Starting phenix.real_space_refine
on Wed Feb  4 20:27:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9w7u_65733/02_2026/9w7u_65733.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9w7u_65733/02_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_65733/02_2026/9w7u_65733.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9w7u_65733/02_2026/9w7u_65733.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9w7u_65733/02_2026/9w7u_65733.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9w7u_65733/02_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-2.0-5952/lib/python3.9/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: 4.30, per 1000 atoms: 0.34
  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: 1.22
  Conformation dependent library (CDL) restraints added in 693.8 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: 1.62
  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: 2.66

  Time building geometry restraints manager: 1.62 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=" C   ILE A1110 "
       pdb=" N   LEU A1111 "
    ideal  model  delta    sigma   weight residual
    1.327  1.351 -0.024 1.71e-02 3.42e+03 1.97e+00
  bond pdb=" CA  VAL A  27 "
       pdb=" C   VAL A  27 "
    ideal  model  delta    sigma   weight residual
    1.528  1.518  0.010 8.10e-03 1.52e+04 1.50e+00
  bond pdb=" CB  LYS A 797 "
       pdb=" CG  LYS A 797 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.15e+00
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.453 -0.031 3.00e-02 1.11e+03 1.08e+00
  bond pdb=" CA  LEU A 306 "
       pdb=" C   LEU A 306 "
    ideal  model  delta    sigma   weight residual
    1.520  1.532 -0.012 1.20e-02 6.94e+03 1.05e+00
  ... (remaining 13285 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.23: 17838
        1.23 -     2.46: 622
        2.46 -     3.69: 90
        3.69 -     4.93: 15
        4.93 -     6.16: 4
  Bond angle restraints: 18569
  Sorted by residual:
  angle pdb=" C   PHE A 164 "
        pdb=" N   ARG A 165 "
        pdb=" CA  ARG A 165 "
      ideal   model   delta    sigma   weight residual
     120.60  125.53   -4.93 1.60e+00 3.91e-01 9.50e+00
  angle pdb=" C   GLU A 480 "
        pdb=" N   VAL A 481 "
        pdb=" CA  VAL A 481 "
      ideal   model   delta    sigma   weight residual
     122.66  120.00    2.66 9.70e-01 1.06e+00 7.52e+00
  angle pdb=" CB  LYS A 797 "
        pdb=" CG  LYS A 797 "
        pdb=" CD  LYS A 797 "
      ideal   model   delta    sigma   weight residual
     111.30  117.46   -6.16 2.30e+00 1.89e-01 7.17e+00
  angle pdb=" N   GLN A 926 "
        pdb=" CA  GLN A 926 "
        pdb=" C   GLN A 926 "
      ideal   model   delta    sigma   weight residual
     110.80  116.19   -5.39 2.13e+00 2.20e-01 6.40e+00
  angle pdb=" C   PHE A1327 "
        pdb=" CA  PHE A1327 "
        pdb=" CB  PHE A1327 "
      ideal   model   delta    sigma   weight residual
     110.42  115.42   -5.00 1.99e+00 2.53e-01 6.32e+00
  ... (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 -    0.028: 1415
       0.028 -    0.055: 463
       0.055 -    0.083: 161
       0.083 -    0.111: 78
       0.111 -    0.138: 12
  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       2.35   -2.48   -0.14 2.00e-01 2.50e+01 4.79e-01
  chirality pdb=" CB  ILE A 795 "
            pdb=" CA  ILE A 795 "
            pdb=" CG1 ILE A 795 "
            pdb=" CG2 ILE A 795 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.60e-01
  chirality pdb=" CA  ILE A 956 "
            pdb=" N   ILE A 956 "
            pdb=" C   ILE A 956 "
            pdb=" CB  ILE A 956 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 4.32e-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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     15.300
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  13290  Z= 0.154
  Angle     :  0.548   6.157  18569  Z= 0.319
  Chirality :  0.035   0.138   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
  covalent geometry    : bond        0.00308 (13290)
  covalent geometry    : angle       0.54794 (18569)
  hydrogen bonds       : bond        0.16378 (  594)
  hydrogen bonds       : angle       6.07783 ( 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  : 0.339 
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: 0.8964 (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: 0.9155 (tt)
REVERT: A  740 THR cc_start: 0.9600 (m) cc_final: 0.9394 (p)
REVERT: A  815 TYR cc_start: 0.9165 (m-80) cc_final: 0.8614 (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: 0.8407 (m-70)
REVERT: A  989 LEU cc_start: 0.9753 (mt) cc_final: 0.9427 (tt)
REVERT: A 1182 LEU cc_start: 0.9715 (mt) cc_final: 0.9491 (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: 0.1255
  time to fit residues: 36.9791
Evaluate side-chains
  125 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.0470
   chunk 55 optimal weight:    0.0980
   chunk 129 optimal weight:   10.0000
   overall best weight:    4.8288

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

Flipped N/Q/H residues before XYZ refinement:
A 309 ASN
A 712 GLN
** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.050307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2616 r_free = 0.2616 target = 0.034509 restraints weight = 139615.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2658 r_free = 0.2658 target = 0.036290 restraints weight = 58370.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2686 r_free = 0.2686 target = 0.037431 restraints weight = 35660.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2705 r_free = 0.2705 target = 0.038192 restraints weight = 26394.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2718 r_free = 0.2718 target = 0.038682 restraints weight = 21830.527|
|-----------------------------------------------------------------------------|
r_work (final): 0.2689
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2690
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.17   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2690 r_free = 0.2690    target_work(ls_wunit_k1) = 0.038         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2690
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.2459

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= 0.204
  Angle     :  0.662  11.105  18569  Z= 0.352
  Chirality :  0.040   0.263   2129
  Planarity :  0.004   0.040   1839
  Dihedral  : 18.578 156.354   3302
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 12.48
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.48 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  :  9.31 %
    Favored  : 89.18 %
  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:  1.29 (0.24), residues: 1173
  helix:  1.44 (0.21), residues: 613
  sheet:  1.62 (0.58), residues: 83
  loop :  0.06 (0.27), residues: 477

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.037   0.001   ARG A  63 
 TYR   0.018   0.002   TYR A 128 
 PHE   0.026   0.002   PHE A1258 
 TRP   0.011   0.001   TRP A 659 
 HIS   0.007   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 (13290)
  covalent geometry    : angle       0.66240 (18569)
  hydrogen bonds       : bond        0.05190 (  594)
  hydrogen bonds       : angle       4.99980 ( 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
  142 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.368 
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   71 ARG cc_start: 0.9669 (mtm180) cc_final: 0.9288 (mtp85)
REVERT: A   90 MET cc_start: 0.9439 (tpt) cc_final: 0.8953 (tpt)
REVERT: A  153 LEU cc_start: 0.9862 (mp) cc_final: 0.9618 (pp)
REVERT: A  321 MET cc_start: 0.9382 (mmm) cc_final: 0.8913 (mmm)
REVERT: A  495 MET cc_start: 0.9254 (mpp) cc_final: 0.9036 (mpp)
REVERT: A  504 ASN cc_start: 0.9475 (m-40) cc_final: 0.8831 (p0)
REVERT: A  631 MET cc_start: 0.9218 (ptp) cc_final: 0.8946 (ptt)
REVERT: A  746 GLU cc_start: 0.9672 (tp30) cc_final: 0.9364 (tt0)
REVERT: A  817 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7408 (mm-40)
REVERT: A  895 ARG cc_start: 0.9238 (tpt90) cc_final: 0.9020 (tpm170)
REVERT: A  930 HIS cc_start: 0.9131 (m170) cc_final: 0.8917 (m90)
REVERT: A 1169 MET cc_start: 0.9478 (tmm) cc_final: 0.9239 (tpt)
REVERT: A 1182 LEU cc_start: 0.9954 (mt) cc_final: 0.9653 (pp)
  outliers start: 15
  outliers final: 10
  residues processed: 136
  average time/residue: 0.1078
  time to fit residues: 20.9738
Evaluate side-chains
  110 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 100
  time to evaluate  : 0.275 
-------------------------------------------------------------------------------
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  634 GLU
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  957 THR
Chi-restraints excluded: chain A residue  997 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 109 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 49 optimal weight:    5.9990
   chunk 20 optimal weight:   10.0000
   chunk 99 optimal weight:    8.9990
   chunk 83 optimal weight:   20.0000
   chunk 66 optimal weight:   20.0000
   chunk 88 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0170
   chunk 98 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   overall best weight:    2.2422

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

Flipped N/Q/H residues before XYZ refinement:
** A 328 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 698 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3082 r_free = 0.3082 target = 0.050746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2635 r_free = 0.2635 target = 0.034767 restraints weight = 167251.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2679 r_free = 0.2679 target = 0.036681 restraints weight = 62266.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2709 r_free = 0.2709 target = 0.037918 restraints weight = 36583.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.038733 restraints weight = 26397.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.039286 restraints weight = 21570.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2711
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2711 r_free = 0.2711    target_work(ls_wunit_k1) = 0.039         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2711
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.2991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13290  Z= 0.131
  Angle     :  0.590   8.451  18569  Z= 0.308
  Chirality :  0.037   0.207   2129
  Planarity :  0.004   0.039   1839
  Dihedral  : 18.529 157.748   3302
  Min Nonbonded Distance : 2.097

Molprobity Statistics.
  All-atom Clashscore : 10.38
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.14 %
    Favored  : 97.69 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.10 %
    Favored  : 87.58 %
  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:  1.28 (0.24), residues: 1173
  helix:  1.39 (0.21), residues: 611
  sheet:  1.43 (0.55), residues: 83
  loop :  0.15 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  71 
 TYR   0.019   0.001   TYR A 128 
 PHE   0.022   0.001   PHE A1258 
 TRP   0.012   0.001   TRP A 659 
 HIS   0.006   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (13290)
  covalent geometry    : angle       0.59023 (18569)
  hydrogen bonds       : bond        0.04474 (  594)
  hydrogen bonds       : angle       4.67218 ( 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
  128 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 0.298 
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   71 ARG cc_start: 0.9618 (mtm180) cc_final: 0.9312 (mtp85)
REVERT: A   90 MET cc_start: 0.9446 (tpt) cc_final: 0.9152 (tpt)
REVERT: A  139 ARG cc_start: 0.9415 (mtp180) cc_final: 0.8988 (mtp180)
REVERT: A  153 LEU cc_start: 0.9883 (mp) cc_final: 0.9642 (pp)
REVERT: A  161 MET cc_start: 0.9343 (mmm) cc_final: 0.9090 (mmt)
REVERT: A  321 MET cc_start: 0.9438 (mmm) cc_final: 0.8854 (mmm)
REVERT: A  504 ASN cc_start: 0.9418 (m-40) cc_final: 0.8832 (p0)
REVERT: A  606 PHE cc_start: 0.9401 (t80) cc_final: 0.9090 (t80)
REVERT: A  631 MET cc_start: 0.9235 (ptp) cc_final: 0.8985 (ptt)
REVERT: A  817 GLN cc_start: 0.7280 (mm-40) cc_final: 0.6938 (mm-40)
REVERT: A  822 MET cc_start: 0.8833 (mmm) cc_final: 0.8609 (mmm)
REVERT: A  858 THR cc_start: 0.6073 (m) cc_final: 0.5763 (m)
REVERT: A 1169 MET cc_start: 0.9466 (tmm) cc_final: 0.9224 (tpt)
REVERT: A 1182 LEU cc_start: 0.9942 (mt) cc_final: 0.9628 (pp)
REVERT: A 1226 LEU cc_start: 0.9357 (tp) cc_final: 0.9124 (tt)
REVERT: A 1313 PHE cc_start: 0.9620 (OUTLIER) cc_final: 0.9302 (t80)
  outliers start: 13
  outliers final: 7
  residues processed: 123
  average time/residue: 0.1053
  time to fit residues: 18.5814
Evaluate side-chains
  109 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  863 ASN
Chi-restraints excluded: chain A residue  957 THR
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
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:    8.9990
   chunk 106 optimal weight:    9.9990
   chunk 55 optimal weight:   10.0000
   chunk 33 optimal weight:    3.9990
   chunk 77 optimal weight:   10.0000
   chunk 81 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 74 optimal weight:    7.9990
   chunk 70 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    6.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 113 HIS
A 328 HIS
A 556 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3004 r_free = 0.3004 target = 0.047063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2551 r_free = 0.2551 target = 0.031961 restraints weight = 170621.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2595 r_free = 0.2595 target = 0.033662 restraints weight = 65110.372|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2625 r_free = 0.2625 target = 0.034799 restraints weight = 38816.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2645 r_free = 0.2645 target = 0.035514 restraints weight = 28379.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2657 r_free = 0.2657 target = 0.035981 restraints weight = 23313.186|
|-----------------------------------------------------------------------------|
r_work (final): 0.2627
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2630
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.12   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2630 r_free = 0.2630    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2630
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8606
moved from start:          0.3851

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037  13290  Z= 0.242
  Angle     :  0.664  12.725  18569  Z= 0.352
  Chirality :  0.040   0.234   2129
  Planarity :  0.004   0.041   1839
  Dihedral  : 18.803 156.317   3302
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 15.21
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.82 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 11.85 %
    Favored  : 86.74 %
  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:  0.87 (0.24), residues: 1173
  helix:  1.12 (0.21), residues: 616
  sheet:  0.83 (0.49), residues: 93
  loop : -0.07 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.025   0.002   TYR A1356 
 PHE   0.024   0.002   PHE A 970 
 TRP   0.012   0.002   TRP A 476 
 HIS   0.009   0.002   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00486 (13290)
  covalent geometry    : angle       0.66404 (18569)
  hydrogen bonds       : bond        0.05187 (  594)
  hydrogen bonds       : angle       4.93458 ( 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
  117 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 103
  time to evaluate  : 0.387 
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   60 GLU cc_start: 0.9682 (pm20) cc_final: 0.9363 (pm20)
REVERT: A   71 ARG cc_start: 0.9646 (mtm180) cc_final: 0.9361 (mtp85)
REVERT: A   90 MET cc_start: 0.9457 (tpt) cc_final: 0.9161 (tpt)
REVERT: A  153 LEU cc_start: 0.9903 (mp) cc_final: 0.9681 (pp)
REVERT: A  321 MET cc_start: 0.9498 (mmm) cc_final: 0.8959 (mmm)
REVERT: A  493 GLU cc_start: 0.9634 (mt-10) cc_final: 0.9422 (mt-10)
REVERT: A  504 ASN cc_start: 0.9433 (m-40) cc_final: 0.8888 (p0)
REVERT: A  606 PHE cc_start: 0.9505 (t80) cc_final: 0.9252 (t80)
REVERT: A  631 MET cc_start: 0.9362 (ptp) cc_final: 0.9159 (ptt)
REVERT: A  694 MET cc_start: 0.8531 (tpt) cc_final: 0.8147 (tmm)
REVERT: A  817 GLN cc_start: 0.7386 (mm-40) cc_final: 0.6456 (mm110)
REVERT: A  939 MET cc_start: 0.9409 (mmm) cc_final: 0.9133 (mmm)
REVERT: A 1108 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8941 (mt-10)
REVERT: A 1169 MET cc_start: 0.9547 (tmm) cc_final: 0.9176 (tpp)
REVERT: A 1182 LEU cc_start: 0.9941 (mt) cc_final: 0.9628 (pp)
  outliers start: 14
  outliers final: 11
  residues processed: 110
  average time/residue: 0.1110
  time to fit residues: 17.6356
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  : 0.457 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  744 VAL
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 1313 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 95 optimal weight:    5.9990
   chunk 8 optimal weight:    5.9990
   chunk 38 optimal weight:   20.0000
   chunk 5 optimal weight:   20.0000
   chunk 29 optimal weight:    6.9990
   chunk 30 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 106 optimal weight:   10.0000
   chunk 57 optimal weight:    9.9990
   chunk 112 optimal weight:   10.0000
   chunk 115 optimal weight:    6.9990
   overall best weight:    5.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 920 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 930 HIS ** 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 = 0.2991 r_free = 0.2991 target = 0.046765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.032272 restraints weight = 113213.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.033691 restraints weight = 51353.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.2624 r_free = 0.2624 target = 0.034645 restraints weight = 33138.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.035271 restraints weight = 25353.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.2650 r_free = 0.2650 target = 0.035661 restraints weight = 21430.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.2624
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2624 r_free = 0.2624    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2624 r_free = 0.2624    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8607
moved from start:          0.4381

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  13290  Z= 0.209
  Angle     :  0.624  10.648  18569  Z= 0.330
  Chirality :  0.038   0.178   2129
  Planarity :  0.004   0.036   1839
  Dihedral  : 18.899 160.930   3302
  Min Nonbonded Distance : 2.092

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.25 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.79 %
    Favored  : 85.98 %
  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:  0.79 (0.24), residues: 1173
  helix:  1.06 (0.21), residues: 608
  sheet:  0.77 (0.49), residues: 92
  loop : -0.10 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.017   0.002   TYR A1356 
 PHE   0.018   0.001   PHE A 970 
 TRP   0.012   0.002   TRP A 476 
 HIS   0.006   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (13290)
  covalent geometry    : angle       0.62383 (18569)
  hydrogen bonds       : bond        0.04760 (  594)
  hydrogen bonds       : angle       4.85543 ( 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
  115 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.403 
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   60 GLU cc_start: 0.9711 (pm20) cc_final: 0.9435 (pm20)
REVERT: A   71 ARG cc_start: 0.9659 (mtm180) cc_final: 0.9383 (mtp85)
REVERT: A   90 MET cc_start: 0.9449 (tpt) cc_final: 0.9228 (tpt)
REVERT: A  125 GLU cc_start: 0.9624 (OUTLIER) cc_final: 0.8874 (mm-30)
REVERT: A  153 LEU cc_start: 0.9908 (mp) cc_final: 0.9671 (pp)
REVERT: A  321 MET cc_start: 0.9501 (mmm) cc_final: 0.9018 (mmm)
REVERT: A  493 GLU cc_start: 0.9649 (mt-10) cc_final: 0.9439 (mt-10)
REVERT: A  504 ASN cc_start: 0.9376 (m-40) cc_final: 0.8916 (p0)
REVERT: A  606 PHE cc_start: 0.9540 (t80) cc_final: 0.9245 (t80)
REVERT: A  631 MET cc_start: 0.9385 (ptp) cc_final: 0.9118 (ptt)
REVERT: A  694 MET cc_start: 0.8475 (tpt) cc_final: 0.8025 (tmm)
REVERT: A  836 TYR cc_start: 0.8745 (m-80) cc_final: 0.8060 (m-80)
REVERT: A  858 THR cc_start: 0.6622 (m) cc_final: 0.6393 (m)
REVERT: A  939 MET cc_start: 0.9495 (mmm) cc_final: 0.9281 (mmm)
REVERT: A 1108 GLU cc_start: 0.9205 (mt-10) cc_final: 0.8928 (mt-10)
REVERT: A 1169 MET cc_start: 0.9584 (tmm) cc_final: 0.9221 (tpp)
REVERT: A 1213 MET cc_start: 0.9360 (tpp) cc_final: 0.9103 (tpp)
REVERT: A 1313 PHE cc_start: 0.9659 (OUTLIER) cc_final: 0.9424 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 110
  average time/residue: 0.1043
  time to fit residues: 17.0265
Evaluate side-chains
  107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  294 LYS
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  748 VAL
Chi-restraints excluded: chain A residue  751 MET
Chi-restraints excluded: chain A residue  863 ASN
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 15 optimal weight:   10.0000
   chunk 50 optimal weight:    9.9990
   chunk 17 optimal weight:    0.3980
   chunk 89 optimal weight:    5.9990
   chunk 85 optimal weight:    8.9990
   chunk 40 optimal weight:    5.9990
   chunk 106 optimal weight:    2.9990
   chunk 90 optimal weight:   10.0000
   chunk 98 optimal weight:    8.9990
   chunk 71 optimal weight:    0.1980
   chunk 53 optimal weight:   10.0000
   overall best weight:    3.1186

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

Flipped N/Q/H residues before XYZ refinement:
A 803 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.047338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.2559 r_free = 0.2559 target = 0.032095 restraints weight = 160700.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2602 r_free = 0.2602 target = 0.033742 restraints weight = 59641.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.2631 r_free = 0.2631 target = 0.034842 restraints weight = 35619.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2651 r_free = 0.2651 target = 0.035557 restraints weight = 26089.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2663 r_free = 0.2663 target = 0.036029 restraints weight = 21454.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.2641
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2648
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2648 r_free = 0.2648    target_work(ls_wunit_k1) = 0.036         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2648
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  13290  Z= 0.143
  Angle     :  0.593  10.226  18569  Z= 0.308
  Chirality :  0.037   0.181   2129
  Planarity :  0.003   0.034   1839
  Dihedral  : 18.821 164.566   3302
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  2.82 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 12.89 %
    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:  0.89 (0.24), residues: 1173
  helix:  1.14 (0.21), residues: 609
  sheet:  0.97 (0.55), residues: 82
  loop : -0.07 (0.28), residues: 482

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  71 
 TYR   0.013   0.001   TYR A 882 
 PHE   0.015   0.001   PHE A1258 
 TRP   0.008   0.001   TRP A1126 
 HIS   0.005   0.001   HIS A 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (13290)
  covalent geometry    : angle       0.59297 (18569)
  hydrogen bonds       : bond        0.04380 (  594)
  hydrogen bonds       : angle       4.65627 ( 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
  113 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.293 
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   60 GLU cc_start: 0.9720 (pm20) cc_final: 0.9441 (pm20)
REVERT: A   71 ARG cc_start: 0.9631 (mtm180) cc_final: 0.9408 (mtp85)
REVERT: A  125 GLU cc_start: 0.9609 (OUTLIER) cc_final: 0.8793 (mm-30)
REVERT: A  153 LEU cc_start: 0.9904 (mp) cc_final: 0.9662 (pp)
REVERT: A  321 MET cc_start: 0.9528 (mmm) cc_final: 0.9015 (mmm)
REVERT: A  493 GLU cc_start: 0.9648 (mt-10) cc_final: 0.9418 (mt-10)
REVERT: A  504 ASN cc_start: 0.9391 (m-40) cc_final: 0.8931 (p0)
REVERT: A  631 MET cc_start: 0.9384 (ptp) cc_final: 0.9109 (ptt)
REVERT: A  836 TYR cc_start: 0.8721 (m-80) cc_final: 0.8207 (m-80)
REVERT: A 1089 MET cc_start: 0.9254 (mmp) cc_final: 0.9045 (mmp)
REVERT: A 1108 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8890 (mt-10)
REVERT: A 1169 MET cc_start: 0.9601 (tmm) cc_final: 0.9210 (tpp)
REVERT: A 1213 MET cc_start: 0.9390 (tpp) cc_final: 0.9124 (tpp)
REVERT: A 1313 PHE cc_start: 0.9657 (OUTLIER) cc_final: 0.9436 (t80)
  outliers start: 12
  outliers final: 9
  residues processed: 107
  average time/residue: 0.1069
  time to fit residues: 16.6806
Evaluate side-chains
  106 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
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  751 MET
Chi-restraints excluded: chain A residue  863 ASN
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 69 optimal weight:    6.9990
   chunk 44 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   chunk 17 optimal weight:    8.9990
   chunk 91 optimal weight:    6.9990
   chunk 113 optimal weight:    8.9990
   chunk 2 optimal weight:    8.9990
   chunk 89 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   chunk 122 optimal weight:   10.0000
   chunk 121 optimal weight:   20.0000
   overall best weight:    6.1988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2964 r_free = 0.2964 target = 0.045370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2508 r_free = 0.2508 target = 0.030510 restraints weight = 170344.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2552 r_free = 0.2552 target = 0.032047 restraints weight = 63735.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2582 r_free = 0.2582 target = 0.033093 restraints weight = 38237.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.033746 restraints weight = 28157.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2612 r_free = 0.2612 target = 0.034183 restraints weight = 23333.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.2589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2589 r_free = 0.2589    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.5104

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= 0.239
  Angle     :  0.666   9.682  18569  Z= 0.351
  Chirality :  0.039   0.178   2129
  Planarity :  0.004   0.050   1839
  Dihedral  : 18.987 166.918   3302
  Min Nonbonded Distance : 2.093

Molprobity Statistics.
  All-atom Clashscore : 16.08
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.33 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 13.64 %
    Favored  : 84.85 %
  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:  0.48 (0.24), residues: 1173
  helix:  0.80 (0.21), residues: 616
  sheet:  0.53 (0.50), residues: 92
  loop : -0.23 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  71 
 TYR   0.023   0.002   TYR A1356 
 PHE   0.023   0.002   PHE A1258 
 TRP   0.012   0.002   TRP A 476 
 HIS   0.004   0.001   HIS A1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 (13290)
  covalent geometry    : angle       0.66618 (18569)
  hydrogen bonds       : bond        0.05111 (  594)
  hydrogen bonds       : angle       4.92026 ( 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: 15
    poor density    : 93
  time to evaluate  : 0.477 
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: A   71 ARG cc_start: 0.9665 (mtm180) cc_final: 0.9336 (mtp85)
REVERT: A  125 GLU cc_start: 0.9566 (OUTLIER) cc_final: 0.8779 (mm-30)
REVERT: A  153 LEU cc_start: 0.9917 (mp) cc_final: 0.9674 (pp)
REVERT: A  321 MET cc_start: 0.9519 (mmm) cc_final: 0.9027 (mmm)
REVERT: A  504 ASN cc_start: 0.9381 (m-40) cc_final: 0.9005 (p0)
REVERT: A  631 MET cc_start: 0.9390 (ptp) cc_final: 0.9180 (ptt)
REVERT: A  836 TYR cc_start: 0.8812 (m-80) cc_final: 0.8259 (m-80)
REVERT: A 1108 GLU cc_start: 0.9180 (mt-10) cc_final: 0.8874 (mt-10)
REVERT: A 1169 MET cc_start: 0.9603 (tmm) cc_final: 0.9180 (tpp)
REVERT: A 1213 MET cc_start: 0.9436 (tpp) cc_final: 0.9172 (tpp)
REVERT: A 1313 PHE cc_start: 0.9692 (OUTLIER) cc_final: 0.9411 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 102
  average time/residue: 0.1231
  time to fit residues: 17.9993
Evaluate side-chains
  103 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 89
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
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  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 1238 LEU
Chi-restraints excluded: chain A residue 1313 PHE
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 105 optimal weight:    8.9990
   chunk 81 optimal weight:    0.9980
   chunk 119 optimal weight:   10.0000
   chunk 118 optimal weight:   10.0000
   chunk 58 optimal weight:    7.9990
   chunk 94 optimal weight:    5.9990
   chunk 72 optimal weight:   30.0000
   chunk 24 optimal weight:    3.9990
   chunk 61 optimal weight:    9.9990
   chunk 5 optimal weight:    7.9990
   chunk 128 optimal weight:   20.0000
   overall best weight:    5.3988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.045558 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2524 r_free = 0.2524 target = 0.030890 restraints weight = 155747.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2568 r_free = 0.2568 target = 0.032405 restraints weight = 60318.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2598 r_free = 0.2598 target = 0.033426 restraints weight = 36627.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.2614 r_free = 0.2614 target = 0.034008 restraints weight = 27103.026|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.2627 r_free = 0.2627 target = 0.034475 restraints weight = 22851.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.2601
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2601
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2601 r_free = 0.2601    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2601
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
moved from start:          0.5448

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  13290  Z= 0.204
  Angle     :  0.635   9.043  18569  Z= 0.335
  Chirality :  0.039   0.171   2129
  Planarity :  0.004   0.042   1839
  Dihedral  : 19.078 174.048   3302
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 14.30
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.16 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 13.83 %
    Favored  : 84.57 %
  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:  0.50 (0.24), residues: 1173
  helix:  0.88 (0.21), residues: 606
  sheet:  0.36 (0.49), residues: 94
  loop : -0.27 (0.28), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 655 
 TYR   0.013   0.001   TYR A1356 
 PHE   0.019   0.001   PHE A1258 
 TRP   0.012   0.002   TRP A 476 
 HIS   0.003   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (13290)
  covalent geometry    : angle       0.63483 (18569)
  hydrogen bonds       : bond        0.04687 (  594)
  hydrogen bonds       : angle       4.88294 ( 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
  107 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 91
  time to evaluate  : 0.454 
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   71 ARG cc_start: 0.9662 (mtm180) cc_final: 0.9328 (mtp85)
REVERT: A  125 GLU cc_start: 0.9605 (OUTLIER) cc_final: 0.8848 (mm-30)
REVERT: A  153 LEU cc_start: 0.9930 (mp) cc_final: 0.9676 (pp)
REVERT: A  321 MET cc_start: 0.9517 (mmm) cc_final: 0.9018 (mmm)
REVERT: A  504 ASN cc_start: 0.9378 (m-40) cc_final: 0.9059 (p0)
REVERT: A  797 LYS cc_start: 0.9798 (tppt) cc_final: 0.9593 (pttt)
REVERT: A  836 TYR cc_start: 0.8899 (m-80) cc_final: 0.8410 (m-80)
REVERT: A  879 MET cc_start: 0.8572 (mmm) cc_final: 0.8308 (mmm)
REVERT: A  939 MET cc_start: 0.9662 (mmm) cc_final: 0.9374 (mmm)
REVERT: A 1108 GLU cc_start: 0.9236 (mt-10) cc_final: 0.8934 (mt-10)
REVERT: A 1213 MET cc_start: 0.9437 (tpp) cc_final: 0.9168 (tpp)
REVERT: A 1313 PHE cc_start: 0.9683 (OUTLIER) cc_final: 0.9446 (t80)
  outliers start: 16
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1240
  time to fit residues: 18.2536
Evaluate side-chains
  102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 86
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
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  957 THR
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 127 optimal weight:   10.0000
   chunk 104 optimal weight:    9.9990
   chunk 93 optimal weight:    7.9990
   chunk 96 optimal weight:    9.9990
   chunk 8 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 0 optimal weight:   20.0000
   chunk 74 optimal weight:   30.0000
   chunk 44 optimal weight:    0.8980
   chunk 82 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9990
   overall best weight:    3.1788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.046028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2555 r_free = 0.2555 target = 0.031732 restraints weight = 114809.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.2596 r_free = 0.2596 target = 0.033166 restraints weight = 51175.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2621 r_free = 0.2621 target = 0.034113 restraints weight = 32609.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2637 r_free = 0.2637 target = 0.034720 restraints weight = 24832.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2647 r_free = 0.2647 target = 0.035064 restraints weight = 21014.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.2618
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2623
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2623 r_free = 0.2623    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2623
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8635
moved from start:          0.5558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  13290  Z= 0.145
  Angle     :  0.611   9.724  18569  Z= 0.316
  Chirality :  0.037   0.181   2129
  Planarity :  0.004   0.042   1839
  Dihedral  : 18.999 175.227   3302
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 11.99
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.25 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.21 %
    Favored  : 84.67 %
  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:  0.70 (0.24), residues: 1173
  helix:  1.03 (0.21), residues: 609
  sheet:  0.47 (0.50), residues: 94
  loop : -0.16 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 895 
 TYR   0.012   0.001   TYR A 882 
 PHE   0.019   0.001   PHE A1258 
 TRP   0.008   0.001   TRP A1126 
 HIS   0.002   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (13290)
  covalent geometry    : angle       0.61073 (18569)
  hydrogen bonds       : bond        0.04387 (  594)
  hydrogen bonds       : angle       4.62599 ( 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
  102 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 91
  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   60 GLU cc_start: 0.9720 (pm20) cc_final: 0.9387 (pm20)
REVERT: A   71 ARG cc_start: 0.9650 (mtm180) cc_final: 0.9319 (mtp85)
REVERT: A  125 GLU cc_start: 0.9602 (OUTLIER) cc_final: 0.8841 (mm-30)
REVERT: A  153 LEU cc_start: 0.9926 (mp) cc_final: 0.9695 (pp)
REVERT: A  321 MET cc_start: 0.9506 (mmm) cc_final: 0.8997 (mmm)
REVERT: A  383 MET cc_start: 0.8390 (mmp) cc_final: 0.8118 (mmp)
REVERT: A  504 ASN cc_start: 0.9368 (m-40) cc_final: 0.9078 (p0)
REVERT: A  836 TYR cc_start: 0.8966 (m-80) cc_final: 0.8555 (m-80)
REVERT: A  879 MET cc_start: 0.8622 (mmm) cc_final: 0.8357 (mmm)
REVERT: A  939 MET cc_start: 0.9673 (mmm) cc_final: 0.9380 (mmm)
REVERT: A 1169 MET cc_start: 0.9639 (tmm) cc_final: 0.9227 (tpp)
REVERT: A 1213 MET cc_start: 0.9411 (tpp) cc_final: 0.9141 (tpp)
  outliers start: 11
  outliers final: 8
  residues processed: 97
  average time/residue: 0.1244
  time to fit residues: 17.7702
Evaluate side-chains
  95 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue  125 GLU
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  748 VAL
Chi-restraints excluded: chain A residue  863 ASN
Chi-restraints excluded: chain A residue 1238 LEU
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 56 optimal weight:    6.9990
   chunk 59 optimal weight:   20.0000
   chunk 34 optimal weight:    3.9990
   chunk 119 optimal weight:   10.0000
   chunk 20 optimal weight:    8.9990
   chunk 127 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 128 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 81 optimal weight:    0.9980
   overall best weight:    3.9988

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.045683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2539 r_free = 0.2539 target = 0.031070 restraints weight = 148820.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2581 r_free = 0.2581 target = 0.032592 restraints weight = 58378.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2610 r_free = 0.2610 target = 0.033625 restraints weight = 35585.712|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2628 r_free = 0.2628 target = 0.034279 restraints weight = 26320.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2640 r_free = 0.2640 target = 0.034706 restraints weight = 21909.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.2614
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2615 r_free = 0.2615    target_work(ls_wunit_k1) = 0.034         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.5689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  13290  Z= 0.168
  Angle     :  0.636  10.622  18569  Z= 0.333
  Chirality :  0.038   0.206   2129
  Planarity :  0.004   0.041   1839
  Dihedral  : 19.026 175.166   3302
  Min Nonbonded Distance : 2.099

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.50 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 14.30 %
    Favored  : 84.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.24), residues: 1173
  helix:  1.00 (0.21), residues: 609
  sheet:  0.43 (0.50), residues: 94
  loop : -0.17 (0.28), residues: 470

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  71 
 TYR   0.013   0.001   TYR A1356 
 PHE   0.018   0.001   PHE A1258 
 TRP   0.009   0.001   TRP A 476 
 HIS   0.007   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00344 (13290)
  covalent geometry    : angle       0.63617 (18569)
  hydrogen bonds       : bond        0.04596 (  594)
  hydrogen bonds       : angle       4.63302 ( 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
  99 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.447 
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   60 GLU cc_start: 0.9721 (pm20) cc_final: 0.9395 (pm20)
REVERT: A   71 ARG cc_start: 0.9658 (mtm180) cc_final: 0.9326 (mtp85)
REVERT: A  125 GLU cc_start: 0.9591 (OUTLIER) cc_final: 0.8823 (mm-30)
REVERT: A  153 LEU cc_start: 0.9930 (mp) cc_final: 0.9699 (pp)
REVERT: A  321 MET cc_start: 0.9504 (mmm) cc_final: 0.9005 (mmm)
REVERT: A  383 MET cc_start: 0.8354 (mmp) cc_final: 0.8109 (mmp)
REVERT: A  504 ASN cc_start: 0.9364 (m-40) cc_final: 0.9080 (p0)
REVERT: A  694 MET cc_start: 0.8231 (tpt) cc_final: 0.7282 (tmm)
REVERT: A  836 TYR cc_start: 0.9030 (m-80) cc_final: 0.8631 (m-80)
REVERT: A  879 MET cc_start: 0.8667 (mmm) cc_final: 0.8431 (mmm)
REVERT: A  939 MET cc_start: 0.9679 (mmm) cc_final: 0.9373 (mmm)
REVERT: A 1169 MET cc_start: 0.9623 (tmm) cc_final: 0.9176 (tpp)
REVERT: A 1213 MET cc_start: 0.9412 (tpp) cc_final: 0.9145 (tpp)
REVERT: A 1313 PHE cc_start: 0.9590 (OUTLIER) cc_final: 0.9377 (t80)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 0.1251
  time to fit residues: 17.4420
Evaluate side-chains
  97 residues out of total 1061 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 VAL
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue  125 GLU
Chi-restraints excluded: chain A residue  134 THR
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  748 VAL
Chi-restraints excluded: chain A residue  863 ASN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 108 optimal weight:   10.0000
   chunk 22 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0270
   chunk 62 optimal weight:    2.9990
   chunk 119 optimal weight:   10.0000
   chunk 86 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 129 optimal weight:   20.0000
   chunk 87 optimal weight:    4.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    2.6044

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

Flipped N/Q/H residues before XYZ refinement:
A  77 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3001 r_free = 0.3001 target = 0.046421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.031999 restraints weight = 117150.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2606 r_free = 0.2606 target = 0.033422 restraints weight = 51193.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.2632 r_free = 0.2632 target = 0.034384 restraints weight = 32574.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2649 r_free = 0.2649 target = 0.034999 restraints weight = 24808.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.2660 r_free = 0.2660 target = 0.035418 restraints weight = 20940.165|
|-----------------------------------------------------------------------------|
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2637
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2637 r_free = 0.2637    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2637 r_free = 0.2637    target_work(ls_wunit_k1) = 0.035         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
r_final: 0.2637
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.5790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13290  Z= 0.130
  Angle     :  0.621  11.295  18569  Z= 0.320
  Chirality :  0.037   0.200   2129
  Planarity :  0.003   0.049   1839
  Dihedral  : 19.009 177.183   3302
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.25 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.58 %
    Favored  : 84.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.25), residues: 1173
  helix:  1.10 (0.21), residues: 608
  sheet:  0.55 (0.51), residues: 94
  loop : -0.11 (0.29), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  71 
 TYR   0.012   0.001   TYR A 882 
 PHE   0.018   0.001   PHE A1258 
 TRP   0.008   0.001   TRP A1126 
 HIS   0.008   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 (13290)
  covalent geometry    : angle       0.62127 (18569)
  hydrogen bonds       : bond        0.04343 (  594)
  hydrogen bonds       : angle       4.51741 ( 1630)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2247.11 seconds
wall clock time: 39 minutes 34.65 seconds (2374.65 seconds total)