Starting phenix.real_space_refine
on Mon Apr 28 05:47:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8iwr_35777/04_2025/8iwr_35777_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8iwr_35777/04_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_35777/04_2025/8iwr_35777.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8iwr_35777/04_2025/8iwr_35777.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8iwr_35777/04_2025/8iwr_35777_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8iwr_35777/04_2025/8iwr_35777_trim.cif"
  }
  resolution = 3.52
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 5.06, per 1000 atoms: 0.74
  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: 1.55
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.92
  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: 2.39

  Time building geometry restraints manager: 1.84 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:             3.580
  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:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     20.730
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.660
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (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
 TRP   0.035   0.002   TRP A  72 
 HIS   0.002   0.000   HIS A 149 
 PHE   0.017   0.001   PHE A 118 
 TYR   0.003   0.000   TYR A 696 
 ARG   0.006   0.000   ARG A 448 

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

*********************** 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  : 0.683 
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: 0.1761
  time to fit residues: 33.5355
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  : 0.790 
-------------------------------------------------------------------------------
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 75 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 37 optimal weight:    0.0570
   chunk 23 optimal weight:    0.0570
   chunk 45 optimal weight:    0.8980
   chunk 36 optimal weight:    0.4980
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 51 optimal weight:    6.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
A 727 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.192229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.157981 restraints weight = 8932.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.161647 restraints weight = 5841.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.164216 restraints weight = 4361.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.1187

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= 0.123
  Angle     :  0.546   6.861   9460  Z= 0.282
  Chirality :  0.041   0.145   1135
  Planarity :  0.004   0.044   1190
  Dihedral  :  7.144  84.374    974
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 29.04 %
    Favored  : 68.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.93 (0.29), residues: 891
  helix:  2.15 (0.24), residues: 461
  sheet: -1.20 (0.55), residues: 99
  loop : -1.03 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  72 
 HIS   0.002   0.001   HIS A 372 
 PHE   0.009   0.001   PHE A 538 
 TYR   0.010   0.001   TYR A 618 
 ARG   0.004   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03338 (  385)
  hydrogen bonds       : angle       4.48525 ( 1149)
  covalent geometry    : bond        0.00275 ( 6981)
  covalent geometry    : angle       0.54645 ( 9460)

*********************** 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
  160 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 143
  time to evaluate  : 0.801 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LEU cc_start: 0.7959 (tt) cc_final: 0.7594 (tp)
  outliers start: 17
  outliers final: 9
  residues processed: 151
  average time/residue: 0.1800
  time to fit residues: 37.2658
Evaluate side-chains
  140 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  502 LEU
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  766 TRP
Chi-restraints excluded: chain A residue  830 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 8 optimal weight:    3.9990
   chunk 71 optimal weight:    3.9990
   chunk 18 optimal weight:    0.0770
   chunk 74 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 66 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.1942

-------------------------------------------------------------------------------
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 381 ASN
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: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.170665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.135619 restraints weight = 9094.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.138086 restraints weight = 6758.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.139721 restraints weight = 5208.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   6981  Z= 0.219
  Angle     :  0.693   7.808   9460  Z= 0.362
  Chirality :  0.046   0.170   1135
  Planarity :  0.005   0.054   1190
  Dihedral  :  6.709  58.742    973
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  6.12 %
    Allowed  : 26.30 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.28), residues: 891
  helix:  1.51 (0.24), residues: 465
  sheet: -1.67 (0.57), residues: 91
  loop : -0.99 (0.33), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 285 
 HIS   0.004   0.001   HIS A 624 
 PHE   0.023   0.002   PHE A 118 
 TYR   0.021   0.002   TYR A 618 
 ARG   0.005   0.001   ARG A 523 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05351 (  385)
  hydrogen bonds       : angle       4.79301 ( 1149)
  covalent geometry    : bond        0.00517 ( 6981)
  covalent geometry    : angle       0.69330 ( 9460)

*********************** 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
  191 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 144
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.7006 (tm-30)
REVERT: A  130 GLU cc_start: 0.7641 (mm-30) cc_final: 0.6413 (mm-30)
REVERT: A  227 LYS cc_start: 0.8623 (mmmt) cc_final: 0.8187 (mmmt)
REVERT: A  264 LEU cc_start: 0.8125 (tt) cc_final: 0.7852 (tp)
REVERT: A  381 ASN cc_start: 0.7843 (p0) cc_final: 0.7513 (p0)
REVERT: A  641 MET cc_start: 0.7785 (OUTLIER) cc_final: 0.7519 (ttm)
REVERT: A  748 SER cc_start: 0.9226 (m) cc_final: 0.8400 (m)
REVERT: A  794 PHE cc_start: 0.8715 (OUTLIER) cc_final: 0.7632 (m-80)
  outliers start: 47
  outliers final: 26
  residues processed: 176
  average time/residue: 0.1820
  time to fit residues: 43.2290
Evaluate side-chains
  160 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 131
  time to evaluate  : 0.865 
-------------------------------------------------------------------------------
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   93 ILE
Chi-restraints excluded: chain A residue   99 GLN
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  354 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  465 CYS
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  550 THR
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  678 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  707 LEU
Chi-restraints excluded: chain A residue  766 TRP
Chi-restraints excluded: chain A residue  772 THR
Chi-restraints excluded: chain A residue  794 PHE
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 73 optimal weight:    0.0170
   chunk 80 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 5 optimal weight:    4.9990
   chunk 72 optimal weight:    0.9980
   chunk 42 optimal weight:    4.9990
   chunk 25 optimal weight:    0.7980
   chunk 4 optimal weight:    0.3980
   chunk 83 optimal weight:    0.9980
   chunk 10 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   overall best weight:    0.5418

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

Flipped N/Q/H residues before XYZ refinement:
A 149 HIS
A 372 HIS
A 727 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.175692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.142271 restraints weight = 9141.983|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.143821 restraints weight = 6891.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.144848 restraints weight = 5263.517|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.3282

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6981  Z= 0.136
  Angle     :  0.593   7.651   9460  Z= 0.304
  Chirality :  0.042   0.158   1135
  Planarity :  0.004   0.065   1190
  Dihedral  :  6.300  55.053    973
  Min Nonbonded Distance : 2.100

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 26.95 %
    Favored  : 68.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.57 (0.29), residues: 891
  helix:  1.74 (0.24), residues: 466
  sheet: -1.46 (0.54), residues: 103
  loop : -0.98 (0.34), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 285 
 HIS   0.002   0.001   HIS A  58 
 PHE   0.021   0.002   PHE A 725 
 TYR   0.009   0.001   TYR A 618 
 ARG   0.003   0.000   ARG A 448 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04147 (  385)
  hydrogen bonds       : angle       4.47138 ( 1149)
  covalent geometry    : bond        0.00309 ( 6981)
  covalent geometry    : angle       0.59311 ( 9460)

*********************** 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
  172 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 136
  time to evaluate  : 0.762 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 LEU cc_start: 0.8145 (tt) cc_final: 0.7856 (tp)
REVERT: A  641 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7445 (ttm)
REVERT: A  748 SER cc_start: 0.9079 (m) cc_final: 0.8321 (m)
REVERT: A  794 PHE cc_start: 0.8619 (OUTLIER) cc_final: 0.7569 (m-80)
  outliers start: 36
  outliers final: 23
  residues processed: 158
  average time/residue: 0.1880
  time to fit residues: 40.0612
Evaluate side-chains
  151 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 126
  time to evaluate  : 0.744 
-------------------------------------------------------------------------------
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  165 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  350 ASP
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  491 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  641 MET
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 41 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 72 optimal weight:    0.5980
   chunk 21 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 23 optimal weight:    0.0770
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 149 HIS
A 727 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.172371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.139069 restraints weight = 8905.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.140898 restraints weight = 6812.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.142097 restraints weight = 5070.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7704
moved from start:          0.3403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6981  Z= 0.140
  Angle     :  0.576   8.456   9460  Z= 0.295
  Chirality :  0.041   0.138   1135
  Planarity :  0.004   0.068   1190
  Dihedral  :  6.135  51.839    973
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 7.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 26.95 %
    Favored  : 67.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.29), residues: 891
  helix:  1.81 (0.24), residues: 464
  sheet: -1.60 (0.53), residues: 103
  loop : -0.99 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  72 
 HIS   0.009   0.001   HIS A 149 
 PHE   0.021   0.001   PHE A 725 
 TYR   0.012   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04056 (  385)
  hydrogen bonds       : angle       4.40962 ( 1149)
  covalent geometry    : bond        0.00328 ( 6981)
  covalent geometry    : angle       0.57599 ( 9460)

*********************** 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
  177 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7257 (mt-10)
REVERT: A  129 GLU cc_start: 0.7001 (pp20) cc_final: 0.6482 (pp20)
REVERT: A  130 GLU cc_start: 0.7306 (mm-30) cc_final: 0.6270 (mm-30)
REVERT: A  264 LEU cc_start: 0.8118 (tt) cc_final: 0.7826 (tp)
REVERT: A  641 MET cc_start: 0.7763 (OUTLIER) cc_final: 0.7476 (ttm)
REVERT: A  748 SER cc_start: 0.9121 (m) cc_final: 0.8511 (m)
REVERT: A  794 PHE cc_start: 0.8659 (OUTLIER) cc_final: 0.7585 (m-80)
  outliers start: 41
  outliers final: 32
  residues processed: 162
  average time/residue: 0.1895
  time to fit residues: 41.1701
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  : 0.799 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   62 GLU
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  165 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  310 LEU
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  491 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  573 SER
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  641 MET
Chi-restraints excluded: chain A residue  642 THR
Chi-restraints excluded: chain A residue  667 ASP
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  727 ASN
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  840 SER
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 31 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 71 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0970
   chunk 42 optimal weight:    3.9990
   chunk 81 optimal weight:    0.7980
   chunk 4 optimal weight:    0.0170
   overall best weight:    0.5016

-------------------------------------------------------------------------------
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 381 ASN
A 727 ASN
A 829 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.181359 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.148833 restraints weight = 8973.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.151392 restraints weight = 7355.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.153132 restraints weight = 5451.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.3479

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6981  Z= 0.129
  Angle     :  0.585   7.613   9460  Z= 0.298
  Chirality :  0.041   0.136   1135
  Planarity :  0.005   0.069   1190
  Dihedral  :  6.042  50.338    973
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 27.21 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.29), residues: 891
  helix:  1.90 (0.24), residues: 460
  sheet: -1.64 (0.53), residues: 103
  loop : -1.03 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  72 
 HIS   0.003   0.001   HIS A 149 
 PHE   0.021   0.001   PHE A 725 
 TYR   0.010   0.001   TYR A 618 
 ARG   0.006   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03891 (  385)
  hydrogen bonds       : angle       4.39138 ( 1149)
  covalent geometry    : bond        0.00296 ( 6981)
  covalent geometry    : angle       0.58452 ( 9460)

*********************** 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
  174 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 133
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLU cc_start: 0.7455 (OUTLIER) cc_final: 0.7059 (mt-10)
REVERT: A  130 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6979 (mm-30)
REVERT: A  264 LEU cc_start: 0.8088 (tt) cc_final: 0.7808 (tp)
REVERT: A  381 ASN cc_start: 0.7943 (p0) cc_final: 0.7692 (p0)
REVERT: A  641 MET cc_start: 0.7669 (OUTLIER) cc_final: 0.7393 (ttm)
REVERT: A  717 ILE cc_start: 0.7288 (mm) cc_final: 0.6470 (mt)
REVERT: A  748 SER cc_start: 0.9082 (m) cc_final: 0.8506 (m)
  outliers start: 41
  outliers final: 30
  residues processed: 160
  average time/residue: 0.1746
  time to fit residues: 37.6237
Evaluate side-chains
  157 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 125
  time to evaluate  : 0.692 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   62 GLU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  350 ASP
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  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  573 SER
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  641 MET
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.0770
   chunk 44 optimal weight:    1.9990
   chunk 61 optimal weight:    0.5980
   chunk 56 optimal weight:    1.9990
   chunk 16 optimal weight:    5.9990
   chunk 45 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9980
   chunk 20 optimal weight:    0.8980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
A 727 ASN
A 765 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.182382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.150973 restraints weight = 8952.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.150183 restraints weight = 7557.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.152018 restraints weight = 6874.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.3655

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= 0.147
  Angle     :  0.598   7.671   9460  Z= 0.306
  Chirality :  0.042   0.240   1135
  Planarity :  0.005   0.075   1190
  Dihedral  :  6.020  49.070    973
  Min Nonbonded Distance : 2.096

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.29), residues: 891
  helix:  1.78 (0.24), residues: 464
  sheet: -1.63 (0.54), residues: 103
  loop : -1.11 (0.34), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A  72 
 HIS   0.001   0.000   HIS A 372 
 PHE   0.023   0.002   PHE A 118 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.003   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04011 (  385)
  hydrogen bonds       : angle       4.43733 ( 1149)
  covalent geometry    : bond        0.00344 ( 6981)
  covalent geometry    : angle       0.59824 ( 9460)

*********************** 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
  175 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6999 (mm-30)
REVERT: A  227 LYS cc_start: 0.8574 (mmmt) cc_final: 0.8138 (mmmt)
REVERT: A  264 LEU cc_start: 0.8105 (tt) cc_final: 0.7845 (tp)
REVERT: A  641 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7394 (ttm)
REVERT: A  717 ILE cc_start: 0.7591 (mm) cc_final: 0.7337 (mm)
REVERT: A  748 SER cc_start: 0.9063 (m) cc_final: 0.8519 (m)
  outliers start: 38
  outliers final: 32
  residues processed: 162
  average time/residue: 0.1836
  time to fit residues: 40.0665
Evaluate side-chains
  165 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 132
  time to evaluate  : 0.703 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  350 ASP
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  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  578 VAL
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  641 MET
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  719 LEU
Chi-restraints excluded: chain A residue  727 ASN
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 65 optimal weight:    0.9980
   chunk 75 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 60 optimal weight:    0.1980
   chunk 73 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 76 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0030
   chunk 20 optimal weight:    0.5980
   chunk 47 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   overall best weight:    0.4390

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

Flipped N/Q/H residues before XYZ refinement:
A 381 ASN
A 727 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.183966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.152029 restraints weight = 9140.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.153041 restraints weight = 7661.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.154549 restraints weight = 6447.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3775
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   6981  Z= 0.126
  Angle     :  0.580   7.450   9460  Z= 0.299
  Chirality :  0.042   0.224   1135
  Planarity :  0.005   0.077   1190
  Dihedral  :  5.941  48.081    973
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 27.47 %
    Favored  : 67.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.29), residues: 891
  helix:  1.91 (0.24), residues: 460
  sheet: -1.51 (0.56), residues: 97
  loop : -1.13 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  72 
 HIS   0.001   0.000   HIS A  58 
 PHE   0.022   0.001   PHE A 725 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.007   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  385)
  hydrogen bonds       : angle       4.36681 ( 1149)
  covalent geometry    : bond        0.00293 ( 6981)
  covalent geometry    : angle       0.57974 ( 9460)

*********************** 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
  176 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 139
  time to evaluate  : 0.790 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLU cc_start: 0.7471 (mt-10) cc_final: 0.7203 (mt-10)
REVERT: A  153 ARG cc_start: 0.8686 (ptm160) cc_final: 0.8225 (ttm-80)
REVERT: A  227 LYS cc_start: 0.8524 (mmmt) cc_final: 0.8084 (mmmt)
REVERT: A  264 LEU cc_start: 0.8077 (tt) cc_final: 0.7829 (tp)
REVERT: A  381 ASN cc_start: 0.8051 (p0) cc_final: 0.7806 (p0)
REVERT: A  641 MET cc_start: 0.7653 (OUTLIER) cc_final: 0.7383 (ttm)
REVERT: A  717 ILE cc_start: 0.7460 (mm) cc_final: 0.7178 (mm)
REVERT: A  748 SER cc_start: 0.9039 (m) cc_final: 0.8598 (m)
  outliers start: 37
  outliers final: 33
  residues processed: 165
  average time/residue: 0.1890
  time to fit residues: 41.9747
Evaluate side-chains
  165 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 131
  time to evaluate  : 0.676 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  350 ASP
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  550 THR
Chi-restraints excluded: chain A residue  552 VAL
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  578 VAL
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  641 MET
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  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 40 optimal weight:    2.9990
   chunk 52 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 56 optimal weight:    0.6980
   chunk 67 optimal weight:    2.9990
   chunk 62 optimal weight:    0.7980
   chunk 88 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
A 727 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.183940 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.150568 restraints weight = 9264.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.151890 restraints weight = 8336.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.153292 restraints weight = 6418.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.3850

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= 0.156
  Angle     :  0.607   7.680   9460  Z= 0.313
  Chirality :  0.042   0.206   1135
  Planarity :  0.005   0.077   1190
  Dihedral  :  5.992  47.050    973
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  5.34 %
    Allowed  : 26.69 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.29), residues: 891
  helix:  1.85 (0.24), residues: 460
  sheet: -1.53 (0.55), residues: 97
  loop : -1.14 (0.33), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A  72 
 HIS   0.002   0.001   HIS A 394 
 PHE   0.025   0.002   PHE A 118 
 TYR   0.020   0.001   TYR A 618 
 ARG   0.006   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04098 (  385)
  hydrogen bonds       : angle       4.46003 ( 1149)
  covalent geometry    : bond        0.00370 ( 6981)
  covalent geometry    : angle       0.60681 ( 9460)

*********************** 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
  177 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 136
  time to evaluate  : 0.768 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.8687 (ptm160) cc_final: 0.8191 (ttm-80)
REVERT: A  227 LYS cc_start: 0.8545 (mmmt) cc_final: 0.8167 (mmmt)
REVERT: A  264 LEU cc_start: 0.8084 (tt) cc_final: 0.7841 (tp)
REVERT: A  381 ASN cc_start: 0.8281 (p0) cc_final: 0.8025 (p0)
REVERT: A  485 GLN cc_start: 0.8591 (OUTLIER) cc_final: 0.7314 (mp10)
REVERT: A  641 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7451 (ttm)
REVERT: A  717 ILE cc_start: 0.7738 (mm) cc_final: 0.7479 (mm)
REVERT: A  748 SER cc_start: 0.9020 (m) cc_final: 0.8596 (m)
  outliers start: 41
  outliers final: 31
  residues processed: 164
  average time/residue: 0.1860
  time to fit residues: 41.2876
Evaluate side-chains
  163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 130
  time to evaluate  : 0.761 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  298 SER
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  350 ASP
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  485 GLN
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  552 VAL
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  578 VAL
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  641 MET
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 80 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 36 optimal weight:    0.8980
   chunk 10 optimal weight:    5.9990
   chunk 59 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   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 140 HIS
** 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 = 0.4041 r_free = 0.4041 target = 0.179319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.147645 restraints weight = 9171.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.147987 restraints weight = 7391.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.149187 restraints weight = 6219.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7793
moved from start:          0.4022

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= 0.158
  Angle     :  0.658  13.259   9460  Z= 0.332
  Chirality :  0.043   0.204   1135
  Planarity :  0.005   0.078   1190
  Dihedral  :  6.042  46.032    973
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 9.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.17 %
    Favored  : 93.83 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 27.73 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.29), residues: 891
  helix:  1.73 (0.24), residues: 465
  sheet: -1.55 (0.55), residues: 97
  loop : -1.14 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A  72 
 HIS   0.003   0.001   HIS A 394 
 PHE   0.025   0.002   PHE A 118 
 TYR   0.027   0.001   TYR A 618 
 ARG   0.007   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04192 (  385)
  hydrogen bonds       : angle       4.49914 ( 1149)
  covalent geometry    : bond        0.00371 ( 6981)
  covalent geometry    : angle       0.65814 ( 9460)

********************** 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
  166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 132
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7084 (mt-10)
REVERT: A  129 GLU cc_start: 0.7047 (pp20) cc_final: 0.6191 (pp20)
REVERT: A  130 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6341 (mm-30)
REVERT: A  153 ARG cc_start: 0.8618 (ptm160) cc_final: 0.8175 (ttm-80)
REVERT: A  227 LYS cc_start: 0.8556 (mmmt) cc_final: 0.8282 (mmmt)
REVERT: A  264 LEU cc_start: 0.8036 (tt) cc_final: 0.7755 (tp)
REVERT: A  274 PHE cc_start: 0.8464 (m-80) cc_final: 0.8085 (m-10)
REVERT: A  485 GLN cc_start: 0.8588 (OUTLIER) cc_final: 0.7306 (mp10)
REVERT: A  536 LEU cc_start: 0.7979 (OUTLIER) cc_final: 0.7777 (mt)
REVERT: A  641 MET cc_start: 0.7741 (OUTLIER) cc_final: 0.7454 (ttm)
REVERT: A  748 SER cc_start: 0.9017 (m) cc_final: 0.8665 (m)
  outliers start: 34
  outliers final: 29
  residues processed: 159
  average time/residue: 0.1982
  time to fit residues: 42.1504
Evaluate side-chains
  162 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.796 
-------------------------------------------------------------------------------
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  147 LEU
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  184 ASP
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  263 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  313 VAL
Chi-restraints excluded: chain A residue  350 ASP
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  485 GLN
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  578 VAL
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  641 MET
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  719 LEU
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    0.2980
   chunk 85 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 140 HIS
** 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 = 0.3954 r_free = 0.3954 target = 0.171793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.139174 restraints weight = 9249.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.139045 restraints weight = 6258.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.140372 restraints weight = 5551.929|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.4198

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6981  Z= 0.162
  Angle     :  0.642   8.431   9460  Z= 0.328
  Chirality :  0.043   0.214   1135
  Planarity :  0.005   0.078   1190
  Dihedral  :  6.077  44.614    973
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 9.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 28.12 %
    Favored  : 67.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.29), residues: 891
  helix:  1.66 (0.24), residues: 471
  sheet: -1.58 (0.55), residues: 97
  loop : -1.16 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  72 
 HIS   0.009   0.001   HIS A 394 
 PHE   0.025   0.002   PHE A 118 
 TYR   0.028   0.001   TYR A 618 
 ARG   0.006   0.000   ARG A 153 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04231 (  385)
  hydrogen bonds       : angle       4.53120 ( 1149)
  covalent geometry    : bond        0.00382 ( 6981)
  covalent geometry    : angle       0.64166 ( 9460)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2656.78 seconds
wall clock time: 46 minutes 46.78 seconds (2806.78 seconds total)