Starting phenix.real_space_refine
on Thu Nov 14 18:45:06 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/11_2024/8iwr_35777_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/11_2024/8iwr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/11_2024/8iwr_35777.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/11_2024/8iwr_35777.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/11_2024/8iwr_35777_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwr_35777/11_2024/8iwr_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): 0.09s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 5.72, per 1000 atoms: 0.83
  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: 2.04
  Conformation dependent library (CDL) restraints added in 1.0 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: 2.48

  Time building geometry restraints manager: 2.37 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:             2.940
  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:             0.000
  Extract box with map and model:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     22.970
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.900
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.340
-------------------------------------------------------------------------------
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= 0.251
  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 

*********************** 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  : 0.690 
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: 0.1898
  time to fit residues: 36.4954
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  : 0.789 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7284
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= 0.175
  Angle     :  0.547   6.862   9460  Z= 0.282
  Chirality :  0.041   0.145   1135
  Planarity :  0.004   0.044   1190
  Dihedral  :  7.144  84.363    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 

*********************** 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  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  264 LEU cc_start: 0.7940 (tt) cc_final: 0.7577 (tp)
  outliers start: 17
  outliers final: 9
  residues processed: 151
  average time/residue: 0.1736
  time to fit residues: 35.5868
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  : 0.683 
-------------------------------------------------------------------------------
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 44 optimal weight:    0.2980
   chunk 25 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 55 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 72 optimal weight:    0.5980
   chunk 27 optimal weight:    0.5980
   chunk 64 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 747 GLN
A 822 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
moved from start:          0.1992

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6981  Z= 0.195
  Angle     :  0.544   6.703   9460  Z= 0.282
  Chirality :  0.042   0.164   1135
  Planarity :  0.004   0.047   1190
  Dihedral  :  6.179  54.152    973
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  5.21 %
    Allowed  : 26.69 %
    Favored  : 68.10 %
  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:  0.95 (0.29), residues: 891
  helix:  2.14 (0.24), residues: 461
  sheet: -1.42 (0.59), residues: 87
  loop : -0.92 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  72 
 HIS   0.003   0.001   HIS A 624 
 PHE   0.019   0.001   PHE A 118 
 TYR   0.011   0.001   TYR A 618 
 ARG   0.005   0.000   ARG A 448 

*********************** 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
  182 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 142
  time to evaluate  : 0.759 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.8743 (ptm160) cc_final: 0.8443 (ptm160)
REVERT: A  184 ASP cc_start: 0.7664 (t0) cc_final: 0.7446 (m-30)
REVERT: A  264 LEU cc_start: 0.7945 (tt) cc_final: 0.7615 (tp)
REVERT: A  298 SER cc_start: 0.8613 (m) cc_final: 0.8360 (m)
REVERT: A  641 MET cc_start: 0.7469 (OUTLIER) cc_final: 0.7251 (ttm)
REVERT: A  717 ILE cc_start: 0.6438 (mm) cc_final: 0.5950 (mm)
REVERT: A  794 PHE cc_start: 0.8065 (OUTLIER) cc_final: 0.7207 (m-80)
  outliers start: 40
  outliers final: 20
  residues processed: 168
  average time/residue: 0.1828
  time to fit residues: 42.2924
Evaluate side-chains
  149 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   47 ASN
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  301 LEU
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  550 THR
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  646 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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 60 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 81 optimal weight:    4.9990
   chunk 86 optimal weight:    0.8980
   chunk 77 optimal weight:    1.9990
   chunk 23 optimal weight:    0.3980
   chunk 71 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 149 HIS
A 506 GLN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6981  Z= 0.241
  Angle     :  0.601   8.089   9460  Z= 0.307
  Chirality :  0.042   0.194   1135
  Planarity :  0.004   0.056   1190
  Dihedral  :  6.067  51.962    973
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.43 %
    Allowed  : 26.69 %
    Favored  : 68.88 %
  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:  0.84 (0.29), residues: 891
  helix:  1.97 (0.24), residues: 463
  sheet: -1.41 (0.53), residues: 105
  loop : -0.83 (0.34), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 624 
 PHE   0.017   0.002   PHE A 274 
 TYR   0.013   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 842 

*********************** 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
  171 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 137
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 TRP cc_start: 0.7934 (m100) cc_final: 0.7602 (m100)
REVERT: A  184 ASP cc_start: 0.7651 (t0) cc_final: 0.7440 (m-30)
REVERT: A  264 LEU cc_start: 0.8030 (tt) cc_final: 0.7746 (tp)
REVERT: A  271 PHE cc_start: 0.7305 (m-10) cc_final: 0.7051 (m-80)
REVERT: A  641 MET cc_start: 0.7583 (OUTLIER) cc_final: 0.7312 (ttm)
REVERT: A  717 ILE cc_start: 0.6974 (mm) cc_final: 0.6210 (mt)
REVERT: A  747 GLN cc_start: 0.8674 (OUTLIER) cc_final: 0.8422 (mp10)
REVERT: A  748 SER cc_start: 0.9068 (m) cc_final: 0.8397 (m)
REVERT: A  794 PHE cc_start: 0.8333 (OUTLIER) cc_final: 0.7363 (m-80)
  outliers start: 34
  outliers final: 22
  residues processed: 159
  average time/residue: 0.1721
  time to fit residues: 37.5992
Evaluate side-chains
  153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.681 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue   93 ILE
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  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  550 THR
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  707 LEU
Chi-restraints excluded: chain A residue  747 GLN
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 1 optimal weight:    0.0670
   chunk 64 optimal weight:    0.4980
   chunk 35 optimal weight:    0.0980
   chunk 73 optimal weight:    0.0030
   chunk 59 optimal weight:    0.5980
   chunk 0 optimal weight:    2.9990
   chunk 43 optimal weight:    2.9990
   chunk 77 optimal weight:    0.8980
   chunk 21 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 17 optimal weight:    0.3980
   overall best weight:    0.2128

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7508
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   6981  Z= 0.149
  Angle     :  0.532   6.650   9460  Z= 0.272
  Chirality :  0.041   0.165   1135
  Planarity :  0.004   0.060   1190
  Dihedral  :  5.822  49.694    973
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 7.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.30 %
    Allowed  : 26.95 %
    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:  1.01 (0.29), residues: 891
  helix:  2.16 (0.24), residues: 463
  sheet: -1.39 (0.54), residues: 103
  loop : -0.81 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  72 
 HIS   0.002   0.000   HIS A 149 
 PHE   0.009   0.001   PHE A 274 
 TYR   0.011   0.001   TYR A 618 
 ARG   0.003   0.000   ARG A 448 

*********************** 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
  166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 133
  time to evaluate  : 0.704 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   37 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.7409 (mt)
REVERT: A   60 TRP cc_start: 0.7960 (m100) cc_final: 0.7644 (m100)
REVERT: A  264 LEU cc_start: 0.7978 (tt) cc_final: 0.7661 (tp)
REVERT: A  298 SER cc_start: 0.8609 (m) cc_final: 0.8068 (m)
REVERT: A  437 MET cc_start: 0.8457 (mmm) cc_final: 0.8152 (tpp)
REVERT: A  641 MET cc_start: 0.7484 (OUTLIER) cc_final: 0.7224 (ttm)
REVERT: A  691 GLU cc_start: 0.5688 (OUTLIER) cc_final: 0.5409 (mp0)
REVERT: A  717 ILE cc_start: 0.6674 (mm) cc_final: 0.6085 (mm)
REVERT: A  794 PHE cc_start: 0.8265 (OUTLIER) cc_final: 0.7353 (m-80)
  outliers start: 33
  outliers final: 16
  residues processed: 153
  average time/residue: 0.1876
  time to fit residues: 39.0040
Evaluate side-chains
  146 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 126
  time to evaluate  : 0.680 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   37 ILE
Chi-restraints excluded: chain A residue  149 HIS
Chi-restraints excluded: chain A residue  165 VAL
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  285 TRP
Chi-restraints excluded: chain A residue  361 THR
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  491 THR
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  614 VAL
Chi-restraints excluded: chain A residue  641 MET
Chi-restraints excluded: chain A residue  646 VAL
Chi-restraints excluded: chain A residue  691 GLU
Chi-restraints excluded: chain A residue  719 LEU
Chi-restraints excluded: chain A residue  766 TRP
Chi-restraints excluded: chain A residue  777 LEU
Chi-restraints excluded: chain A residue  794 PHE
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 50 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 86 optimal weight:    0.6980
   chunk 71 optimal weight:    0.0980
   chunk 39 optimal weight:    0.4980
   chunk 7 optimal weight:    0.8980
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    3.9990
   chunk 83 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 49 optimal weight:    0.6980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A  47 ASN
A 506 GLN
A 605 GLN
A 727 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7584
moved from start:          0.2930

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= 0.194
  Angle     :  0.556   6.869   9460  Z= 0.284
  Chirality :  0.041   0.144   1135
  Planarity :  0.004   0.061   1190
  Dihedral  :  5.743  48.325    973
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 27.86 %
    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:  0.90 (0.29), residues: 891
  helix:  2.05 (0.24), residues: 463
  sheet: -1.45 (0.54), residues: 103
  loop : -0.82 (0.35), residues: 325

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 460 
 HIS   0.001   0.000   HIS A  58 
 PHE   0.016   0.001   PHE A 274 
 TYR   0.020   0.001   TYR A 618 
 ARG   0.003   0.000   ARG A 448 

*********************** 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
  164 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.8682 (ptm160) cc_final: 0.8414 (ptm160)
REVERT: A  227 LYS cc_start: 0.8716 (mmmt) cc_final: 0.7988 (mmmt)
REVERT: A  264 LEU cc_start: 0.8016 (tt) cc_final: 0.7738 (tp)
REVERT: A  437 MET cc_start: 0.8538 (mmm) cc_final: 0.8218 (tpp)
REVERT: A  641 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7321 (ttm)
REVERT: A  691 GLU cc_start: 0.5905 (OUTLIER) cc_final: 0.5583 (mp0)
REVERT: A  717 ILE cc_start: 0.6978 (mm) cc_final: 0.6527 (mm)
REVERT: A  748 SER cc_start: 0.9027 (m) cc_final: 0.8436 (m)
REVERT: A  794 PHE cc_start: 0.8445 (OUTLIER) cc_final: 0.7412 (m-80)
  outliers start: 29
  outliers final: 22
  residues processed: 152
  average time/residue: 0.1823
  time to fit residues: 37.6867
Evaluate side-chains
  149 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 124
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
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  244 VAL
Chi-restraints excluded: chain A residue  285 TRP
Chi-restraints excluded: chain A residue  313 VAL
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  609 GLN
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 52 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    6.9990
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7638
moved from start:          0.3178

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= 0.229
  Angle     :  0.575   7.495   9460  Z= 0.294
  Chirality :  0.042   0.134   1135
  Planarity :  0.004   0.065   1190
  Dihedral  :  5.820  47.893    973
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 27.34 %
    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:  0.76 (0.29), residues: 891
  helix:  2.00 (0.24), residues: 461
  sheet: -1.54 (0.56), residues: 97
  loop : -0.98 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 460 
 HIS   0.001   0.001   HIS A  58 
 PHE   0.013   0.001   PHE A 725 
 TYR   0.014   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 796 

*********************** 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
  166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 136
  time to evaluate  : 0.785 
Fit side-chains
   revert: symmetry clash
REVERT: A  153 ARG cc_start: 0.8696 (ptm160) cc_final: 0.8390 (ptm160)
REVERT: A  264 LEU cc_start: 0.8032 (tt) cc_final: 0.7742 (tp)
REVERT: A  274 PHE cc_start: 0.8510 (m-80) cc_final: 0.8006 (m-10)
REVERT: A  437 MET cc_start: 0.8489 (mmm) cc_final: 0.8250 (tpp)
REVERT: A  641 MET cc_start: 0.7642 (OUTLIER) cc_final: 0.7374 (ttm)
REVERT: A  691 GLU cc_start: 0.6019 (OUTLIER) cc_final: 0.5691 (mp0)
REVERT: A  748 SER cc_start: 0.9043 (m) cc_final: 0.8478 (m)
REVERT: A  794 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7453 (m-80)
  outliers start: 30
  outliers final: 24
  residues processed: 154
  average time/residue: 0.1839
  time to fit residues: 38.3866
Evaluate side-chains
  153 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.757 
-------------------------------------------------------------------------------
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  111 LEU
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  244 VAL
Chi-restraints excluded: chain A residue  313 VAL
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  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  678 VAL
Chi-restraints excluded: chain A residue  691 GLU
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 54 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 42 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 74 optimal weight:    0.8980
   chunk 79 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 419 ASN
** A 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 765 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.3566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6981  Z= 0.287
  Angle     :  0.630   8.119   9460  Z= 0.322
  Chirality :  0.043   0.161   1135
  Planarity :  0.004   0.068   1190
  Dihedral  :  5.970  47.190    973
  Min Nonbonded Distance : 2.091

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 27.34 %
    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:  0.57 (0.29), residues: 891
  helix:  1.79 (0.24), residues: 467
  sheet: -1.63 (0.56), residues: 97
  loop : -1.04 (0.33), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 285 
 HIS   0.002   0.001   HIS A 140 
 PHE   0.011   0.002   PHE A 274 
 TYR   0.026   0.002   TYR A 618 
 ARG   0.003   0.000   ARG A 796 

*********************** 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
  166 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 129
  time to evaluate  : 0.749 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7126 (tm-30)
REVERT: A  153 ARG cc_start: 0.8692 (ptm160) cc_final: 0.8329 (ptm160)
REVERT: A  227 LYS cc_start: 0.8808 (mmmt) cc_final: 0.8113 (mmmt)
REVERT: A  264 LEU cc_start: 0.8017 (tt) cc_final: 0.7746 (tp)
REVERT: A  308 GLU cc_start: 0.8356 (pm20) cc_final: 0.8145 (pm20)
REVERT: A  437 MET cc_start: 0.8500 (mmm) cc_final: 0.8284 (tpp)
REVERT: A  560 ILE cc_start: 0.8951 (tp) cc_final: 0.8580 (mt)
REVERT: A  641 MET cc_start: 0.7750 (OUTLIER) cc_final: 0.7460 (ttm)
REVERT: A  748 SER cc_start: 0.9099 (m) cc_final: 0.8654 (m)
  outliers start: 37
  outliers final: 28
  residues processed: 155
  average time/residue: 0.1899
  time to fit residues: 39.6894
Evaluate side-chains
  157 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 127
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  100 PHE
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLU
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  244 VAL
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  310 LEU
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  492 THR
Chi-restraints excluded: chain A residue  550 THR
Chi-restraints excluded: chain A residue  552 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  678 VAL
Chi-restraints excluded: chain A residue  766 TRP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 34 optimal weight:    0.0000
   chunk 62 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 52 optimal weight:    0.5980
   chunk 84 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5584

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

Flipped N/Q/H residues before XYZ refinement:
A 443 GLN
A 727 ASN
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3659

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= 0.212
  Angle     :  0.615  12.999   9460  Z= 0.310
  Chirality :  0.042   0.147   1135
  Planarity :  0.004   0.075   1190
  Dihedral  :  5.900  45.767    973
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.04 %
    Allowed  : 28.52 %
    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:  0.63 (0.29), residues: 891
  helix:  1.89 (0.24), residues: 462
  sheet: -1.57 (0.56), residues: 97
  loop : -1.07 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 795 
 HIS   0.002   0.001   HIS A 394 
 PHE   0.016   0.001   PHE A 274 
 TYR   0.015   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 842 

*********************** 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
  168 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.740 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7744 (tp30) cc_final: 0.7538 (tp30)
REVERT: A  148 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7098 (tm-30)
REVERT: A  153 ARG cc_start: 0.8664 (ptm160) cc_final: 0.8305 (ptm160)
REVERT: A  227 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8209 (mmmt)
REVERT: A  264 LEU cc_start: 0.7972 (tt) cc_final: 0.7726 (tp)
REVERT: A  437 MET cc_start: 0.8576 (mmm) cc_final: 0.8363 (tpp)
REVERT: A  505 GLN cc_start: 0.7922 (pp30) cc_final: 0.7363 (pp30)
REVERT: A  560 ILE cc_start: 0.8910 (tp) cc_final: 0.8526 (mt)
REVERT: A  641 MET cc_start: 0.7675 (OUTLIER) cc_final: 0.7323 (ttm)
REVERT: A  748 SER cc_start: 0.9011 (m) cc_final: 0.8570 (m)
  outliers start: 31
  outliers final: 25
  residues processed: 158
  average time/residue: 0.1859
  time to fit residues: 39.8298
Evaluate side-chains
  155 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 128
  time to evaluate  : 0.766 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   83 LEU
Chi-restraints excluded: chain A residue   93 ILE
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  149 HIS
Chi-restraints excluded: chain A residue  150 THR
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  369 ASP
Chi-restraints excluded: chain A residue  378 VAL
Chi-restraints excluded: chain A residue  461 MET
Chi-restraints excluded: chain A residue  492 THR
Chi-restraints excluded: chain A residue  552 VAL
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  727 ASN
Chi-restraints excluded: chain A residue  766 TRP
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 88 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 54 optimal weight:    0.6980
   chunk 43 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 10 optimal weight:    2.9990
   overall best weight:    0.8584

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7717
moved from start:          0.3821

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= 0.264
  Angle     :  0.638   8.275   9460  Z= 0.327
  Chirality :  0.043   0.267   1135
  Planarity :  0.004   0.075   1190
  Dihedral  :  5.952  44.934    973
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.96 %
    Favored  : 93.04 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 29.04 %
    Favored  : 67.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.74 (0.24), residues: 466
  sheet: -1.55 (0.57), residues: 97
  loop : -1.16 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 795 
 HIS   0.001   0.001   HIS A  58 
 PHE   0.014   0.002   PHE A 274 
 TYR   0.032   0.001   TYR A 618 
 ARG   0.002   0.000   ARG A 796 

********************** 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
  163 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.655 
Fit side-chains
   revert: symmetry clash
REVERT: A   33 GLU cc_start: 0.7781 (tp30) cc_final: 0.7548 (tp30)
REVERT: A  148 GLU cc_start: 0.7835 (OUTLIER) cc_final: 0.7114 (tm-30)
REVERT: A  153 ARG cc_start: 0.8712 (ptm160) cc_final: 0.8336 (ptm160)
REVERT: A  227 LYS cc_start: 0.8771 (mmmt) cc_final: 0.8258 (mmmt)
REVERT: A  264 LEU cc_start: 0.7959 (tt) cc_final: 0.7716 (tp)
REVERT: A  437 MET cc_start: 0.8635 (mmm) cc_final: 0.8412 (tpp)
REVERT: A  505 GLN cc_start: 0.7975 (pp30) cc_final: 0.7393 (pp30)
REVERT: A  641 MET cc_start: 0.7759 (OUTLIER) cc_final: 0.7422 (ttm)
REVERT: A  717 ILE cc_start: 0.7234 (mm) cc_final: 0.6925 (mm)
  outliers start: 30
  outliers final: 25
  residues processed: 154
  average time/residue: 0.1977
  time to fit residues: 40.6114
Evaluate side-chains
  157 residues out of total 768 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 130
  time to evaluate  : 0.776 
-------------------------------------------------------------------------------
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  100 PHE
Chi-restraints excluded: chain A residue  111 LEU
Chi-restraints excluded: chain A residue  115 THR
Chi-restraints excluded: chain A residue  147 LEU
Chi-restraints excluded: chain A residue  148 GLU
Chi-restraints excluded: chain A residue  149 HIS
Chi-restraints excluded: chain A residue  150 THR
Chi-restraints excluded: chain A residue  244 VAL
Chi-restraints excluded: chain A residue  298 SER
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  492 THR
Chi-restraints excluded: chain A residue  552 VAL
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  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 19 optimal weight:   10.0000
   chunk 70 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 8 optimal weight:    3.9990
   chunk 13 optimal weight:    7.9990
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 80 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 727 ASN
** 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 = 0.4027 r_free = 0.4027 target = 0.177620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.146194 restraints weight = 8995.232|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.146813 restraints weight = 7243.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.148291 restraints weight = 6071.719|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.4210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6981  Z= 0.313
  Angle     :  0.697  13.327   9460  Z= 0.358
  Chirality :  0.045   0.253   1135
  Planarity :  0.005   0.081   1190
  Dihedral  :  6.200  43.780    973
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.41 %
    Favored  : 92.59 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 29.30 %
    Favored  : 67.19 %
  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:  0.34 (0.29), residues: 891
  helix:  1.61 (0.24), residues: 465
  sheet: -1.59 (0.58), residues: 97
  loop : -1.21 (0.33), residues: 329

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  60 
 HIS   0.002   0.001   HIS A 140 
 PHE   0.015   0.002   PHE A 274 
 TYR   0.037   0.002   TYR A 618 
 ARG   0.004   0.000   ARG A 842 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1861.61 seconds
wall clock time: 35 minutes 8.69 seconds (2108.69 seconds total)