Starting phenix.real_space_refine
on Fri Aug 22 19:00:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwr_35777/08_2025/8iwr_35777_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwr_35777/08_2025/8iwr_35777.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8iwr_35777/08_2025/8iwr_35777.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwr_35777/08_2025/8iwr_35777.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwr_35777/08_2025/8iwr_35777_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwr_35777/08_2025/8iwr_35777_trim.cif"
  }
  resolution = 3.52
  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=   0.019
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: 7
    Type Number    sf(0)   Gaussians
     Ca      1      9.91       5
     P       3      5.49       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    4371      2.51       5
     N    1149      2.21       5
     O    1294      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6871
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6838
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 893, 6838
          Classifications: {'peptide': 893}
          Link IDs: {'PTRANS': 35, 'TRANS': 857}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' CA': 1, ' MG': 1, 'ACP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.11, per 1000 atoms: 0.31
  Number of scatterers: 6871
  At special positions: 0
  Unit cell: (115.08, 100.8, 107.52, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Ca      1     19.99
     S      52     16.00
     P       3     15.00
     Mg      1     11.99
     O    1294      8.00
     N    1149      7.00
     C    4371      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: 0.60
  Conformation dependent library (CDL) restraints added in 408.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1664

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 7 sheets defined
      55.3% alpha, 15.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.30
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 29
    Processing helix  chain 'A' and resid 30 through 39
    Processing helix  chain 'A' and resid 47 through 59
    Processing helix  chain 'A' and resid 70 through 78
      removed outlier: 3.675A  pdb=" N   LYS A  74 " --> pdb=" O   PRO A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 97
    Processing helix  chain 'A' and resid 100 through 131
    Processing helix  chain 'A' and resid 153 through 155
      No H-bonds generated for 'chain 'A' and resid 153 through 155'
    Processing helix  chain 'A' and resid 185 through 190
    Processing helix  chain 'A' and resid 235 through 239
      removed outlier: 3.758A  pdb=" N   ASN A 238 " --> pdb=" O   THR A 235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 249
    Processing helix  chain 'A' and resid 256 through 287
    Processing helix  chain 'A' and resid 291 through 306
      removed outlier: 3.501A  pdb=" N   ILE A 306 " --> pdb=" O   ALA A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
      removed outlier: 3.749A  pdb=" N   LYS A 328 " --> pdb=" O   ARG A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 342
      removed outlier: 4.018A  pdb=" N   VAL A 338 " --> pdb=" O   LYS A 334 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLU A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   THR A 340 " --> pdb=" O   PRO A 336 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY A 342 " --> pdb=" O   VAL A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 412
    Processing helix  chain 'A' and resid 424 through 438
    Processing helix  chain 'A' and resid 439 through 443
      removed outlier: 3.626A  pdb=" N   GLN A 443 " --> pdb=" O   ASP A 440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 519
      removed outlier: 4.221A  pdb=" N   VAL A 509 " --> pdb=" O   GLN A 505 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 552 through 563
      removed outlier: 4.021A  pdb=" N   SER A 562 " --> pdb=" O   THR A 558 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   GLY A 563 " --> pdb=" O   LEU A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 584
    Processing helix  chain 'A' and resid 595 through 602
      removed outlier: 3.545A  pdb=" N   MET A 602 " --> pdb=" O   GLU A 598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 609
      removed outlier: 4.218A  pdb=" N   GLN A 609 " --> pdb=" O   GLN A 605 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 610 through 612
      No H-bonds generated for 'chain 'A' and resid 610 through 612'
    Processing helix  chain 'A' and resid 621 through 636
    Processing helix  chain 'A' and resid 645 through 647
      No H-bonds generated for 'chain 'A' and resid 645 through 647'
    Processing helix  chain 'A' and resid 648 through 655
    Processing helix  chain 'A' and resid 666 through 673
    Processing helix  chain 'A' and resid 683 through 723
      removed outlier: 3.530A  pdb=" N   SER A 687 " --> pdb=" O   GLN A 683 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 742
    Processing helix  chain 'A' and resid 743 through 751
    Processing helix  chain 'A' and resid 772 through 798
    Processing helix  chain 'A' and resid 804 through 825
      removed outlier: 3.806A  pdb=" N   THR A 808 " --> pdb=" O   THR A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 841 through 860
      removed outlier: 3.538A  pdb=" N   CYS A 845 " --> pdb=" O   ASN A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 861 through 869
    Processing helix  chain 'A' and resid 874 through 886
      removed outlier: 3.662A  pdb=" N   SER A 886 " --> pdb=" O   LEU A 882 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 886 through 909
    Processing sheet with id=AA1, first strand: chain 'A' and resid 138 through 143
      removed outlier: 3.747A  pdb=" N   THR A 150 " --> pdb=" O   CYS A 139 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 163
      removed outlier: 6.481A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 160 through 163
      removed outlier: 6.481A  pdb=" N   SER A 182 " --> pdb=" O   ARG A 224 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY A 226 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ASP A 180 " --> pdb=" O   GLY A 226 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   ALA A 228 " --> pdb=" O   ALA A 178 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ALA A 178 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 7.720A  pdb=" N   GLY A 230 " --> pdb=" O   PHE A 176 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   PHE A 176 " --> pdb=" O   GLY A 230 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   VAL A 232 " --> pdb=" O   ARG A 174 " (cutoff:3.500A)
      removed outlier: 6.066A  pdb=" N   ARG A 174 " --> pdb=" O   VAL A 232 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   GLY A 234 " --> pdb=" O   ASP A 172 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ASP A 172 " --> pdb=" O   GLY A 234 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 331 through 332
    Processing sheet with id=AA5, first strand: chain 'A' and resid 592 through 594
      removed outlier: 6.601A  pdb=" N   GLN A 592 " --> pdb=" O   VAL A 616 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   MET A 568 " --> pdb=" O   PHE A 617 " (cutoff:3.500A)
      removed outlier: 6.510A  pdb=" N   ILE A 347 " --> pdb=" O   LYS A 567 " (cutoff:3.500A)
      removed outlier: 7.268A  pdb=" N   ILE A 569 " --> pdb=" O   ILE A 347 " (cutoff:3.500A)
      removed outlier: 5.773A  pdb=" N   SER A 349 " --> pdb=" O   ILE A 569 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 386 through 387
      removed outlier: 4.470A  pdb=" N   THR A 363 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   THR A 361 " --> pdb=" O   ILE A 545 " (cutoff:3.500A)
      removed outlier: 6.418A  pdb=" N   GLY A 543 " --> pdb=" O   THR A 363 " (cutoff:3.500A)
      removed outlier: 4.940A  pdb=" N   ILE A 365 " --> pdb=" O   LEU A 541 " (cutoff:3.500A)
      removed outlier: 6.943A  pdb=" N   LEU A 541 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 4.603A  pdb=" N   THR A 367 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   LEU A 539 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
      removed outlier: 5.604A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
      removed outlier: 6.656A  pdb=" N   PHE A 538 " --> pdb=" O   CYS A 490 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   THR A 492 " --> pdb=" O   PHE A 538 " (cutoff:3.500A)
      removed outlier: 8.688A  pdb=" N   GLY A 540 " --> pdb=" O   THR A 492 " (cutoff:3.500A)
      removed outlier: 10.962A  pdb=" N   GLN A 494 " --> pdb=" O   GLY A 540 " (cutoff:3.500A)
      removed outlier: 14.625A  pdb=" N   VAL A 542 " --> pdb=" O   GLN A 494 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 447 through 452
      removed outlier: 6.888A  pdb=" N   ARG A 448 " --> pdb=" O   VAL A 466 " (cutoff:3.500A)
      removed outlier: 7.762A  pdb=" N   VAL A 466 " --> pdb=" O   ARG A 448 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   ALA A 450 " --> pdb=" O   LYS A 464 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   ALA A 462 " --> pdb=" O   TYR A 452 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   CYS A 465 " --> pdb=" O   ILE A 476 " (cutoff:3.500A)
      removed outlier: 4.253A  pdb=" N   ILE A 476 " --> pdb=" O   CYS A 465 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   LEU A 527 " --> pdb=" O   LEU A 539 " (cutoff:3.500A)
      removed outlier: 7.656A  pdb=" N   GLN A 535 " --> pdb=" O   PRO A 531 " (cutoff:3.500A)

    392 hydrogen bonds defined for protein.
    1149 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.42

  Time building geometry restraints manager: 0.83 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: 1395
        1.33 -     1.45: 1425
        1.45 -     1.57: 4070
        1.57 -     1.69: 5
        1.69 -     1.81: 86
  Bond restraints: 6981
  Sorted by residual:
  bond pdb=" O3A ACP A1003 "
       pdb=" PB  ACP A1003 "
    ideal  model  delta    sigma   weight residual
    1.698  1.578  0.120 2.00e-02 2.50e+03 3.59e+01
  bond pdb=" C3B ACP A1003 "
       pdb=" PG  ACP A1003 "
    ideal  model  delta    sigma   weight residual
    1.875  1.785  0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" CA  THR A 352 "
       pdb=" C   THR A 352 "
    ideal  model  delta    sigma   weight residual
    1.526  1.470  0.057 1.35e-02 5.49e+03 1.76e+01
  bond pdb=" O5' ACP A1003 "
       pdb=" PA  ACP A1003 "
    ideal  model  delta    sigma   weight residual
    1.659  1.581  0.078 2.00e-02 2.50e+03 1.53e+01
  bond pdb=" O1G ACP A1003 "
       pdb=" PG  ACP A1003 "
    ideal  model  delta    sigma   weight residual
    1.533  1.459  0.074 2.00e-02 2.50e+03 1.38e+01
  ... (remaining 6976 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.61: 9340
        2.61 -     5.23: 96
        5.23 -     7.84: 12
        7.84 -    10.46: 9
       10.46 -    13.07: 3
  Bond angle restraints: 9460
  Sorted by residual:
  angle pdb=" N   PRO A 201 "
        pdb=" CD  PRO A 201 "
        pdb=" CG  PRO A 201 "
      ideal   model   delta    sigma   weight residual
     103.20   95.23    7.97 1.50e+00 4.44e-01 2.82e+01
  angle pdb=" CA  PRO A 201 "
        pdb=" CB  PRO A 201 "
        pdb=" CG  PRO A 201 "
      ideal   model   delta    sigma   weight residual
     104.50   94.66    9.84 1.90e+00 2.77e-01 2.68e+01
  angle pdb=" CA  PRO A 201 "
        pdb=" N   PRO A 201 "
        pdb=" CD  PRO A 201 "
      ideal   model   delta    sigma   weight residual
     112.00  105.98    6.02 1.40e+00 5.10e-01 1.85e+01
  angle pdb=" CB  PRO A 201 "
        pdb=" CG  PRO A 201 "
        pdb=" CD  PRO A 201 "
      ideal   model   delta    sigma   weight residual
     106.10   93.03   13.07 3.20e+00 9.77e-02 1.67e+01
  angle pdb=" O1B ACP A1003 "
        pdb=" PB  ACP A1003 "
        pdb=" O2B ACP A1003 "
      ideal   model   delta    sigma   weight residual
     119.60  108.46   11.14 3.00e+00 1.11e-01 1.38e+01
  ... (remaining 9455 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    19.74: 3654
       19.74 -    39.49: 508
       39.49 -    59.23: 98
       59.23 -    78.98: 11
       78.98 -    98.72: 8
  Dihedral angle restraints: 4279
    sinusoidal: 1707
      harmonic: 2572
  Sorted by residual:
  dihedral pdb=" O1A ACP A1003 "
           pdb=" O3A ACP A1003 "
           pdb=" PA  ACP A1003 "
           pdb=" PB  ACP A1003 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -48.75   49.97  -98.72     1      3.00e+01 1.11e-03 1.23e+01
  dihedral pdb=" CA  GLU A 129 "
           pdb=" C   GLU A 129 "
           pdb=" N   GLU A 130 "
           pdb=" CA  GLU A 130 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.01   16.99     0      5.00e+00 4.00e-02 1.15e+01
  dihedral pdb=" CA  ASN A 822 "
           pdb=" CB  ASN A 822 "
           pdb=" CG  ASN A 822 "
           pdb=" OD1 ASN A 822 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -159.44   69.44     2      2.00e+01 2.50e-03 1.05e+01
  ... (remaining 4276 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 843
       0.040 -    0.079: 206
       0.079 -    0.119: 78
       0.119 -    0.158: 5
       0.158 -    0.198: 3
  Chirality restraints: 1135
  Sorted by residual:
  chirality pdb=" C2' ACP A1003 "
            pdb=" C1' ACP A1003 "
            pdb=" C3' ACP A1003 "
            pdb=" O2' ACP A1003 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.75   -2.55   -0.20 2.00e-01 2.50e+01 9.80e-01
  chirality pdb=" CB  ILE A 894 "
            pdb=" CA  ILE A 894 "
            pdb=" CG1 ILE A 894 "
            pdb=" CG2 ILE A 894 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.47    0.18 2.00e-01 2.50e+01 8.07e-01
  chirality pdb=" CA  THR A 354 "
            pdb=" N   THR A 354 "
            pdb=" C   THR A 354 "
            pdb=" CB  THR A 354 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.96e-01
  ... (remaining 1132 not shown)

  Planarity restraints: 1190
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 136 "   -0.038 5.00e-02 4.00e+02   5.65e-02 5.10e+00
        pdb=" N   PRO A 137 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO A 137 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 137 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  72 "    0.012 2.00e-02 2.50e+03   1.29e-02 4.17e+00
        pdb=" CG  TRP A  72 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  72 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  72 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  72 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  72 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  72 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  72 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 861 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO A 862 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 862 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 862 "   -0.027 5.00e-02 4.00e+02
  ... (remaining 1187 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 188
        2.70 -     3.25: 6741
        3.25 -     3.80: 10892
        3.80 -     4.35: 13106
        4.35 -     4.90: 22292
  Nonbonded interactions: 53219
  Sorted by model distance:
  nonbonded pdb="MG    MG A1002 "
            pdb=" O1G ACP A1003 "
     model   vdw
     2.149 2.170
  nonbonded pdb=" OD1 ASN A 701 "
            pdb=" NE2 GLN A 829 "
     model   vdw
     2.206 3.120
  nonbonded pdb=" O   ILE A 836 "
            pdb=" OG  SER A 840 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" NE2 GLN A 865 "
            pdb=" O   GLU A 871 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" O   PRO A 744 "
            pdb=" OG  SER A 748 "
     model   vdw
     2.293 3.040
  ... (remaining 53214 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             4.820
  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:                    0.030
  Process input model:                     8.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7052
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      :  0.004   0.120   6981  Z= 0.222
  Angle     :  0.701  13.074   9460  Z= 0.343
  Chirality :  0.040   0.198   1135
  Planarity :  0.004   0.056   1190
  Dihedral  : 18.077  98.719   2615
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 30.73 %
    Favored  : 69.01 %
  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:  0.89 (0.29), residues: 891
  helix:  2.07 (0.24), residues: 465
  sheet: -1.15 (0.72), residues: 67
  loop : -1.09 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 448 
 TYR   0.003   0.000   TYR A 696 
 PHE   0.017   0.001   PHE A 118 
 TRP   0.035   0.002   TRP A  72 
 HIS   0.002   0.000   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6981)
  covalent geometry    : angle       0.70137 ( 9460)
  hydrogen bonds       : bond        0.14213 (  385)
  hydrogen bonds       : angle       5.80848 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 139
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 LYS cc_start: 0.8348 (mmmt) cc_final: 0.7222 (mmmt)
REVERT: A  264 LEU cc_start: 0.7846 (tt) cc_final: 0.7517 (tp)
  outliers start: 2
  outliers final: 1
  residues processed: 140
  average time/residue: 0.0721
  time to fit residues: 13.7904
Evaluate side-chains
  130 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 129
  time to evaluate  : 0.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 74 optimal weight:   10.0000
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
A 149 HIS
A 829 GLN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.184056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.148156 restraints weight = 9053.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.151752 restraints weight = 5930.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.154201 restraints weight = 4457.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.155858 restraints weight = 3665.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.156643 restraints weight = 3211.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7458
moved from start:          0.1780

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6981  Z= 0.167
  Angle     :  0.616   6.924   9460  Z= 0.317
  Chirality :  0.043   0.156   1135
  Planarity :  0.005   0.046   1190
  Dihedral  :  6.839  72.262    974
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 28.12 %
    Favored  : 67.97 %
  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:  0.73 (0.29), residues: 891
  helix:  1.93 (0.24), residues: 461
  sheet: -1.44 (0.59), residues: 87
  loop : -1.00 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 448 
 TYR   0.017   0.001   TYR A 618 
 PHE   0.013   0.001   PHE A 821 
 TRP   0.014   0.001   TRP A  72 
 HIS   0.003   0.001   HIS A 624 

Details of bonding type rmsd
  covalent geometry    : bond        0.00375 ( 6981)
  covalent geometry    : angle       0.61623 ( 9460)
  hydrogen bonds       : bond        0.03953 (  385)
  hydrogen bonds       : angle       4.54927 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 144
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8365 (OUTLIER) cc_final: 0.7843 (mt)
REVERT: A   62 GLU cc_start: 0.7625 (mt-10) cc_final: 0.7317 (mt-10)
REVERT: A  153 ARG cc_start: 0.8478 (ptm160) cc_final: 0.8250 (ptm160)
REVERT: A  264 LEU cc_start: 0.8037 (tt) cc_final: 0.7689 (tp)
REVERT: A  717 ILE cc_start: 0.6577 (mm) cc_final: 0.6035 (mm)
REVERT: A  794 PHE cc_start: 0.8030 (OUTLIER) cc_final: 0.7223 (m-80)
  outliers start: 30
  outliers final: 14
  residues processed: 161
  average time/residue: 0.0660
  time to fit residues: 14.5962
Evaluate side-chains
  143 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 127
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  594 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  766 TRP
Chi-restraints excluded: chain A residue  794 PHE
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 2 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 32 optimal weight:    2.9990
   chunk 18 optimal weight:    7.9990
   chunk 56 optimal weight:    0.5980
   chunk 20 optimal weight:    0.7980
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 120 GLN
A 140 HIS
A 372 HIS
A 419 ASN
A 506 GLN
A 605 GLN
A 633 GLN
A 822 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.168317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.134587 restraints weight = 9220.235|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.136230 restraints weight = 6686.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.137731 restraints weight = 5266.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138201 restraints weight = 4515.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.138279 restraints weight = 4070.046|
|-----------------------------------------------------------------------------|
r_work (final): 0.3582
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.3630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   6981  Z= 0.250
  Angle     :  0.727   9.679   9460  Z= 0.377
  Chirality :  0.047   0.190   1135
  Planarity :  0.005   0.056   1190
  Dihedral  :  6.769  54.813    973
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.07 %
    Favored  : 92.93 %
  Rotamer:
    Outliers :  7.03 %
    Allowed  : 25.00 %
    Favored  : 67.97 %
  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:  0.14 (0.28), residues: 891
  helix:  1.30 (0.24), residues: 469
  sheet: -1.90 (0.55), residues: 93
  loop : -1.01 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 842 
 TYR   0.023   0.002   TYR A 618 
 PHE   0.020   0.002   PHE A 821 
 TRP   0.012   0.001   TRP A 285 
 HIS   0.005   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00587 ( 6981)
  covalent geometry    : angle       0.72702 ( 9460)
  hydrogen bonds       : bond        0.05822 (  385)
  hydrogen bonds       : angle       5.01587 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 144
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLU cc_start: 0.7675 (mt-10) cc_final: 0.7069 (mt-10)
REVERT: A  130 GLU cc_start: 0.7434 (mm-30) cc_final: 0.7229 (mm-30)
REVERT: A  153 ARG cc_start: 0.8520 (ptm160) cc_final: 0.8150 (ptm160)
REVERT: A  264 LEU cc_start: 0.8157 (tt) cc_final: 0.7874 (tp)
REVERT: A  485 GLN cc_start: 0.8579 (OUTLIER) cc_final: 0.7280 (mp10)
REVERT: A  513 GLU cc_start: 0.8176 (tp30) cc_final: 0.7886 (tp30)
REVERT: A  748 SER cc_start: 0.9262 (m) cc_final: 0.8325 (m)
REVERT: A  794 PHE cc_start: 0.8865 (OUTLIER) cc_final: 0.7735 (m-80)
  outliers start: 54
  outliers final: 36
  residues processed: 181
  average time/residue: 0.0741
  time to fit residues: 18.2105
Evaluate side-chains
  169 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 131
  time to evaluate  : 0.184 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  100 PHE
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  149 HIS
Chi-restraints excluded: chain A residue  151 LEU
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  354 THR
Chi-restraints excluded: chain A residue  356 THR
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  485 GLN
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  503 THR
Chi-restraints excluded: chain A residue  524 VAL
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  578 VAL
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  766 TRP
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  775 LEU
Chi-restraints excluded: chain A residue  794 PHE
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 25 optimal weight:    0.6980
   chunk 67 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0020
   chunk 37 optimal weight:    3.9990
   chunk 2 optimal weight:    2.9990
   chunk 86 optimal weight:    0.6980
   chunk 78 optimal weight:    0.0030
   chunk 52 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.3998

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.179049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.146871 restraints weight = 9242.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.147226 restraints weight = 7936.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.148821 restraints weight = 6529.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.150668 restraints weight = 4954.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.150856 restraints weight = 4170.611|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
moved from start:          0.3615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6981  Z= 0.129
  Angle     :  0.585   8.038   9460  Z= 0.298
  Chirality :  0.042   0.206   1135
  Planarity :  0.004   0.068   1190
  Dihedral  :  6.277  51.444    973
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 28.78 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.29), residues: 891
  helix:  1.73 (0.24), residues: 464
  sheet: -1.54 (0.55), residues: 103
  loop : -0.97 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 448 
 TYR   0.011   0.001   TYR A 618 
 PHE   0.015   0.001   PHE A 274 
 TRP   0.014   0.002   TRP A  72 
 HIS   0.003   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 6981)
  covalent geometry    : angle       0.58543 ( 9460)
  hydrogen bonds       : bond        0.04128 (  385)
  hydrogen bonds       : angle       4.55435 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7859 (OUTLIER) cc_final: 0.7594 (tt)
REVERT: A  130 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7033 (mm-30)
REVERT: A  153 ARG cc_start: 0.8407 (ptm160) cc_final: 0.8175 (ptm160)
REVERT: A  229 LYS cc_start: 0.8414 (ttmm) cc_final: 0.8120 (ttmm)
REVERT: A  264 LEU cc_start: 0.8074 (tt) cc_final: 0.7795 (tp)
REVERT: A  748 SER cc_start: 0.9082 (m) cc_final: 0.8376 (m)
  outliers start: 28
  outliers final: 15
  residues processed: 158
  average time/residue: 0.0822
  time to fit residues: 17.1622
Evaluate side-chains
  148 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  149 HIS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 19 optimal weight:    5.9990
   chunk 63 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 75 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 53 optimal weight:    6.9990
   chunk 22 optimal weight:    0.7980
   chunk 50 optimal weight:    0.3980
   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  47 ASN
A 381 ASN
A 765 ASN
** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.180282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.148683 restraints weight = 9156.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.150574 restraints weight = 7591.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.152287 restraints weight = 6180.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.152523 restraints weight = 4709.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.152938 restraints weight = 4193.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7745
moved from start:          0.3756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6981  Z= 0.143
  Angle     :  0.582   8.206   9460  Z= 0.298
  Chirality :  0.042   0.164   1135
  Planarity :  0.004   0.074   1190
  Dihedral  :  6.092  48.635    973
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 8.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 27.73 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.29), residues: 891
  helix:  1.79 (0.24), residues: 465
  sheet: -1.69 (0.54), residues: 103
  loop : -1.00 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 842 
 TYR   0.014   0.001   TYR A 618 
 PHE   0.022   0.001   PHE A 118 
 TRP   0.015   0.001   TRP A  72 
 HIS   0.002   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6981)
  covalent geometry    : angle       0.58230 ( 9460)
  hydrogen bonds       : bond        0.04093 (  385)
  hydrogen bonds       : angle       4.45665 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 139
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7860 (OUTLIER) cc_final: 0.7582 (tt)
REVERT: A  130 GLU cc_start: 0.7224 (mm-30) cc_final: 0.6976 (mm-30)
REVERT: A  227 LYS cc_start: 0.8619 (mmmt) cc_final: 0.8206 (mmmt)
REVERT: A  264 LEU cc_start: 0.8091 (tt) cc_final: 0.7828 (tp)
REVERT: A  381 ASN cc_start: 0.8092 (p0) cc_final: 0.7818 (p0)
REVERT: A  536 LEU cc_start: 0.7883 (OUTLIER) cc_final: 0.7638 (mt)
REVERT: A  641 MET cc_start: 0.7462 (ttm) cc_final: 0.7245 (ttm)
REVERT: A  717 ILE cc_start: 0.7665 (mm) cc_final: 0.7369 (mm)
REVERT: A  748 SER cc_start: 0.9107 (m) cc_final: 0.8395 (m)
  outliers start: 36
  outliers final: 27
  residues processed: 163
  average time/residue: 0.0782
  time to fit residues: 17.1287
Evaluate side-chains
  157 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  149 HIS
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 64 optimal weight:    0.9980
   chunk 71 optimal weight:    0.1980
   chunk 5 optimal weight:    5.9990
   chunk 86 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 75 optimal weight:    0.9990
   chunk 17 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 28 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.180858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.149267 restraints weight = 9090.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.150087 restraints weight = 7547.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.151580 restraints weight = 6047.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.151949 restraints weight = 4872.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.152373 restraints weight = 4505.148|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.3870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6981  Z= 0.132
  Angle     :  0.577   8.108   9460  Z= 0.297
  Chirality :  0.042   0.237   1135
  Planarity :  0.004   0.074   1190
  Dihedral  :  6.000  46.976    973
  Min Nonbonded Distance : 2.116

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.72 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 27.34 %
    Favored  : 67.45 %
  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:  0.54 (0.29), residues: 891
  helix:  1.79 (0.24), residues: 465
  sheet: -1.72 (0.55), residues: 103
  loop : -1.04 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 448 
 TYR   0.015   0.001   TYR A 618 
 PHE   0.021   0.001   PHE A 118 
 TRP   0.018   0.001   TRP A  72 
 HIS   0.002   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6981)
  covalent geometry    : angle       0.57679 ( 9460)
  hydrogen bonds       : bond        0.03966 (  385)
  hydrogen bonds       : angle       4.43187 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 142
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7863 (OUTLIER) cc_final: 0.7583 (tt)
REVERT: A  148 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7394 (tm-30)
REVERT: A  227 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8189 (mmmt)
REVERT: A  264 LEU cc_start: 0.8101 (tt) cc_final: 0.7851 (tp)
REVERT: A  536 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7719 (mt)
REVERT: A  641 MET cc_start: 0.7483 (ttm) cc_final: 0.7273 (ttm)
REVERT: A  717 ILE cc_start: 0.7758 (mm) cc_final: 0.7497 (mm)
REVERT: A  748 SER cc_start: 0.9059 (m) cc_final: 0.8415 (m)
  outliers start: 40
  outliers final: 29
  residues processed: 171
  average time/residue: 0.0749
  time to fit residues: 17.1916
Evaluate side-chains
  163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 12 optimal weight:    8.9990
   chunk 44 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 727 ASN
** A 829 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.177430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.145392 restraints weight = 9060.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.145534 restraints weight = 8142.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.147281 restraints weight = 6656.894|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.148389 restraints weight = 4984.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.148761 restraints weight = 4420.391|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.4019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6981  Z= 0.152
  Angle     :  0.590   7.145   9460  Z= 0.305
  Chirality :  0.042   0.205   1135
  Planarity :  0.005   0.076   1190
  Dihedral  :  6.043  45.698    973
  Min Nonbonded Distance : 2.115

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  4.95 %
    Allowed  : 27.47 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.29), residues: 891
  helix:  1.67 (0.24), residues: 472
  sheet: -1.80 (0.55), residues: 103
  loop : -1.02 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 153 
 TYR   0.020   0.001   TYR A 618 
 PHE   0.023   0.002   PHE A 118 
 TRP   0.020   0.001   TRP A  72 
 HIS   0.002   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6981)
  covalent geometry    : angle       0.58990 ( 9460)
  hydrogen bonds       : bond        0.04142 (  385)
  hydrogen bonds       : angle       4.48523 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 133
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7660 (tt)
REVERT: A  129 GLU cc_start: 0.6947 (pp20) cc_final: 0.6649 (pp20)
REVERT: A  148 GLU cc_start: 0.8033 (OUTLIER) cc_final: 0.7438 (tm-30)
REVERT: A  227 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8379 (mmmt)
REVERT: A  264 LEU cc_start: 0.8070 (tt) cc_final: 0.7827 (tp)
REVERT: A  513 GLU cc_start: 0.7972 (tp30) cc_final: 0.7766 (tp30)
REVERT: A  641 MET cc_start: 0.7510 (ttm) cc_final: 0.7291 (ttm)
REVERT: A  717 ILE cc_start: 0.7814 (mm) cc_final: 0.7585 (mm)
REVERT: A  748 SER cc_start: 0.9090 (m) cc_final: 0.8503 (m)
  outliers start: 38
  outliers final: 32
  residues processed: 160
  average time/residue: 0.0755
  time to fit residues: 16.0815
Evaluate side-chains
  161 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 127
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue   97 MET
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 82 optimal weight:    0.6980
   chunk 70 optimal weight:    0.5980
   chunk 14 optimal weight:    8.9990
   chunk 77 optimal weight:    0.5980
   chunk 11 optimal weight:    0.0370
   chunk 58 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0870
   overall best weight:    0.4036

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

Flipped N/Q/H residues before XYZ refinement:
A 727 ASN
A 829 GLN
A 855 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.180234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.148367 restraints weight = 9151.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.149646 restraints weight = 7566.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.150917 restraints weight = 5997.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.151229 restraints weight = 5100.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.153169 restraints weight = 4606.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.4026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6981  Z= 0.123
  Angle     :  0.591   8.393   9460  Z= 0.304
  Chirality :  0.042   0.203   1135
  Planarity :  0.005   0.077   1190
  Dihedral  :  5.948  45.043    973
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 28.12 %
    Favored  : 67.06 %
  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:  0.55 (0.29), residues: 891
  helix:  1.81 (0.24), residues: 466
  sheet: -1.76 (0.54), residues: 103
  loop : -1.05 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 153 
 TYR   0.019   0.001   TYR A 618 
 PHE   0.024   0.001   PHE A 118 
 TRP   0.022   0.001   TRP A  72 
 HIS   0.002   0.001   HIS A  58 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 6981)
  covalent geometry    : angle       0.59057 ( 9460)
  hydrogen bonds       : bond        0.03826 (  385)
  hydrogen bonds       : angle       4.39309 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7825 (OUTLIER) cc_final: 0.7551 (tt)
REVERT: A  148 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7518 (tm-30)
REVERT: A  227 LYS cc_start: 0.8666 (mmmt) cc_final: 0.8363 (mmmt)
REVERT: A  264 LEU cc_start: 0.8051 (tt) cc_final: 0.7836 (tp)
REVERT: A  360 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.7768 (mtt)
REVERT: A  641 MET cc_start: 0.7472 (ttm) cc_final: 0.7255 (ttm)
REVERT: A  717 ILE cc_start: 0.7640 (mm) cc_final: 0.7383 (mm)
REVERT: A  748 SER cc_start: 0.9011 (m) cc_final: 0.8475 (m)
  outliers start: 37
  outliers final: 29
  residues processed: 162
  average time/residue: 0.0784
  time to fit residues: 16.7318
Evaluate side-chains
  163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 131
  time to evaluate  : 0.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 54 optimal weight:    0.5980
   chunk 22 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 727 ASN
A 855 GLN
A 869 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.178251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.146390 restraints weight = 9138.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.147044 restraints weight = 7092.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.147683 restraints weight = 6253.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3712 r_free = 0.3712 target = 0.148310 restraints weight = 5579.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.149408 restraints weight = 4818.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3717
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   6981  Z= 0.157
  Angle     :  0.618   7.018   9460  Z= 0.323
  Chirality :  0.043   0.186   1135
  Planarity :  0.005   0.079   1190
  Dihedral  :  5.982  43.980    973
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 27.99 %
    Favored  : 66.80 %
  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:  0.49 (0.29), residues: 891
  helix:  1.71 (0.24), residues: 472
  sheet: -1.78 (0.55), residues: 103
  loop : -1.02 (0.34), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 153 
 TYR   0.028   0.001   TYR A 618 
 PHE   0.024   0.002   PHE A 118 
 TRP   0.023   0.002   TRP A  72 
 HIS   0.002   0.001   HIS A 149 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 6981)
  covalent geometry    : angle       0.61839 ( 9460)
  hydrogen bonds       : bond        0.04130 (  385)
  hydrogen bonds       : angle       4.48857 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 127
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7643 (tt)
REVERT: A  129 GLU cc_start: 0.6995 (pp20) cc_final: 0.6628 (pp20)
REVERT: A  130 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6600 (mm-30)
REVERT: A  148 GLU cc_start: 0.8051 (OUTLIER) cc_final: 0.7424 (tm-30)
REVERT: A  227 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8411 (mmmt)
REVERT: A  264 LEU cc_start: 0.8059 (tt) cc_final: 0.7837 (tp)
REVERT: A  641 MET cc_start: 0.7516 (ttm) cc_final: 0.7311 (ttm)
REVERT: A  717 ILE cc_start: 0.7807 (mm) cc_final: 0.7569 (mm)
REVERT: A  748 SER cc_start: 0.9081 (m) cc_final: 0.8687 (m)
REVERT: A  869 GLN cc_start: 0.5746 (OUTLIER) cc_final: 0.5537 (pp30)
  outliers start: 40
  outliers final: 32
  residues processed: 159
  average time/residue: 0.0762
  time to fit residues: 16.1209
Evaluate side-chains
  162 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 127
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  727 ASN
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  840 SER
Chi-restraints excluded: chain A residue  869 GLN
Chi-restraints excluded: chain A residue  870 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 62 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0060
   chunk 10 optimal weight:    5.9990
   chunk 64 optimal weight:    0.9980
   chunk 75 optimal weight:    0.5980
   chunk 83 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
A 855 GLN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.178495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.144081 restraints weight = 9132.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.147200 restraints weight = 6238.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.149357 restraints weight = 4850.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.150771 restraints weight = 4062.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.151810 restraints weight = 3600.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.4197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6981  Z= 0.149
  Angle     :  0.629   8.195   9460  Z= 0.328
  Chirality :  0.043   0.187   1135
  Planarity :  0.005   0.081   1190
  Dihedral  :  5.994  43.717    973
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 28.91 %
    Favored  : 66.54 %
  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:  0.51 (0.29), residues: 891
  helix:  1.71 (0.24), residues: 472
  sheet: -1.77 (0.54), residues: 103
  loop : -0.99 (0.35), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 153 
 TYR   0.032   0.001   TYR A 618 
 PHE   0.025   0.002   PHE A 118 
 TRP   0.025   0.002   TRP A  72 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6981)
  covalent geometry    : angle       0.62854 ( 9460)
  hydrogen bonds       : bond        0.04099 (  385)
  hydrogen bonds       : angle       4.55595 ( 1149)

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

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

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1782 Ramachandran restraints generated.
    891 Oldfield, 0 Emsley, 891 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 129
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
REVERT: A   93 ILE cc_start: 0.7952 (OUTLIER) cc_final: 0.7633 (tt)
REVERT: A  129 GLU cc_start: 0.6941 (pp20) cc_final: 0.6621 (pp20)
REVERT: A  130 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6521 (mm-30)
REVERT: A  148 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7314 (tm-30)
REVERT: A  227 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8415 (mmmt)
REVERT: A  264 LEU cc_start: 0.8034 (tt) cc_final: 0.7824 (tp)
REVERT: A  360 MET cc_start: 0.8304 (OUTLIER) cc_final: 0.7815 (mtt)
REVERT: A  641 MET cc_start: 0.7491 (ttm) cc_final: 0.7285 (ttm)
REVERT: A  717 ILE cc_start: 0.7787 (mm) cc_final: 0.7557 (mm)
REVERT: A  748 SER cc_start: 0.9074 (m) cc_final: 0.8758 (m)
  outliers start: 35
  outliers final: 29
  residues processed: 156
  average time/residue: 0.0779
  time to fit residues: 16.2696
Evaluate side-chains
  159 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  231 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  360 MET
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  570 THR
Chi-restraints excluded: chain A residue  609 GLN
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  623 ARG
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  741 MET
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  830 THR
Chi-restraints excluded: chain A residue  840 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 67 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    0.2980
   chunk 28 optimal weight:    0.9990
   chunk 59 optimal weight:    0.0870
   chunk 9 optimal weight:    0.9980
   chunk 66 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   chunk 55 optimal weight:    0.3980
   chunk 16 optimal weight:    4.9990
   overall best weight:    0.4758

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

Flipped N/Q/H residues before XYZ refinement:
A 855 GLN
A 869 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.181676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.149793 restraints weight = 9163.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.150128 restraints weight = 9056.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.152791 restraints weight = 6803.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.152959 restraints weight = 4803.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.153411 restraints weight = 4591.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6981  Z= 0.130
  Angle     :  0.595   6.454   9460  Z= 0.309
  Chirality :  0.042   0.193   1135
  Planarity :  0.005   0.081   1190
  Dihedral  :  5.842  42.821    973
  Min Nonbonded Distance : 2.153

Molprobity Statistics.
  All-atom Clashscore : 8.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 28.91 %
    Favored  : 66.80 %
  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:  0.65 (0.29), residues: 891
  helix:  1.87 (0.24), residues: 468
  sheet: -1.74 (0.54), residues: 103
  loop : -0.97 (0.34), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 153 
 TYR   0.029   0.001   TYR A 618 
 PHE   0.024   0.001   PHE A 118 
 TRP   0.025   0.002   TRP A  72 
 HIS   0.003   0.001   HIS A 394 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 6981)
  covalent geometry    : angle       0.59516 ( 9460)
  hydrogen bonds       : bond        0.03751 (  385)
  hydrogen bonds       : angle       4.39492 ( 1149)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1229.21 seconds
wall clock time: 21 minutes 52.80 seconds (1312.80 seconds total)