Starting phenix.real_space_refine
on Thu Jan 16 15:31:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9b5x_44228/01_2025/9b5x_44228.cif"
  }
  resolution = 4.16
  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=   0.034
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: 6
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     Mg      2      5.21       5
     S      42      5.16       5
     C    6074      2.51       5
     N    1573      2.21       5
     O    1833      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 9527
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 7734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 985, 7734
          Classifications: {'peptide': 985}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 1, 'PTRANS': 55, 'TRANS': 928}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 1158
          Classifications: {'peptide': 147}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 131}
    Chain: "D"
      Number of atoms: 596
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 596
          Classifications: {'peptide': 75}
          Link IDs: {'PTRANS': 2, 'TRANS': 72}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 33
          Unusual residues: {' MG': 2, 'ATP': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 6
          Unusual residues: {'A1AIV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 6.30, per 1000 atoms: 0.66
  Number of scatterers: 9527
  At special positions: 0
  Unit cell: (94.696, 97.888, 119.168, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      42     16.00
     P       3     15.00
     Mg      2     11.99
     O    1833      8.00
     N    1573      7.00
     C    6074      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 593 " - pdb=" SG  CYS C  85 " distance=2.92

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.37
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 11 sheets defined
      46.1% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 20 through 25
      removed outlier: 3.825A  pdb=" N   TYR A  25 " --> pdb=" O   SER A  21 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 36
    Processing helix  chain 'A' and resid 46 through 60
    Processing helix  chain 'A' and resid 74 through 79
      removed outlier: 3.686A  pdb=" N   SER A  79 " --> pdb=" O   ASP A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 84 through 88
      removed outlier: 3.958A  pdb=" N   ILE A  88 " --> pdb=" O   GLU A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 91 through 101
      removed outlier: 4.221A  pdb=" N   SER A  98 " --> pdb=" O   LYS A  94 " (cutoff:3.500A)
      removed outlier: 4.682A  pdb=" N   LYS A  99 " --> pdb=" O   VAL A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 123
    Processing helix  chain 'A' and resid 132 through 144
      removed outlier: 3.705A  pdb=" N   PHE A 142 " --> pdb=" O   GLU A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 218 through 223
    Processing helix  chain 'A' and resid 267 through 274
      removed outlier: 4.220A  pdb=" N   LYS A 273 " --> pdb=" O   ARG A 269 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ASP A 274 " --> pdb=" O   GLU A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 304
      removed outlier: 3.950A  pdb=" N   GLN A 290 " --> pdb=" O   MET A 286 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A 293 " --> pdb=" O   PRO A 289 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   GLN A 296 " --> pdb=" O   HIS A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 332
    Processing helix  chain 'A' and resid 339 through 349
    Processing helix  chain 'A' and resid 354 through 375
    Processing helix  chain 'A' and resid 389 through 392
    Processing helix  chain 'A' and resid 399 through 404
    Processing helix  chain 'A' and resid 410 through 418
      removed outlier: 4.465A  pdb=" N   VAL A 416 " --> pdb=" O   GLY A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 427
    Processing helix  chain 'A' and resid 436 through 450
    Processing helix  chain 'A' and resid 468 through 474
      removed outlier: 3.864A  pdb=" N   ASN A 473 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ARG A 474 " --> pdb=" O   ASN A 471 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 483
    Processing helix  chain 'A' and resid 486 through 499
      removed outlier: 3.601A  pdb=" N   CYS A 490 " --> pdb=" O   LEU A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 500 through 503
    Processing helix  chain 'A' and resid 514 through 518
      removed outlier: 3.899A  pdb=" N   GLU A 518 " --> pdb=" O   PRO A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 527
    Processing helix  chain 'A' and resid 538 through 553
    Processing helix  chain 'A' and resid 591 through 597
    Processing helix  chain 'A' and resid 601 through 618
    Processing helix  chain 'A' and resid 618 through 628
    Processing helix  chain 'A' and resid 632 through 641
      removed outlier: 3.511A  pdb=" N   LYS A 639 " --> pdb=" O   GLU A 635 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 656
    Processing helix  chain 'A' and resid 662 through 679
      removed outlier: 3.528A  pdb=" N   CYS A 666 " --> pdb=" O   SER A 662 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 689
      removed outlier: 3.766A  pdb=" N   GLN A 683 " --> pdb=" O   ASN A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 718 through 736
    Processing helix  chain 'A' and resid 743 through 753
      removed outlier: 3.928A  pdb=" N   TYR A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   GLY A 753 " --> pdb=" O   ARG A 749 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 794
      removed outlier: 4.112A  pdb=" N   GLN A 785 " --> pdb=" O   ASN A 781 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 794 " --> pdb=" O   ILE A 790 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 818 through 834
    Processing helix  chain 'A' and resid 840 through 849
    Processing helix  chain 'A' and resid 855 through 876
      removed outlier: 3.532A  pdb=" N   VAL A 871 " --> pdb=" O   CYS A 867 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   LYS A 872 " --> pdb=" O   LEU A 868 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 937
    Processing helix  chain 'A' and resid 958 through 966
    Processing helix  chain 'A' and resid 969 through 979
    Processing helix  chain 'C' and resid 3 through 16
    Processing helix  chain 'C' and resid 86 through 90
      removed outlier: 3.530A  pdb=" N   LEU C  89 " --> pdb=" O   LEU C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 98 through 112
    Processing helix  chain 'C' and resid 120 through 130
    Processing helix  chain 'C' and resid 130 through 145
    Processing helix  chain 'D' and resid 22 through 35
    Processing helix  chain 'D' and resid 37 through 41
    Processing helix  chain 'D' and resid 56 through 60
    Processing sheet with id=AA1, first strand: chain 'A' and resid 109 through 111
      removed outlier: 6.637A  pdb=" N   VAL A  64 " --> pdb=" O   SER A 110 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   VAL A 126 " --> pdb=" O   ILE A 151 " (cutoff:3.500A)
      removed outlier: 7.650A  pdb=" N   ALA A 153 " --> pdb=" O   VAL A 126 " (cutoff:3.500A)
      removed outlier: 6.196A  pdb=" N   VAL A 128 " --> pdb=" O   ALA A 153 " (cutoff:3.500A)
      removed outlier: 8.165A  pdb=" N   SER A 155 " --> pdb=" O   VAL A 128 " (cutoff:3.500A)
      removed outlier: 4.570A  pdb=" N   TYR A 385 " --> pdb=" O   VAL A 278 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172
    Processing sheet with id=AA3, first strand: chain 'A' and resid 227 through 228
      removed outlier: 7.089A  pdb=" N   THR A 195 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE A 188 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 6.484A  pdb=" N   VAL A 193 " --> pdb=" O   ILE A 188 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 227 through 228
    Processing sheet with id=AA5, first strand: chain 'A' and resid 506 through 509
      removed outlier: 6.599A  pdb=" N   ILE A 459 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 7.854A  pdb=" N   TYR A 509 " --> pdb=" O   ILE A 459 " (cutoff:3.500A)
      removed outlier: 6.584A  pdb=" N   VAL A 461 " --> pdb=" O   TYR A 509 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   SER A 460 " --> pdb=" O   THR A 430 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR A 462 " --> pdb=" O   LEU A 432 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   LEU A 531 " --> pdb=" O   SER A 429 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   SER A 559 " --> pdb=" O   ASN A 534 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 905 through 908
    Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.258A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 6.015A  pdb=" N   ASP A 996 " --> pdb=" O   VAL A 942 " (cutoff:3.500A)
      removed outlier: 5.099A  pdb=" N   VAL A 942 " --> pdb=" O   ASP A 996 " (cutoff:3.500A)
      removed outlier: 6.934A  pdb=" N   SER A 947 " --> pdb=" O   LEU A 951 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   LEU A 951 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 920 through 922
      removed outlier: 6.258A  pdb=" N   TYR A 920 " --> pdb=" O   CYS A1009 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LYS A1011 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   LEU A 922 " --> pdb=" O   LYS A1011 " (cutoff:3.500A)
      removed outlier: 4.249A  pdb=" N   CYS A 995 " --> pdb=" O   VAL A1003 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 21 through 22
      removed outlier: 6.141A  pdb=" N   HIS C  32 " --> pdb=" O   VAL C  26 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 21 through 22
    Processing sheet with id=AB2, first strand: chain 'D' and resid 12 through 16
      removed outlier: 4.029A  pdb=" N   SER D  65 " --> pdb=" O   GLN D   2 " (cutoff:3.500A)

    465 hydrogen bonds defined for protein.
    1269 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: 3.15

  Time building geometry restraints manager: 2.75 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1616
        1.27 -     1.40: 2291
        1.40 -     1.54: 5677
        1.54 -     1.67: 90
        1.67 -     1.81: 64
  Bond restraints: 9738
  Sorted by residual:
  bond pdb=" C04 A1AIV D 101 "
       pdb=" C05 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.453  1.526 -0.073 2.00e-02 2.50e+03 1.32e+01
  bond pdb=" N   MET D   1 "
       pdb=" CA  MET D   1 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 1.90e-02 2.77e+03 2.71e+00
  bond pdb=" C1' ATP A1103 "
       pdb=" C2' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.531  1.520  0.011 1.20e-02 6.94e+03 9.05e-01
  bond pdb=" C05 A1AIV D 101 "
       pdb=" N06 A1AIV D 101 "
    ideal  model  delta    sigma   weight residual
    1.151  1.132  0.019 2.00e-02 2.50e+03 8.85e-01
  bond pdb=" C1' ATP A1103 "
       pdb=" O4' ATP A1103 "
    ideal  model  delta    sigma   weight residual
    1.416  1.407  0.009 1.30e-02 5.92e+03 4.96e-01
  ... (remaining 9733 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.20: 12982
        1.20 -     2.40: 134
        2.40 -     3.59: 60
        3.59 -     4.79: 14
        4.79 -     5.99: 5
  Bond angle restraints: 13195
  Sorted by residual:
  angle pdb=" C   LYS A 381 "
        pdb=" N   GLN A 382 "
        pdb=" CA  GLN A 382 "
      ideal   model   delta    sigma   weight residual
     121.70  127.69   -5.99 1.80e+00 3.09e-01 1.11e+01
  angle pdb=" C2' ATP A1103 "
        pdb=" C1' ATP A1103 "
        pdb=" O4' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     106.53  103.47    3.06 1.18e+00 7.24e-01 6.80e+00
  angle pdb=" C3' ATP A1103 "
        pdb=" C4' ATP A1103 "
        pdb=" C5' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     115.19  110.99    4.20 1.76e+00 3.23e-01 5.69e+00
  angle pdb=" C4' ATP A1103 "
        pdb=" C3' ATP A1103 "
        pdb=" O3' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     111.06  105.26    5.80 2.50e+00 1.60e-01 5.39e+00
  angle pdb=" C1' ATP A1103 "
        pdb=" C2' ATP A1103 "
        pdb=" O2' ATP A1103 "
      ideal   model   delta    sigma   weight residual
     110.58  104.61    5.97 2.79e+00 1.28e-01 4.57e+00
  ... (remaining 13190 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.21: 5626
       15.21 -    30.42: 238
       30.42 -    45.63: 46
       45.63 -    60.84: 16
       60.84 -    76.05: 3
  Dihedral angle restraints: 5929
    sinusoidal: 2424
      harmonic: 3505
  Sorted by residual:
  dihedral pdb=" CB  CYS A 593 "
           pdb=" SG  CYS A 593 "
           pdb=" SG  CYS C  85 "
           pdb=" CB  CYS C  85 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -162.05   76.05     1      1.00e+01 1.00e-02 7.29e+01
  dihedral pdb=" CA  LYS A 884 "
           pdb=" C   LYS A 884 "
           pdb=" N   ASN A 885 "
           pdb=" CA  ASN A 885 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.83   16.17     0      5.00e+00 4.00e-02 1.05e+01
  dihedral pdb=" N   GLU A 869 "
           pdb=" CA  GLU A 869 "
           pdb=" CB  GLU A 869 "
           pdb=" CG  GLU A 869 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -118.79   58.79     3      1.50e+01 4.44e-03 9.47e+00
  ... (remaining 5926 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.055: 1287
       0.055 -    0.111: 159
       0.111 -    0.166: 22
       0.166 -    0.221: 1
       0.221 -    0.276: 2
  Chirality restraints: 1471
  Sorted by residual:
  chirality pdb=" C2' ATP A1103 "
            pdb=" C1' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" O2' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.96    0.28 2.00e-01 2.50e+01 1.91e+00
  chirality pdb=" C3' ATP A1103 "
            pdb=" C2' ATP A1103 "
            pdb=" C4' ATP A1103 "
            pdb=" O3' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.90    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C4' ATP A1103 "
            pdb=" C3' ATP A1103 "
            pdb=" C5' ATP A1103 "
            pdb=" O4' ATP A1103 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.49   -2.71    0.21 2.00e-01 2.50e+01 1.13e+00
  ... (remaining 1468 not shown)

  Planarity restraints: 1707
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 105 "    0.009 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   SER C 105 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   SER C 105 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ILE C 106 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS C 101 "    0.008 2.00e-02 2.50e+03   1.67e-02 2.78e+00
        pdb=" C   LYS C 101 "   -0.029 2.00e-02 2.50e+03
        pdb=" O   LYS C 101 "    0.011 2.00e-02 2.50e+03
        pdb=" N   VAL C 102 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 543 "    0.006 2.00e-02 2.50e+03   1.25e-02 1.55e+00
        pdb=" C   MET A 543 "   -0.022 2.00e-02 2.50e+03
        pdb=" O   MET A 543 "    0.008 2.00e-02 2.50e+03
        pdb=" N   TYR A 544 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1704 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.58: 97
        2.58 -     3.16: 8160
        3.16 -     3.74: 14407
        3.74 -     4.32: 20344
        4.32 -     4.90: 34294
  Nonbonded interactions: 77302
  Sorted by model distance:
  nonbonded pdb="MG    MG A1101 "
            pdb=" O2A ATP A1103 "
     model   vdw
     2.006 2.170
  nonbonded pdb="MG    MG A1102 "
            pdb=" O1B ATP A1103 "
     model   vdw
     2.027 2.170
  nonbonded pdb=" O   PRO C  18 "
            pdb=" OG  SER C  19 "
     model   vdw
     2.109 3.040
  nonbonded pdb=" OD1 ASP A 154 "
            pdb=" NH1 ARG A 156 "
     model   vdw
     2.160 3.120
  nonbonded pdb=" OG  SER A 488 "
            pdb=" OE1 GLU A 489 "
     model   vdw
     2.184 3.040
  ... (remaining 77297 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             2.680
  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:             0.020
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     24.800
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:2.720
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.880
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
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      :  0.002   0.073   9738  Z= 0.133
  Angle     :  0.442   5.988  13195  Z= 0.228
  Chirality :  0.040   0.276   1471
  Planarity :  0.003   0.023   1707
  Dihedral  :  9.372  73.529   3662
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  2.83 %
    Favored  : 95.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  0.97 (0.25), residues: 1199
  helix:  1.52 (0.25), residues: 484
  sheet:  0.11 (0.35), residues: 208
  loop :  0.15 (0.28), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C  93 
 HIS   0.002   0.001   HIS D  68 
 PHE   0.008   0.001   PHE A 521 
 TYR   0.006   0.001   TYR A 277 
 ARG   0.002   0.000   ARG A 474 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 167
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9561 (ttp) cc_final: 0.9078 (tmm)
REVERT: A  158 LEU cc_start: 0.9603 (mt) cc_final: 0.9380 (mp)
REVERT: A  349 GLN cc_start: 0.8940 (mt0) cc_final: 0.8715 (pp30)
REVERT: A  413 GLN cc_start: 0.9359 (tt0) cc_final: 0.9116 (mt0)
REVERT: A  442 MET cc_start: 0.9785 (tpp) cc_final: 0.9224 (tpp)
REVERT: A  448 MET cc_start: 0.9193 (mmp) cc_final: 0.8493 (mmm)
REVERT: A  449 MET cc_start: 0.9468 (mtp) cc_final: 0.8874 (mmm)
REVERT: A  533 THR cc_start: 0.9247 (m) cc_final: 0.8611 (p)
REVERT: A  832 MET cc_start: 0.9308 (mtp) cc_final: 0.9008 (mtp)
REVERT: A  869 GLU cc_start: 0.9529 (OUTLIER) cc_final: 0.9288 (mm-30)
REVERT: A  941 GLU cc_start: 0.9373 (tt0) cc_final: 0.9049 (tm-30)
REVERT: C   74 TYR cc_start: 0.9130 (t80) cc_final: 0.8067 (t80)
REVERT: D    1 MET cc_start: 0.3807 (ptt) cc_final: 0.2537 (ptt)
REVERT: D   18 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8098 (mm-30)
  outliers start: 16
  outliers final: 6
  residues processed: 180
  average time/residue: 0.2614
  time to fit residues: 63.4552
Evaluate side-chains
  92 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 1.186 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 50 optimal weight:    7.9990
   chunk 30 optimal weight:   10.0000
   chunk 60 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0050
   chunk 93 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 69 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    1.3798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.035047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.026369 restraints weight = 83336.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2674 r_free = 0.2674 target = 0.027306 restraints weight = 56048.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2697 r_free = 0.2697 target = 0.027971 restraints weight = 41408.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.2695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8505
moved from start:          0.2179

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069   9738  Z= 0.228
  Angle     :  0.543   6.102  13195  Z= 0.285
  Chirality :  0.042   0.165   1471
  Planarity :  0.004   0.064   1707
  Dihedral  :  5.206  56.390   1325
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 6.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.70 %
    Favored  : 98.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.27 (0.25), residues: 1199
  helix:  1.51 (0.24), residues: 499
  sheet:  0.65 (0.39), residues: 194
  loop :  0.39 (0.29), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP C  93 
 HIS   0.004   0.001   HIS C  55 
 PHE   0.010   0.001   PHE A 170 
 TYR   0.012   0.001   TYR A  81 
 ARG   0.014   0.001   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 105
  time to evaluate  : 0.941 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9635 (ttp) cc_final: 0.9105 (tmm)
REVERT: A   55 ASN cc_start: 0.9374 (m-40) cc_final: 0.9004 (m110)
REVERT: A  334 PHE cc_start: 0.6928 (m-80) cc_final: 0.6650 (m-80)
REVERT: A  413 GLN cc_start: 0.9365 (tt0) cc_final: 0.9043 (mt0)
REVERT: A  442 MET cc_start: 0.9722 (tpp) cc_final: 0.9283 (tpp)
REVERT: A  449 MET cc_start: 0.9421 (mtp) cc_final: 0.8775 (mmm)
REVERT: A  464 MET cc_start: 0.9344 (pmm) cc_final: 0.8972 (pmm)
REVERT: A  855 MET cc_start: 0.9314 (tpt) cc_final: 0.8865 (tpp)
REVERT: C   30 LEU cc_start: 0.9682 (mm) cc_final: 0.9399 (mm)
REVERT: C   74 TYR cc_start: 0.9059 (t80) cc_final: 0.8500 (t80)
REVERT: D    1 MET cc_start: 0.8272 (ptt) cc_final: 0.7931 (ptt)
REVERT: D   23 ILE cc_start: 0.8952 (mm) cc_final: 0.8686 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 106
  average time/residue: 0.2087
  time to fit residues: 32.0156
Evaluate side-chains
  69 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 1.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 60 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 85 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 67 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 92 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2936 r_free = 0.2936 target = 0.035401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.026764 restraints weight = 85591.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.027679 restraints weight = 56912.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2702 r_free = 0.2702 target = 0.028355 restraints weight = 42396.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.2696
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.2565

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.044   9738  Z= 0.162
  Angle     :  0.477   5.864  13195  Z= 0.248
  Chirality :  0.041   0.139   1471
  Planarity :  0.003   0.048   1707
  Dihedral  :  5.071  58.375   1325
  Min Nonbonded Distance : 1.969

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.83 %
    Favored  : 98.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.39 (0.26), residues: 1199
  helix:  1.59 (0.24), residues: 499
  sheet:  0.55 (0.40), residues: 193
  loop :  0.56 (0.29), residues: 507

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  93 
 HIS   0.002   0.000   HIS D  68 
 PHE   0.008   0.001   PHE A 888 
 TYR   0.009   0.001   TYR C 134 
 ARG   0.006   0.000   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 88
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9628 (ttp) cc_final: 0.9084 (tmm)
REVERT: A   55 ASN cc_start: 0.9339 (m-40) cc_final: 0.8988 (m110)
REVERT: A  334 PHE cc_start: 0.7077 (m-80) cc_final: 0.6862 (m-80)
REVERT: A  413 GLN cc_start: 0.9337 (tt0) cc_final: 0.8941 (mt0)
REVERT: A  442 MET cc_start: 0.9657 (tpp) cc_final: 0.9244 (tpp)
REVERT: A  448 MET cc_start: 0.9140 (mmp) cc_final: 0.8830 (mmm)
REVERT: A  464 MET cc_start: 0.9433 (pmm) cc_final: 0.9066 (pmm)
REVERT: A  832 MET cc_start: 0.9151 (mtm) cc_final: 0.8759 (ptm)
REVERT: A  855 MET cc_start: 0.9263 (tpt) cc_final: 0.8882 (tpp)
REVERT: C   30 LEU cc_start: 0.9735 (mm) cc_final: 0.9461 (mm)
REVERT: C  126 VAL cc_start: 0.9591 (t) cc_final: 0.9379 (p)
REVERT: D    1 MET cc_start: 0.8493 (ptt) cc_final: 0.8084 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 88
  average time/residue: 0.2095
  time to fit residues: 27.3377
Evaluate side-chains
  66 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 1.067 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 65 optimal weight:    0.0770
   chunk 82 optimal weight:    5.9990
   chunk 69 optimal weight:    7.9990
   chunk 35 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 95 optimal weight:    0.0980
   overall best weight:    1.6344

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.034806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.026621 restraints weight = 86447.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2664 r_free = 0.2664 target = 0.027523 restraints weight = 57530.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2688 r_free = 0.2688 target = 0.028185 restraints weight = 42454.190|
|-----------------------------------------------------------------------------|
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8567
moved from start:          0.2961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9738  Z= 0.225
  Angle     :  0.523   5.868  13195  Z= 0.273
  Chirality :  0.040   0.129   1471
  Planarity :  0.004   0.053   1707
  Dihedral  :  5.271  59.963   1325
  Min Nonbonded Distance : 1.869

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.41 %
    Favored  : 98.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.42 (0.25), residues: 1199
  helix:  1.64 (0.24), residues: 497
  sheet:  0.49 (0.40), residues: 193
  loop :  0.60 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  93 
 HIS   0.003   0.001   HIS A  29 
 PHE   0.030   0.001   PHE C  50 
 TYR   0.014   0.001   TYR C  45 
 ARG   0.014   0.001   ARG D  74 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 1.141 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9639 (ttp) cc_final: 0.9118 (tmm)
REVERT: A   55 ASN cc_start: 0.9312 (m-40) cc_final: 0.9006 (m110)
REVERT: A  334 PHE cc_start: 0.7244 (m-80) cc_final: 0.6998 (m-80)
REVERT: A  413 GLN cc_start: 0.9361 (tt0) cc_final: 0.8923 (mt0)
REVERT: A  442 MET cc_start: 0.9668 (tpp) cc_final: 0.9178 (tpp)
REVERT: A  449 MET cc_start: 0.9599 (mtp) cc_final: 0.8969 (mmt)
REVERT: A  533 THR cc_start: 0.9248 (m) cc_final: 0.8630 (p)
REVERT: A  832 MET cc_start: 0.9169 (mtm) cc_final: 0.8852 (ptm)
REVERT: A  855 MET cc_start: 0.9335 (tpt) cc_final: 0.8947 (tpp)
REVERT: A  941 GLU cc_start: 0.9384 (tt0) cc_final: 0.9025 (tm-30)
REVERT: C   74 TYR cc_start: 0.8729 (t80) cc_final: 0.8292 (t80)
REVERT: D    1 MET cc_start: 0.8441 (ptt) cc_final: 0.7999 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.2102
  time to fit residues: 24.0295
Evaluate side-chains
  62 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 85 optimal weight:    0.9990
   chunk 33 optimal weight:    0.8980
   chunk 43 optimal weight:    2.9990
   chunk 76 optimal weight:    0.7980
   chunk 89 optimal weight:    7.9990
   chunk 17 optimal weight:    9.9990
   chunk 104 optimal weight:    0.7980
   chunk 59 optimal weight:    4.9990
   chunk 8 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    0.8984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.035278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.026983 restraints weight = 85446.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.2677 r_free = 0.2677 target = 0.027906 restraints weight = 56964.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.028561 restraints weight = 41974.519|
|-----------------------------------------------------------------------------|
r_work (final): 0.2683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8551
moved from start:          0.3099

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9738  Z= 0.161
  Angle     :  0.480   5.664  13195  Z= 0.247
  Chirality :  0.040   0.131   1471
  Planarity :  0.004   0.061   1707
  Dihedral  :  5.336  59.816   1325
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.45 (0.25), residues: 1199
  helix:  1.65 (0.24), residues: 498
  sheet:  0.53 (0.40), residues: 193
  loop :  0.61 (0.29), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  93 
 HIS   0.002   0.001   HIS A 292 
 PHE   0.016   0.001   PHE C  50 
 TYR   0.010   0.001   TYR C 134 
 ARG   0.009   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9647 (ttp) cc_final: 0.9386 (ppp)
REVERT: A   55 ASN cc_start: 0.9329 (m-40) cc_final: 0.9023 (m110)
REVERT: A  286 MET cc_start: 0.9180 (pmm) cc_final: 0.8957 (pmm)
REVERT: A  413 GLN cc_start: 0.9364 (tt0) cc_final: 0.8998 (mt0)
REVERT: A  442 MET cc_start: 0.9629 (tpp) cc_final: 0.9245 (tpp)
REVERT: A  448 MET cc_start: 0.9194 (mmp) cc_final: 0.8832 (mmm)
REVERT: A  449 MET cc_start: 0.9591 (mtp) cc_final: 0.8764 (mmm)
REVERT: A  533 THR cc_start: 0.9253 (m) cc_final: 0.8597 (p)
REVERT: A  832 MET cc_start: 0.9164 (mtm) cc_final: 0.8732 (ptp)
REVERT: A  855 MET cc_start: 0.9337 (tpt) cc_final: 0.8945 (tpp)
REVERT: A  866 VAL cc_start: 0.9613 (p) cc_final: 0.9198 (m)
REVERT: A  869 GLU cc_start: 0.9167 (mp0) cc_final: 0.8741 (mp0)
REVERT: A  941 GLU cc_start: 0.9395 (tt0) cc_final: 0.9033 (tm-30)
REVERT: C   74 TYR cc_start: 0.8634 (t80) cc_final: 0.8310 (t80)
REVERT: D    1 MET cc_start: 0.8355 (ptt) cc_final: 0.7967 (ptt)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.2035
  time to fit residues: 23.8166
Evaluate side-chains
  63 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 1.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 84 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 90 optimal weight:    5.9990
   chunk 99 optimal weight:    0.9990
   chunk 61 optimal weight:    0.5980
   chunk 100 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 37 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0020
   chunk 102 optimal weight:    5.9990
   overall best weight:    1.1194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.034947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.026650 restraints weight = 86418.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2662 r_free = 0.2662 target = 0.027558 restraints weight = 57797.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.028217 restraints weight = 42727.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.2669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8568
moved from start:          0.3316

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9738  Z= 0.178
  Angle     :  0.495   6.114  13195  Z= 0.256
  Chirality :  0.040   0.171   1471
  Planarity :  0.004   0.064   1707
  Dihedral  :  5.188  59.999   1325
  Min Nonbonded Distance : 1.901

Molprobity Statistics.
  All-atom Clashscore : 7.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.85 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.54 (0.25), residues: 1199
  helix:  1.70 (0.24), residues: 497
  sheet:  0.54 (0.39), residues: 193
  loop :  0.71 (0.29), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  93 
 HIS   0.002   0.001   HIS C  75 
 PHE   0.022   0.001   PHE A 526 
 TYR   0.010   0.001   TYR C  60 
 ARG   0.007   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.062 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9596 (ttp) cc_final: 0.9370 (ppp)
REVERT: A   55 ASN cc_start: 0.9316 (m-40) cc_final: 0.9023 (m110)
REVERT: A  286 MET cc_start: 0.9178 (pmm) cc_final: 0.8962 (pmm)
REVERT: A  413 GLN cc_start: 0.9368 (tt0) cc_final: 0.8998 (mt0)
REVERT: A  442 MET cc_start: 0.9642 (tpp) cc_final: 0.9238 (tpp)
REVERT: A  448 MET cc_start: 0.9165 (mmp) cc_final: 0.8902 (mmm)
REVERT: A  449 MET cc_start: 0.9583 (mtp) cc_final: 0.8709 (mmm)
REVERT: A  533 THR cc_start: 0.9250 (m) cc_final: 0.8615 (p)
REVERT: A  832 MET cc_start: 0.9180 (mtm) cc_final: 0.8808 (mtp)
REVERT: A  855 MET cc_start: 0.9348 (tpt) cc_final: 0.8946 (tpp)
REVERT: A  941 GLU cc_start: 0.9409 (tt0) cc_final: 0.9042 (tm-30)
REVERT: C   74 TYR cc_start: 0.8658 (t80) cc_final: 0.8317 (t80)
REVERT: C  101 LYS cc_start: 0.9544 (pttt) cc_final: 0.9301 (pttm)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.2116
  time to fit residues: 23.4046
Evaluate side-chains
  60 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 69 optimal weight:    9.9990
   chunk 43 optimal weight:    5.9990
   chunk 61 optimal weight:    4.9990
   chunk 85 optimal weight:    0.5980
   chunk 33 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   chunk 104 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9990
   chunk 30 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   overall best weight:    1.4586

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.034454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.026338 restraints weight = 88254.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.027201 restraints weight = 58934.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.027836 restraints weight = 43801.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.2652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9738  Z= 0.204
  Angle     :  0.502   5.444  13195  Z= 0.262
  Chirality :  0.041   0.163   1471
  Planarity :  0.004   0.066   1707
  Dihedral  :  5.228  59.694   1325
  Min Nonbonded Distance : 1.874

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.94 %
    Favored  : 99.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.58 (0.25), residues: 1199
  helix:  1.73 (0.24), residues: 498
  sheet:  0.46 (0.39), residues: 193
  loop :  0.77 (0.30), residues: 508

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  93 
 HIS   0.003   0.001   HIS C  55 
 PHE   0.015   0.001   PHE C  50 
 TYR   0.012   0.001   TYR C  60 
 ARG   0.006   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.938 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9651 (ttp) cc_final: 0.9410 (ppp)
REVERT: A   55 ASN cc_start: 0.9342 (m-40) cc_final: 0.9063 (m110)
REVERT: A  286 MET cc_start: 0.9150 (pmm) cc_final: 0.8891 (pmm)
REVERT: A  413 GLN cc_start: 0.9384 (tt0) cc_final: 0.9030 (mt0)
REVERT: A  442 MET cc_start: 0.9659 (tpp) cc_final: 0.9238 (tpp)
REVERT: A  449 MET cc_start: 0.9586 (mtp) cc_final: 0.8687 (mmm)
REVERT: A  533 THR cc_start: 0.9234 (m) cc_final: 0.8599 (p)
REVERT: A  832 MET cc_start: 0.9182 (mtm) cc_final: 0.8816 (mtp)
REVERT: A  855 MET cc_start: 0.9344 (tpt) cc_final: 0.8960 (tpp)
REVERT: A  869 GLU cc_start: 0.9294 (mp0) cc_final: 0.8904 (mp0)
REVERT: A  941 GLU cc_start: 0.9408 (tt0) cc_final: 0.9055 (tm-30)
REVERT: C   74 TYR cc_start: 0.8737 (t80) cc_final: 0.8329 (t80)
REVERT: C  101 LYS cc_start: 0.9494 (pttt) cc_final: 0.9251 (pttm)
REVERT: D    1 MET cc_start: 0.8290 (ptt) cc_final: 0.8082 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2095
  time to fit residues: 22.5788
Evaluate side-chains
  60 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 82 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 31 optimal weight:    0.7980
   chunk 66 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 71 optimal weight:    0.7980
   chunk 55 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 118 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2902 r_free = 0.2902 target = 0.034415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.025917 restraints weight = 88450.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.026799 restraints weight = 58738.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.027468 restraints weight = 43795.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.2671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   9738  Z= 0.144
  Angle     :  0.470   5.288  13195  Z= 0.244
  Chirality :  0.041   0.160   1471
  Planarity :  0.004   0.060   1707
  Dihedral  :  5.175  59.609   1325
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.26), residues: 1199
  helix:  1.80 (0.24), residues: 497
  sheet:  0.51 (0.39), residues: 191
  loop :  0.81 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C  33 
 HIS   0.002   0.000   HIS A 292 
 PHE   0.026   0.001   PHE A  82 
 TYR   0.015   0.001   TYR A  81 
 ARG   0.012   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9659 (ttp) cc_final: 0.9404 (ppp)
REVERT: A   55 ASN cc_start: 0.9333 (m-40) cc_final: 0.9035 (m110)
REVERT: A  413 GLN cc_start: 0.9358 (tt0) cc_final: 0.9075 (mt0)
REVERT: A  442 MET cc_start: 0.9615 (tpp) cc_final: 0.9260 (tpp)
REVERT: A  448 MET cc_start: 0.9267 (mmp) cc_final: 0.8967 (mmm)
REVERT: A  449 MET cc_start: 0.9588 (mtp) cc_final: 0.8693 (mmm)
REVERT: A  533 THR cc_start: 0.9218 (m) cc_final: 0.8604 (p)
REVERT: A  832 MET cc_start: 0.9190 (mtm) cc_final: 0.8795 (mtp)
REVERT: A  855 MET cc_start: 0.9355 (tpt) cc_final: 0.8975 (tpp)
REVERT: A  869 GLU cc_start: 0.9221 (mp0) cc_final: 0.8947 (mp0)
REVERT: A  941 GLU cc_start: 0.9419 (tt0) cc_final: 0.9074 (tm-30)
REVERT: C   74 TYR cc_start: 0.8748 (t80) cc_final: 0.8295 (t80)
REVERT: C  101 LYS cc_start: 0.9518 (pttt) cc_final: 0.9273 (pttm)
REVERT: C  126 VAL cc_start: 0.9638 (t) cc_final: 0.9324 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.2099
  time to fit residues: 23.6484
Evaluate side-chains
  64 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 19 optimal weight:    0.8980
   chunk 6 optimal weight:    2.9990
   chunk 48 optimal weight:    0.9990
   chunk 105 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 17 optimal weight:    9.9990
   chunk 15 optimal weight:    0.0570
   chunk 30 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.7300

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2912 r_free = 0.2912 target = 0.034552 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.026085 restraints weight = 84804.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.026936 restraints weight = 57122.607|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2680 r_free = 0.2680 target = 0.027585 restraints weight = 42978.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.2674
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8582
moved from start:          0.3669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   9738  Z= 0.146
  Angle     :  0.467   5.263  13195  Z= 0.240
  Chirality :  0.040   0.154   1471
  Planarity :  0.003   0.043   1707
  Dihedral  :  5.150  59.320   1325
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.09 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    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:  1.64 (0.26), residues: 1199
  helix:  1.77 (0.24), residues: 498
  sheet:  0.49 (0.39), residues: 192
  loop :  0.81 (0.30), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C  93 
 HIS   0.002   0.001   HIS A 819 
 PHE   0.023   0.001   PHE A  82 
 TYR   0.009   0.001   TYR C  60 
 ARG   0.005   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 1.069 
Fit side-chains
   revert: symmetry clash
REVERT: A   35 MET cc_start: 0.9646 (ttp) cc_final: 0.9403 (ppp)
REVERT: A   55 ASN cc_start: 0.9329 (m-40) cc_final: 0.9037 (m110)
REVERT: A  413 GLN cc_start: 0.9346 (tt0) cc_final: 0.9088 (mt0)
REVERT: A  442 MET cc_start: 0.9605 (tpp) cc_final: 0.9240 (tpp)
REVERT: A  448 MET cc_start: 0.9244 (mmp) cc_final: 0.8977 (mmm)
REVERT: A  449 MET cc_start: 0.9581 (mtp) cc_final: 0.8687 (mmm)
REVERT: A  533 THR cc_start: 0.9252 (m) cc_final: 0.8622 (p)
REVERT: A  832 MET cc_start: 0.9175 (mtm) cc_final: 0.8781 (mtp)
REVERT: A  855 MET cc_start: 0.9335 (tpt) cc_final: 0.8972 (tpp)
REVERT: A  869 GLU cc_start: 0.9199 (mp0) cc_final: 0.8776 (mp0)
REVERT: A  941 GLU cc_start: 0.9425 (tt0) cc_final: 0.9066 (tm-30)
REVERT: C   74 TYR cc_start: 0.8729 (t80) cc_final: 0.8357 (t80)
REVERT: C  101 LYS cc_start: 0.9490 (pttt) cc_final: 0.9227 (pttm)
REVERT: C  126 VAL cc_start: 0.9627 (t) cc_final: 0.9310 (p)
REVERT: D    1 MET cc_start: 0.8367 (ptt) cc_final: 0.8112 (ptp)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.2063
  time to fit residues: 22.8347
Evaluate side-chains
  63 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 13 optimal weight:    5.9990
   chunk 10 optimal weight:    3.9990
   chunk 2 optimal weight:    6.9990
   chunk 61 optimal weight:    0.9980
   chunk 17 optimal weight:    8.9990
   chunk 46 optimal weight:    0.6980
   chunk 100 optimal weight:    6.9990
   chunk 79 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 90 optimal weight:    0.6980
   overall best weight:    1.0782

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.034053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2609 r_free = 0.2609 target = 0.025792 restraints weight = 87574.666|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.026677 restraints weight = 59212.654|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.027328 restraints weight = 43968.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.2661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8592
moved from start:          0.3759

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9738  Z= 0.167
  Angle     :  0.473   5.618  13195  Z= 0.245
  Chirality :  0.040   0.154   1471
  Planarity :  0.004   0.087   1707
  Dihedral  :  5.098  59.149   1325
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.25), residues: 1199
  helix:  1.80 (0.24), residues: 498
  sheet:  0.49 (0.39), residues: 192
  loop :  0.82 (0.30), residues: 509

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C  33 
 HIS   0.002   0.001   HIS A 292 
 PHE   0.019   0.001   PHE A  82 
 TYR   0.011   0.001   TYR C  60 
 ARG   0.013   0.000   ARG C   8 

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

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

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2398 Ramachandran restraints generated.
    1199 Oldfield, 0 Emsley, 1199 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 1.073 
Fit side-chains
REVERT: A   35 MET cc_start: 0.9658 (ttp) cc_final: 0.9405 (ppp)
REVERT: A   55 ASN cc_start: 0.9336 (m-40) cc_final: 0.9028 (m-40)
REVERT: A  413 GLN cc_start: 0.9406 (tt0) cc_final: 0.9109 (mt0)
REVERT: A  442 MET cc_start: 0.9638 (tpp) cc_final: 0.9227 (tpp)
REVERT: A  448 MET cc_start: 0.9272 (mmp) cc_final: 0.9048 (mmm)
REVERT: A  449 MET cc_start: 0.9598 (mtp) cc_final: 0.8697 (mmm)
REVERT: A  533 THR cc_start: 0.9263 (m) cc_final: 0.8661 (p)
REVERT: A  832 MET cc_start: 0.9202 (mtm) cc_final: 0.8798 (mtp)
REVERT: A  855 MET cc_start: 0.9339 (tpt) cc_final: 0.8963 (tpp)
REVERT: A  865 LEU cc_start: 0.9683 (mt) cc_final: 0.9481 (mt)
REVERT: A  869 GLU cc_start: 0.9225 (mp0) cc_final: 0.8804 (mp0)
REVERT: A  941 GLU cc_start: 0.9420 (tt0) cc_final: 0.9070 (tm-30)
REVERT: C   74 TYR cc_start: 0.8772 (t80) cc_final: 0.8343 (t80)
REVERT: C  101 LYS cc_start: 0.9492 (pttt) cc_final: 0.9223 (pttm)
REVERT: C  126 VAL cc_start: 0.9637 (t) cc_final: 0.9312 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.2030
  time to fit residues: 21.8769
Evaluate side-chains
  64 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 1.056 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 89 optimal weight:    0.0770
   chunk 78 optimal weight:    3.9990
   chunk 112 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 93 optimal weight:    0.4980
   chunk 60 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 34 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6538

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.034578 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2623 r_free = 0.2623 target = 0.026132 restraints weight = 86906.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.027023 restraints weight = 57841.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.027666 restraints weight = 42911.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.2676
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8588
moved from start:          0.3782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9738  Z= 0.142
  Angle     :  0.475   7.326  13195  Z= 0.246
  Chirality :  0.040   0.153   1471
  Planarity :  0.003   0.043   1707
  Dihedral  :  5.141  59.060   1325
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.39 %
    Cis-general     : 0.09 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  1.68 (0.25), residues: 1199
  helix:  1.79 (0.24), residues: 497
  sheet:  0.59 (0.39), residues: 191
  loop :  0.82 (0.29), residues: 511

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 917 
 HIS   0.003   0.001   HIS A 292 
 PHE   0.019   0.001   PHE A  82 
 TYR   0.009   0.001   TYR C  60 
 ARG   0.003   0.000   ARG C   8 
Origin is already at (0, 0, 0), no shifts will be applied
Model does not fit in PDB format.

===============================================================================
Job complete
usr+sys time: 2676.49 seconds
wall clock time: 48 minutes 50.74 seconds (2930.74 seconds total)