Starting phenix.real_space_refine
on Wed Jun  3 17:58:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9wsp_66202/06_2026/9wsp_66202.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9wsp_66202/06_2026/9wsp_66202.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.55
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9wsp_66202/06_2026/9wsp_66202.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9wsp_66202/06_2026/9wsp_66202.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9wsp_66202/06_2026/9wsp_66202.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9wsp_66202/06_2026/9wsp_66202.cif"
  }
  resolution = 4.55
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    4866      2.51       5
     N    1263      2.21       5
     O    1447      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 7609
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 7609
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 972, 7609
          Classifications: {'peptide': 972}
          Link IDs: {'PTRANS': 48, 'TRANS': 923}
          Chain breaks: 11
  Time building chain proxies: 2.05, per 1000 atoms: 0.27
  Number of scatterers: 7609
  At special positions: 0
  Unit cell: (100.28, 98.44, 172.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      33     16.00
     O    1447      8.00
     N    1263      7.00
     C    4866      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 131 " - pdb=" SG  CYS B 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 291 " - pdb=" SG  CYS B 301 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 538 " - pdb=" SG  CYS B 590 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 617 " - pdb=" SG  CYS B 649 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 662 " - pdb=" SG  CYS B 671 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 738 " - pdb=" SG  CYS B 760 " distance=2.02
    Simple disulfide: pdb=" SG  CYS B 743 " - pdb=" SG  CYS B 749 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1032 " - pdb=" SG  CYS B1043 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B1082 " - pdb=" SG  CYS B1126 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.79
  Conformation dependent library (CDL) restraints added in 308.9 milliseconds
  

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1828

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 13 sheets defined
      26.1% alpha, 27.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'B' and resid 294 through 304
    Processing helix  chain 'B' and resid 338 through 343
    Processing helix  chain 'B' and resid 349 through 353
      removed outlier: 3.615A  pdb=" N   TRP B 353 " --> pdb=" O   VAL B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 371
      removed outlier: 4.115A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 389
    Processing helix  chain 'B' and resid 405 through 407
      No H-bonds generated for 'chain 'B' and resid 405 through 407'
    Processing helix  chain 'B' and resid 737 through 744
    Processing helix  chain 'B' and resid 746 through 754
    Processing helix  chain 'B' and resid 755 through 757
      No H-bonds generated for 'chain 'B' and resid 755 through 757'
    Processing helix  chain 'B' and resid 760 through 783
      removed outlier: 3.956A  pdb=" N   ASN B 764 " --> pdb=" O   CYS B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 816 through 824
    Processing helix  chain 'B' and resid 866 through 885
    Processing helix  chain 'B' and resid 886 through 891
      removed outlier: 4.238A  pdb=" N   ALA B 890 " --> pdb=" O   TRP B 886 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 897 through 908
    Processing helix  chain 'B' and resid 912 through 919
      removed outlier: 4.021A  pdb=" N   LEU B 916 " --> pdb=" O   THR B 912 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 919 through 941
    Processing helix  chain 'B' and resid 942 through 944
      No H-bonds generated for 'chain 'B' and resid 942 through 944'
    Processing helix  chain 'B' and resid 945 through 966
      removed outlier: 4.170A  pdb=" N   VAL B 951 " --> pdb=" O   LYS B 947 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL B 952 " --> pdb=" O   LEU B 948 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   LEU B 966 " --> pdb=" O   LEU B 962 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 976 through 984
    Processing helix  chain 'B' and resid 985 through 1033
      removed outlier: 4.771A  pdb=" N   VAL B 991 " --> pdb=" O   PRO B 987 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1116 through 1118
      No H-bonds generated for 'chain 'B' and resid 1116 through 1118'
    Processing helix  chain 'B' and resid 1140 through 1147
      removed outlier: 4.236A  pdb=" N   GLU B1144 " --> pdb=" O   PRO B1140 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 28 through 30
      removed outlier: 8.539A  pdb=" N   ASN B  61 " --> pdb=" O   TYR B 269 " (cutoff:3.500A)
      removed outlier: 6.452A  pdb=" N   TYR B 269 " --> pdb=" O   ASN B  61 " (cutoff:3.500A)
      removed outlier: 6.079A  pdb=" N   PHE B 201 " --> pdb=" O   ASP B 228 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ASP B 228 " --> pdb=" O   PHE B 201 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   ILE B 203 " --> pdb=" O   LEU B 226 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 55
      removed outlier: 4.048A  pdb=" N   ASP B 287 " --> pdb=" O   LYS B 278 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85
      removed outlier: 6.427A  pdb=" N   LEU B 141 " --> pdb=" O   LEU B 244 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 83 through 85
      removed outlier: 6.183A  pdb=" N   ALA B 243 " --> pdb=" O   ILE B 101 " (cutoff:3.500A)
      removed outlier: 5.928A  pdb=" N   ILE B 101 " --> pdb=" O   ALA B 243 " (cutoff:3.500A)
      removed outlier: 5.541A  pdb=" N   ARG B 102 " --> pdb=" O   ASN B 121 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 311 through 319
      removed outlier: 5.297A  pdb=" N   ILE B 312 " --> pdb=" O   THR B 599 " (cutoff:3.500A)
      removed outlier: 7.585A  pdb=" N   THR B 599 " --> pdb=" O   ILE B 312 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   GLN B 314 " --> pdb=" O   VAL B 597 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   VAL B 597 " --> pdb=" O   GLN B 314 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   GLY B 594 " --> pdb=" O   GLN B 613 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 325 through 328
      removed outlier: 5.853A  pdb=" N   ASP B 574 " --> pdb=" O   ILE B 587 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   GLY B 566 " --> pdb=" O   ASP B 574 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 354 through 358
    Processing sheet with id=AA8, first strand: chain 'B' and resid 448 through 453
      removed outlier: 5.860A  pdb=" N   TYR B 449 " --> pdb=" O   PHE B 497 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   PHE B 497 " --> pdb=" O   TYR B 449 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   TYR B 451 " --> pdb=" O   TYR B 495 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 654 through 655
      removed outlier: 6.036A  pdb=" N   GLU B 654 " --> pdb=" O   ALA B 694 " (cutoff:3.500A)
      removed outlier: 8.390A  pdb=" N   THR B 696 " --> pdb=" O   GLU B 654 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   ALA B 672 " --> pdb=" O   PRO B 665 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 711 through 728
      removed outlier: 3.709A  pdb=" N   PHE B1075 " --> pdb=" O   ILE B 712 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   ILE B 714 " --> pdb=" O   LYS B1073 " (cutoff:3.500A)
      removed outlier: 6.255A  pdb=" N   GLN B1071 " --> pdb=" O   THR B 716 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   PHE B 718 " --> pdb=" O   PRO B1069 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   ILE B 720 " --> pdb=" O   TYR B1067 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   TYR B1067 " --> pdb=" O   ILE B 720 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   VAL B 722 " --> pdb=" O   VAL B1065 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL B1065 " --> pdb=" O   VAL B 722 " (cutoff:3.500A)
      removed outlier: 6.966A  pdb=" N   THR B 724 " --> pdb=" O   LEU B1063 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LEU B1063 " --> pdb=" O   THR B 724 " (cutoff:3.500A)
      removed outlier: 6.809A  pdb=" N   ILE B 726 " --> pdb=" O   VAL B1061 " (cutoff:3.500A)
      removed outlier: 6.888A  pdb=" N   VAL B1061 " --> pdb=" O   ILE B 726 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   GLY B1059 " --> pdb=" O   PRO B 728 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   TYR B1067 " --> pdb=" O   HIS B1048 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   HIS B1048 " --> pdb=" O   TYR B1067 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 734 through 736
    Processing sheet with id=AB3, first strand: chain 'B' and resid 1120 through 1125
      removed outlier: 4.300A  pdb=" N   ALA B1087 " --> pdb=" O   SER B1123 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE B1081 " --> pdb=" O   HIS B1088 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 1094 through 1096
      removed outlier: 3.577A  pdb=" N   GLN B1113 " --> pdb=" O   VAL B1104 " (cutoff:3.500A)

    321 hydrogen bonds defined for protein.
    888 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.60

  Time building geometry restraints manager: 1.01 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2454
        1.35 -     1.47: 1952
        1.47 -     1.59: 3331
        1.59 -     1.72: 0
        1.72 -     1.84: 41
  Bond restraints: 7778
  Sorted by residual:
  bond pdb=" C   VAL B 860 "
       pdb=" N   LEU B 861 "
    ideal  model  delta    sigma   weight residual
    1.331  1.302  0.029 2.07e-02 2.33e+03 1.92e+00
  bond pdb=" C   TYR B 505 "
       pdb=" N   GLN B 506 "
    ideal  model  delta    sigma   weight residual
    1.330  1.350 -0.020 1.47e-02 4.63e+03 1.84e+00
  bond pdb=" N   ASP B 614 "
       pdb=" CA  ASP B 614 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.017 1.29e-02 6.01e+03 1.81e+00
  bond pdb=" N   PRO B 986 "
       pdb=" CA  PRO B 986 "
    ideal  model  delta    sigma   weight residual
    1.465  1.488 -0.023 2.03e-02 2.43e+03 1.31e+00
  bond pdb=" N   ASP B1041 "
       pdb=" CA  ASP B1041 "
    ideal  model  delta    sigma   weight residual
    1.457  1.471 -0.013 1.29e-02 6.01e+03 1.06e+00
  ... (remaining 7773 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.77: 10337
        1.77 -     3.54: 213
        3.54 -     5.31: 19
        5.31 -     7.09: 11
        7.09 -     8.86: 1
  Bond angle restraints: 10581
  Sorted by residual:
  angle pdb=" C   ASN B  87 "
        pdb=" CA  ASN B  87 "
        pdb=" CB  ASN B  87 "
      ideal   model   delta    sigma   weight residual
     117.23  110.51    6.72 1.36e+00 5.41e-01 2.44e+01
  angle pdb=" N   THR B 618 "
        pdb=" CA  THR B 618 "
        pdb=" C   THR B 618 "
      ideal   model   delta    sigma   weight residual
     113.28  107.93    5.35 1.22e+00 6.72e-01 1.92e+01
  angle pdb=" N   PRO B 986 "
        pdb=" CA  PRO B 986 "
        pdb=" C   PRO B 986 "
      ideal   model   delta    sigma   weight residual
     110.70  115.25   -4.55 1.22e+00 6.72e-01 1.39e+01
  angle pdb=" C   TYR B 505 "
        pdb=" N   GLN B 506 "
        pdb=" CA  GLN B 506 "
      ideal   model   delta    sigma   weight residual
     120.68  126.14   -5.46 1.52e+00 4.33e-01 1.29e+01
  angle pdb=" CA  ASN B  87 "
        pdb=" C   ASN B  87 "
        pdb=" N   ASP B  88 "
      ideal   model   delta    sigma   weight residual
     119.98  117.08    2.90 8.50e-01 1.38e+00 1.16e+01
  ... (remaining 10576 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.62: 4352
       17.62 -    35.24: 225
       35.24 -    52.85: 29
       52.85 -    70.47: 16
       70.47 -    88.09: 14
  Dihedral angle restraints: 4636
    sinusoidal: 1807
      harmonic: 2829
  Sorted by residual:
  dihedral pdb=" CB  CYS B1032 "
           pdb=" SG  CYS B1032 "
           pdb=" SG  CYS B1043 "
           pdb=" CB  CYS B1043 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.06  -76.06     1      1.00e+01 1.00e-02 7.29e+01
  dihedral pdb=" CB  CYS B1082 "
           pdb=" SG  CYS B1082 "
           pdb=" SG  CYS B1126 "
           pdb=" CB  CYS B1126 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.35   68.35     1      1.00e+01 1.00e-02 6.06e+01
  dihedral pdb=" CA  CYS B 391 "
           pdb=" C   CYS B 391 "
           pdb=" N   PHE B 392 "
           pdb=" CA  PHE B 392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.30  -29.70     0      5.00e+00 4.00e-02 3.53e+01
  ... (remaining 4633 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 822
       0.037 -    0.074: 256
       0.074 -    0.112: 114
       0.112 -    0.149: 17
       0.149 -    0.186: 3
  Chirality restraints: 1212
  Sorted by residual:
  chirality pdb=" CA  ASP B1041 "
            pdb=" N   ASP B1041 "
            pdb=" C   ASP B1041 "
            pdb=" CB  ASP B1041 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 8.64e-01
  chirality pdb=" CB  ILE B 909 "
            pdb=" CA  ILE B 909 "
            pdb=" CG1 ILE B 909 "
            pdb=" CG2 ILE B 909 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.83   -0.19 2.00e-01 2.50e+01 8.58e-01
  chirality pdb=" CA  ASP B 985 "
            pdb=" N   ASP B 985 "
            pdb=" C   ASP B 985 "
            pdb=" CB  ASP B 985 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.67   -0.16 2.00e-01 2.50e+01 6.66e-01
  ... (remaining 1209 not shown)

  Planarity restraints: 1367
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B1040 "    0.010 2.00e-02 2.50e+03   2.02e-02 4.08e+00
        pdb=" C   VAL B1040 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   VAL B1040 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ASP B1041 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 392 "   -0.010 2.00e-02 2.50e+03   1.37e-02 3.28e+00
        pdb=" CG  PHE B 392 "    0.031 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 392 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 392 "   -0.011 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 392 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 392 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 392 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 237 "   -0.148 9.50e-02 1.11e+02   6.62e-02 2.71e+00
        pdb=" NE  ARG B 237 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 237 "    0.004 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 237 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 237 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1364 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 263
        2.71 -     3.26: 7655
        3.26 -     3.81: 12085
        3.81 -     4.35: 14473
        4.35 -     4.90: 24346
  Nonbonded interactions: 58822
  Sorted by model distance:
  nonbonded pdb=" O   ALA B 958 "
            pdb=" OG1 THR B 961 "
     model   vdw
     2.164 3.040
  nonbonded pdb=" O   TYR B1047 "
            pdb=" OG1 THR B1066 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   THR B 393 "
            pdb=" OG1 THR B 523 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   ASN B  81 "
            pdb=" NE2 GLN B 239 "
     model   vdw
     2.212 3.120
  nonbonded pdb=" O   ARG B 983 "
            pdb=" NH1 ARG B 983 "
     model   vdw
     2.248 3.120
  ... (remaining 58817 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.630
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.790
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.180
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7995
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      :  0.003   0.031   7790  Z= 0.157
  Angle     :  0.641   8.858  10605  Z= 0.368
  Chirality :  0.044   0.186   1212
  Planarity :  0.004   0.066   1367
  Dihedral  : 12.235  88.087   2772
  Min Nonbonded Distance : 2.164

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  1.90 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.00 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.27), residues: 948
  helix:  1.60 (0.38), residues: 211
  sheet:  0.04 (0.33), residues: 221
  loop : -0.12 (0.27), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 995 
 TYR   0.019   0.001   TYR B 204 
 PHE   0.031   0.001   PHE B 392 
 TRP   0.009   0.001   TRP B 104 
 HIS   0.003   0.001   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.16 ( 7778)
  covalent geometry    : angle       0.63832 /  0.37 (10581)
  SS BOND              : bond        0.00466 /  0.35 (   12)
  SS BOND              : angle       1.29116 /  0.75 (   24)
  hydrogen bonds       : bond        0.14234 /  9.80 (  319)
  hydrogen bonds       : angle       6.70086 /  4.64 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
REVERT: B  238 PHE cc_start: 0.8411 (p90) cc_final: 0.7944 (p90)
REVERT: B  338 PHE cc_start: 0.8050 (m-10) cc_final: 0.7760 (m-80)
REVERT: B  423 TYR cc_start: 0.8833 (t80) cc_final: 0.8494 (t80)
REVERT: B  697 MET cc_start: 0.9152 (ppp) cc_final: 0.8828 (ppp)
REVERT: B  900 MET cc_start: 0.9454 (mmp) cc_final: 0.9187 (mmt)
REVERT: B  936 ASP cc_start: 0.9252 (m-30) cc_final: 0.9011 (m-30)
REVERT: B  966 LEU cc_start: 0.9656 (mt) cc_final: 0.9379 (mp)
REVERT: B  968 SER cc_start: 0.9297 (m) cc_final: 0.8668 (t)
REVERT: B  970 PHE cc_start: 0.8156 (m-10) cc_final: 0.7883 (m-10)
REVERT: B  984 LEU cc_start: 0.8215 (mt) cc_final: 0.7980 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 46
  average time/residue: 0.0721
  time to fit residues: 5.1588
Evaluate side-chains
  34 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 34
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 49 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    8.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:   30.0000
   chunk 61 optimal weight:    5.9990
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    4.9990
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B 450 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.065543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.043316 restraints weight = 44439.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.044770 restraints weight = 25471.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.045744 restraints weight = 17321.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.046414 restraints weight = 13090.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.046867 restraints weight = 10644.707|
|-----------------------------------------------------------------------------|
r_work (final): 0.2825
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.1333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   7790  Z= 0.180
  Angle     :  0.574   8.550  10605  Z= 0.302
  Chirality :  0.043   0.163   1212
  Planarity :  0.004   0.047   1367
  Dihedral  :  4.358  22.664   1032
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.27), residues: 948
  helix:  1.64 (0.36), residues: 218
  sheet: -0.08 (0.33), residues: 226
  loop : -0.12 (0.27), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 237 
 TYR   0.012   0.001   TYR B 269 
 PHE   0.021   0.001   PHE B 392 
 TRP   0.005   0.001   TRP B 365 
 HIS   0.005   0.001   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00382 /  0.18 ( 7778)
  covalent geometry    : angle       0.57241 /  0.30 (10581)
  SS BOND              : bond        0.00458 /  0.33 (   12)
  SS BOND              : angle       1.05169 /  0.60 (   24)
  hydrogen bonds       : bond        0.04110 /  2.70 (  319)
  hydrogen bonds       : angle       5.58197 /  3.87 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  48 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  238 PHE cc_start: 0.8555 (p90) cc_final: 0.8030 (p90)
REVERT: B  338 PHE cc_start: 0.8129 (m-10) cc_final: 0.7865 (m-80)
REVERT: B  423 TYR cc_start: 0.8700 (t80) cc_final: 0.8487 (t80)
REVERT: B  697 MET cc_start: 0.9208 (ppp) cc_final: 0.8860 (ppp)
REVERT: B  731 MET cc_start: 0.8597 (ppp) cc_final: 0.8371 (ppp)
REVERT: B  936 ASP cc_start: 0.9133 (m-30) cc_final: 0.8868 (m-30)
REVERT: B  968 SER cc_start: 0.9404 (m) cc_final: 0.8735 (p)
REVERT: B  970 PHE cc_start: 0.8316 (m-10) cc_final: 0.7869 (m-10)
REVERT: B  984 LEU cc_start: 0.8254 (mt) cc_final: 0.8011 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 48
  average time/residue: 0.0689
  time to fit residues: 5.1924
Evaluate side-chains
  31 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 66 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 96 optimal weight:    4.9990
   chunk 42 optimal weight:    0.8980
   chunk 54 optimal weight:    6.9990
   chunk 44 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 52 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0170
   chunk 62 optimal weight:    8.9990
   overall best weight:    1.7824

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B 450 ASN
B 804 GLN
B 913 GLN
B1048 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.066252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.044153 restraints weight = 42569.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 20)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.045638 restraints weight = 24229.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.046658 restraints weight = 16345.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2849 r_free = 0.2849 target = 0.047339 restraints weight = 12256.530|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2862 r_free = 0.2862 target = 0.047823 restraints weight = 9989.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7790  Z= 0.116
  Angle     :  0.504   7.239  10605  Z= 0.263
  Chirality :  0.043   0.195   1212
  Planarity :  0.004   0.047   1367
  Dihedral  :  4.065  21.842   1032
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.27), residues: 948
  helix:  2.03 (0.37), residues: 219
  sheet: -0.01 (0.33), residues: 225
  loop : -0.16 (0.28), residues: 504

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 237 
 TYR   0.008   0.001   TYR B 279 
 PHE   0.020   0.001   PHE B 392 
 TRP   0.003   0.001   TRP B 365 
 HIS   0.002   0.001   HIS B  49 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00251 /  0.12 ( 7778)
  covalent geometry    : angle       0.50216 /  0.26 (10581)
  SS BOND              : bond        0.00416 /  0.31 (   12)
  SS BOND              : angle       1.07870 /  0.50 (   24)
  hydrogen bonds       : bond        0.03914 /  2.59 (  319)
  hydrogen bonds       : angle       5.26598 /  3.65 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8437 (mt-10) cc_final: 0.7774 (mt-10)
REVERT: B  238 PHE cc_start: 0.8505 (p90) cc_final: 0.7893 (p90)
REVERT: B  338 PHE cc_start: 0.8219 (m-10) cc_final: 0.7925 (m-80)
REVERT: B  423 TYR cc_start: 0.8751 (t80) cc_final: 0.8468 (t80)
REVERT: B  697 MET cc_start: 0.9161 (ppp) cc_final: 0.8868 (ppp)
REVERT: B  731 MET cc_start: 0.8573 (ppp) cc_final: 0.8315 (ppp)
REVERT: B  936 ASP cc_start: 0.9125 (m-30) cc_final: 0.8825 (m-30)
REVERT: B  968 SER cc_start: 0.9273 (m) cc_final: 0.8595 (p)
REVERT: B  970 PHE cc_start: 0.8334 (m-10) cc_final: 0.7812 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0691
  time to fit residues: 5.3378
Evaluate side-chains
  33 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 60 optimal weight:    9.9990
   chunk 38 optimal weight:   20.0000
   chunk 71 optimal weight:    7.9990
   chunk 77 optimal weight:    9.9990
   chunk 82 optimal weight:    6.9990
   chunk 3 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 14 optimal weight:    8.9990
   chunk 26 optimal weight:    6.9990
   chunk 58 optimal weight:   10.0000
   chunk 24 optimal weight:   10.0000
   overall best weight:    7.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  69 HIS
B  87 ASN
B 239 GLN
B 321 GLN
B 644 GLN
** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.061103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2618 r_free = 0.2618 target = 0.039768 restraints weight = 47193.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.041093 restraints weight = 27402.726|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.041967 restraints weight = 18760.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2703 r_free = 0.2703 target = 0.042570 restraints weight = 14368.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.042999 restraints weight = 11868.861|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.105   7790  Z= 0.401
  Angle     :  0.840  12.561  10605  Z= 0.444
  Chirality :  0.048   0.223   1212
  Planarity :  0.006   0.079   1367
  Dihedral  :  5.319  21.531   1032
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.22 %
    Favored  : 95.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.56 (0.26), residues: 948
  helix:  0.76 (0.35), residues: 219
  sheet: -0.59 (0.36), residues: 182
  loop : -0.73 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 237 
 TYR   0.026   0.003   TYR B 904 
 PHE   0.033   0.003   PHE B 392 
 TRP   0.012   0.002   TRP B1102 
 HIS   0.008   0.002   HIS B1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00823 /  0.40 ( 7778)
  covalent geometry    : angle       0.83771 /  0.44 (10581)
  SS BOND              : bond        0.00563 /  0.41 (   12)
  SS BOND              : angle       1.46487 /  0.80 (   24)
  hydrogen bonds       : bond        0.05638 /  3.79 (  319)
  hydrogen bonds       : angle       6.28119 /  4.37 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 44
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8623 (mt-10) cc_final: 0.7980 (mt-10)
REVERT: B  338 PHE cc_start: 0.8434 (m-10) cc_final: 0.8078 (m-10)
REVERT: B  380 TYR cc_start: 0.8321 (m-80) cc_final: 0.8020 (m-80)
REVERT: B  423 TYR cc_start: 0.8589 (t80) cc_final: 0.8205 (t80)
REVERT: B  568 ASP cc_start: 0.8533 (t0) cc_final: 0.8301 (m-30)
REVERT: B  697 MET cc_start: 0.9137 (ppp) cc_final: 0.8752 (ppp)
REVERT: B  731 MET cc_start: 0.8681 (ppp) cc_final: 0.8350 (ppp)
REVERT: B  900 MET cc_start: 0.7424 (mmt) cc_final: 0.7161 (mmt)
REVERT: B  936 ASP cc_start: 0.9206 (m-30) cc_final: 0.8944 (m-30)
REVERT: B  968 SER cc_start: 0.9375 (m) cc_final: 0.8987 (t)
REVERT: B  984 LEU cc_start: 0.8615 (mt) cc_final: 0.8359 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 44
  average time/residue: 0.0898
  time to fit residues: 5.7512
Evaluate side-chains
  31 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 31
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 77 optimal weight:    2.9990
   chunk 4 optimal weight:   20.0000
   chunk 61 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 24 optimal weight:    7.9990
   chunk 79 optimal weight:    4.9990
   chunk 51 optimal weight:   10.0000
   chunk 53 optimal weight:    0.9990
   chunk 11 optimal weight:   30.0000
   chunk 69 optimal weight:    4.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B 450 ASN
** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1088 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.062686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.041740 restraints weight = 45505.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2712 r_free = 0.2712 target = 0.043135 restraints weight = 25649.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2740 r_free = 0.2740 target = 0.044058 restraints weight = 17194.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.044689 restraints weight = 12869.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2773 r_free = 0.2773 target = 0.045137 restraints weight = 10424.065|
|-----------------------------------------------------------------------------|
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.3507

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7790  Z= 0.160
  Angle     :  0.571   9.907  10605  Z= 0.297
  Chirality :  0.044   0.160   1212
  Planarity :  0.004   0.052   1367
  Dihedral  :  4.660  22.069   1032
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.20 (0.26), residues: 948
  helix:  1.37 (0.35), residues: 219
  sheet: -0.53 (0.35), residues: 195
  loop : -0.57 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 237 
 TYR   0.012   0.001   TYR B  37 
 PHE   0.019   0.001   PHE B 392 
 TRP   0.004   0.001   TRP B 104 
 HIS   0.003   0.001   HIS B1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.16 ( 7778)
  covalent geometry    : angle       0.56717 /  0.30 (10581)
  SS BOND              : bond        0.00415 /  0.31 (   12)
  SS BOND              : angle       1.41615 /  0.66 (   24)
  hydrogen bonds       : bond        0.04481 /  2.96 (  319)
  hydrogen bonds       : angle       5.59816 /  3.85 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8113 (mt-10)
REVERT: B  423 TYR cc_start: 0.8580 (t80) cc_final: 0.8151 (t80)
REVERT: B  568 ASP cc_start: 0.8433 (t0) cc_final: 0.8207 (m-30)
REVERT: B  697 MET cc_start: 0.9224 (ppp) cc_final: 0.8873 (ppp)
REVERT: B  731 MET cc_start: 0.8580 (ppp) cc_final: 0.8349 (ppp)
REVERT: B  936 ASP cc_start: 0.9157 (m-30) cc_final: 0.8862 (m-30)
REVERT: B  968 SER cc_start: 0.9373 (m) cc_final: 0.8981 (t)
REVERT: B  984 LEU cc_start: 0.8562 (mt) cc_final: 0.8322 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 42
  average time/residue: 0.0705
  time to fit residues: 4.5367
Evaluate side-chains
  33 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 15 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 5 optimal weight:   10.0000
   chunk 61 optimal weight:    0.7980
   chunk 63 optimal weight:    1.9990
   chunk 77 optimal weight:   10.0000
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B1088 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.063402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.042627 restraints weight = 44890.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.044054 restraints weight = 24803.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2774 r_free = 0.2774 target = 0.045001 restraints weight = 16349.655|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.045639 restraints weight = 12111.656|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 57)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.046096 restraints weight = 9766.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.3744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7790  Z= 0.110
  Angle     :  0.518   7.948  10605  Z= 0.271
  Chirality :  0.043   0.167   1212
  Planarity :  0.004   0.052   1367
  Dihedral  :  4.182  21.252   1032
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.17 %
    Favored  : 98.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.14 (0.27), residues: 948
  helix:  1.81 (0.36), residues: 219
  sheet: -0.34 (0.34), residues: 204
  loop : -0.43 (0.27), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 237 
 TYR   0.006   0.001   TYR B 279 
 PHE   0.019   0.001   PHE B 392 
 TRP   0.006   0.001   TRP B 104 
 HIS   0.002   0.000   HIS B1064 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.11 ( 7778)
  covalent geometry    : angle       0.51516 /  0.27 (10581)
  SS BOND              : bond        0.00409 /  0.31 (   12)
  SS BOND              : angle       1.22019 /  0.58 (   24)
  hydrogen bonds       : bond        0.03970 /  2.58 (  319)
  hydrogen bonds       : angle       5.19250 /  3.60 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  43 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8093 (mt-10)
REVERT: B  423 TYR cc_start: 0.8612 (t80) cc_final: 0.8087 (t80)
REVERT: B  568 ASP cc_start: 0.8279 (t0) cc_final: 0.7978 (m-30)
REVERT: B  697 MET cc_start: 0.9238 (ppp) cc_final: 0.8914 (ppp)
REVERT: B  936 ASP cc_start: 0.9169 (m-30) cc_final: 0.8855 (m-30)
REVERT: B  968 SER cc_start: 0.9397 (m) cc_final: 0.8990 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 43
  average time/residue: 0.0703
  time to fit residues: 4.6957
Evaluate side-chains
  30 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 30
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 57 optimal weight:    6.9990
   chunk 10 optimal weight:   10.0000
   chunk 63 optimal weight:    5.9990
   chunk 49 optimal weight:    9.9990
   chunk 15 optimal weight:    8.9990
   chunk 5 optimal weight:    9.9990
   chunk 0 optimal weight:    9.9990
   chunk 35 optimal weight:   50.0000
   chunk 40 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    6.3990

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B 450 ASN
** B 953 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.060328 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.039229 restraints weight = 46985.132|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2642 r_free = 0.2642 target = 0.040574 restraints weight = 26519.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.041467 restraints weight = 17900.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 51)----------------|
| r_work = 0.2687 r_free = 0.2687 target = 0.042066 restraints weight = 13517.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.042475 restraints weight = 11041.686|
|-----------------------------------------------------------------------------|
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.4567

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.079   7790  Z= 0.315
  Angle     :  0.738  11.870  10605  Z= 0.387
  Chirality :  0.046   0.155   1212
  Planarity :  0.005   0.052   1367
  Dihedral  :  5.073  21.251   1032
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.49 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.26), residues: 948
  helix:  1.06 (0.35), residues: 219
  sheet: -0.62 (0.35), residues: 189
  loop : -0.88 (0.25), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 102 
 TYR   0.025   0.002   TYR B 904 
 PHE   0.023   0.002   PHE B 392 
 TRP   0.012   0.002   TRP B1102 
 HIS   0.009   0.002   HIS B1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00656 /  0.31 ( 7778)
  covalent geometry    : angle       0.73554 /  0.39 (10581)
  SS BOND              : bond        0.00930 /  0.68 (   12)
  SS BOND              : angle       1.43641 /  0.82 (   24)
  hydrogen bonds       : bond        0.05184 /  3.50 (  319)
  hydrogen bonds       : angle       5.96520 /  4.13 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  38 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 38
  time to evaluate  : 0.302 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8048 (mt-10)
REVERT: B  423 TYR cc_start: 0.8535 (t80) cc_final: 0.8162 (t80)
REVERT: B  568 ASP cc_start: 0.8360 (t0) cc_final: 0.7936 (m-30)
REVERT: B  697 MET cc_start: 0.9200 (ppp) cc_final: 0.8803 (ppp)
REVERT: B  731 MET cc_start: 0.8674 (ppp) cc_final: 0.8309 (ppp)
REVERT: B  936 ASP cc_start: 0.9277 (m-30) cc_final: 0.8997 (m-30)
REVERT: B  968 SER cc_start: 0.9282 (m) cc_final: 0.9013 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 38
  average time/residue: 0.0713
  time to fit residues: 4.2808
Evaluate side-chains
  29 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 15 optimal weight:    6.9990
   chunk 84 optimal weight:    3.9990
   chunk 20 optimal weight:    5.9990
   chunk 94 optimal weight:    0.0980
   chunk 56 optimal weight:    5.9990
   chunk 39 optimal weight:    7.9990
   chunk 80 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9980
   chunk 85 optimal weight:    1.9990
   chunk 25 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
B1048 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.062175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.041615 restraints weight = 45492.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.043026 restraints weight = 25230.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2744 r_free = 0.2744 target = 0.043965 restraints weight = 16691.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2764 r_free = 0.2764 target = 0.044616 restraints weight = 12372.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.045060 restraints weight = 9956.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7790  Z= 0.124
  Angle     :  0.537   7.789  10605  Z= 0.280
  Chirality :  0.044   0.163   1212
  Planarity :  0.004   0.053   1367
  Dihedral  :  4.399  21.221   1032
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.27), residues: 948
  helix:  1.60 (0.35), residues: 226
  sheet: -0.33 (0.34), residues: 193
  loop : -0.68 (0.26), residues: 529

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 237 
 TYR   0.010   0.001   TYR B 917 
 PHE   0.021   0.001   PHE B 392 
 TRP   0.009   0.001   TRP B 104 
 HIS   0.002   0.001   HIS B1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00262 /  0.12 ( 7778)
  covalent geometry    : angle       0.53522 /  0.28 (10581)
  SS BOND              : bond        0.00405 /  0.30 (   12)
  SS BOND              : angle       1.11647 /  0.60 (   24)
  hydrogen bonds       : bond        0.04187 /  2.75 (  319)
  hydrogen bonds       : angle       5.35795 /  3.70 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  41 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 41
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8767 (mt-10) cc_final: 0.8161 (mt-10)
REVERT: B  423 TYR cc_start: 0.8608 (t80) cc_final: 0.8124 (t80)
REVERT: B  697 MET cc_start: 0.9259 (ppp) cc_final: 0.8922 (ppp)
REVERT: B  731 MET cc_start: 0.8629 (ppp) cc_final: 0.8410 (ppp)
REVERT: B  740 MET cc_start: 0.8947 (ttt) cc_final: 0.8085 (tmm)
REVERT: B  936 ASP cc_start: 0.9212 (m-30) cc_final: 0.8915 (m-30)
REVERT: B  968 SER cc_start: 0.9296 (m) cc_final: 0.9021 (t)
REVERT: B  984 LEU cc_start: 0.8718 (mt) cc_final: 0.8417 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 41
  average time/residue: 0.0717
  time to fit residues: 4.6193
Evaluate side-chains
  29 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 29
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 23 optimal weight:    7.9990
   chunk 29 optimal weight:    5.9990
   chunk 44 optimal weight:    9.9990
   chunk 70 optimal weight:    8.9990
   chunk 36 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 54 optimal weight:    3.9990
   chunk 9 optimal weight:   20.0000
   overall best weight:    5.1990

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B 450 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.060439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.039487 restraints weight = 46167.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.040851 restraints weight = 25920.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2683 r_free = 0.2683 target = 0.041743 restraints weight = 17383.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2701 r_free = 0.2701 target = 0.042374 restraints weight = 13099.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 50)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.042780 restraints weight = 10635.136|
|-----------------------------------------------------------------------------|
r_work (final): 0.2698
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.5088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   7790  Z= 0.262
  Angle     :  0.662  10.274  10605  Z= 0.349
  Chirality :  0.045   0.223   1212
  Planarity :  0.005   0.051   1367
  Dihedral  :  4.819  21.284   1032
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.17 %
    Favored  : 94.83 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.50 (0.26), residues: 948
  helix:  1.27 (0.35), residues: 225
  sheet: -0.61 (0.34), residues: 197
  loop : -0.93 (0.26), residues: 526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 102 
 TYR   0.018   0.002   TYR B 904 
 PHE   0.020   0.002   PHE B 392 
 TRP   0.010   0.002   TRP B1102 
 HIS   0.005   0.001   HIS B1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00548 /  0.26 ( 7778)
  covalent geometry    : angle       0.65841 /  0.35 (10581)
  SS BOND              : bond        0.00513 /  0.37 (   12)
  SS BOND              : angle       1.61769 /  0.76 (   24)
  hydrogen bonds       : bond        0.04817 /  3.24 (  319)
  hydrogen bonds       : angle       5.69923 /  3.96 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  33 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 33
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8681 (mt-10) cc_final: 0.8112 (mt-10)
REVERT: B  697 MET cc_start: 0.9244 (ppp) cc_final: 0.8880 (ppp)
REVERT: B  731 MET cc_start: 0.8675 (ppp) cc_final: 0.8383 (ppp)
REVERT: B  740 MET cc_start: 0.9054 (ttt) cc_final: 0.8817 (ttp)
REVERT: B  936 ASP cc_start: 0.9258 (m-30) cc_final: 0.8963 (m-30)
REVERT: B  968 SER cc_start: 0.9283 (m) cc_final: 0.9078 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 33
  average time/residue: 0.0725
  time to fit residues: 3.7970
Evaluate side-chains
  26 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 26
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 10 optimal weight:    9.9990
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 67 optimal weight:    8.9990
   chunk 74 optimal weight:    0.6980
   chunk 55 optimal weight:    6.9990
   chunk 77 optimal weight:    8.9990
   chunk 71 optimal weight:    7.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    2.1384

-------------------------------------------------------------------------------
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 = 0.3247 r_free = 0.3247 target = 0.061675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2655 r_free = 0.2655 target = 0.040808 restraints weight = 45308.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2699 r_free = 0.2699 target = 0.042221 restraints weight = 25196.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 59)----------------|
| r_work = 0.2726 r_free = 0.2726 target = 0.043157 restraints weight = 16804.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2745 r_free = 0.2745 target = 0.043762 restraints weight = 12512.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2758 r_free = 0.2758 target = 0.044222 restraints weight = 10174.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.2745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.5142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7790  Z= 0.132
  Angle     :  0.553   9.108  10605  Z= 0.287
  Chirality :  0.044   0.220   1212
  Planarity :  0.004   0.054   1367
  Dihedral  :  4.424  21.434   1032
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.38 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.27), residues: 948
  helix:  1.71 (0.36), residues: 223
  sheet: -0.45 (0.33), residues: 208
  loop : -0.84 (0.26), residues: 517

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 237 
 TYR   0.012   0.001   TYR B 917 
 PHE   0.019   0.001   PHE B 392 
 TRP   0.005   0.001   TRP B 104 
 HIS   0.007   0.001   HIS B1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 7778)
  covalent geometry    : angle       0.54969 /  0.29 (10581)
  SS BOND              : bond        0.00421 /  0.31 (   12)
  SS BOND              : angle       1.38181 /  0.66 (   24)
  hydrogen bonds       : bond        0.04322 /  2.86 (  319)
  hydrogen bonds       : angle       5.37707 /  3.73 (  888)

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

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

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1896 Ramachandran restraints generated.
    948 Oldfield, 0 Emsley, 948 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  35 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 35
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: B  191 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8190 (mt-10)
REVERT: B  697 MET cc_start: 0.9256 (ppp) cc_final: 0.8921 (ppp)
REVERT: B  731 MET cc_start: 0.8606 (ppp) cc_final: 0.8364 (ppp)
REVERT: B  740 MET cc_start: 0.9062 (ttt) cc_final: 0.8832 (ttp)
REVERT: B  936 ASP cc_start: 0.9217 (m-30) cc_final: 0.8907 (m-30)
REVERT: B  968 SER cc_start: 0.9265 (m) cc_final: 0.9065 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 35
  average time/residue: 0.0840
  time to fit residues: 4.5217
Evaluate side-chains
  25 residues out of total 853 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 25
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 97
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 72 optimal weight:    0.0270
   chunk 49 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9980
   chunk 32 optimal weight:   30.0000
   chunk 50 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   chunk 62 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    3.0044

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

Flipped N/Q/H residues before XYZ refinement:
B  87 ASN
B 450 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.061342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.040534 restraints weight = 46389.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2689 r_free = 0.2689 target = 0.041949 restraints weight = 25594.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.042867 restraints weight = 16970.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.043484 restraints weight = 12614.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.043930 restraints weight = 10237.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.5383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   7790  Z= 0.162
  Angle     :  0.564   8.822  10605  Z= 0.293
  Chirality :  0.044   0.211   1212
  Planarity :  0.004   0.053   1367
  Dihedral  :  4.398  21.200   1032
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.12 %
    Favored  : 99.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.27), residues: 948
  helix:  1.73 (0.35), residues: 226
  sheet: -0.48 (0.33), residues: 208
  loop : -0.88 (0.27), residues: 514

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 237 
 TYR   0.012   0.001   TYR B 917 
 PHE   0.021   0.001   PHE B 377 
 TRP   0.005   0.001   TRP B 353 
 HIS   0.005   0.001   HIS B1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.16 ( 7778)
  covalent geometry    : angle       0.56022 /  0.29 (10581)
  SS BOND              : bond        0.00421 /  0.31 (   12)
  SS BOND              : angle       1.43883 /  0.70 (   24)
  hydrogen bonds       : bond        0.04268 /  2.84 (  319)
  hydrogen bonds       : angle       5.35473 /  3.72 (  888)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1474.26 seconds
wall clock time: 26 minutes 11.30 seconds (1571.30 seconds total)