Starting phenix.real_space_refine
on Wed Aug  5 00:03:40 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jjf_61525/08_2026/9jjf_61525.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jjf_61525/08_2026/9jjf_61525.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.65
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jjf_61525/08_2026/9jjf_61525.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jjf_61525/08_2026/9jjf_61525.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jjf_61525/08_2026/9jjf_61525.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jjf_61525/08_2026/9jjf_61525.cif"
  }
  resolution = 2.65
  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=   0.001 sd=   0.022
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
     Ca      1      9.91       5
     P       3      5.49       5
     S      41      5.16       5
     C    4937      2.51       5
     N    1250      2.21       5
     O    1386      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 7618
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7549
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 941, 7549
          Classifications: {'peptide': 941}
          Link IDs: {'PTRANS': 35, 'TRANS': 905}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 41
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 41
          Unusual residues: {' CA': 1, 'A2R': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.65, per 1000 atoms: 0.22
  Number of scatterers: 7618
  At special positions: 0
  Unit cell: (111.28, 71.69, 145.52, 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)
     Ca      1     19.99
     S      41     16.00
     P       3     15.00
     O    1386      8.00
     N    1250      7.00
     C    4937      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A1017 "
  Time building additional restraints: 0.43
  Conformation dependent library (CDL) restraints added in 342.7 milliseconds
  

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1774

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 1 sheets defined
      70.0% alpha, 3.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 119 through 130
      removed outlier: 3.753A  pdb=" N   VAL A 123 " --> pdb=" O   ASP A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 169
      removed outlier: 3.654A  pdb=" N   THR A 169 " --> pdb=" O   LYS A 165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 193
      removed outlier: 3.641A  pdb=" N   HIS A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 281
      removed outlier: 4.150A  pdb=" N   ILE A 268 " --> pdb=" O   TYR A 264 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   GLY A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET A 270 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   GLU A 275 " --> pdb=" O   ARG A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 317
    Processing helix  chain 'A' and resid 330 through 339
      removed outlier: 3.625A  pdb=" N   VAL A 334 " --> pdb=" O   ALA A 330 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   GLY A 335 " --> pdb=" O   ALA A 331 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ASN A 339 " --> pdb=" O   GLY A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 369
    Processing helix  chain 'A' and resid 374 through 386
      removed outlier: 4.360A  pdb=" N   THR A 378 " --> pdb=" O   GLY A 374 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   LEU A 386 " --> pdb=" O   ILE A 382 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 417
      removed outlier: 4.037A  pdb=" N   ALA A 408 " --> pdb=" O   ASP A 404 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ASN A 417 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 432
    Processing helix  chain 'A' and resid 433 through 441
    Processing helix  chain 'A' and resid 453 through 463
    Processing helix  chain 'A' and resid 465 through 476
      removed outlier: 3.512A  pdb=" N   GLY A 476 " --> pdb=" O   PHE A 472 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 483
    Processing helix  chain 'A' and resid 484 through 492
    Processing helix  chain 'A' and resid 500 through 513
    Processing helix  chain 'A' and resid 518 through 531
    Processing helix  chain 'A' and resid 536 through 541
      removed outlier: 3.728A  pdb=" N   LYS A 540 " --> pdb=" O   SER A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 545
      removed outlier: 3.769A  pdb=" N   PHE A 545 " --> pdb=" O   GLY A 542 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 542 through 545'
    Processing helix  chain 'A' and resid 578 through 590
    Processing helix  chain 'A' and resid 592 through 603
      removed outlier: 3.580A  pdb=" N   GLY A 603 " --> pdb=" O   LEU A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 605 through 627
    Processing helix  chain 'A' and resid 633 through 658
      removed outlier: 3.994A  pdb=" N   GLU A 658 " --> pdb=" O   GLU A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 659 through 667
    Processing helix  chain 'A' and resid 671 through 675
      removed outlier: 3.969A  pdb=" N   SER A 675 " --> pdb=" O   ASP A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 686
      removed outlier: 3.521A  pdb=" N   ALA A 686 " --> pdb=" O   LEU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 688 through 693
    Processing helix  chain 'A' and resid 694 through 706
    Processing helix  chain 'A' and resid 714 through 721
    Processing helix  chain 'A' and resid 727 through 732
      removed outlier: 4.462A  pdb=" N   ILE A 731 " --> pdb=" O   LEU A 727 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ILE A 732 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 727 through 732'
    Processing helix  chain 'A' and resid 827 through 835
    Processing helix  chain 'A' and resid 836 through 861
    Processing helix  chain 'A' and resid 870 through 875
      removed outlier: 3.771A  pdb=" N   GLY A 873 " --> pdb=" O   LYS A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 899
    Processing helix  chain 'A' and resid 904 through 913
    Processing helix  chain 'A' and resid 915 through 935
      removed outlier: 3.912A  pdb=" N   PHE A 919 " --> pdb=" O   ASP A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 961
      removed outlier: 4.954A  pdb=" N   ILE A 955 " --> pdb=" O   SER A 951 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   PHE A 956 " --> pdb=" O   LEU A 952 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 961 through 966
      removed outlier: 4.009A  pdb=" N   PHE A 965 " --> pdb=" O   SER A 961 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 970 through 1008
      removed outlier: 3.825A  pdb=" N   LYS A 974 " --> pdb=" O   LEU A 970 " (cutoff:3.500A)
      removed outlier: 4.821A  pdb=" N   ILE A 990 " --> pdb=" O   ALA A 986 " (cutoff:3.500A)
      removed outlier: 4.992A  pdb=" N   ILE A 991 " --> pdb=" O   GLN A 987 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ALA A1002 " --> pdb=" O   ALA A 998 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1018 through 1035
      Proline residue:  A1030  - end of helix
      removed outlier: 3.720A  pdb=" N   TYR A1035 " --> pdb=" O   TYR A1031 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1044
    Processing helix  chain 'A' and resid 1057 through 1074
      removed outlier: 4.017A  pdb=" N   LEU A1061 " --> pdb=" O   ASP A1057 " (cutoff:3.500A)
      Proline residue:  A1063  - end of helix
    Processing helix  chain 'A' and resid 1076 through 1094
    Processing helix  chain 'A' and resid 1095 through 1113
      removed outlier: 3.813A  pdb=" N   TYR A1105 " --> pdb=" O   LYS A1101 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ASP A1106 " --> pdb=" O   PHE A1102 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR A1111 " --> pdb=" O   LEU A1107 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER A1113 " --> pdb=" O   GLN A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1121 through 1131
    Processing helix  chain 'A' and resid 1154 through 1182
    Processing helix  chain 'A' and resid 1183 through 1206
    Processing sheet with id=AA1, first strand: chain 'A' and resid 95 through 98
      removed outlier: 7.938A  pdb=" N   LEU A 255 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      removed outlier: 6.512A  pdb=" N   LEU A 112 " --> pdb=" O   LEU A 255 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   ILE A 174 " --> pdb=" O   ILE A 207 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   ILE A 209 " --> pdb=" O   ILE A 174 " (cutoff:3.500A)
      removed outlier: 6.134A  pdb=" N   THR A 176 " --> pdb=" O   ILE A 209 " (cutoff:3.500A)
      removed outlier: 8.285A  pdb=" N   THR A 211 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ILE A 140 " --> pdb=" O   ILE A 175 " (cutoff:3.500A)
      removed outlier: 6.224A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   LEU A 299 " --> pdb=" O   VAL A 139 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   SER A 141 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
      removed outlier: 7.603A  pdb=" N   LEU A 301 " --> pdb=" O   SER A 141 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   THR A 143 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 8.556A  pdb=" N   VAL A 322 " --> pdb=" O   VAL A 296 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU A 298 " --> pdb=" O   VAL A 322 " (cutoff:3.500A)

    441 hydrogen bonds defined for protein.
    1308 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: 1.06

  Time building geometry restraints manager: 0.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2144
        1.34 -     1.45: 1361
        1.45 -     1.57: 4197
        1.57 -     1.69: 7
        1.69 -     1.81: 77
  Bond restraints: 7786
  Sorted by residual:
  bond pdb="C12' A2R A4001 "
       pdb="C13' A2R A4001 "
    ideal  model  delta    sigma   weight residual
    1.524  1.309  0.215 2.00e-02 2.50e+03 1.15e+02
  bond pdb=" C2  A2R A4001 "
       pdb=" N3  A2R A4001 "
    ideal  model  delta    sigma   weight residual
    1.321  1.473 -0.152 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" C5  A2R A4001 "
       pdb=" C6  A2R A4001 "
    ideal  model  delta    sigma   weight residual
    1.406  1.532 -0.126 2.00e-02 2.50e+03 3.97e+01
  bond pdb=" C2' A2R A4001 "
       pdb=" O2' A2R A4001 "
    ideal  model  delta    sigma   weight residual
    1.375  1.494 -0.119 2.00e-02 2.50e+03 3.53e+01
  bond pdb="C14' A2R A4001 "
       pdb="O14' A2R A4001 "
    ideal  model  delta    sigma   weight residual
    1.424  1.541 -0.117 2.00e-02 2.50e+03 3.44e+01
  ... (remaining 7781 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.70: 10269
        2.70 -     5.40: 243
        5.40 -     8.09: 38
        8.09 -    10.79: 6
       10.79 -    13.49: 6
  Bond angle restraints: 10562
  Sorted by residual:
  angle pdb=" O1  A2R A4001 "
        pdb=" P   A2R A4001 "
        pdb=" O2  A2R A4001 "
      ideal   model   delta    sigma   weight residual
     122.24  108.75   13.49 3.00e+00 1.11e-01 2.02e+01
  angle pdb=" N   PRO A 901 "
        pdb=" CA  PRO A 901 "
        pdb=" C   PRO A 901 "
      ideal   model   delta    sigma   weight residual
     110.70  115.97   -5.27 1.22e+00 6.72e-01 1.86e+01
  angle pdb=" O3  A2R A4001 "
        pdb=" P1  A2R A4001 "
        pdb="O15' A2R A4001 "
      ideal   model   delta    sigma   weight residual
      97.52  109.77  -12.25 3.00e+00 1.11e-01 1.67e+01
  angle pdb=" O11 A2R A4001 "
        pdb=" P1  A2R A4001 "
        pdb=" O12 A2R A4001 "
      ideal   model   delta    sigma   weight residual
     122.43  110.19   12.24 3.00e+00 1.11e-01 1.66e+01
  angle pdb=" C   PHE A 937 "
        pdb=" N   THR A 938 "
        pdb=" CA  THR A 938 "
      ideal   model   delta    sigma   weight residual
     122.61  128.61   -6.00 1.56e+00 4.11e-01 1.48e+01
  ... (remaining 10557 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.80: 4359
       14.80 -    29.60: 238
       29.60 -    44.40: 61
       44.40 -    59.20: 19
       59.20 -    74.00: 19
  Dihedral angle restraints: 4696
    sinusoidal: 1952
      harmonic: 2744
  Sorted by residual:
  dihedral pdb=" CA  PRO A 730 "
           pdb=" C   PRO A 730 "
           pdb=" N   ILE A 731 "
           pdb=" CA  ILE A 731 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.92  -22.08     0      5.00e+00 4.00e-02 1.95e+01
  dihedral pdb=" CA  VAL A 735 "
           pdb=" C   VAL A 735 "
           pdb=" N   PRO A 736 "
           pdb=" CA  PRO A 736 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.99   20.01     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  PRO A1009 "
           pdb=" C   PRO A1009 "
           pdb=" N   SER A1010 "
           pdb=" CA  SER A1010 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.07  -18.93     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 4693 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.123: 1158
       0.123 -    0.245: 50
       0.245 -    0.368: 1
       0.368 -    0.491: 0
       0.491 -    0.613: 1
  Chirality restraints: 1210
  Sorted by residual:
  chirality pdb=" C2' A2R A4001 "
            pdb=" C1' A2R A4001 "
            pdb=" C3' A2R A4001 "
            pdb=" O2' A2R A4001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42   -3.04    0.61 2.00e-01 2.50e+01 9.41e+00
  chirality pdb="C13' A2R A4001 "
            pdb="C12' A2R A4001 "
            pdb="C14' A2R A4001 "
            pdb="O13' A2R A4001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.42   -0.32 2.00e-01 2.50e+01 2.58e+00
  chirality pdb="C14' A2R A4001 "
            pdb="C13' A2R A4001 "
            pdb="C15' A2R A4001 "
            pdb="O14' A2R A4001 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.64    0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1207 not shown)

  Planarity restraints: 1319
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1010 "   -0.055 5.00e-02 4.00e+02   8.25e-02 1.09e+01
        pdb=" N   PRO A1011 "    0.143 5.00e-02 4.00e+02
        pdb=" CA  PRO A1011 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A1011 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A1118 "    0.043 5.00e-02 4.00e+02   6.43e-02 6.62e+00
        pdb=" N   PRO A1119 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO A1119 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A1119 "    0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A1119 "    0.042 5.00e-02 4.00e+02   6.32e-02 6.39e+00
        pdb=" N   PRO A1120 "   -0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO A1120 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A1120 "    0.037 5.00e-02 4.00e+02
  ... (remaining 1316 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1772
        2.79 -     3.31: 7216
        3.31 -     3.84: 13138
        3.84 -     4.37: 15684
        4.37 -     4.90: 26162
  Nonbonded interactions: 63972
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 984 "
            pdb=" OG1 THR A1088 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OG  SER A 484 "
            pdb=" OD1 ASP A 486 "
     model   vdw
     2.281 3.040
  nonbonded pdb=" OE1 GLU A 893 "
            pdb=" OH  TYR A 912 "
     model   vdw
     2.293 3.040
  nonbonded pdb=" OG1 THR A 176 "
            pdb=" NE2 HIS A 250 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" OH  TYR A 395 "
            pdb=" O   GLN A 403 "
     model   vdw
     2.312 3.040
  ... (remaining 63967 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 individual isotropic
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:             3.130
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.570
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:6.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
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      :  0.009   0.215   7788  Z= 0.395
  Angle     :  1.029  13.492  10568  Z= 0.521
  Chirality :  0.061   0.613   1210
  Planarity :  0.008   0.082   1318
  Dihedral  : 11.856  74.002   2922
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.31 %
    Favored  : 95.69 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.69 (0.21), residues: 929
  helix: -2.17 (0.16), residues: 604
  sheet: -2.57 (0.58), residues: 53
  loop : -2.60 (0.32), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 592 
 TYR   0.035   0.003   TYR A 638 
 PHE   0.024   0.003   PHE A 838 
 TRP   0.029   0.004   TRP A 431 
 HIS   0.010   0.003   HIS A 250 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00865 /  0.40 ( 7786)
  covalent geometry    : angle       1.02813 /  0.52 (10562)
  hydrogen bonds       : bond        0.11407 /  7.41 (  441)
  hydrogen bonds       : angle       6.13207 /  4.23 ( 1308)
  link_BETA1-4         : bond        0.00383 /  0.20 (    1)
  link_BETA1-4         : angle       2.33457 /  1.55 (    3)
  link_NAG-ASN         : bond        0.00668 /  0.35 (    1)
  link_NAG-ASN         : angle       2.47463 /  1.64 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.228 
Fit side-chains
   revert: symmetry clash
REVERT: A  249 ASN cc_start: 0.8400 (m110) cc_final: 0.8181 (m-40)
REVERT: A  273 ARG cc_start: 0.8068 (mtm180) cc_final: 0.7857 (mtm180)
REVERT: A  308 VAL cc_start: 0.8599 (p) cc_final: 0.8308 (t)
REVERT: A  433 ARG cc_start: 0.8572 (mmt180) cc_final: 0.8328 (mmt180)
REVERT: A  438 LYS cc_start: 0.8146 (mtmm) cc_final: 0.7855 (mttt)
REVERT: A  479 MET cc_start: 0.8140 (mmt) cc_final: 0.7893 (mmt)
REVERT: A  540 LYS cc_start: 0.7939 (mtmt) cc_final: 0.7721 (mtmt)
REVERT: A  594 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7284 (mm-30)
REVERT: A  709 MET cc_start: 0.7559 (ttp) cc_final: 0.7230 (ttp)
REVERT: A  714 ARG cc_start: 0.7587 (mmm-85) cc_final: 0.6666 (mmp-170)
REVERT: A  829 ARG cc_start: 0.7159 (mtt-85) cc_final: 0.6462 (mpp-170)
REVERT: A  892 GLU cc_start: 0.7342 (tp30) cc_final: 0.6860 (tm-30)
REVERT: A 1070 MET cc_start: 0.8800 (mmm) cc_final: 0.8590 (mmm)
REVERT: A 1162 ASP cc_start: 0.7215 (m-30) cc_final: 0.6926 (m-30)
REVERT: A 1189 ARG cc_start: 0.7615 (ttt180) cc_final: 0.7321 (tpp80)
  outliers start: 0
  outliers final: 3
  residues processed: 199
  average time/residue: 0.4908
  time to fit residues: 102.6989
Evaluate side-chains
  144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 0.308 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  426 ASN
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  486 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.0370
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 51 optimal weight:    0.7980
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0980
   chunk 45 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   overall best weight:    0.3658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1103 GLN
A1160 GLN
A1175 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.185394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.148512 restraints weight = 7954.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3660 rms_B_bonded: 1.58
r_work: 0.3445 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.3302 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3302
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1723

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7788  Z= 0.125
  Angle     :  0.618  10.250  10568  Z= 0.307
  Chirality :  0.042   0.174   1210
  Planarity :  0.006   0.062   1318
  Dihedral  :  8.686  59.836   1124
  Min Nonbonded Distance : 2.317

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 10.15 %
    Favored  : 87.65 %
  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: -1.55 (0.25), residues: 929
  helix: -0.29 (0.19), residues: 601
  sheet: -1.98 (0.65), residues: 52
  loop : -2.29 (0.35), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 329 
 TYR   0.013   0.001   TYR A 855 
 PHE   0.012   0.001   PHE A 254 
 TRP   0.012   0.001   TRP A1100 
 HIS   0.004   0.001   HIS A 116 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.13 ( 7786)
  covalent geometry    : angle       0.61734 /  0.31 (10562)
  hydrogen bonds       : bond        0.04145 /  2.75 (  441)
  hydrogen bonds       : angle       4.52274 /  3.18 ( 1308)
  link_BETA1-4         : bond        0.00069 /  0.04 (    1)
  link_BETA1-4         : angle       1.35174 /  0.85 (    3)
  link_NAG-ASN         : bond        0.00199 /  0.10 (    1)
  link_NAG-ASN         : angle       0.85989 /  0.56 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 143
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  245 MET cc_start: 0.6900 (tmt) cc_final: 0.6369 (tmt)
REVERT: A  249 ASN cc_start: 0.8718 (m110) cc_final: 0.8497 (m110)
REVERT: A  261 GLU cc_start: 0.6375 (mp0) cc_final: 0.5475 (tt0)
REVERT: A  273 ARG cc_start: 0.8192 (mtm180) cc_final: 0.7933 (mtm180)
REVERT: A  308 VAL cc_start: 0.8374 (p) cc_final: 0.8123 (t)
REVERT: A  336 PHE cc_start: 0.6439 (t80) cc_final: 0.6205 (t80)
REVERT: A  433 ARG cc_start: 0.8720 (mmt180) cc_final: 0.8449 (mmt-90)
REVERT: A  463 ASP cc_start: 0.7528 (m-30) cc_final: 0.7158 (m-30)
REVERT: A  509 MET cc_start: 0.7432 (OUTLIER) cc_final: 0.5644 (mtp)
REVERT: A  511 LYS cc_start: 0.7559 (mttm) cc_final: 0.6759 (mmtt)
REVERT: A  528 GLU cc_start: 0.7830 (pp20) cc_final: 0.7575 (mp0)
REVERT: A  540 LYS cc_start: 0.7899 (mtmt) cc_final: 0.7674 (mtmt)
REVERT: A  714 ARG cc_start: 0.8149 (mmm-85) cc_final: 0.6781 (mmp-170)
REVERT: A  831 MET cc_start: 0.7436 (tpp) cc_final: 0.7075 (ppp)
REVERT: A  892 GLU cc_start: 0.8042 (tp30) cc_final: 0.7668 (tm-30)
REVERT: A  997 ILE cc_start: 0.8810 (OUTLIER) cc_final: 0.8556 (mp)
REVERT: A 1157 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7111 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8287 (ttt180) cc_final: 0.7278 (tpp80)
  outliers start: 18
  outliers final: 6
  residues processed: 150
  average time/residue: 0.5043
  time to fit residues: 79.3567
Evaluate side-chains
  137 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 ASP
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  627 ASP
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  997 ILE
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 62 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 73 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9980
   chunk 59 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.8180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1074 ASN
A1160 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.182102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.145104 restraints weight = 7896.959|
|-----------------------------------------------------------------------------|
r_work (start): 0.3622 rms_B_bonded: 1.64
r_work: 0.3416 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.2101

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7788  Z= 0.155
  Angle     :  0.601   9.315  10568  Z= 0.297
  Chirality :  0.043   0.157   1210
  Planarity :  0.005   0.060   1318
  Dihedral  :  6.223  48.668   1120
  Min Nonbonded Distance : 2.274

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 11.37 %
    Favored  : 86.43 %
  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: 929
  helix:  0.54 (0.20), residues: 605
  sheet: -1.87 (0.67), residues: 52
  loop : -1.96 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1016 
 TYR   0.019   0.002   TYR A 855 
 PHE   0.011   0.001   PHE A1089 
 TRP   0.013   0.002   TRP A1100 
 HIS   0.004   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.15 ( 7786)
  covalent geometry    : angle       0.60063 /  0.30 (10562)
  hydrogen bonds       : bond        0.03957 /  2.62 (  441)
  hydrogen bonds       : angle       4.22446 /  3.00 ( 1308)
  link_BETA1-4         : bond        0.00405 /  0.21 (    1)
  link_BETA1-4         : angle       1.41707 /  0.90 (    3)
  link_NAG-ASN         : bond        0.00127 /  0.07 (    1)
  link_NAG-ASN         : angle       1.11210 /  0.67 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 141
  time to evaluate  : 0.166 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.4732 (OUTLIER) cc_final: 0.2826 (mpt-90)
REVERT: A  267 GLU cc_start: 0.6910 (tm-30) cc_final: 0.6582 (tt0)
REVERT: A  273 ARG cc_start: 0.8180 (mtm180) cc_final: 0.7960 (mtm180)
REVERT: A  308 VAL cc_start: 0.8390 (p) cc_final: 0.8183 (t)
REVERT: A  336 PHE cc_start: 0.6508 (t80) cc_final: 0.6263 (t80)
REVERT: A  447 GLN cc_start: 0.7533 (pm20) cc_final: 0.7133 (mt0)
REVERT: A  457 MET cc_start: 0.8925 (tpt) cc_final: 0.8622 (tpt)
REVERT: A  463 ASP cc_start: 0.7487 (m-30) cc_final: 0.7018 (m-30)
REVERT: A  509 MET cc_start: 0.7568 (OUTLIER) cc_final: 0.6154 (mtp)
REVERT: A  512 ARG cc_start: 0.7542 (tpp80) cc_final: 0.7276 (mmm-85)
REVERT: A  517 ILE cc_start: 0.7896 (OUTLIER) cc_final: 0.7595 (tp)
REVERT: A  540 LYS cc_start: 0.7942 (mtmt) cc_final: 0.7598 (mtmt)
REVERT: A  623 ARG cc_start: 0.8162 (tpt90) cc_final: 0.7899 (mmm160)
REVERT: A  714 ARG cc_start: 0.8207 (mmm-85) cc_final: 0.7253 (mmm160)
REVERT: A  831 MET cc_start: 0.7368 (tpp) cc_final: 0.7001 (mpp)
REVERT: A  885 TRP cc_start: 0.7296 (t-100) cc_final: 0.6721 (t60)
REVERT: A  892 GLU cc_start: 0.8072 (tp30) cc_final: 0.7715 (tm-30)
REVERT: A  893 GLU cc_start: 0.8652 (mm-30) cc_final: 0.8443 (mm-30)
REVERT: A  992 LEU cc_start: 0.8218 (mt) cc_final: 0.7920 (tp)
REVERT: A 1157 GLU cc_start: 0.7361 (OUTLIER) cc_final: 0.7057 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8284 (ttt180) cc_final: 0.7261 (tpp80)
  outliers start: 18
  outliers final: 6
  residues processed: 148
  average time/residue: 0.4778
  time to fit residues: 74.5448
Evaluate side-chains
  140 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  509 MET
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 63 optimal weight:    0.6980
   chunk 5 optimal weight:    6.9990
   chunk 62 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0870
   chunk 67 optimal weight:    2.9990
   chunk 38 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 75 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    0.9562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 403 GLN
A1160 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.180539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.143420 restraints weight = 7931.612|
|-----------------------------------------------------------------------------|
r_work (start): 0.3597 rms_B_bonded: 1.53
r_work: 0.3398 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 3.81 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2366

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7788  Z= 0.162
  Angle     :  0.602   9.197  10568  Z= 0.297
  Chirality :  0.043   0.163   1210
  Planarity :  0.005   0.055   1318
  Dihedral  :  5.923  51.201   1118
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.44 %
    Allowed  : 12.47 %
    Favored  : 85.09 %
  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: -0.07 (0.27), residues: 929
  helix:  0.90 (0.21), residues: 607
  sheet: -1.87 (0.64), residues: 52
  loop : -1.79 (0.36), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 647 
 TYR   0.017   0.002   TYR A 855 
 PHE   0.011   0.001   PHE A 956 
 TRP   0.012   0.002   TRP A1100 
 HIS   0.004   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00384 /  0.16 ( 7786)
  covalent geometry    : angle       0.60116 /  0.30 (10562)
  hydrogen bonds       : bond        0.03964 /  2.61 (  441)
  hydrogen bonds       : angle       4.18865 /  2.98 ( 1308)
  link_BETA1-4         : bond        0.00196 /  0.10 (    1)
  link_BETA1-4         : angle       1.52241 /  0.96 (    3)
  link_NAG-ASN         : bond        0.00079 /  0.04 (    1)
  link_NAG-ASN         : angle       1.17743 /  0.74 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 141
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.4829 (OUTLIER) cc_final: 0.2870 (mpt-90)
REVERT: A  267 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6784 (tt0)
REVERT: A  273 ARG cc_start: 0.8226 (mtm180) cc_final: 0.7892 (mtm180)
REVERT: A  308 VAL cc_start: 0.8394 (p) cc_final: 0.8169 (t)
REVERT: A  447 GLN cc_start: 0.7521 (pm20) cc_final: 0.7115 (mt0)
REVERT: A  457 MET cc_start: 0.8946 (tpt) cc_final: 0.8579 (tpt)
REVERT: A  512 ARG cc_start: 0.7515 (tpp80) cc_final: 0.7279 (mmm-85)
REVERT: A  517 ILE cc_start: 0.7986 (OUTLIER) cc_final: 0.7636 (tp)
REVERT: A  540 LYS cc_start: 0.7999 (mtmt) cc_final: 0.7656 (mtmt)
REVERT: A  623 ARG cc_start: 0.8215 (tpt90) cc_final: 0.7989 (mmm160)
REVERT: A  885 TRP cc_start: 0.7427 (t-100) cc_final: 0.6953 (t60)
REVERT: A  892 GLU cc_start: 0.8138 (tp30) cc_final: 0.7790 (tm-30)
REVERT: A  893 GLU cc_start: 0.8632 (mm-30) cc_final: 0.8430 (mm-30)
REVERT: A  992 LEU cc_start: 0.8289 (mt) cc_final: 0.8005 (tp)
REVERT: A 1157 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.7167 (mt-10)
REVERT: A 1159 GLU cc_start: 0.7886 (tp30) cc_final: 0.7665 (tp30)
REVERT: A 1189 ARG cc_start: 0.8268 (ttt180) cc_final: 0.7275 (tpp80)
  outliers start: 20
  outliers final: 9
  residues processed: 150
  average time/residue: 0.4970
  time to fit residues: 78.4561
Evaluate side-chains
  141 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 129
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  426 ASN
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 42 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 27 optimal weight:    5.9990
   chunk 61 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.180454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.144091 restraints weight = 7936.117|
|-----------------------------------------------------------------------------|
r_work (start): 0.3606 rms_B_bonded: 1.51
r_work: 0.3390 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3247 rms_B_bonded: 3.90 restraints_weight: 0.2500
r_work (final): 0.3247
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8232
moved from start:          0.2531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7788  Z= 0.153
  Angle     :  0.589   6.912  10568  Z= 0.291
  Chirality :  0.042   0.163   1210
  Planarity :  0.004   0.053   1318
  Dihedral  :  5.882  50.380   1118
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 14.06 %
    Favored  : 83.62 %
  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:  0.21 (0.27), residues: 929
  helix:  1.13 (0.21), residues: 605
  sheet: -1.80 (0.65), residues: 52
  loop : -1.66 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 935 
 TYR   0.015   0.002   TYR A 855 
 PHE   0.010   0.001   PHE A 956 
 TRP   0.012   0.001   TRP A1100 
 HIS   0.003   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00363 /  0.15 ( 7786)
  covalent geometry    : angle       0.58841 /  0.29 (10562)
  hydrogen bonds       : bond        0.03863 /  2.55 (  441)
  hydrogen bonds       : angle       4.11466 /  2.92 ( 1308)
  link_BETA1-4         : bond        0.00038 /  0.02 (    1)
  link_BETA1-4         : angle       1.51139 /  0.95 (    3)
  link_NAG-ASN         : bond        0.00022 /  0.01 (    1)
  link_NAG-ASN         : angle       1.07937 /  0.67 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 137
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.4875 (OUTLIER) cc_final: 0.2901 (mpt-90)
REVERT: A  197 MET cc_start: -0.0425 (ttp) cc_final: -0.0749 (mtm)
REVERT: A  261 GLU cc_start: 0.6439 (mp0) cc_final: 0.5613 (tt0)
REVERT: A  267 GLU cc_start: 0.7060 (tm-30) cc_final: 0.6744 (tt0)
REVERT: A  273 ARG cc_start: 0.8260 (mtm180) cc_final: 0.8034 (mtm180)
REVERT: A  275 GLU cc_start: 0.8241 (OUTLIER) cc_final: 0.7956 (mp0)
REVERT: A  276 GLU cc_start: 0.7681 (tt0) cc_final: 0.7399 (tt0)
REVERT: A  308 VAL cc_start: 0.8361 (p) cc_final: 0.8155 (t)
REVERT: A  447 GLN cc_start: 0.7534 (pm20) cc_final: 0.7074 (mt0)
REVERT: A  457 MET cc_start: 0.8972 (tpt) cc_final: 0.8586 (tpt)
REVERT: A  512 ARG cc_start: 0.7500 (tpp80) cc_final: 0.7299 (mmm-85)
REVERT: A  540 LYS cc_start: 0.8028 (mtmt) cc_final: 0.7705 (mtmt)
REVERT: A  623 ARG cc_start: 0.8222 (tpt90) cc_final: 0.8003 (mmm160)
REVERT: A  885 TRP cc_start: 0.7378 (t-100) cc_final: 0.7040 (t60)
REVERT: A  892 GLU cc_start: 0.8159 (tp30) cc_final: 0.7820 (tm-30)
REVERT: A  893 GLU cc_start: 0.8560 (mm-30) cc_final: 0.8349 (mm-30)
REVERT: A  992 LEU cc_start: 0.8282 (mt) cc_final: 0.8010 (tp)
REVERT: A 1090 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7935 (pt0)
REVERT: A 1157 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.7290 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8246 (ttt180) cc_final: 0.7282 (tpp80)
  outliers start: 19
  outliers final: 12
  residues processed: 147
  average time/residue: 0.4561
  time to fit residues: 70.6578
Evaluate side-chains
  144 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 0.194 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 33 optimal weight:    3.9990
   chunk 47 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 80 optimal weight:    0.0270
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    5.9990
   overall best weight:    1.4046

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.177782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.140332 restraints weight = 7905.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3557 rms_B_bonded: 1.52
r_work: 0.3358 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3216 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3216
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8269
moved from start:          0.2704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.058   7788  Z= 0.211
  Angle     :  0.643   6.941  10568  Z= 0.319
  Chirality :  0.045   0.185   1210
  Planarity :  0.005   0.055   1318
  Dihedral  :  6.059  49.664   1118
  Min Nonbonded Distance : 2.254

Molprobity Statistics.
  All-atom Clashscore : 9.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.01 %
    Favored  : 96.99 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.43 %
    Favored  : 82.89 %
  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: 929
  helix:  1.04 (0.21), residues: 614
  sheet: -1.76 (0.66), residues: 52
  loop : -1.50 (0.37), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 935 
 TYR   0.018   0.002   TYR A 855 
 PHE   0.014   0.002   PHE A 956 
 TRP   0.014   0.002   TRP A1100 
 HIS   0.004   0.001   HIS A 832 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00505 /  0.21 ( 7786)
  covalent geometry    : angle       0.64241 /  0.32 (10562)
  hydrogen bonds       : bond        0.04220 /  2.77 (  441)
  hydrogen bonds       : angle       4.21921 /  2.99 ( 1308)
  link_BETA1-4         : bond        0.00222 /  0.12 (    1)
  link_BETA1-4         : angle       1.74636 /  1.11 (    3)
  link_NAG-ASN         : bond        0.00273 /  0.14 (    1)
  link_NAG-ASN         : angle       1.42273 /  0.90 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 138
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.4966 (OUTLIER) cc_final: 0.2942 (mpt-90)
REVERT: A  197 MET cc_start: -0.0165 (ttp) cc_final: -0.0408 (ptt)
REVERT: A  267 GLU cc_start: 0.7251 (tm-30) cc_final: 0.6890 (tt0)
REVERT: A  274 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8116 (mp)
REVERT: A  276 GLU cc_start: 0.7780 (tt0) cc_final: 0.7508 (tt0)
REVERT: A  308 VAL cc_start: 0.8466 (p) cc_final: 0.8225 (t)
REVERT: A  418 ARG cc_start: 0.7969 (mmm160) cc_final: 0.7751 (mtm110)
REVERT: A  447 GLN cc_start: 0.7643 (pm20) cc_final: 0.7153 (mt0)
REVERT: A  540 LYS cc_start: 0.8280 (mtmt) cc_final: 0.7967 (mtmt)
REVERT: A  623 ARG cc_start: 0.8238 (tpt90) cc_final: 0.7965 (mmm160)
REVERT: A  728 ILE cc_start: 0.6892 (OUTLIER) cc_final: 0.6434 (mt)
REVERT: A  885 TRP cc_start: 0.7517 (t-100) cc_final: 0.7230 (t60)
REVERT: A  892 GLU cc_start: 0.8158 (tp30) cc_final: 0.7818 (tm-30)
REVERT: A  893 GLU cc_start: 0.8578 (mm-30) cc_final: 0.8374 (mm-30)
REVERT: A  992 LEU cc_start: 0.8378 (mt) cc_final: 0.8084 (tp)
REVERT: A 1157 GLU cc_start: 0.7576 (OUTLIER) cc_final: 0.7289 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8285 (ttt180) cc_final: 0.7288 (tpp80)
  outliers start: 22
  outliers final: 12
  residues processed: 145
  average time/residue: 0.4756
  time to fit residues: 72.5600
Evaluate side-chains
  145 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.175 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 82 optimal weight:    1.9990
   chunk 10 optimal weight:    4.9990
   chunk 67 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 0 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 47 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 18 optimal weight:    0.5980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 352 ASN
A1160 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.178854 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.141724 restraints weight = 7895.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3579 rms_B_bonded: 1.51
r_work: 0.3381 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.2806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   7788  Z= 0.176
  Angle     :  0.625   7.195  10568  Z= 0.311
  Chirality :  0.044   0.203   1210
  Planarity :  0.004   0.054   1318
  Dihedral  :  6.000  49.455   1118
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 14.55 %
    Favored  : 82.89 %
  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:  0.33 (0.28), residues: 929
  helix:  1.13 (0.21), residues: 614
  sheet: -1.72 (0.66), residues: 52
  loop : -1.47 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 604 
 TYR   0.014   0.002   TYR A 855 
 PHE   0.011   0.001   PHE A 956 
 TRP   0.013   0.001   TRP A1100 
 HIS   0.003   0.001   HIS A 876 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00419 /  0.18 ( 7786)
  covalent geometry    : angle       0.62462 /  0.31 (10562)
  hydrogen bonds       : bond        0.04015 /  2.63 (  441)
  hydrogen bonds       : angle       4.18410 /  2.94 ( 1308)
  link_BETA1-4         : bond        0.00039 /  0.02 (    1)
  link_BETA1-4         : angle       1.63690 /  1.03 (    3)
  link_NAG-ASN         : bond        0.00114 /  0.06 (    1)
  link_NAG-ASN         : angle       1.18814 /  0.74 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 135
  time to evaluate  : 0.282 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.4888 (OUTLIER) cc_final: 0.2938 (mpt-90)
REVERT: A  261 GLU cc_start: 0.6441 (mp0) cc_final: 0.5562 (tt0)
REVERT: A  267 GLU cc_start: 0.7320 (tm-30) cc_final: 0.7006 (tt0)
REVERT: A  274 ILE cc_start: 0.8383 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: A  275 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.8174 (mp0)
REVERT: A  276 GLU cc_start: 0.7736 (tt0) cc_final: 0.7463 (tt0)
REVERT: A  308 VAL cc_start: 0.8402 (p) cc_final: 0.8179 (t)
REVERT: A  447 GLN cc_start: 0.7623 (pm20) cc_final: 0.7119 (mt0)
REVERT: A  463 ASP cc_start: 0.7635 (m-30) cc_final: 0.7229 (m-30)
REVERT: A  509 MET cc_start: 0.8104 (mtm) cc_final: 0.7894 (mpp)
REVERT: A  540 LYS cc_start: 0.8110 (mtmt) cc_final: 0.7851 (mtmt)
REVERT: A  612 MET cc_start: 0.9102 (OUTLIER) cc_final: 0.8591 (ttt)
REVERT: A  623 ARG cc_start: 0.8228 (tpt90) cc_final: 0.7974 (mmm160)
REVERT: A  728 ILE cc_start: 0.6791 (OUTLIER) cc_final: 0.6480 (mt)
REVERT: A  885 TRP cc_start: 0.7501 (t-100) cc_final: 0.7236 (t60)
REVERT: A  892 GLU cc_start: 0.8157 (tp30) cc_final: 0.7821 (tm-30)
REVERT: A  893 GLU cc_start: 0.8583 (mm-30) cc_final: 0.8355 (mm-30)
REVERT: A  992 LEU cc_start: 0.8353 (OUTLIER) cc_final: 0.8062 (tp)
REVERT: A 1157 GLU cc_start: 0.7580 (OUTLIER) cc_final: 0.7297 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8125 (ttt180) cc_final: 0.7254 (tpp80)
  outliers start: 21
  outliers final: 12
  residues processed: 141
  average time/residue: 0.4394
  time to fit residues: 65.5700
Evaluate side-chains
  149 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 130
  time to evaluate  : 0.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  612 MET
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 29 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:    0.7980
   chunk 57 optimal weight:    3.9990
   chunk 61 optimal weight:    1.9990
   chunk 92 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 116 HIS
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.178832 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.141619 restraints weight = 7971.953|
|-----------------------------------------------------------------------------|
r_work (start): 0.3578 rms_B_bonded: 1.52
r_work: 0.3381 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8248
moved from start:          0.2881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7788  Z= 0.173
  Angle     :  0.625   7.254  10568  Z= 0.311
  Chirality :  0.044   0.292   1210
  Planarity :  0.004   0.053   1318
  Dihedral  :  5.975  49.921   1118
  Min Nonbonded Distance : 2.263

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.16 %
    Favored  : 81.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.28), residues: 929
  helix:  1.17 (0.21), residues: 617
  sheet: -1.70 (0.67), residues: 52
  loop : -1.43 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 604 
 TYR   0.015   0.002   TYR A 395 
 PHE   0.011   0.001   PHE A 956 
 TRP   0.013   0.001   TRP A1100 
 HIS   0.003   0.001   HIS A 832 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00413 /  0.17 ( 7786)
  covalent geometry    : angle       0.62413 /  0.31 (10562)
  hydrogen bonds       : bond        0.03963 /  2.60 (  441)
  hydrogen bonds       : angle       4.16374 /  2.94 ( 1308)
  link_BETA1-4         : bond        0.00077 /  0.04 (    1)
  link_BETA1-4         : angle       1.63785 /  1.03 (    3)
  link_NAG-ASN         : bond        0.00116 /  0.06 (    1)
  link_NAG-ASN         : angle       1.20174 /  0.75 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 133
  time to evaluate  : 0.281 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.4883 (OUTLIER) cc_final: 0.2940 (mpt-90)
REVERT: A  261 GLU cc_start: 0.6408 (mp0) cc_final: 0.5611 (tt0)
REVERT: A  267 GLU cc_start: 0.7329 (tm-30) cc_final: 0.6998 (tt0)
REVERT: A  274 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8210 (mm)
REVERT: A  275 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8138 (mp0)
REVERT: A  276 GLU cc_start: 0.7756 (tt0) cc_final: 0.7486 (tt0)
REVERT: A  308 VAL cc_start: 0.8441 (p) cc_final: 0.8210 (t)
REVERT: A  418 ARG cc_start: 0.7905 (mmm160) cc_final: 0.7691 (mtm110)
REVERT: A  447 GLN cc_start: 0.7620 (pm20) cc_final: 0.7130 (mt0)
REVERT: A  463 ASP cc_start: 0.7630 (m-30) cc_final: 0.7203 (m-30)
REVERT: A  540 LYS cc_start: 0.8096 (mtmt) cc_final: 0.7832 (mtmt)
REVERT: A  612 MET cc_start: 0.9094 (OUTLIER) cc_final: 0.8581 (ttt)
REVERT: A  623 ARG cc_start: 0.8211 (tpt90) cc_final: 0.7945 (mmm160)
REVERT: A  728 ILE cc_start: 0.6764 (OUTLIER) cc_final: 0.6450 (mt)
REVERT: A  885 TRP cc_start: 0.7450 (t-100) cc_final: 0.7244 (t60)
REVERT: A  892 GLU cc_start: 0.8161 (tp30) cc_final: 0.7828 (tm-30)
REVERT: A  992 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8059 (tp)
REVERT: A 1157 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7287 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8162 (ttt180) cc_final: 0.7321 (tpp80)
  outliers start: 27
  outliers final: 15
  residues processed: 141
  average time/residue: 0.4538
  time to fit residues: 67.6732
Evaluate side-chains
  153 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  381 MET
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  612 MET
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  720 VAL
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  828 ASP
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 30 optimal weight:    0.7980
   chunk 50 optimal weight:    0.8980
   chunk 24 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 39 optimal weight:    0.6980
   chunk 14 optimal weight:    0.2980
   chunk 55 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.179936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.144128 restraints weight = 7921.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.3607 rms_B_bonded: 1.57
r_work: 0.3403 rms_B_bonded: 2.20 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8208
moved from start:          0.2947

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   7788  Z= 0.143
  Angle     :  0.600   7.411  10568  Z= 0.298
  Chirality :  0.043   0.281   1210
  Planarity :  0.004   0.051   1318
  Dihedral  :  5.859  50.234   1118
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 9.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 16.38 %
    Favored  : 81.42 %
  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:  0.51 (0.28), residues: 929
  helix:  1.26 (0.21), residues: 617
  sheet: -1.72 (0.67), residues: 52
  loop : -1.39 (0.38), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 604 
 TYR   0.014   0.001   TYR A 395 
 PHE   0.009   0.001   PHE A 956 
 TRP   0.012   0.001   TRP A1100 
 HIS   0.002   0.001   HIS A 186 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00337 /  0.14 ( 7786)
  covalent geometry    : angle       0.59927 /  0.30 (10562)
  hydrogen bonds       : bond        0.03750 /  2.45 (  441)
  hydrogen bonds       : angle       4.08494 /  2.88 ( 1308)
  link_BETA1-4         : bond        0.00157 /  0.08 (    1)
  link_BETA1-4         : angle       1.48916 /  0.92 (    3)
  link_NAG-ASN         : bond        0.00031 /  0.02 (    1)
  link_NAG-ASN         : angle       0.97798 /  0.60 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 136
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.5072 (OUTLIER) cc_final: 0.3028 (mpt-90)
REVERT: A  261 GLU cc_start: 0.6447 (mp0) cc_final: 0.5584 (tt0)
REVERT: A  267 GLU cc_start: 0.7301 (tm-30) cc_final: 0.6912 (tt0)
REVERT: A  274 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8128 (mm)
REVERT: A  275 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.8069 (mp0)
REVERT: A  276 GLU cc_start: 0.7686 (tt0) cc_final: 0.7424 (tt0)
REVERT: A  308 VAL cc_start: 0.8380 (p) cc_final: 0.8157 (t)
REVERT: A  418 ARG cc_start: 0.7884 (mmm160) cc_final: 0.7668 (mtm110)
REVERT: A  447 GLN cc_start: 0.7503 (pm20) cc_final: 0.7067 (mt0)
REVERT: A  463 ASP cc_start: 0.7617 (m-30) cc_final: 0.7211 (m-30)
REVERT: A  540 LYS cc_start: 0.7917 (mtmt) cc_final: 0.7651 (mtmt)
REVERT: A  612 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8527 (ttt)
REVERT: A  623 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7912 (mmm160)
REVERT: A  892 GLU cc_start: 0.8083 (tp30) cc_final: 0.7656 (tm-30)
REVERT: A  992 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.8007 (tp)
REVERT: A 1090 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7938 (pt0)
REVERT: A 1157 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.7262 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8031 (ttt180) cc_final: 0.7224 (tpp80)
  outliers start: 18
  outliers final: 13
  residues processed: 143
  average time/residue: 0.4655
  time to fit residues: 70.5237
Evaluate side-chains
  150 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 131
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  367 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  506 GLN
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  612 MET
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  828 ASP
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 93 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 79 optimal weight:    0.5980
   chunk 28 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.180242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.142916 restraints weight = 7934.272|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 1.57
r_work: 0.3420 rms_B_bonded: 2.17 restraints_weight: 0.5000
r_work: 0.3282 rms_B_bonded: 3.59 restraints_weight: 0.2500
r_work (final): 0.3282
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   7788  Z= 0.136
  Angle     :  0.605   7.571  10568  Z= 0.300
  Chirality :  0.045   0.507   1210
  Planarity :  0.004   0.050   1318
  Dihedral  :  5.775  50.524   1118
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 9.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 16.87 %
    Favored  : 81.17 %
  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:  0.66 (0.28), residues: 929
  helix:  1.40 (0.21), residues: 611
  sheet: -1.69 (0.67), residues: 52
  loop : -1.34 (0.38), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 604 
 TYR   0.012   0.001   TYR A 395 
 PHE   0.009   0.001   PHE A 956 
 TRP   0.018   0.001   TRP A 885 
 HIS   0.004   0.001   HIS A 116 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 ( 7786)
  covalent geometry    : angle       0.60496 /  0.30 (10562)
  hydrogen bonds       : bond        0.03665 /  2.39 (  441)
  hydrogen bonds       : angle       4.07289 /  2.88 ( 1308)
  link_BETA1-4         : bond        0.00031 /  0.02 (    1)
  link_BETA1-4         : angle       1.43144 /  0.90 (    3)
  link_NAG-ASN         : bond        0.00069 /  0.04 (    1)
  link_NAG-ASN         : angle       0.91147 /  0.55 (    3)

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

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

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1858 Ramachandran restraints generated.
    929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 132
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 ARG cc_start: 0.5037 (OUTLIER) cc_final: 0.2988 (mpt-90)
REVERT: A  261 GLU cc_start: 0.6403 (mp0) cc_final: 0.5556 (tt0)
REVERT: A  267 GLU cc_start: 0.7268 (tm-30) cc_final: 0.6980 (tt0)
REVERT: A  274 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8109 (OUTLIER)
REVERT: A  275 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8055 (mp0)
REVERT: A  276 GLU cc_start: 0.7661 (tt0) cc_final: 0.7403 (tt0)
REVERT: A  308 VAL cc_start: 0.8396 (p) cc_final: 0.8166 (t)
REVERT: A  418 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7654 (mtm110)
REVERT: A  447 GLN cc_start: 0.7508 (pm20) cc_final: 0.7084 (mt0)
REVERT: A  463 ASP cc_start: 0.7609 (m-30) cc_final: 0.7207 (m-30)
REVERT: A  540 LYS cc_start: 0.7937 (mtmt) cc_final: 0.7610 (mtmt)
REVERT: A  623 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7926 (mmm160)
REVERT: A  728 ILE cc_start: 0.6687 (OUTLIER) cc_final: 0.6366 (mt)
REVERT: A  892 GLU cc_start: 0.8150 (tp30) cc_final: 0.7807 (tm-30)
REVERT: A  992 LEU cc_start: 0.8255 (OUTLIER) cc_final: 0.7999 (tp)
REVERT: A 1090 GLU cc_start: 0.8465 (mm-30) cc_final: 0.7949 (pt0)
REVERT: A 1157 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.7254 (mt-10)
REVERT: A 1189 ARG cc_start: 0.8036 (ttt180) cc_final: 0.7263 (tpp80)
  outliers start: 16
  outliers final: 13
  residues processed: 137
  average time/residue: 0.4783
  time to fit residues: 69.1958
Evaluate side-chains
  146 residues out of total 818 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 128
  time to evaluate  : 0.289 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  126 LEU
Chi-restraints excluded: chain A residue  130 ARG
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  274 ILE
Chi-restraints excluded: chain A residue  275 GLU
Chi-restraints excluded: chain A residue  346 VAL
Chi-restraints excluded: chain A residue  382 ILE
Chi-restraints excluded: chain A residue  435 ASP
Chi-restraints excluded: chain A residue  479 MET
Chi-restraints excluded: chain A residue  578 THR
Chi-restraints excluded: chain A residue  620 MET
Chi-restraints excluded: chain A residue  664 GLN
Chi-restraints excluded: chain A residue  728 ILE
Chi-restraints excluded: chain A residue  828 ASP
Chi-restraints excluded: chain A residue  992 LEU
Chi-restraints excluded: chain A residue 1041 ASP
Chi-restraints excluded: chain A residue 1157 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 94
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 77 optimal weight:    2.9990
   chunk 68 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   chunk 10 optimal weight:    7.9990
   overall best weight:    1.3186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 186 HIS
** A 205 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1160 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.177542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.141233 restraints weight = 7890.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.3575 rms_B_bonded: 1.56
r_work: 0.3346 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.3200 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.3200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.3081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059   7788  Z= 0.205
  Angle     :  0.663   7.287  10568  Z= 0.329
  Chirality :  0.045   0.162   1210
  Planarity :  0.005   0.053   1318
  Dihedral  :  5.978  50.483   1118
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 16.14 %
    Favored  : 81.17 %
  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 (0.28), residues: 929
  helix:  1.24 (0.21), residues: 616
  sheet: -1.65 (0.67), residues: 52
  loop : -1.38 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 273 
 TYR   0.016   0.002   TYR A 855 
 PHE   0.015   0.002   PHE A 956 
 TRP   0.024   0.002   TRP A 885 
 HIS   0.004   0.001   HIS A 832 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00490 /  0.20 ( 7786)
  covalent geometry    : angle       0.66221 /  0.33 (10562)
  hydrogen bonds       : bond        0.04159 /  2.73 (  441)
  hydrogen bonds       : angle       4.20278 /  2.97 ( 1308)
  link_BETA1-4         : bond        0.00163 /  0.09 (    1)
  link_BETA1-4         : angle       1.74876 /  1.09 (    3)
  link_NAG-ASN         : bond        0.00300 /  0.16 (    1)
  link_NAG-ASN         : angle       1.44502 /  0.90 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2723.35 seconds
wall clock time: 46 minutes 48.51 seconds (2808.51 seconds total)