tpt) cc_final: 0.7812 (tpp)
REVERT: A  521 MET cc_start: 0.6102 (OUTLIER) cc_final: 0.5866 (tpt)
REVERT: A  694 PHE cc_start: 0.7309 (OUTLIER) cc_final: 0.6760 (t80)
REVERT: B  165 TYR cc_start: 0.7977 (m-80) cc_final: 0.7698 (m-80)
REVERT: B  170 TYR cc_start: 0.7150 (m-80) cc_final: 0.6878 (m-80)
REVERT: B  179 MET cc_start: 0.7434 (mtm) cc_final: 0.6972 (ptt)
REVERT: B  282 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7786 (mm)
REVERT: B  292 LEU cc_start: 0.7141 (OUTLIER) cc_final: 0.6808 (mm)
REVERT: B  365 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8655 (mm)
REVERT: B  394 LEU cc_start: 0.9084 (pp) cc_final: 0.8817 (tp)
REVERT: B  413 MET cc_start: 0.3902 (mmt) cc_final: 0.3287 (ptt)
REVERT: B  528 LEU cc_start: 0.9508 (tt) cc_final: 0.9178 (mp)
REVERT: B  694 PHE cc_start: 0.7468 (OUTLIER) cc_final: 0.7154 (t80)
  outliers start: 36
  outliers final: 22
  residues processed: 192
  average time/residue: 0.0694
  time to fit residues: 18.8521
Evaluate side-chains
  188 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 158
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  681 PHE
Chi-restraints excluded: chain A residue  694 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 78 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9990
   chunk 80 optimal weight:    8.9990
   chunk 1 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 50 optimal weight:    0.9980
   chunk 11 optimal weight:    0.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.150397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.122718 restraints weight = 16354.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.125975 restraints weight = 9376.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.128046 restraints weight = 6578.630|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.129463 restraints weight = 5219.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.130104 restraints weight = 4468.495|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7196
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7339  Z= 0.140
  Angle     :  0.706  12.415   9981  Z= 0.342
  Chirality :  0.043   0.165   1242
  Planarity :  0.004   0.040   1203
  Dihedral  :  3.913  17.115    975
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.85 %
    Favored  : 98.15 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 26.23 %
    Favored  : 69.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.28), residues: 917
  helix:  0.70 (0.19), residues: 725
  sheet:  None (None), residues: 0
  loop : -0.98 (0.49), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 130 
 TYR   0.017   0.001   TYR A 104 
 PHE   0.040   0.002   PHE B 336 
 TRP   0.013   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 7339)
  covalent geometry    : angle       0.70607 ( 9981)
  hydrogen bonds       : bond        0.04332 (  476)
  hydrogen bonds       : angle       4.95872 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 169
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.8173 (m-10) cc_final: 0.7700 (m-80)
REVERT: A  170 TYR cc_start: 0.7141 (m-80) cc_final: 0.6919 (m-80)
REVERT: A  176 SER cc_start: 0.8875 (m) cc_final: 0.8471 (m)
REVERT: A  179 MET cc_start: 0.7226 (mtm) cc_final: 0.6754 (mtt)
REVERT: A  215 LEU cc_start: 0.7694 (OUTLIER) cc_final: 0.7336 (mm)
REVERT: A  282 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7883 (mm)
REVERT: A  296 GLU cc_start: 0.8021 (mm-30) cc_final: 0.7570 (mm-30)
REVERT: A  360 VAL cc_start: 0.8645 (t) cc_final: 0.8443 (t)
REVERT: A  394 LEU cc_start: 0.9061 (pp) cc_final: 0.8746 (tp)
REVERT: A  413 MET cc_start: 0.3767 (mmt) cc_final: 0.3025 (pmm)
REVERT: A  429 MET cc_start: 0.8593 (tpt) cc_final: 0.7857 (tpp)
REVERT: A  521 MET cc_start: 0.6219 (OUTLIER) cc_final: 0.5958 (tpt)
REVERT: A  694 PHE cc_start: 0.7288 (OUTLIER) cc_final: 0.6847 (t80)
REVERT: A  695 PHE cc_start: 0.7764 (OUTLIER) cc_final: 0.6937 (m-80)
REVERT: B  165 TYR cc_start: 0.7992 (m-80) cc_final: 0.7746 (m-80)
REVERT: B  170 TYR cc_start: 0.7153 (m-80) cc_final: 0.6943 (m-80)
REVERT: B  179 MET cc_start: 0.7403 (mtm) cc_final: 0.6883 (ptt)
REVERT: B  282 LEU cc_start: 0.8137 (OUTLIER) cc_final: 0.7841 (mm)
REVERT: B  292 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6722 (mm)
REVERT: B  365 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8693 (mm)
REVERT: B  394 LEU cc_start: 0.9085 (pp) cc_final: 0.8882 (tp)
REVERT: B  413 MET cc_start: 0.3860 (mmt) cc_final: 0.3299 (ptt)
REVERT: B  694 PHE cc_start: 0.7425 (OUTLIER) cc_final: 0.7149 (t80)
  outliers start: 33
  outliers final: 22
  residues processed: 189
  average time/residue: 0.0709
  time to fit residues: 18.9496
Evaluate side-chains
  189 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 158
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   63 ASN
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  237 VAL
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  300 LEU
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  694 PHE
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  282 LEU
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    9.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 34 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 87 optimal weight:    7.9990
   chunk 73 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 36 optimal weight:    1.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.148993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.121244 restraints weight = 15772.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.124283 restraints weight = 9200.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.126255 restraints weight = 6484.086|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.127457 restraints weight = 5174.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.128436 restraints weight = 4489.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.4023
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.4065

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   7339  Z= 0.164
  Angle     :  0.744  12.523   9981  Z= 0.367
  Chirality :  0.045   0.184   1242
  Planarity :  0.004   0.040   1203
  Dihedral  :  4.032  18.216    975
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 14.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 26.87 %
    Favored  : 68.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.28), residues: 917
  helix:  0.68 (0.19), residues: 723
  sheet:  None (None), residues: 0
  loop : -0.97 (0.49), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 130 
 TYR   0.017   0.002   TYR A 104 
 PHE   0.047   0.002   PHE B 336 
 TRP   0.014   0.001   TRP A 432 
 HIS   0.001   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00366 ( 7339)
  covalent geometry    : angle       0.74442 ( 9981)
  hydrogen bonds       : bond        0.04561 (  476)
  hydrogen bonds       : angle       5.05756 ( 1428)

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

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

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1834 Ramachandran restraints generated.
    917 Oldfield, 0 Emsley, 917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 161
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 TYR cc_start: 0.8250 (m-10) cc_final: 0.7777 (m-80)
REVERT: A  170 TYR cc_start: 0.7187 (m-80) cc_final: 0.6911 (m-80)
REVERT: A  176 SER cc_start: 0.8894 (m) cc_final: 0.8505 (m)
REVERT: A  179 MET cc_start: 0.7319 (mtm) cc_final: 0.6801 (mtt)
REVERT: A  215 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7344 (mm)
REVERT: A  282 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7874 (mm)
REVERT: A  394 LEU cc_start: 0.9017 (pp) cc_final: 0.8767 (tp)
REVERT: A  413 MET cc_start: 0.3741 (mmt) cc_final: 0.3110 (pmm)
REVERT: A  521 MET cc_start: 0.6181 (OUTLIER) cc_final: 0.5893 (tpt)
REVERT: A  695 PHE cc_start: 0.7810 (OUTLIER) cc_final: 0.6993 (m-80)
REVERT: B  170 TYR cc_start: 0.7263 (m-80) cc_final: 0.7003 (m-80)
REVERT: B  179 MET cc_start: 0.7346 (mtm) cc_final: 0.6924 (ptt)
REVERT: B  292 LEU cc_start: 0.7052 (OUTLIER) cc_final: 0.6664 (mm)
REVERT: B  365 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8639 (mm)
REVERT: B  413 MET cc_start: 0.3752 (mmt) cc_final: 0.3257 (ptt)
REVERT: B  694 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.7207 (t80)
  outliers start: 32
  outliers final: 20
  residues processed: 180
  average time/residue: 0.0715
  time to fit residues: 18.2309
Evaluate side-chains
  184 residues out of total 824 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 157
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   93 LEU
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  215 LEU
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  283 ILE
Chi-restraints excluded: chain A residue  306 SER
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  461 THR
Chi-restraints excluded: chain A residue  494 LEU
Chi-restraints excluded: chain A residue  495 LEU
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  521 MET
Chi-restraints excluded: chain A residue  695 PHE
Chi-restraints excluded: chain B residue   98 VAL
Chi-restraints excluded: chain B residue  124 VAL
Chi-restraints excluded: chain B residue  215 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  292 LEU
Chi-restraints excluded: chain B residue  345 SER
Chi-restraints excluded: chain B residue  351 THR
Chi-restraints excluded: chain B residue  365 LEU
Chi-restraints excluded: chain B residue  457 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  694 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 5 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0770
   chunk 3 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 23 optimal weight:    0.2980
   chunk 64 optimal weight:    9.9990
   chunk 62 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4342 r_free = 0.4342 target = 0.151413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.123219 restraints weight = 15920.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.126489 restraints weight = 9039.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.128625 restraints weight = 6281.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.129998 restraints weight = 4959.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.130641 restraints weight = 4249.740|
|-----------------------------------------------------------------------------|
r_work (final): 0.4057
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.4193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7339  Z= 0.133
  Angle     :  0.717  13.318   9981  Z= 0.345
  Chirality :  0.044   0.183   1242
  Planarity :  0.004   0.040   1203
  Dihedral  :  3.930  17.189    975
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Rotamer:
    Outliers :  3.36 %
    Allowed  : 27.52 %
    Favored  : 69.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.28), residues: 917
  helix:  0.75 (0.19), residues: 725
  sheet:  None (None), residues: 0
  loop : -1.03 (0.48), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 130 
 TYR   0.015   0.001   TYR A 104 
 PHE   0.043   0.002   PHE B 336 
 TRP   0.015   0.001   TRP A 432 
 HIS   0.000   0.000   HIS B 310 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 7339)
  covalent geometry    : angle       0.71673 ( 9981)
  hydrogen bonds       : bond        0.04249 (  476)
  hydrogen bonds       : angle       4.91552 ( 1428)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1371.57 seconds
wall clock time: 24 minutes 26.53 seconds (1466.53 seconds total)