Starting phenix.real_space_refine
on Thu Aug  6 02:22:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w7u_65733/08_2026/9w7u_65733.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w7u_65733/08_2026/9w7u_65733.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.83
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9w7u_65733/08_2026/9w7u_65733.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w7u_65733/08_2026/9w7u_65733.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w7u_65733/08_2026/9w7u_65733.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w7u_65733/08_2026/9w7u_65733.map"
  }
  resolution = 3.83
  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=   0.006 sd=   0.046
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: 5
    Type Number    sf(0)   Gaussians
     P     144      5.49       5
     S      22      5.16       5
     C    7549      2.51       5
     N    2263      2.21       5
     O    2771      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 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: 12749
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9657
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1176, 9646
          Classifications: {'peptide': 1176}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 1145}
          Chain breaks: 2
      Conformer: "B"
        Number of residues, atoms: 1176, 9646
          Classifications: {'peptide': 1176}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 1145}
          Chain breaks: 2
          bond proxies already assigned to first conformer: 9803
    Chain: "B"
      Number of atoms: 698
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 34, 698
          Classifications: {'DNA': 34}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 33}
    Chain: "C"
      Number of atoms: 305
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 305
          Classifications: {'DNA': 15}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 14}
    Chain: "D"
      Number of atoms: 2089
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2089
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 48, 'rna3p_pyr': 38}
          Link IDs: {'rna2p': 11, 'rna3p': 86}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AARG A 783 " occ=0.83
      ... (20 atoms not shown)
      pdb=" NH2BARG A 783 " occ=0.17
  Time building chain proxies: 4.13, per 1000 atoms: 0.32
  Number of scatterers: 12749
  At special positions: 0
  Unit cell: (119.658, 103.488, 139.062, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      22     16.00
     P     144     15.00
     O    2771      8.00
     N    2263      7.00
     C    7549      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 849.9 milliseconds
  

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2238

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 8 sheets defined
      56.1% alpha, 10.5% beta
      51 base pairs and 86 stacking pairs defined.
    Time for finding SS restraints: 1.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 4.873A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.534A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 295 through 306
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 346 through 353
      removed outlier: 3.548A  pdb=" N   ASP A 353 " --> pdb=" O   GLU A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 364
    Processing helix  chain 'A' and resid 368 through 382
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.672A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.290A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.726A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 477 through 482
      removed outlier: 3.665A  pdb=" N   VAL A 481 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 483 through 494
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 4.160A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 603 through 609
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 640
      No H-bonds generated for 'chain 'A' and resid 638 through 640'
    Processing helix  chain 'A' and resid 644 through 654
      removed outlier: 3.681A  pdb=" N   ARG A 653 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ARG A 654 " --> pdb=" O   GLN A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 663 through 669
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 751
    Processing helix  chain 'A' and resid 769 through 778
    Processing helix  chain 'A' and resid 779 through 792
      removed outlier: 3.541A  pdb=" N  AARG A 783 " --> pdb=" O   GLU A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 794 through 799
    Processing helix  chain 'A' and resid 802 through 807
    Processing helix  chain 'A' and resid 808 through 817
    Processing helix  chain 'A' and resid 829 through 833
      removed outlier: 3.780A  pdb=" N   LEU A 833 " --> pdb=" O   ILE A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 859 through 866
    Processing helix  chain 'A' and resid 872 through 890
      removed outlier: 4.825A  pdb=" N   ASN A 881 " --> pdb=" O   LYS A 877 " (cutoff:3.500A)
      removed outlier: 5.343A  pdb=" N   TYR A 882 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 893 through 901
    Processing helix  chain 'A' and resid 901 through 906
    Processing helix  chain 'A' and resid 909 through 914
      removed outlier: 3.652A  pdb=" N   ALA A 914 " --> pdb=" O   GLU A 910 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 917 through 925
      removed outlier: 4.189A  pdb=" N   LEU A 921 " --> pdb=" O   ILE A 917 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG A 925 " --> pdb=" O   LEU A 921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 980 through 999
      removed outlier: 4.406A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
      removed outlier: 3.534A  pdb=" N   VAL A1233 " --> pdb=" O   PRO A1229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1262
    Processing helix  chain 'A' and resid 1264 through 1281
      removed outlier: 3.556A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1313
    Processing helix  chain 'A' and resid 1314 through 1316
      No H-bonds generated for 'chain 'A' and resid 1314 through 1316'
    Processing helix  chain 'A' and resid 1339 through 1344
      removed outlier: 3.523A  pdb=" N   VAL A1342 " --> pdb=" O   THR A1339 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 959
      removed outlier: 3.551A  pdb=" N   MET A 763 " --> pdb=" O   LEU A 958 " (cutoff:3.500A)
      removed outlier: 4.335A  pdb=" N   ASN A 758 " --> pdb=" O   TYR A   5 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLU A 762 " --> pdb=" O   LEU A   9 " (cutoff:3.500A)
      removed outlier: 4.949A  pdb=" N   ILE A  11 " --> pdb=" O   GLU A 762 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46
      removed outlier: 10.040A  pdb=" N   GLU A1357 " --> pdb=" O   LYS A  31 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   LYS A  33 " --> pdb=" O   GLU A1357 " (cutoff:3.500A)
      removed outlier: 8.282A  pdb=" N   ARG A1359 " --> pdb=" O   LYS A  33 " (cutoff:3.500A)
      removed outlier: 6.279A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.318A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.562A  pdb=" N   LYS A 528 " --> pdb=" O   SER A 581 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 837 through 840
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.791A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 3.791A  pdb=" N   TYR A1141 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 3.858A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    476 hydrogen bonds defined for protein.
    1384 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      129 hydrogen bonds
      246 hydrogen bond angles
      0 basepair planarities
      51 basepair parallelities
      86 stacking parallelities
  Total time for adding SS restraints: 3.15

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3119
        1.33 -     1.45: 3186
        1.45 -     1.57: 6655
        1.57 -     1.69: 288
        1.69 -     1.81: 42
  Bond restraints: 13290
  Sorted by residual:
  bond pdb=" C3'  DA B   8 "
       pdb=" C2'  DA B   8 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.32e+01
  bond pdb=" C3'  DG B   7 "
       pdb=" C2'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.12e+01
  bond pdb=" C3'  DC B   3 "
       pdb=" C2'  DC B   3 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.03e+01
  bond pdb=" C3'  DA C  11 "
       pdb=" C2'  DA C  11 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 9.67e+00
  bond pdb=" C3'  DT C   9 "
       pdb=" C2'  DT C   9 "
    ideal  model  delta    sigma   weight residual
    1.516  1.540 -0.024 8.00e-03 1.56e+04 8.76e+00
  ... (remaining 13285 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 17401
        1.23 -     2.46: 928
        2.46 -     3.69: 220
        3.69 -     4.93: 16
        4.93 -     6.16: 4
  Bond angle restraints: 18569
  Sorted by residual:
  angle pdb=" O4'  DA B  22 "
        pdb=" C4'  DA B  22 "
        pdb=" C3'  DA B  22 "
      ideal   model   delta    sigma   weight residual
     106.00  102.84    3.16 6.00e-01 2.78e+00 2.78e+01
  angle pdb=" O4'  DG B  23 "
        pdb=" C4'  DG B  23 "
        pdb=" C3'  DG B  23 "
      ideal   model   delta    sigma   weight residual
     106.00  103.12    2.88 6.00e-01 2.78e+00 2.31e+01
  angle pdb=" O4'  DA B  24 "
        pdb=" C4'  DA B  24 "
        pdb=" C3'  DA B  24 "
      ideal   model   delta    sigma   weight residual
     106.00  103.38    2.62 6.00e-01 2.78e+00 1.91e+01
  angle pdb=" N3   DT B  10 "
        pdb=" C4   DT B  10 "
        pdb=" O4   DT B  10 "
      ideal   model   delta    sigma   weight residual
     119.90  122.51   -2.61 6.00e-01 2.78e+00 1.89e+01
  angle pdb=" O4'  DT B  17 "
        pdb=" C4'  DT B  17 "
        pdb=" C3'  DT B  17 "
      ideal   model   delta    sigma   weight residual
     106.00  103.42    2.58 6.00e-01 2.78e+00 1.85e+01
  ... (remaining 18564 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.48: 7638
       31.48 -    62.97: 381
       62.97 -    94.45: 54
       94.45 -   125.94: 0
      125.94 -   157.42: 1
  Dihedral angle restraints: 8074
    sinusoidal: 4615
      harmonic: 3459
  Sorted by residual:
  dihedral pdb=" CA  ARG A 925 "
           pdb=" C   ARG A 925 "
           pdb=" N   GLN A 926 "
           pdb=" CA  GLN A 926 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.85  -47.15     0      5.00e+00 4.00e-02 8.89e+01
  dihedral pdb=" CA  LEU A 625 "
           pdb=" C   LEU A 625 "
           pdb=" N   PHE A 626 "
           pdb=" CA  PHE A 626 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.81  -20.19     0      5.00e+00 4.00e-02 1.63e+01
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   62.58  157.42     1      3.50e+01 8.16e-04 1.51e+01
  ... (remaining 8071 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 1307
       0.030 -    0.059: 457
       0.059 -    0.089: 181
       0.089 -    0.119: 88
       0.119 -    0.149: 96
  Chirality restraints: 2129
  Sorted by residual:
  chirality pdb=" P    DA B   8 "
            pdb=" OP1  DA B   8 "
            pdb=" OP2  DA B   8 "
            pdb=" O5'  DA B   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.48   -0.15 2.00e-01 2.50e+01 5.53e-01
  chirality pdb=" C2'   C D  11 "
            pdb=" C3'   C D  11 "
            pdb=" O2'   C D  11 "
            pdb=" C1'   C D  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.77    0.15 2.00e-01 2.50e+01 5.43e-01
  chirality pdb=" C2'   A D   5 "
            pdb=" C3'   A D   5 "
            pdb=" O2'   A D   5 "
            pdb=" C1'   A D   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.62   -2.76    0.14 2.00e-01 2.50e+01 5.05e-01
  ... (remaining 2126 not shown)

  Planarity restraints: 1839
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U D  97 "    0.020 2.00e-02 2.50e+03   1.04e-02 2.42e+00
        pdb=" N1    U D  97 "   -0.022 2.00e-02 2.50e+03
        pdb=" C2    U D  97 "   -0.001 2.00e-02 2.50e+03
        pdb=" O2    U D  97 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    U D  97 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    U D  97 "    0.003 2.00e-02 2.50e+03
        pdb=" O4    U D  97 "    0.005 2.00e-02 2.50e+03
        pdb=" C5    U D  97 "   -0.001 2.00e-02 2.50e+03
        pdb=" C6    U D  97 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  49 "    0.018 2.00e-02 2.50e+03   8.49e-03 1.98e+00
        pdb=" N9    A D  49 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8    A D  49 "   -0.000 2.00e-02 2.50e+03
        pdb=" N7    A D  49 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    A D  49 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    A D  49 "    0.001 2.00e-02 2.50e+03
        pdb=" N6    A D  49 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    A D  49 "    0.004 2.00e-02 2.50e+03
        pdb=" C2    A D  49 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  49 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  49 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  42 "    0.019 2.00e-02 2.50e+03   8.37e-03 1.93e+00
        pdb=" N9    A D  42 "   -0.019 2.00e-02 2.50e+03
        pdb=" C8    A D  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  42 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" N6    A D  42 "    0.005 2.00e-02 2.50e+03
        pdb=" N1    A D  42 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  42 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  42 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4    A D  42 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 1836 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 2
        2.02 -     2.74: 1187
        2.74 -     3.46: 17770
        3.46 -     4.18: 32376
        4.18 -     4.90: 51869
  Nonbonded interactions: 103204
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A  77 "
            pdb=" O2    U D  59 "
     model   vdw
     1.299 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" C5    C D  18 "
     model   vdw
     1.431 3.420
  nonbonded pdb=" O   ARG A 925 "
            pdb=" N   ILE A 927 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" N2   DG B   9 "
            pdb=" O2   DC C   8 "
     model   vdw
     2.164 2.496
  nonbonded pdb=" OD1 ASN A  14 "
            pdb=" OG  SER A  55 "
     model   vdw
     2.188 3.040
  ... (remaining 103199 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=0.17 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     15.770
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  13290  Z= 0.286
  Angle     :  0.652   6.157  18569  Z= 0.492
  Chirality :  0.047   0.149   2129
  Planarity :  0.004   0.034   1839
  Dihedral  : 16.464 157.423   5836
  Min Nonbonded Distance : 1.299

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  1.79 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.00 %
    Favored  : 99.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  1.61 (0.24), residues: 1173
  helix:  1.83 (0.21), residues: 595
  sheet:  1.15 (0.56), residues: 100
  loop :  0.16 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 780 
 TYR   0.017   0.001   TYR A 882 
 PHE   0.014   0.001   PHE A 462 
 TRP   0.019   0.002   TRP A1126 
 HIS   0.008   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.29 (13290)
  covalent geometry    : angle       0.65160 /  0.49 (18569)
  hydrogen bonds       : bond        0.16378 / 10.49 (  594)
  hydrogen bonds       : angle       6.07783 /  4.41 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 0.410 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  398 LEU cc_start: 0.9320 (tp) cc_final: 0.8963 (tt)
REVERT: A  504 ASN cc_start: 0.9337 (m-40) cc_final: 0.8713 (p0)
REVERT: A  623 LEU cc_start: 0.9553 (mt) cc_final: 0.9156 (tt)
REVERT: A  740 THR cc_start: 0.9600 (m) cc_final: 0.9397 (p)
REVERT: A  815 TYR cc_start: 0.9165 (m-80) cc_final: 0.8613 (m-80)
REVERT: A  895 ARG cc_start: 0.9093 (tpt90) cc_final: 0.8830 (tpm170)
REVERT: A  930 HIS cc_start: 0.8666 (m170) cc_final: 0.8408 (m-70)
REVERT: A  989 LEU cc_start: 0.9753 (mt) cc_final: 0.9426 (tt)
REVERT: A 1182 LEU cc_start: 0.9715 (mt) cc_final: 0.9490 (pp)
REVERT: A 1236 LEU cc_start: 0.9795 (mt) cc_final: 0.9593 (pp)
REVERT: A 1313 PHE cc_start: 0.9213 (m-80) cc_final: 0.8967 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.1307
  time to fit residues: 38.8784
Evaluate side-chains
  127 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.393 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:   20.0000
   chunk 124 optimal weight:   50.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:   30.0000
   chunk 91 optimal weight:    0.3980
   chunk 55 optimal weight:    0.0980
   chunk 129 optimal weight:   40.0000
   overall best weight:    4.8990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 309 ASN
A 712 GLN
A1091 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.051457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2643 r_free = 0.2643 target = 0.035485 restraints weight = 137366.268|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.037301 restraints weight = 57134.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.038488 restraints weight = 34779.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.039266 restraints weight = 25669.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2743 r_free = 0.2743 target = 0.039705 restraints weight = 21185.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13290  Z= 0.206
  Angle     :  0.694  10.953  18569  Z= 0.380
  Chirality :  0.046   0.426   2129
  Planarity :  0.005   0.063   1839
  Dihedral  : 18.508 162.306   3302
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 12.98
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.56 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  8.94 %
    Favored  : 89.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  1.36 (0.24), residues: 1173
  helix:  1.53 (0.21), residues: 612
  sheet:  1.76 (0.59), residues: 83
  loop : -0.00 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A  71 
 TYR   0.018   0.002   TYR A 823 
 PHE   0.027   0.002   PHE A1258 
 TRP   0.018   0.002   TRP A 659 
 HIS   0.008   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00399 /  0.21 (13290)
  covalent geometry    : angle       0.69418 /  0.38 (18569)
  hydrogen bonds       : bond        0.06112 /  4.00 (  594)
  hydrogen bonds       : angle       5.17954 /  3.73 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 128
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9524 (t0) cc_final: 0.9233 (p0)
REVERT: A   71 ARG cc_start: 0.9695 (mtm180) cc_final: 0.9380 (mtp85)
REVERT: A   90 MET cc_start: 0.9420 (tpt) cc_final: 0.9064 (tpt)
REVERT: A  153 LEU cc_start: 0.9885 (mp) cc_final: 0.9625 (pp)
REVERT: A  504 ASN cc_start: 0.9451 (m-40) cc_final: 0.8771 (p0)
REVERT: A  606 PHE cc_start: 0.9296 (t80) cc_final: 0.8700 (t80)
REVERT: A  737 ILE cc_start: 0.9848 (mt) cc_final: 0.9627 (mm)
REVERT: A  930 HIS cc_start: 0.9010 (m170) cc_final: 0.8777 (m90)
REVERT: A  963 VAL cc_start: 0.9699 (t) cc_final: 0.9497 (p)
REVERT: A  989 LEU cc_start: 0.9828 (mt) cc_final: 0.9567 (tt)
REVERT: A 1257 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9245 (pp)
  outliers start: 17
  outliers final: 9
  residues processed: 137
  average time/residue: 0.1170
  time to fit residues: 23.1889
Evaluate side-chains
  116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 106
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1257 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    9.9990
   chunk 43 optimal weight:    8.9990
   chunk 49 optimal weight:    7.9990
   chunk 20 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 66 optimal weight:    5.9990
   chunk 88 optimal weight:   20.0000
   chunk 46 optimal weight:    1.9990
   chunk 98 optimal weight:    0.7980
   chunk 0 optimal weight:   20.0000
   overall best weight:    4.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 698 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.050683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.034729 restraints weight = 170293.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2666 r_free = 0.2666 target = 0.036609 restraints weight = 63693.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.037834 restraints weight = 37709.047|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2716 r_free = 0.2716 target = 0.038626 restraints weight = 27255.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.039146 restraints weight = 22288.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.2697
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2697
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2697 r_free = 0.2697    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (7 function evaluations)
r_final: 0.2697
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.2448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  13290  Z= 0.191
  Angle     :  0.658  11.222  18569  Z= 0.362
  Chirality :  0.044   0.326   2129
  Planarity :  0.004   0.048   1839
  Dihedral  : 18.554 159.852   3302
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 12.94
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.65 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.72 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  1.07 (0.24), residues: 1173
  helix:  1.25 (0.21), residues: 612
  sheet:  1.51 (0.58), residues: 83
  loop : -0.05 (0.27), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A  71 
 TYR   0.016   0.002   TYR A 823 
 PHE   0.025   0.002   PHE A1258 
 TRP   0.016   0.001   TRP A 659 
 HIS   0.016   0.002   HIS A 698 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00375 /  0.19 (13290)
  covalent geometry    : angle       0.65836 /  0.36 (18569)
  hydrogen bonds       : bond        0.05575 /  3.66 (  594)
  hydrogen bonds       : angle       5.09079 /  3.65 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.312 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9553 (t0) cc_final: 0.9161 (p0)
REVERT: A   71 ARG cc_start: 0.9702 (mtm180) cc_final: 0.9416 (mtp85)
REVERT: A   90 MET cc_start: 0.9433 (tpt) cc_final: 0.9039 (tpt)
REVERT: A  153 LEU cc_start: 0.9895 (mp) cc_final: 0.9630 (pp)
REVERT: A  504 ASN cc_start: 0.9451 (m-40) cc_final: 0.8788 (p0)
REVERT: A  930 HIS cc_start: 0.9058 (m170) cc_final: 0.8852 (m90)
REVERT: A  939 MET cc_start: 0.9330 (mmm) cc_final: 0.8968 (mmp)
REVERT: A 1108 GLU cc_start: 0.9310 (mt-10) cc_final: 0.9072 (mt-10)
  outliers start: 19
  outliers final: 13
  residues processed: 117
  average time/residue: 0.1212
  time to fit residues: 20.4929
Evaluate side-chains
  109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1139 VAL
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 43 optimal weight:   10.0000
   chunk 67 optimal weight:   10.0000
   chunk 106 optimal weight:    5.9990
   chunk 55 optimal weight:    9.9990
   chunk 33 optimal weight:   10.0000
   chunk 77 optimal weight:    9.9990
   chunk 81 optimal weight:    6.9990
   chunk 57 optimal weight:    9.9990
   chunk 74 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 26 optimal weight:    0.5980
   overall best weight:    4.9188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1091 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.049809 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2604 r_free = 0.2604 target = 0.033993 restraints weight = 164549.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2648 r_free = 0.2648 target = 0.035785 restraints weight = 64103.883|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2678 r_free = 0.2678 target = 0.036973 restraints weight = 38413.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2698 r_free = 0.2698 target = 0.037769 restraints weight = 28017.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.038274 restraints weight = 22850.632|
|-----------------------------------------------------------------------------|
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2680
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.10   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2680 r_free = 0.2680    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (10 function evaluations)
r_final: 0.2680
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8408
moved from start:          0.2851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  13290  Z= 0.188
  Angle     :  0.668  15.144  18569  Z= 0.361
  Chirality :  0.042   0.254   2129
  Planarity :  0.004   0.045   1839
  Dihedral  : 18.663 159.396   3302
  Min Nonbonded Distance : 2.108

Molprobity Statistics.
  All-atom Clashscore : 12.44
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.82 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 11.57 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.85 (0.24), residues: 1173
  helix:  1.06 (0.21), residues: 617
  sheet:  1.26 (0.57), residues: 83
  loop : -0.11 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  71 
 TYR   0.025   0.002   TYR A 823 
 PHE   0.034   0.002   PHE A1105 
 TRP   0.009   0.001   TRP A 659 
 HIS   0.008   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.19 (13290)
  covalent geometry    : angle       0.66835 /  0.36 (18569)
  hydrogen bonds       : bond        0.05371 /  3.55 (  594)
  hydrogen bonds       : angle       5.01084 /  3.59 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9466 (t0) cc_final: 0.9198 (p0)
REVERT: A   71 ARG cc_start: 0.9703 (mtm180) cc_final: 0.9432 (mtp85)
REVERT: A   90 MET cc_start: 0.9449 (tpt) cc_final: 0.9057 (tpt)
REVERT: A  153 LEU cc_start: 0.9899 (mp) cc_final: 0.9657 (pp)
REVERT: A  504 ASN cc_start: 0.9414 (m-40) cc_final: 0.8790 (p0)
REVERT: A  746 GLU cc_start: 0.9635 (tt0) cc_final: 0.9356 (tt0)
REVERT: A  817 GLN cc_start: 0.7314 (mm-40) cc_final: 0.6964 (mm-40)
REVERT: A  930 HIS cc_start: 0.9048 (m170) cc_final: 0.8729 (m90)
REVERT: A  939 MET cc_start: 0.9400 (mmm) cc_final: 0.9077 (mmm)
REVERT: A 1108 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9015 (mt-10)
REVERT: A 1228 LEU cc_start: 0.9269 (tp) cc_final: 0.8924 (tt)
  outliers start: 16
  outliers final: 14
  residues processed: 114
  average time/residue: 0.1148
  time to fit residues: 19.1526
Evaluate side-chains
  112 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 98
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  751 MET
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 95 optimal weight:   10.0000
   chunk 8 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 5 optimal weight:    8.9990
   chunk 29 optimal weight:    9.9990
   chunk 30 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 57 optimal weight:   20.0000
   chunk 112 optimal weight:    9.9990
   chunk 115 optimal weight:    8.9990
   overall best weight:    7.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 113 HIS
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 556 ASN
** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3006 r_free = 0.3006 target = 0.047469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2567 r_free = 0.2567 target = 0.032828 restraints weight = 114488.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.034274 restraints weight = 53916.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2633 r_free = 0.2633 target = 0.035245 restraints weight = 35134.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.035861 restraints weight = 26927.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 47)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.036258 restraints weight = 22843.805|
|-----------------------------------------------------------------------------|
r_work (final): 0.2635
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2636
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2636 r_free = 0.2636    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (6 function evaluations)
r_final: 0.2636
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8486
moved from start:          0.3443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  13290  Z= 0.269
  Angle     :  0.714  11.147  18569  Z= 0.389
  Chirality :  0.044   0.388   2129
  Planarity :  0.005   0.046   1839
  Dihedral  : 18.878 163.593   3302
  Min Nonbonded Distance : 2.105

Molprobity Statistics.
  All-atom Clashscore : 17.36
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.68 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 11.76 %
    Favored  : 86.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.41 (0.24), residues: 1173
  helix:  0.78 (0.20), residues: 616
  sheet:  0.79 (0.54), residues: 83
  loop : -0.37 (0.27), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  71 
 TYR   0.038   0.002   TYR A 823 
 PHE   0.029   0.002   PHE A1105 
 TRP   0.012   0.002   TRP A 476 
 HIS   0.006   0.002   HIS A1241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00509 /  0.27 (13290)
  covalent geometry    : angle       0.71400 /  0.39 (18569)
  hydrogen bonds       : bond        0.05951 /  4.00 (  594)
  hydrogen bonds       : angle       5.14637 /  3.66 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9572 (t0) cc_final: 0.9343 (t0)
REVERT: A   71 ARG cc_start: 0.9718 (mtm180) cc_final: 0.9269 (mtp85)
REVERT: A   90 MET cc_start: 0.9469 (tpt) cc_final: 0.9093 (tpt)
REVERT: A  153 LEU cc_start: 0.9915 (mp) cc_final: 0.9663 (pp)
REVERT: A  504 ASN cc_start: 0.9418 (m-40) cc_final: 0.8795 (p0)
REVERT: A  746 GLU cc_start: 0.9571 (tt0) cc_final: 0.9273 (tt0)
REVERT: A  939 MET cc_start: 0.9482 (mmm) cc_final: 0.9136 (mmm)
REVERT: A 1108 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8949 (mt-10)
  outliers start: 22
  outliers final: 17
  residues processed: 109
  average time/residue: 0.1109
  time to fit residues: 17.7037
Evaluate side-chains
  107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.346 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  309 ASN
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  737 ILE
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  751 MET
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  858 THR
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue  963 VAL
Chi-restraints excluded: chain A residue  997 LEU
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 15 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 17 optimal weight:    0.3980
   chunk 89 optimal weight:    5.9990
   chunk 85 optimal weight:    9.9990
   chunk 40 optimal weight:    9.9990
   chunk 106 optimal weight:    6.9990
   chunk 90 optimal weight:    6.9990
   chunk 98 optimal weight:    7.9990
   chunk 71 optimal weight:   20.0000
   chunk 53 optimal weight:   10.0000
   overall best weight:    3.8788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 328 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3019 r_free = 0.3019 target = 0.048382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2572 r_free = 0.2572 target = 0.032716 restraints weight = 158047.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.034449 restraints weight = 61380.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2641 r_free = 0.2641 target = 0.035574 restraints weight = 36872.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.2659 r_free = 0.2659 target = 0.036290 restraints weight = 27089.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2672 r_free = 0.2672 target = 0.036770 restraints weight = 22410.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.2639
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2639
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2639 r_free = 0.2639    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (5 function evaluations)
r_final: 0.2639
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8445
moved from start:          0.3561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13290  Z= 0.160
  Angle     :  0.644  15.599  18569  Z= 0.346
  Chirality :  0.041   0.283   2129
  Planarity :  0.004   0.043   1839
  Dihedral  : 18.846 164.217   3302
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.82 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.70 %
    Favored  : 85.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.69 (0.24), residues: 1173
  helix:  0.98 (0.21), residues: 609
  sheet:  0.88 (0.55), residues: 83
  loop : -0.17 (0.28), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  71 
 TYR   0.026   0.002   TYR A 823 
 PHE   0.025   0.001   PHE A1105 
 TRP   0.008   0.002   TRP A 659 
 HIS   0.007   0.001   HIS A 328 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.16 (13290)
  covalent geometry    : angle       0.64378 /  0.35 (18569)
  hydrogen bonds       : bond        0.05113 /  3.39 (  594)
  hydrogen bonds       : angle       4.88206 /  3.49 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 97
  time to evaluate  : 0.290 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9588 (t0) cc_final: 0.9368 (t0)
REVERT: A   71 ARG cc_start: 0.9711 (mtm180) cc_final: 0.9210 (mtp85)
REVERT: A   90 MET cc_start: 0.9445 (tpt) cc_final: 0.9096 (tpt)
REVERT: A  125 GLU cc_start: 0.9615 (OUTLIER) cc_final: 0.8781 (mm-30)
REVERT: A  153 LEU cc_start: 0.9901 (mp) cc_final: 0.9655 (pp)
REVERT: A  504 ASN cc_start: 0.9436 (m-40) cc_final: 0.8857 (p0)
REVERT: A  746 GLU cc_start: 0.9615 (tt0) cc_final: 0.9278 (tt0)
REVERT: A  817 GLN cc_start: 0.6910 (mm-40) cc_final: 0.6688 (mm-40)
REVERT: A  939 MET cc_start: 0.9495 (mmm) cc_final: 0.9193 (mmm)
REVERT: A 1108 GLU cc_start: 0.9244 (mt-10) cc_final: 0.8952 (mt-10)
  outliers start: 14
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1111
  time to fit residues: 17.0624
Evaluate side-chains
  103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 92
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  309 ASN
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue  931 VAL
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 69 optimal weight:    0.9990
   chunk 44 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 17 optimal weight:    6.9990
   chunk 91 optimal weight:   10.0000
   chunk 113 optimal weight:   20.0000
   chunk 2 optimal weight:    1.9990
   chunk 89 optimal weight:    3.9990
   chunk 71 optimal weight:   20.0000
   chunk 122 optimal weight:   30.0000
   chunk 121 optimal weight:   40.0000
   overall best weight:    4.7992

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 723 HIS
A 803 ASN
** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.047799 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.032227 restraints weight = 161566.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.033882 restraints weight = 62540.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.034980 restraints weight = 37512.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.035699 restraints weight = 27582.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.036159 restraints weight = 22695.885|
|-----------------------------------------------------------------------------|
r_work (final): 0.2630
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2631
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2631 r_free = 0.2631    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (9 function evaluations)
r_final: 0.2631
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3775

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13290  Z= 0.183
  Angle     :  0.641  10.006  18569  Z= 0.348
  Chirality :  0.042   0.369   2129
  Planarity :  0.004   0.041   1839
  Dihedral  : 18.873 166.680   3302
  Min Nonbonded Distance : 2.109

Molprobity Statistics.
  All-atom Clashscore : 13.31
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.25 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 12.79 %
    Favored  : 85.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.67 (0.24), residues: 1173
  helix:  0.97 (0.21), residues: 611
  sheet:  0.94 (0.56), residues: 83
  loop : -0.21 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.033   0.002   TYR A 823 
 PHE   0.019   0.002   PHE A 970 
 TRP   0.008   0.002   TRP A 476 
 HIS   0.004   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00344 /  0.18 (13290)
  covalent geometry    : angle       0.64094 /  0.35 (18569)
  hydrogen bonds       : bond        0.05204 /  3.47 (  594)
  hydrogen bonds       : angle       4.86949 /  3.49 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 94
  time to evaluate  : 0.448 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9586 (t0) cc_final: 0.9375 (t0)
REVERT: A   71 ARG cc_start: 0.9718 (mtm180) cc_final: 0.9228 (mtp85)
REVERT: A   90 MET cc_start: 0.9467 (tpt) cc_final: 0.9195 (tpt)
REVERT: A  125 GLU cc_start: 0.9613 (OUTLIER) cc_final: 0.8765 (mm-30)
REVERT: A  153 LEU cc_start: 0.9899 (mp) cc_final: 0.9654 (pp)
REVERT: A  321 MET cc_start: 0.9512 (mmm) cc_final: 0.9109 (mmm)
REVERT: A  504 ASN cc_start: 0.9425 (m-40) cc_final: 0.8865 (p0)
REVERT: A  746 GLU cc_start: 0.9610 (tt0) cc_final: 0.9248 (tt0)
REVERT: A  939 MET cc_start: 0.9508 (mmm) cc_final: 0.9174 (mmm)
REVERT: A 1089 MET cc_start: 0.9153 (mmm) cc_final: 0.8922 (mmm)
REVERT: A 1108 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8952 (mt-10)
REVERT: A 1169 MET cc_start: 0.9486 (mmm) cc_final: 0.9141 (tpp)
REVERT: A 1257 LEU cc_start: 0.9518 (OUTLIER) cc_final: 0.9254 (pp)
  outliers start: 14
  outliers final: 11
  residues processed: 102
  average time/residue: 0.1214
  time to fit residues: 18.1090
Evaluate side-chains
  105 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  309 ASN
Chi-restraints excluded: chain A residue  440 ILE
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  744 VAL
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1257 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 105 optimal weight:    9.9990
   chunk 81 optimal weight:    0.0980
   chunk 119 optimal weight:   30.0000
   chunk 118 optimal weight:   40.0000
   chunk 58 optimal weight:    2.9990
   chunk 94 optimal weight:   10.0000
   chunk 72 optimal weight:    7.9990
   chunk 24 optimal weight:   10.0000
   chunk 61 optimal weight:   10.0000
   chunk 5 optimal weight:    6.9990
   chunk 128 optimal weight:   40.0000
   overall best weight:    5.6188

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.047262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.031901 restraints weight = 151987.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.033492 restraints weight = 61032.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.034612 restraints weight = 37235.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.2638 r_free = 0.2638 target = 0.035311 restraints weight = 27415.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.035740 restraints weight = 22688.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.2619
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2620
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2620 r_free = 0.2620    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2620 r_free = 0.2620    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (19 function evaluations)
r_final: 0.2620
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8477
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13290  Z= 0.200
  Angle     :  0.644  10.105  18569  Z= 0.353
  Chirality :  0.041   0.336   2129
  Planarity :  0.004   0.040   1839
  Dihedral  : 18.911 168.388   3302
  Min Nonbonded Distance : 2.112

Molprobity Statistics.
  All-atom Clashscore : 14.34
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.33 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.45 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.55 (0.24), residues: 1173
  helix:  0.86 (0.21), residues: 615
  sheet:  0.89 (0.55), residues: 83
  loop : -0.26 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 820 
 TYR   0.027   0.002   TYR A 823 
 PHE   0.019   0.001   PHE A 970 
 TRP   0.010   0.002   TRP A 476 
 HIS   0.005   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00377 /  0.20 (13290)
  covalent geometry    : angle       0.64435 /  0.35 (18569)
  hydrogen bonds       : bond        0.05237 /  3.52 (  594)
  hydrogen bonds       : angle       4.90245 /  3.52 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9594 (t0) cc_final: 0.9376 (t0)
REVERT: A   71 ARG cc_start: 0.9704 (mtm180) cc_final: 0.9148 (mtp85)
REVERT: A   90 MET cc_start: 0.9450 (tpt) cc_final: 0.9174 (tpt)
REVERT: A  125 GLU cc_start: 0.9609 (OUTLIER) cc_final: 0.8778 (mm-30)
REVERT: A  153 LEU cc_start: 0.9901 (mp) cc_final: 0.9656 (pp)
REVERT: A  321 MET cc_start: 0.9517 (mmm) cc_final: 0.9107 (mmm)
REVERT: A  504 ASN cc_start: 0.9434 (m-40) cc_final: 0.8889 (p0)
REVERT: A  746 GLU cc_start: 0.9588 (tt0) cc_final: 0.9228 (tt0)
REVERT: A  939 MET cc_start: 0.9535 (mmm) cc_final: 0.9194 (mmm)
REVERT: A 1108 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8941 (mt-10)
REVERT: A 1169 MET cc_start: 0.9429 (mmm) cc_final: 0.9039 (tpp)
  outliers start: 13
  outliers final: 9
  residues processed: 102
  average time/residue: 0.0996
  time to fit residues: 15.1675
Evaluate side-chains
  101 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  309 ASN
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 127 optimal weight:   30.0000
   chunk 104 optimal weight:    0.6980
   chunk 93 optimal weight:    6.9990
   chunk 96 optimal weight:    7.9990
   chunk 8 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 74 optimal weight:   20.0000
   chunk 44 optimal weight:    6.9990
   chunk 82 optimal weight:   20.0000
   chunk 24 optimal weight:    2.9990
   overall best weight:    4.3388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  14 ASN
** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.047305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.032475 restraints weight = 115332.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2603 r_free = 0.2603 target = 0.033945 restraints weight = 52132.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2630 r_free = 0.2630 target = 0.034941 restraints weight = 33357.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.2646 r_free = 0.2646 target = 0.035577 restraints weight = 25333.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.035954 restraints weight = 21360.466|
|-----------------------------------------------------------------------------|
r_work (final): 0.2628
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2629
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2629 r_free = 0.2629    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2629
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8454
moved from start:          0.4165

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  13290  Z= 0.164
  Angle     :  0.626   9.947  18569  Z= 0.340
  Chirality :  0.040   0.274   2129
  Planarity :  0.004   0.040   1839
  Dihedral  : 18.928 171.548   3302
  Min Nonbonded Distance : 2.107

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.33 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 13.45 %
    Favored  : 85.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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 (0.24), residues: 1173
  helix:  0.96 (0.21), residues: 611
  sheet:  0.94 (0.52), residues: 92
  loop : -0.24 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.023   0.001   TYR A 823 
 PHE   0.024   0.001   PHE A 606 
 TRP   0.008   0.002   TRP A 476 
 HIS   0.003   0.001   HIS A 113 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00308 /  0.16 (13290)
  covalent geometry    : angle       0.62639 /  0.34 (18569)
  hydrogen bonds       : bond        0.04979 /  3.33 (  594)
  hydrogen bonds       : angle       4.81203 /  3.44 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 93
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9607 (t0) cc_final: 0.9372 (t0)
REVERT: A   71 ARG cc_start: 0.9707 (mtm180) cc_final: 0.9127 (mtp85)
REVERT: A   90 MET cc_start: 0.9440 (tpt) cc_final: 0.9203 (tpt)
REVERT: A  125 GLU cc_start: 0.9600 (OUTLIER) cc_final: 0.8741 (mm-30)
REVERT: A  153 LEU cc_start: 0.9896 (mp) cc_final: 0.9646 (pp)
REVERT: A  321 MET cc_start: 0.9528 (mmm) cc_final: 0.9114 (mmm)
REVERT: A  504 ASN cc_start: 0.9449 (m-40) cc_final: 0.8921 (p0)
REVERT: A  653 ARG cc_start: 0.9470 (mtt180) cc_final: 0.9073 (mmm-85)
REVERT: A  722 GLU cc_start: 0.9703 (tm-30) cc_final: 0.9467 (pt0)
REVERT: A  746 GLU cc_start: 0.9570 (tt0) cc_final: 0.9220 (tt0)
REVERT: A  939 MET cc_start: 0.9554 (mmm) cc_final: 0.9232 (mmm)
REVERT: A 1108 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8944 (mt-10)
REVERT: A 1169 MET cc_start: 0.9448 (mmm) cc_final: 0.9026 (tpp)
REVERT: A 1257 LEU cc_start: 0.9594 (mm) cc_final: 0.9352 (pp)
  outliers start: 13
  outliers final: 10
  residues processed: 101
  average time/residue: 0.1042
  time to fit residues: 15.5341
Evaluate side-chains
  104 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
Chi-restraints excluded: chain A residue  303 SER
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue 1164 LEU
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 56 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   chunk 34 optimal weight:    0.1980
   chunk 119 optimal weight:   30.0000
   chunk 20 optimal weight:   10.0000
   chunk 127 optimal weight:   30.0000
   chunk 23 optimal weight:    0.8980
   chunk 128 optimal weight:   40.0000
   chunk 14 optimal weight:    3.9990
   chunk 1 optimal weight:   10.0000
   chunk 81 optimal weight:    0.0970
   overall best weight:    0.6382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3026 r_free = 0.3026 target = 0.048428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.032940 restraints weight = 141055.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2629 r_free = 0.2629 target = 0.034623 restraints weight = 56746.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2656 r_free = 0.2656 target = 0.035727 restraints weight = 34489.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2675 r_free = 0.2675 target = 0.036453 restraints weight = 25540.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2685 r_free = 0.2685 target = 0.036862 restraints weight = 21168.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.2658
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2659
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2659 r_free = 0.2659    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2659
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8419
moved from start:          0.4193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  13290  Z= 0.119
  Angle     :  0.627  12.574  18569  Z= 0.332
  Chirality :  0.040   0.278   2129
  Planarity :  0.003   0.040   1839
  Dihedral  : 18.895 172.844   3302
  Min Nonbonded Distance : 2.114

Molprobity Statistics.
  All-atom Clashscore : 10.29
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.91 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  : 14.21 %
    Favored  : 85.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.80 (0.24), residues: 1173
  helix:  1.08 (0.21), residues: 606
  sheet:  1.07 (0.56), residues: 82
  loop : -0.15 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 895 
 TYR   0.021   0.001   TYR A 823 
 PHE   0.019   0.001   PHE A1258 
 TRP   0.010   0.001   TRP A 659 
 HIS   0.003   0.001   HIS A 930 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00222 /  0.12 (13290)
  covalent geometry    : angle       0.62709 /  0.33 (18569)
  hydrogen bonds       : bond        0.04685 /  3.07 (  594)
  hydrogen bonds       : angle       4.63510 /  3.32 ( 1630)

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

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

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2346 Ramachandran restraints generated.
    1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 0.413 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ASP cc_start: 0.9585 (t0) cc_final: 0.9385 (t0)
REVERT: A   71 ARG cc_start: 0.9695 (mtm180) cc_final: 0.9083 (mtp85)
REVERT: A   90 MET cc_start: 0.9461 (tpt) cc_final: 0.9255 (tpt)
REVERT: A  153 LEU cc_start: 0.9884 (mp) cc_final: 0.9644 (pp)
REVERT: A  321 MET cc_start: 0.9512 (mmm) cc_final: 0.9096 (mmm)
REVERT: A  504 ASN cc_start: 0.9452 (m-40) cc_final: 0.8933 (p0)
REVERT: A  653 ARG cc_start: 0.9445 (mtt180) cc_final: 0.9053 (mmm-85)
REVERT: A  722 GLU cc_start: 0.9704 (tm-30) cc_final: 0.9489 (pt0)
REVERT: A  746 GLU cc_start: 0.9574 (tt0) cc_final: 0.9200 (tt0)
REVERT: A  836 TYR cc_start: 0.8768 (m-80) cc_final: 0.8315 (m-80)
REVERT: A  939 MET cc_start: 0.9553 (mmm) cc_final: 0.9254 (mmm)
REVERT: A 1089 MET cc_start: 0.9165 (mmm) cc_final: 0.8849 (mmm)
REVERT: A 1108 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8973 (mt-10)
  outliers start: 7
  outliers final: 6
  residues processed: 103
  average time/residue: 0.1015
  time to fit residues: 15.0851
Evaluate side-chains
  98 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  693 PHE
Chi-restraints excluded: chain A residue  840 HIS
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 22 optimal weight:    8.9990
   chunk 8 optimal weight:    0.3980
   chunk 93 optimal weight:    7.9990
   chunk 62 optimal weight:    0.7980
   chunk 119 optimal weight:   30.0000
   chunk 86 optimal weight:    0.9980
   chunk 73 optimal weight:   20.0000
   chunk 129 optimal weight:   40.0000
   chunk 87 optimal weight:    8.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    2.2382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 817 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 854 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3023 r_free = 0.3023 target = 0.048283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.033074 restraints weight = 118672.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.034625 restraints weight = 53162.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2654 r_free = 0.2654 target = 0.035655 restraints weight = 33740.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2670 r_free = 0.2670 target = 0.036250 restraints weight = 25566.993|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2681 r_free = 0.2681 target = 0.036720 restraints weight = 21772.916|
|-----------------------------------------------------------------------------|
r_work (final): 0.2654
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2654
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2654 r_free = 0.2654    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 5 (11 function evaluations)
r_final: 0.2654
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.4300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13290  Z= 0.126
  Angle     :  0.613  11.697  18569  Z= 0.327
  Chirality :  0.039   0.266   2129
  Planarity :  0.003   0.039   1839
  Dihedral  : 18.881 173.250   3302
  Min Nonbonded Distance : 2.130

Molprobity Statistics.
  All-atom Clashscore : 10.76
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.25 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 14.58 %
    Favored  : 84.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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:  0.82 (0.24), residues: 1173
  helix:  1.10 (0.21), residues: 606
  sheet:  1.07 (0.56), residues: 82
  loop : -0.16 (0.27), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 778 
 TYR   0.018   0.001   TYR A 823 
 PHE   0.029   0.001   PHE A 606 
 TRP   0.012   0.002   TRP A 464 
 HIS   0.003   0.001   HIS A 412 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00235 /  0.13 (13290)
  covalent geometry    : angle       0.61257 /  0.33 (18569)
  hydrogen bonds       : bond        0.04731 /  3.12 (  594)
  hydrogen bonds       : angle       4.60361 /  3.29 ( 1630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2208.29 seconds
wall clock time: 38 minutes 56.15 seconds (2336.15 seconds total)