Starting phenix.real_space_refine
on Fri Jul  3 07:20:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9xd6_66756/07_2026/9xd6_66756.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9xd6_66756/07_2026/9xd6_66756.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.74
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9xd6_66756/07_2026/9xd6_66756.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9xd6_66756/07_2026/9xd6_66756.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9xd6_66756/07_2026/9xd6_66756.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9xd6_66756/07_2026/9xd6_66756.cif"
  }
  resolution = 2.74
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.027
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P       7      5.49       5
     S      87      5.16       5
     C    7757      2.51       5
     N    2114      2.21       5
     O    2329      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12295
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 12144
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1520, 12144
          Classifications: {'peptide': 1520}
          Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 1472}
          Chain breaks: 11
    Chain: "C"
      Number of atoms: 150
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 150
          Classifications: {'RNA': 7}
          Modifications used: {'rna2p_pur': 2, 'rna2p_pyr': 3, 'rna3p_pur': 2}
          Link IDs: {'rna2p': 4, 'rna3p': 2}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    816  SG  CYS A1028      36.694  92.760  35.115  1.00 77.36           S
  ATOM    835  SG  CYS A1031      39.577  95.081  34.766  1.00 87.01           S
  ATOM   1078  SG  CYS A1062      36.683  96.467  36.602  1.00 82.68           S
  ATOM   1098  SG  CYS A1065      38.475  93.899  38.321  1.00 75.54           S

  Time building chain proxies: 2.92, per 1000 atoms: 0.24
  Number of scatterers: 12295
  At special positions: 0
  Unit cell: (109.5, 111.252, 126.144, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      87     16.00
     P       7     15.00
     O    2329      8.00
     N    2114      7.00
     C    7757      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: 1.00
  Conformation dependent library (CDL) restraints added in 510.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A4001 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1062 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1031 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1065 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1028 "
      Number of angles added : 6


  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2912

  Finding SS restraints...
    Secondary structure from input PDB file:
      73 helices and 10 sheets defined
      60.7% alpha, 6.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'A' and resid 930 through 947
      removed outlier: 5.012A  pdb=" N   GLU A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      removed outlier: 5.305A  pdb=" N   HIS A 944 " --> pdb=" O   LYS A 940 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ASN A 947 " --> pdb=" O   GLU A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 955 through 967
    Processing helix  chain 'A' and resid 973 through 987
    Processing helix  chain 'A' and resid 987 through 997
    Processing helix  chain 'A' and resid 1008 through 1024
    Processing helix  chain 'A' and resid 1028 through 1041
    Processing helix  chain 'A' and resid 1044 through 1057
      removed outlier: 3.763A  pdb=" N   GLN A1057 " --> pdb=" O   ALA A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1061
    Processing helix  chain 'A' and resid 1076 through 1081
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.572A  pdb=" N   VAL A1088 " --> pdb=" O   ILE A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1104 through 1111
      removed outlier: 3.564A  pdb=" N   ARG A1111 " --> pdb=" O   ASP A1107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1139
    Processing helix  chain 'A' and resid 1175 through 1186
    Processing helix  chain 'A' and resid 1196 through 1208
      removed outlier: 3.595A  pdb=" N   LYS A1208 " --> pdb=" O   SER A1204 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1234
      removed outlier: 4.019A  pdb=" N   LEU A1225 " --> pdb=" O   PRO A1221 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   VAL A1234 " --> pdb=" O   PHE A1230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1278
      removed outlier: 3.644A  pdb=" N   VAL A1276 " --> pdb=" O   LYS A1272 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   GLN A1277 " --> pdb=" O   CYS A1273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1296
      removed outlier: 3.796A  pdb=" N   ILE A1295 " --> pdb=" O   GLN A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1309
      removed outlier: 3.518A  pdb=" N   ALA A1301 " --> pdb=" O   PHE A1297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1315 through 1328
    Processing helix  chain 'A' and resid 1330 through 1350
    Processing helix  chain 'A' and resid 1401 through 1426
      removed outlier: 4.505A  pdb=" N   LEU A1412 " --> pdb=" O   GLY A1408 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   TYR A1413 " --> pdb=" O   SER A1409 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   GLN A1424 " --> pdb=" O   ILE A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1429 through 1435
      removed outlier: 3.707A  pdb=" N   ASN A1433 " --> pdb=" O   GLU A1430 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   VAL A1435 " --> pdb=" O   ILE A1432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1463
    Processing helix  chain 'A' and resid 1465 through 1481
      removed outlier: 3.552A  pdb=" N   SER A1469 " --> pdb=" O   ARG A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1487 through 1505
    Processing helix  chain 'A' and resid 1507 through 1514
      removed outlier: 4.059A  pdb=" N   ASN A1514 " --> pdb=" O   ASN A1510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1524
    Processing helix  chain 'A' and resid 1524 through 1531
    Processing helix  chain 'A' and resid 1532 through 1534
      No H-bonds generated for 'chain 'A' and resid 1532 through 1534'
    Processing helix  chain 'A' and resid 1543 through 1547
    Processing helix  chain 'A' and resid 1552 through 1572
      removed outlier: 4.734A  pdb=" N   ASP A1572 " --> pdb=" O   CYS A1568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 3.588A  pdb=" N   LYS A1578 " --> pdb=" O   GLU A1574 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   LYS A1581 " --> pdb=" O   VAL A1577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1611
    Processing helix  chain 'A' and resid 1612 through 1616
      removed outlier: 3.720A  pdb=" N   HIS A1615 " --> pdb=" O   TYR A1612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1631 through 1651
      removed outlier: 3.663A  pdb=" N   THR A1635 " --> pdb=" O   VAL A1631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1758 through 1773
    Processing helix  chain 'A' and resid 1780 through 1792
    Processing helix  chain 'A' and resid 1793 through 1795
      No H-bonds generated for 'chain 'A' and resid 1793 through 1795'
    Processing helix  chain 'A' and resid 1796 through 1805
    Processing helix  chain 'A' and resid 2295 through 2305
    Processing helix  chain 'A' and resid 2317 through 2335
      removed outlier: 4.076A  pdb=" N   LEU A2322 " --> pdb=" O   LYS A2318 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   ASN A2323 " --> pdb=" O   GLU A2319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2367 through 2379
      removed outlier: 3.626A  pdb=" N   PHE A2371 " --> pdb=" O   CYS A2367 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   GLY A2373 " --> pdb=" O   SER A2369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2382 through 2396
      removed outlier: 3.985A  pdb=" N   PHE A2388 " --> pdb=" O   ASP A2384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2447 through 2457
    Processing helix  chain 'A' and resid 2478 through 2503
      removed outlier: 3.979A  pdb=" N   VAL A2489 " --> pdb=" O   SER A2485 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   LEU A2490 " --> pdb=" O   LEU A2486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2559
      removed outlier: 5.053A  pdb=" N   TRP A2542 " --> pdb=" O   ASP A2538 " (cutoff:3.500A)
      removed outlier: 5.322A  pdb=" N   LYS A2543 " --> pdb=" O   GLU A2539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2589 through 2594
      removed outlier: 3.783A  pdb=" N   MET A2594 " --> pdb=" O   ILE A2591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2595 through 2600
      removed outlier: 3.510A  pdb=" N   ILE A2599 " --> pdb=" O   PHE A2595 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ASN A2600 " --> pdb=" O   THR A2596 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 2595 through 2600'
    Processing helix  chain 'A' and resid 2605 through 2623
    Processing helix  chain 'A' and resid 2626 through 2645
      removed outlier: 3.713A  pdb=" N   PHE A2641 " --> pdb=" O   ARG A2637 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   HIS A2644 " --> pdb=" O   ILE A2640 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   VAL A2645 " --> pdb=" O   PHE A2641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2645 through 2652
    Processing helix  chain 'A' and resid 2652 through 2657
    Processing helix  chain 'A' and resid 2658 through 2659
      No H-bonds generated for 'chain 'A' and resid 2658 through 2659'
    Processing helix  chain 'A' and resid 2660 through 2664
      removed outlier: 3.729A  pdb=" N   GLY A2664 " --> pdb=" O   SER A2661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2671 through 2675
      removed outlier: 3.874A  pdb=" N   VAL A2675 " --> pdb=" O   SER A2672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2678 through 2697
    Processing helix  chain 'A' and resid 2753 through 2764
    Processing helix  chain 'A' and resid 2771 through 2783
    Processing helix  chain 'A' and resid 2801 through 2805
    Processing helix  chain 'A' and resid 2806 through 2816
    Processing helix  chain 'A' and resid 2818 through 2836
    Processing helix  chain 'A' and resid 2899 through 2910
      removed outlier: 3.615A  pdb=" N   LEU A2910 " --> pdb=" O   LYS A2906 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2945 through 2953
    Processing helix  chain 'A' and resid 2994 through 3003
    Processing helix  chain 'A' and resid 3043 through 3060
    Processing helix  chain 'A' and resid 3062 through 3073
    Processing helix  chain 'A' and resid 3093 through 3100
      removed outlier: 4.196A  pdb=" N   GLU A3097 " --> pdb=" O   PHE A3093 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLN A3098 " --> pdb=" O   SER A3094 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3104 through 3112
      removed outlier: 3.522A  pdb=" N   LEU A3112 " --> pdb=" O   VAL A3108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3116 through 3122
      removed outlier: 3.515A  pdb=" N   VAL A3121 " --> pdb=" O   ALA A3117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3131 through 3141
    Processing helix  chain 'A' and resid 3142 through 3163
      removed outlier: 3.553A  pdb=" N   PHE A3146 " --> pdb=" O   PHE A3142 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP A3158 " --> pdb=" O   ASP A3154 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   GLU A3160 " --> pdb=" O   SER A3156 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   LYS A3161 " --> pdb=" O   SER A3157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3166 through 3185
      removed outlier: 4.189A  pdb=" N   GLN A3170 " --> pdb=" O   PRO A3166 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A3171 " --> pdb=" O   ASP A3167 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ASN A3176 " --> pdb=" O   ALA A3172 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   MET A3184 " --> pdb=" O   LEU A3180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3208 through 3217
      removed outlier: 3.557A  pdb=" N   LEU A3212 " --> pdb=" O   THR A3208 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   VAL A3213 " --> pdb=" O   VAL A3209 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   ILE A3217 " --> pdb=" O   VAL A3213 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 971 through 972
      removed outlier: 6.584A  pdb=" N   VAL A 971 " --> pdb=" O   TYR A1755 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1003 through 1004
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1151 through 1152
      removed outlier: 3.687A  pdb=" N   CYS A1143 " --> pdb=" O   VAL A1220 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1357 through 1362
      removed outlier: 4.304A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU A1386 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      removed outlier: 5.438A  pdb=" N   GLY A1396 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2507 through 2511
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2574 through 2576
      removed outlier: 4.763A  pdb=" N   PHE A2580 " --> pdb=" O   THR A2587 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2956 through 2959
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3004 through 3009
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3078 through 3081
      removed outlier: 3.873A  pdb=" N   SER A3078 " --> pdb=" O   ARG A3224 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3086 through 3089

    650 hydrogen bonds defined for protein.
    1881 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.53

  Time building geometry restraints manager: 1.33 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: 3416
        1.33 -     1.45: 2021
        1.45 -     1.57: 6939
        1.57 -     1.69: 13
        1.69 -     1.81: 126
  Bond restraints: 12515
  Sorted by residual:
  bond pdb=" N9    A C   7 "
       pdb=" C4    A C   7 "
    ideal  model  delta    sigma   weight residual
    1.374  1.384 -0.010 6.00e-03 2.78e+04 2.78e+00
  bond pdb=" C   VAL A1288 "
       pdb=" N   PRO A1289 "
    ideal  model  delta    sigma   weight residual
    1.334  1.370 -0.036 2.34e-02 1.83e+03 2.39e+00
  bond pdb=" C8    G C   6 "
       pdb=" N7    G C   6 "
    ideal  model  delta    sigma   weight residual
    1.305  1.296  0.009 6.00e-03 2.78e+04 2.37e+00
  bond pdb=" N7    G C   6 "
       pdb=" C5    G C   6 "
    ideal  model  delta    sigma   weight residual
    1.388  1.381  0.007 6.00e-03 2.78e+04 1.42e+00
  bond pdb=" CB  GLN A1785 "
       pdb=" CG  GLN A1785 "
    ideal  model  delta    sigma   weight residual
    1.520  1.485  0.035 3.00e-02 1.11e+03 1.39e+00
  ... (remaining 12510 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.48: 16300
        1.48 -     2.97: 490
        2.97 -     4.45: 80
        4.45 -     5.94: 27
        5.94 -     7.42: 8
  Bond angle restraints: 16905
  Sorted by residual:
  angle pdb=" C1'   U C   5 "
        pdb=" N1    U C   5 "
        pdb=" C2    U C   5 "
      ideal   model   delta    sigma   weight residual
     117.70  123.00   -5.30 1.20e+00 6.94e-01 1.95e+01
  angle pdb=" C1'   G C   6 "
        pdb=" N9    G C   6 "
        pdb=" C4    G C   6 "
      ideal   model   delta    sigma   weight residual
     126.50  131.66   -5.16 1.30e+00 5.92e-01 1.58e+01
  angle pdb=" O2    U C   5 "
        pdb=" C2    U C   5 "
        pdb=" N3    U C   5 "
      ideal   model   delta    sigma   weight residual
     122.20  119.42    2.78 7.00e-01 2.04e+00 1.57e+01
  angle pdb=" N1    U C   5 "
        pdb=" C2    U C   5 "
        pdb=" O2    U C   5 "
      ideal   model   delta    sigma   weight residual
     122.80  125.30   -2.50 7.00e-01 2.04e+00 1.28e+01
  angle pdb=" C1'   G C   6 "
        pdb=" N9    G C   6 "
        pdb=" C8    G C   6 "
      ideal   model   delta    sigma   weight residual
     127.00  122.53    4.47 1.30e+00 5.92e-01 1.18e+01
  ... (remaining 16900 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.63: 7594
       33.63 -    67.26: 84
       67.26 -   100.90: 7
      100.90 -   134.53: 0
      134.53 -   168.16: 1
  Dihedral angle restraints: 7686
    sinusoidal: 3220
      harmonic: 4466
  Sorted by residual:
  dihedral pdb=" O4'   U C   5 "
           pdb=" C1'   U C   5 "
           pdb=" N1    U C   5 "
           pdb=" C2    U C   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   40.16 -168.16     1      1.70e+01 3.46e-03 6.57e+01
  dihedral pdb=" O4'   A C   7 "
           pdb=" C1'   A C   7 "
           pdb=" N9    A C   7 "
           pdb=" C4    A C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.00  151.50  -83.50     1      1.70e+01 3.46e-03 2.95e+01
  dihedral pdb=" CA  PHE A1505 "
           pdb=" C   PHE A1505 "
           pdb=" N   LEU A1506 "
           pdb=" CA  LEU A1506 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.68  -20.32     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 7683 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 1200
       0.036 -    0.072: 577
       0.072 -    0.107: 130
       0.107 -    0.143: 41
       0.143 -    0.179: 5
  Chirality restraints: 1953
  Sorted by residual:
  chirality pdb=" CB  ILE A2365 "
            pdb=" CA  ILE A2365 "
            pdb=" CG1 ILE A2365 "
            pdb=" CG2 ILE A2365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.82   -0.18 2.00e-01 2.50e+01 8.02e-01
  chirality pdb=" CA  ILE A2365 "
            pdb=" N   ILE A2365 "
            pdb=" C   ILE A2365 "
            pdb=" CB  ILE A2365 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.47e-01
  chirality pdb=" CB  THR A2587 "
            pdb=" CA  THR A2587 "
            pdb=" OG1 THR A2587 "
            pdb=" CG2 THR A2587 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.40    0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 1950 not shown)

  Planarity restraints: 2114
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A2503 "   -0.040 5.00e-02 4.00e+02   6.01e-02 5.78e+00
        pdb=" N   PRO A2504 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A2504 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A2504 "   -0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A2324 "    0.010 2.00e-02 2.50e+03   1.97e-02 3.87e+00
        pdb=" C   VAL A2324 "   -0.034 2.00e-02 2.50e+03
        pdb=" O   VAL A2324 "    0.013 2.00e-02 2.50e+03
        pdb=" N   GLY A2325 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A2326 "   -0.010 2.00e-02 2.50e+03   1.96e-02 3.83e+00
        pdb=" C   LEU A2326 "    0.034 2.00e-02 2.50e+03
        pdb=" O   LEU A2326 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ASP A2327 "   -0.011 2.00e-02 2.50e+03
  ... (remaining 2111 not shown)

  Histogram of nonbonded interaction distances:
        2.56 -     3.03: 6953
        3.03 -     3.50: 12716
        3.50 -     3.96: 20335
        3.96 -     4.43: 24576
        4.43 -     4.90: 37716
  Nonbonded interactions: 102296
  Sorted by model distance:
  nonbonded pdb=" O5'   A C   7 "
            pdb=" O4'   A C   7 "
     model   vdw
     2.561 2.432
  nonbonded pdb=" N1    G C   8 "
            pdb=" C4    G C   8 "
     model   vdw
     2.602 2.672
  nonbonded pdb=" N1    G C   6 "
            pdb=" C4    G C   6 "
     model   vdw
     2.605 2.672
  nonbonded pdb=" N   ILE A1616 "
            pdb=" N   TYR A1617 "
     model   vdw
     2.614 2.560
  nonbonded pdb=" N   SER A2515 "
            pdb=" O   SER A2515 "
     model   vdw
     2.619 2.496
  ... (remaining 102291 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.420
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.410
  Find NCS groups from input model:        0.160
  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:             0.010
  Load rotamer database and sin/cos tables:6.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8305
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  12519  Z= 0.176
  Angle     :  0.645   9.027  16911  Z= 0.351
  Chirality :  0.043   0.179   1953
  Planarity :  0.005   0.062   2114
  Dihedral  : 12.059 168.162   4774
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.07 %
    Favored  : 99.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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: -0.71 (0.20), residues: 1496
  helix:  0.07 (0.17), residues: 851
  sheet:  0.23 (0.64), residues: 65
  loop : -1.27 (0.24), residues: 580

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A2585 
 TYR   0.013   0.002   TYR A2949 
 PHE   0.026   0.002   PHE A3049 
 TRP   0.018   0.002   TRP A2542 
 HIS   0.011   0.001   HIS A3177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.18 (12515)
  covalent geometry    : angle       0.63547 /  0.35 (16905)
  hydrogen bonds       : bond        0.13813 /  9.44 (  650)
  hydrogen bonds       : angle       5.94780 /  4.18 ( 1881)
  metal coordination   : bond        0.00925 /  0.41 (    4)
  metal coordination   : angle       5.95130 /  3.57 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  431 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 431
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
REVERT: A  936 GLU cc_start: 0.7580 (mt-10) cc_final: 0.7187 (mt-10)
REVERT: A  947 ASN cc_start: 0.8129 (m-40) cc_final: 0.7922 (m-40)
REVERT: A  968 GLU cc_start: 0.7825 (mp0) cc_final: 0.7246 (mp0)
REVERT: A 1021 GLU cc_start: 0.7941 (tp30) cc_final: 0.7711 (tp30)
REVERT: A 1024 LYS cc_start: 0.8297 (tttt) cc_final: 0.7999 (ttpp)
REVERT: A 1037 LYS cc_start: 0.8536 (tttt) cc_final: 0.8215 (ttmm)
REVERT: A 1073 SER cc_start: 0.8316 (t) cc_final: 0.8113 (p)
REVERT: A 1079 CYS cc_start: 0.7978 (t) cc_final: 0.7728 (m)
REVERT: A 1086 GLU cc_start: 0.7717 (mp0) cc_final: 0.7365 (mp0)
REVERT: A 1094 LYS cc_start: 0.8045 (mttt) cc_final: 0.7810 (mttm)
REVERT: A 1117 LYS cc_start: 0.8372 (tmtt) cc_final: 0.8144 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7352 (tp30) cc_final: 0.6982 (tp30)
REVERT: A 1179 LYS cc_start: 0.7687 (tttt) cc_final: 0.7456 (tttp)
REVERT: A 1181 ASP cc_start: 0.7501 (t0) cc_final: 0.7200 (t0)
REVERT: A 1209 ASN cc_start: 0.7730 (m-40) cc_final: 0.6326 (m110)
REVERT: A 1282 LYS cc_start: 0.8827 (mttt) cc_final: 0.8604 (mttm)
REVERT: A 1348 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7758 (ttp80)
REVERT: A 1361 VAL cc_start: 0.8631 (t) cc_final: 0.8312 (p)
REVERT: A 1373 LYS cc_start: 0.8362 (tttt) cc_final: 0.8159 (tttm)
REVERT: A 1380 GLU cc_start: 0.7797 (tt0) cc_final: 0.7425 (mt-10)
REVERT: A 1535 ARG cc_start: 0.8501 (mtp180) cc_final: 0.8214 (mmm160)
REVERT: A 1578 LYS cc_start: 0.8520 (tttt) cc_final: 0.8299 (ttpp)
REVERT: A 1608 ILE cc_start: 0.8143 (mt) cc_final: 0.7934 (mm)
REVERT: A 1643 GLU cc_start: 0.8129 (mm-30) cc_final: 0.7722 (mp0)
REVERT: A 1647 MET cc_start: 0.8188 (ttp) cc_final: 0.7925 (ttp)
REVERT: A 1648 ASN cc_start: 0.8097 (m-40) cc_final: 0.7869 (m-40)
REVERT: A 1758 ASN cc_start: 0.8169 (t0) cc_final: 0.7939 (t0)
REVERT: A 1764 LYS cc_start: 0.8245 (mtpp) cc_final: 0.7980 (mtmm)
REVERT: A 1792 MET cc_start: 0.8593 (mmm) cc_final: 0.8285 (mmm)
REVERT: A 2301 ARG cc_start: 0.8422 (ttm110) cc_final: 0.7937 (ttm110)
REVERT: A 2309 ASP cc_start: 0.7651 (p0) cc_final: 0.7362 (p0)
REVERT: A 2318 LYS cc_start: 0.7860 (ttmt) cc_final: 0.6906 (ttpp)
REVERT: A 2358 ASP cc_start: 0.6512 (m-30) cc_final: 0.6303 (m-30)
REVERT: A 2468 TYR cc_start: 0.8425 (t80) cc_final: 0.8103 (t80)
REVERT: A 2471 MET cc_start: 0.6818 (mmp) cc_final: 0.6566 (mmt)
REVERT: A 2511 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7752 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7926 (ttpp)
REVERT: A 2547 ARG cc_start: 0.8720 (mtp85) cc_final: 0.8453 (mmm160)
REVERT: A 2579 GLU cc_start: 0.7426 (mp0) cc_final: 0.6722 (mp0)
REVERT: A 2811 ASP cc_start: 0.8069 (t0) cc_final: 0.7857 (t0)
REVERT: A 2902 LEU cc_start: 0.8173 (mt) cc_final: 0.7891 (mt)
REVERT: A 2905 LYS cc_start: 0.8300 (mttt) cc_final: 0.7768 (mttt)
REVERT: A 2966 LEU cc_start: 0.8559 (mt) cc_final: 0.8291 (mt)
REVERT: A 3004 CYS cc_start: 0.8159 (m) cc_final: 0.7938 (m)
REVERT: A 3014 VAL cc_start: 0.8944 (t) cc_final: 0.8642 (p)
REVERT: A 3089 LYS cc_start: 0.8437 (ttmt) cc_final: 0.8163 (ttmt)
REVERT: A 3107 VAL cc_start: 0.8371 (t) cc_final: 0.8137 (p)
REVERT: A 3150 LYS cc_start: 0.7828 (mmpt) cc_final: 0.7576 (mmpt)
REVERT: A 3203 MET cc_start: 0.6091 (mpp) cc_final: 0.5565 (mpp)
  outliers start: 0
  outliers final: 1
  residues processed: 431
  average time/residue: 0.6170
  time to fit residues: 286.8324
Evaluate side-chains
  345 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 344
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 3062 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    0.3980
   chunk 130 optimal weight:    0.9980
   chunk 124 optimal weight:    0.9990
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 149 optimal weight:    0.8980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A 987 ASN
A1100 ASN
A1127 ASN
A1277 GLN
A1325 ASN
A1354 ASN
A1401 ASN
A1556 ASN
A2302 ASN
A2345 ASN
A2536 GLN
A2643 ASN
** A2695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2777 ASN
A2857 ASN
A3186 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.124287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.110212 restraints weight = 16765.308|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 1.67
r_work: 0.3373 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 3.75 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1610

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12519  Z= 0.176
  Angle     :  0.587   7.810  16911  Z= 0.298
  Chirality :  0.042   0.173   1953
  Planarity :  0.005   0.052   2114
  Dihedral  :  8.946 169.995   1742
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 10.87 %
    Favored  : 87.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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: -0.08 (0.21), residues: 1496
  helix:  0.80 (0.17), residues: 852
  sheet:  0.35 (0.59), residues: 75
  loop : -1.40 (0.24), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A1212 
 TYR   0.012   0.001   TYR A2836 
 PHE   0.034   0.002   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00410 /  0.18 (12515)
  covalent geometry    : angle       0.58098 /  0.30 (16905)
  hydrogen bonds       : bond        0.04352 /  2.85 (  650)
  hydrogen bonds       : angle       4.55981 /  3.24 ( 1881)
  metal coordination   : bond        0.00733 /  0.34 (    4)
  metal coordination   : angle       4.64789 /  2.85 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  375 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 347
  time to evaluate  : 0.520 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7461 (t0) cc_final: 0.7250 (t0)
REVERT: A  968 GLU cc_start: 0.7869 (mp0) cc_final: 0.7283 (mp0)
REVERT: A 1024 LYS cc_start: 0.8348 (tttt) cc_final: 0.8081 (mtpp)
REVERT: A 1037 LYS cc_start: 0.8414 (tttt) cc_final: 0.8171 (mtpp)
REVERT: A 1073 SER cc_start: 0.8411 (t) cc_final: 0.8136 (p)
REVERT: A 1079 CYS cc_start: 0.7992 (t) cc_final: 0.7626 (m)
REVERT: A 1094 LYS cc_start: 0.8148 (mttt) cc_final: 0.7873 (mttm)
REVERT: A 1117 LYS cc_start: 0.8378 (tmtt) cc_final: 0.8135 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7352 (tp30) cc_final: 0.6936 (tp30)
REVERT: A 1181 ASP cc_start: 0.7532 (t0) cc_final: 0.7258 (t0)
REVERT: A 1350 CYS cc_start: 0.7812 (m) cc_final: 0.7452 (t)
REVERT: A 1373 LYS cc_start: 0.8454 (tttt) cc_final: 0.8248 (tttm)
REVERT: A 1380 GLU cc_start: 0.7930 (tt0) cc_final: 0.7565 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7787 (ttmm)
REVERT: A 1535 ARG cc_start: 0.8474 (mtp180) cc_final: 0.8162 (mmm-85)
REVERT: A 1578 LYS cc_start: 0.8555 (tttt) cc_final: 0.8329 (ttpp)
REVERT: A 1608 ILE cc_start: 0.8223 (mt) cc_final: 0.8014 (mm)
REVERT: A 1638 ARG cc_start: 0.7739 (ttm110) cc_final: 0.7408 (ttm-80)
REVERT: A 1643 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7727 (mp0)
REVERT: A 1647 MET cc_start: 0.8228 (ttp) cc_final: 0.7927 (ttp)
REVERT: A 1648 ASN cc_start: 0.8130 (m-40) cc_final: 0.7910 (m-40)
REVERT: A 1792 MET cc_start: 0.8601 (mmm) cc_final: 0.8283 (mmm)
REVERT: A 2301 ARG cc_start: 0.8445 (ttm110) cc_final: 0.8023 (ttm110)
REVERT: A 2309 ASP cc_start: 0.7512 (p0) cc_final: 0.7306 (p0)
REVERT: A 2318 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7142 (ttpp)
REVERT: A 2468 TYR cc_start: 0.8366 (t80) cc_final: 0.8117 (t80)
REVERT: A 2511 GLU cc_start: 0.7937 (mm-30) cc_final: 0.7733 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7965 (ttpp)
REVERT: A 2560 GLN cc_start: 0.8060 (OUTLIER) cc_final: 0.7835 (mm-40)
REVERT: A 2579 GLU cc_start: 0.7411 (mp0) cc_final: 0.6955 (mp0)
REVERT: A 2902 LEU cc_start: 0.8170 (mt) cc_final: 0.7933 (mt)
REVERT: A 2905 LYS cc_start: 0.8287 (mttt) cc_final: 0.7782 (mttt)
REVERT: A 2966 LEU cc_start: 0.8581 (mt) cc_final: 0.8326 (mt)
REVERT: A 3014 VAL cc_start: 0.8903 (t) cc_final: 0.8645 (p)
REVERT: A 3016 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7853 (mt-10)
REVERT: A 3107 VAL cc_start: 0.8550 (t) cc_final: 0.8346 (p)
REVERT: A 3150 LYS cc_start: 0.7843 (mmpt) cc_final: 0.7607 (mmpt)
REVERT: A 3203 MET cc_start: 0.6121 (mpp) cc_final: 0.5574 (mpp)
  outliers start: 28
  outliers final: 9
  residues processed: 360
  average time/residue: 0.6489
  time to fit residues: 250.7617
Evaluate side-chains
  336 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 326
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  945 ILE
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1133 LYS
Chi-restraints excluded: chain A residue 1137 SER
Chi-restraints excluded: chain A residue 1298 LYS
Chi-restraints excluded: chain A residue 1356 SER
Chi-restraints excluded: chain A residue 1454 SER
Chi-restraints excluded: chain A residue 2560 GLN
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 3135 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 105 optimal weight:    0.9980
   chunk 73 optimal weight:    0.7980
   chunk 81 optimal weight:    0.6980
   chunk 4 optimal weight:    0.7980
   chunk 121 optimal weight:    0.6980
   chunk 75 optimal weight:    0.0270
   chunk 38 optimal weight:    0.1980
   chunk 66 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 125 optimal weight:    5.9990
   chunk 78 optimal weight:    0.5980
   overall best weight:    0.4438

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A1100 ASN
A1354 ASN
A1401 ASN
A1424 GLN
A2345 ASN
A2536 GLN
** A2695 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2777 ASN
A3064 ASN
A3186 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.124786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.110655 restraints weight = 16983.018|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.68
r_work: 0.3373 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8346
moved from start:          0.1901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12519  Z= 0.124
  Angle     :  0.528   6.840  16911  Z= 0.268
  Chirality :  0.039   0.160   1953
  Planarity :  0.004   0.045   2114
  Dihedral  :  8.749 171.221   1740
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 13.88 %
    Favored  : 83.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  0.28 (0.21), residues: 1496
  helix:  1.14 (0.18), residues: 855
  sheet:  0.44 (0.61), residues: 75
  loop : -1.34 (0.25), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1638 
 TYR   0.009   0.001   TYR A2836 
 PHE   0.031   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.12 (12515)
  covalent geometry    : angle       0.52288 /  0.27 (16905)
  hydrogen bonds       : bond        0.03720 /  2.46 (  650)
  hydrogen bonds       : angle       4.24090 /  3.03 ( 1881)
  metal coordination   : bond        0.00372 /  0.17 (    4)
  metal coordination   : angle       3.98189 /  2.43 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 335
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7454 (t0) cc_final: 0.7222 (t0)
REVERT: A  968 GLU cc_start: 0.7829 (mp0) cc_final: 0.7273 (mp0)
REVERT: A  999 LYS cc_start: 0.8616 (ptmm) cc_final: 0.8320 (pttp)
REVERT: A 1021 GLU cc_start: 0.8001 (tp30) cc_final: 0.7668 (tp30)
REVERT: A 1024 LYS cc_start: 0.8332 (tttt) cc_final: 0.8122 (ttpp)
REVERT: A 1037 LYS cc_start: 0.8413 (tttt) cc_final: 0.8169 (mtpp)
REVERT: A 1079 CYS cc_start: 0.7985 (t) cc_final: 0.7643 (m)
REVERT: A 1086 GLU cc_start: 0.7708 (mp0) cc_final: 0.7396 (mp0)
REVERT: A 1094 LYS cc_start: 0.8150 (mttt) cc_final: 0.7899 (mttm)
REVERT: A 1104 THR cc_start: 0.7891 (OUTLIER) cc_final: 0.7630 (t)
REVERT: A 1117 LYS cc_start: 0.8357 (tmtt) cc_final: 0.8121 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7301 (tp30) cc_final: 0.6892 (tp30)
REVERT: A 1134 LEU cc_start: 0.8518 (mt) cc_final: 0.8184 (mp)
REVERT: A 1181 ASP cc_start: 0.7513 (t0) cc_final: 0.7251 (t0)
REVERT: A 1350 CYS cc_start: 0.7616 (m) cc_final: 0.7315 (t)
REVERT: A 1380 GLU cc_start: 0.7808 (tt0) cc_final: 0.7461 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8039 (ttmm) cc_final: 0.7735 (ttmm)
REVERT: A 1535 ARG cc_start: 0.8479 (mtp180) cc_final: 0.8224 (mmm160)
REVERT: A 1541 GLU cc_start: 0.7481 (mm-30) cc_final: 0.7171 (mm-30)
REVERT: A 1578 LYS cc_start: 0.8533 (tttt) cc_final: 0.8318 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7281 (ttm-80)
REVERT: A 1640 MET cc_start: 0.8160 (ttp) cc_final: 0.7885 (ttm)
REVERT: A 1647 MET cc_start: 0.8217 (ttp) cc_final: 0.7952 (ttp)
REVERT: A 1648 ASN cc_start: 0.8148 (m-40) cc_final: 0.7926 (m-40)
REVERT: A 1792 MET cc_start: 0.8579 (mmm) cc_final: 0.8204 (mmm)
REVERT: A 2299 PHE cc_start: 0.8379 (t80) cc_final: 0.8134 (t80)
REVERT: A 2301 ARG cc_start: 0.8451 (ttm110) cc_final: 0.8086 (ttm110)
REVERT: A 2309 ASP cc_start: 0.7484 (p0) cc_final: 0.7257 (p0)
REVERT: A 2318 LYS cc_start: 0.8015 (ttmt) cc_final: 0.7477 (ttpp)
REVERT: A 2511 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7750 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8275 (ptmt) cc_final: 0.8008 (ttpp)
REVERT: A 2579 GLU cc_start: 0.7455 (mp0) cc_final: 0.7019 (mp0)
REVERT: A 2675 VAL cc_start: 0.7987 (t) cc_final: 0.7731 (m)
REVERT: A 2802 MET cc_start: 0.8555 (ttm) cc_final: 0.8330 (ttm)
REVERT: A 2902 LEU cc_start: 0.8200 (mt) cc_final: 0.7940 (mt)
REVERT: A 2905 LYS cc_start: 0.8275 (mttt) cc_final: 0.7773 (mttt)
REVERT: A 2966 LEU cc_start: 0.8582 (mt) cc_final: 0.8336 (mt)
REVERT: A 3014 VAL cc_start: 0.8894 (t) cc_final: 0.8643 (p)
REVERT: A 3150 LYS cc_start: 0.7886 (mmpt) cc_final: 0.7639 (mmpt)
REVERT: A 3203 MET cc_start: 0.6125 (mpp) cc_final: 0.5590 (mpp)
  outliers start: 33
  outliers final: 12
  residues processed: 349
  average time/residue: 0.6402
  time to fit residues: 239.8210
Evaluate side-chains
  332 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 319
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1097 GLU
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1549 SER
Chi-restraints excluded: chain A residue 2396 ASN
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2793 ARG
Chi-restraints excluded: chain A residue 3080 LEU
Chi-restraints excluded: chain A residue 3135 ARG
Chi-restraints excluded: chain A residue 3151 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 142 optimal weight:    1.9990
   chunk 71 optimal weight:    0.6980
   chunk 58 optimal weight:    2.9990
   chunk 151 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 139 optimal weight:    0.8980
   chunk 103 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 95 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A1100 ASN
A1354 ASN
A1401 ASN
A2536 GLN
** A2560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2607 GLN
A2777 ASN
A3186 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.122096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.108340 restraints weight = 16852.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3451 rms_B_bonded: 1.63
r_work: 0.3343 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3205 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.045  12519  Z= 0.239
  Angle     :  0.578   7.576  16911  Z= 0.294
  Chirality :  0.043   0.179   1953
  Planarity :  0.004   0.050   2114
  Dihedral  :  8.791 170.565   1740
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.41 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 14.74 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  0.25 (0.21), residues: 1496
  helix:  1.14 (0.18), residues: 857
  sheet:  0.39 (0.59), residues: 75
  loop : -1.40 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1212 
 TYR   0.019   0.002   TYR A1617 
 PHE   0.029   0.002   PHE A2633 
 TRP   0.012   0.002   TRP A2542 
 HIS   0.005   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00569 /  0.24 (12515)
  covalent geometry    : angle       0.57226 /  0.29 (16905)
  hydrogen bonds       : bond        0.04187 /  2.72 (  650)
  hydrogen bonds       : angle       4.23543 /  3.06 ( 1881)
  metal coordination   : bond        0.00896 /  0.42 (    4)
  metal coordination   : angle       4.22631 /  2.64 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  376 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 342
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7500 (t0) cc_final: 0.7250 (t0)
REVERT: A  946 LEU cc_start: 0.8390 (mm) cc_final: 0.8176 (mp)
REVERT: A  968 GLU cc_start: 0.7825 (mp0) cc_final: 0.7285 (mp0)
REVERT: A 1021 GLU cc_start: 0.7997 (tp30) cc_final: 0.7701 (tp30)
REVERT: A 1024 LYS cc_start: 0.8367 (tttt) cc_final: 0.8136 (ttpp)
REVERT: A 1037 LYS cc_start: 0.8399 (tttt) cc_final: 0.8168 (mtpp)
REVERT: A 1079 CYS cc_start: 0.8037 (t) cc_final: 0.7662 (m)
REVERT: A 1094 LYS cc_start: 0.8182 (mttt) cc_final: 0.7933 (mttm)
REVERT: A 1104 THR cc_start: 0.8033 (OUTLIER) cc_final: 0.7728 (t)
REVERT: A 1117 LYS cc_start: 0.8368 (tmtt) cc_final: 0.8166 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7334 (tp30) cc_final: 0.6891 (tp30)
REVERT: A 1134 LEU cc_start: 0.8537 (mt) cc_final: 0.8196 (mp)
REVERT: A 1181 ASP cc_start: 0.7532 (t0) cc_final: 0.7267 (t0)
REVERT: A 1189 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7111 (mm-30)
REVERT: A 1262 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8151 (mp)
REVERT: A 1350 CYS cc_start: 0.7593 (m) cc_final: 0.7391 (t)
REVERT: A 1380 GLU cc_start: 0.7861 (tt0) cc_final: 0.7488 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7745 (ttmm)
REVERT: A 1535 ARG cc_start: 0.8561 (mtp180) cc_final: 0.8300 (mmm160)
REVERT: A 1578 LYS cc_start: 0.8544 (tttt) cc_final: 0.8317 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7736 (ttm110) cc_final: 0.7303 (ttm-80)
REVERT: A 1640 MET cc_start: 0.8125 (ttp) cc_final: 0.7811 (ttm)
REVERT: A 1647 MET cc_start: 0.8360 (ttp) cc_final: 0.8056 (ttp)
REVERT: A 1648 ASN cc_start: 0.8240 (m-40) cc_final: 0.8013 (m-40)
REVERT: A 1792 MET cc_start: 0.8598 (mmm) cc_final: 0.8210 (mmm)
REVERT: A 2301 ARG cc_start: 0.8475 (ttm110) cc_final: 0.8107 (ttm110)
REVERT: A 2302 ASN cc_start: 0.8621 (m-40) cc_final: 0.8302 (m-40)
REVERT: A 2309 ASP cc_start: 0.7503 (p0) cc_final: 0.7258 (p0)
REVERT: A 2318 LYS cc_start: 0.8159 (ttmt) cc_final: 0.7929 (ttpp)
REVERT: A 2397 LEU cc_start: 0.8611 (mp) cc_final: 0.8403 (mt)
REVERT: A 2468 TYR cc_start: 0.8219 (t80) cc_final: 0.7998 (t80)
REVERT: A 2471 MET cc_start: 0.7091 (OUTLIER) cc_final: 0.6533 (mmm)
REVERT: A 2511 GLU cc_start: 0.7981 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8292 (ptmt) cc_final: 0.8014 (ttpp)
REVERT: A 2579 GLU cc_start: 0.7442 (mp0) cc_final: 0.7021 (mp0)
REVERT: A 2587 THR cc_start: 0.7656 (t) cc_final: 0.7433 (t)
REVERT: A 2902 LEU cc_start: 0.8234 (mt) cc_final: 0.7980 (mt)
REVERT: A 2905 LYS cc_start: 0.8309 (mttt) cc_final: 0.7813 (mttt)
REVERT: A 2966 LEU cc_start: 0.8598 (mt) cc_final: 0.8357 (mt)
REVERT: A 3014 VAL cc_start: 0.8908 (t) cc_final: 0.8670 (p)
REVERT: A 3150 LYS cc_start: 0.7924 (mmpt) cc_final: 0.7655 (mmpt)
REVERT: A 3199 LYS cc_start: 0.8589 (tttt) cc_final: 0.8348 (tttt)
REVERT: A 3203 MET cc_start: 0.6137 (mpp) cc_final: 0.5533 (mpp)
  outliers start: 34
  outliers final: 12
  residues processed: 353
  average time/residue: 0.6946
  time to fit residues: 263.1681
Evaluate side-chains
  339 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 324
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1112 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1262 LEU
Chi-restraints excluded: chain A residue 1454 SER
Chi-restraints excluded: chain A residue 2471 MET
Chi-restraints excluded: chain A residue 2704 SER
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2793 ARG
Chi-restraints excluded: chain A residue 2861 GLU
Chi-restraints excluded: chain A residue 3135 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 58 optimal weight:    2.9990
   chunk 119 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 98 optimal weight:    0.5980
   chunk 101 optimal weight:    0.5980
   chunk 1 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 82 optimal weight:    0.4980
   chunk 75 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A1100 ASN
A1354 ASN
** A1768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2345 ASN
A2536 GLN
A2692 GLN
A2695 GLN
A2777 ASN
A3186 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.123310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.109295 restraints weight = 16921.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 1.66
r_work: 0.3350 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3210 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8378
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  12519  Z= 0.154
  Angle     :  0.529   6.963  16911  Z= 0.270
  Chirality :  0.040   0.159   1953
  Planarity :  0.004   0.045   2114
  Dihedral  :  8.754 171.693   1740
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.48
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.48 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 16.24 %
    Favored  : 81.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  0.42 (0.21), residues: 1496
  helix:  1.29 (0.18), residues: 858
  sheet:  0.52 (0.61), residues: 75
  loop : -1.37 (0.25), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1348 
 TYR   0.011   0.001   TYR A3196 
 PHE   0.028   0.002   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.006   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00361 /  0.15 (12515)
  covalent geometry    : angle       0.52448 /  0.27 (16905)
  hydrogen bonds       : bond        0.03726 /  2.44 (  650)
  hydrogen bonds       : angle       4.12582 /  2.98 ( 1881)
  metal coordination   : bond        0.00451 /  0.21 (    4)
  metal coordination   : angle       3.84279 /  2.36 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  358 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 327
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7481 (t0) cc_final: 0.7212 (t0)
REVERT: A  946 LEU cc_start: 0.8355 (mm) cc_final: 0.8094 (mp)
REVERT: A  962 MET cc_start: 0.8617 (OUTLIER) cc_final: 0.8296 (mtm)
REVERT: A  968 GLU cc_start: 0.7809 (mp0) cc_final: 0.7285 (mp0)
REVERT: A 1021 GLU cc_start: 0.7999 (tp30) cc_final: 0.7649 (tp30)
REVERT: A 1037 LYS cc_start: 0.8405 (tttt) cc_final: 0.8161 (mtpp)
REVERT: A 1079 CYS cc_start: 0.8058 (t) cc_final: 0.7626 (m)
REVERT: A 1086 GLU cc_start: 0.7754 (mp0) cc_final: 0.7431 (mp0)
REVERT: A 1094 LYS cc_start: 0.8201 (mttt) cc_final: 0.7945 (mttm)
REVERT: A 1104 THR cc_start: 0.7961 (OUTLIER) cc_final: 0.7673 (t)
REVERT: A 1117 LYS cc_start: 0.8380 (tmtt) cc_final: 0.8089 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7264 (tp30) cc_final: 0.6841 (tp30)
REVERT: A 1134 LEU cc_start: 0.8499 (mt) cc_final: 0.8205 (mp)
REVERT: A 1181 ASP cc_start: 0.7569 (t0) cc_final: 0.7296 (t0)
REVERT: A 1189 GLU cc_start: 0.7299 (mm-30) cc_final: 0.7099 (mm-30)
REVERT: A 1262 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8110 (mp)
REVERT: A 1380 GLU cc_start: 0.7840 (tt0) cc_final: 0.7461 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8045 (ttmm) cc_final: 0.7748 (ttmm)
REVERT: A 1452 GLU cc_start: 0.7849 (tp30) cc_final: 0.7589 (tp30)
REVERT: A 1578 LYS cc_start: 0.8537 (tttt) cc_final: 0.8318 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7745 (ttm110) cc_final: 0.7291 (ttm-80)
REVERT: A 1640 MET cc_start: 0.8114 (ttp) cc_final: 0.7828 (ttm)
REVERT: A 1647 MET cc_start: 0.8355 (ttp) cc_final: 0.8044 (ttp)
REVERT: A 1648 ASN cc_start: 0.8232 (m-40) cc_final: 0.7985 (m-40)
REVERT: A 2301 ARG cc_start: 0.8421 (ttm110) cc_final: 0.8047 (ttm110)
REVERT: A 2302 ASN cc_start: 0.8603 (m-40) cc_final: 0.8295 (m-40)
REVERT: A 2309 ASP cc_start: 0.7459 (p0) cc_final: 0.7178 (p0)
REVERT: A 2318 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7940 (ttpp)
REVERT: A 2468 TYR cc_start: 0.8194 (t80) cc_final: 0.7957 (t80)
REVERT: A 2471 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6483 (mmm)
REVERT: A 2511 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7766 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8294 (ptmt) cc_final: 0.8016 (ttpp)
REVERT: A 2579 GLU cc_start: 0.7478 (mp0) cc_final: 0.6966 (mp0)
REVERT: A 2675 VAL cc_start: 0.8073 (t) cc_final: 0.7806 (m)
REVERT: A 2902 LEU cc_start: 0.8219 (mt) cc_final: 0.7961 (mt)
REVERT: A 2905 LYS cc_start: 0.8306 (mttt) cc_final: 0.7812 (mttt)
REVERT: A 2966 LEU cc_start: 0.8596 (mt) cc_final: 0.8361 (mt)
REVERT: A 3014 VAL cc_start: 0.8887 (t) cc_final: 0.8649 (p)
REVERT: A 3199 LYS cc_start: 0.8598 (tttt) cc_final: 0.8359 (tttt)
REVERT: A 3203 MET cc_start: 0.6172 (mpp) cc_final: 0.5557 (mpp)
  outliers start: 31
  outliers final: 12
  residues processed: 336
  average time/residue: 0.6580
  time to fit residues: 237.6577
Evaluate side-chains
  337 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 321
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1262 LEU
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 2471 MET
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2793 ARG
Chi-restraints excluded: chain A residue 2857 ASN
Chi-restraints excluded: chain A residue 2861 GLU
Chi-restraints excluded: chain A residue 3029 LEU
Chi-restraints excluded: chain A residue 3135 ARG
Chi-restraints excluded: chain A residue 3140 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 126 optimal weight:    0.3980
   chunk 0 optimal weight:    6.9990
   chunk 74 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 69 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 136 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A1100 ASN
A1401 ASN
** A1768 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2477 HIS
A2536 GLN
** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN
A2695 GLN
A2777 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.123231 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.109171 restraints weight = 16909.111|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 1.66
r_work: 0.3353 rms_B_bonded: 2.13 restraints_weight: 0.5000
r_work: 0.3212 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.3212
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.2359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  12519  Z= 0.150
  Angle     :  0.524   8.203  16911  Z= 0.268
  Chirality :  0.040   0.159   1953
  Planarity :  0.004   0.045   2114
  Dihedral  :  8.715 171.979   1740
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 6.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.08 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  2.43 %
    Allowed  : 17.10 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.53 (0.21), residues: 1496
  helix:  1.39 (0.18), residues: 858
  sheet:  0.52 (0.61), residues: 75
  loop : -1.34 (0.25), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1348 
 TYR   0.011   0.001   TYR A3196 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.007   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.15 (12515)
  covalent geometry    : angle       0.51971 /  0.27 (16905)
  hydrogen bonds       : bond        0.03636 /  2.38 (  650)
  hydrogen bonds       : angle       4.07011 /  2.95 ( 1881)
  metal coordination   : bond        0.00480 /  0.22 (    4)
  metal coordination   : angle       3.69069 /  2.28 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  360 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 326
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7474 (t0) cc_final: 0.7202 (t0)
REVERT: A  964 LYS cc_start: 0.8051 (ttmt) cc_final: 0.7807 (ttmt)
REVERT: A  968 GLU cc_start: 0.7833 (mp0) cc_final: 0.7298 (mp0)
REVERT: A 1037 LYS cc_start: 0.8407 (tttt) cc_final: 0.8157 (mtpp)
REVERT: A 1079 CYS cc_start: 0.8069 (t) cc_final: 0.7639 (m)
REVERT: A 1086 GLU cc_start: 0.7745 (mp0) cc_final: 0.7431 (mp0)
REVERT: A 1094 LYS cc_start: 0.8226 (mttt) cc_final: 0.7964 (mttm)
REVERT: A 1104 THR cc_start: 0.7982 (OUTLIER) cc_final: 0.7699 (t)
REVERT: A 1117 LYS cc_start: 0.8331 (tmtt) cc_final: 0.8093 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7281 (tp30) cc_final: 0.6853 (tp30)
REVERT: A 1134 LEU cc_start: 0.8502 (mt) cc_final: 0.8211 (mp)
REVERT: A 1181 ASP cc_start: 0.7580 (t0) cc_final: 0.7292 (t0)
REVERT: A 1213 GLN cc_start: 0.7984 (mm-40) cc_final: 0.7309 (mt0)
REVERT: A 1380 GLU cc_start: 0.7858 (tt0) cc_final: 0.7470 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8052 (ttmm) cc_final: 0.7756 (ttmm)
REVERT: A 1578 LYS cc_start: 0.8540 (tttt) cc_final: 0.8322 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7738 (ttm110) cc_final: 0.7290 (ttm-80)
REVERT: A 1640 MET cc_start: 0.8113 (ttp) cc_final: 0.7782 (ttm)
REVERT: A 1647 MET cc_start: 0.8364 (ttp) cc_final: 0.8041 (ttp)
REVERT: A 1648 ASN cc_start: 0.8229 (m-40) cc_final: 0.7962 (m-40)
REVERT: A 1764 LYS cc_start: 0.8321 (mtpp) cc_final: 0.8104 (mtpp)
REVERT: A 1792 MET cc_start: 0.8586 (mmp) cc_final: 0.8323 (mmm)
REVERT: A 2301 ARG cc_start: 0.8431 (ttm110) cc_final: 0.8061 (ttm110)
REVERT: A 2302 ASN cc_start: 0.8625 (m-40) cc_final: 0.8311 (m-40)
REVERT: A 2318 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7936 (ttpp)
REVERT: A 2358 ASP cc_start: 0.6640 (m-30) cc_final: 0.6369 (m-30)
REVERT: A 2471 MET cc_start: 0.6910 (OUTLIER) cc_final: 0.6563 (mmm)
REVERT: A 2511 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7765 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8343 (ptmt) cc_final: 0.8064 (ttpp)
REVERT: A 2575 GLU cc_start: 0.7004 (pp20) cc_final: 0.6708 (tm-30)
REVERT: A 2675 VAL cc_start: 0.8074 (t) cc_final: 0.7821 (m)
REVERT: A 2760 ILE cc_start: 0.8187 (OUTLIER) cc_final: 0.7977 (mp)
REVERT: A 2802 MET cc_start: 0.8656 (ttm) cc_final: 0.8368 (ttm)
REVERT: A 2902 LEU cc_start: 0.8232 (mt) cc_final: 0.7972 (mt)
REVERT: A 2905 LYS cc_start: 0.8313 (mttt) cc_final: 0.7818 (mttt)
REVERT: A 2966 LEU cc_start: 0.8600 (mt) cc_final: 0.8364 (mt)
REVERT: A 3014 VAL cc_start: 0.8883 (t) cc_final: 0.8653 (p)
REVERT: A 3199 LYS cc_start: 0.8604 (tttt) cc_final: 0.8369 (tttt)
REVERT: A 3203 MET cc_start: 0.6181 (mpp) cc_final: 0.5573 (mpp)
  outliers start: 34
  outliers final: 14
  residues processed: 338
  average time/residue: 0.6682
  time to fit residues: 242.2588
Evaluate side-chains
  337 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 320
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  975 GLU
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1196 SER
Chi-restraints excluded: chain A residue 1454 SER
Chi-restraints excluded: chain A residue 2471 MET
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2861 GLU
Chi-restraints excluded: chain A residue 3029 LEU
Chi-restraints excluded: chain A residue 3135 ARG
Chi-restraints excluded: chain A residue 3140 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 137 optimal weight:    0.2980
   chunk 112 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 146 optimal weight:    0.0970
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A1100 ASN
A2477 HIS
A2536 GLN
** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN
A2695 GLN
A2777 ASN
** A2911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.123729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.109689 restraints weight = 16701.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3468 rms_B_bonded: 1.65
r_work: 0.3358 rms_B_bonded: 2.12 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 3.74 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.2431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12519  Z= 0.145
  Angle     :  0.523   7.529  16911  Z= 0.268
  Chirality :  0.040   0.157   1953
  Planarity :  0.004   0.044   2114
  Dihedral  :  8.703 172.413   1740
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.28 %
    Favored  : 95.66 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 17.74 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  0.59 (0.21), residues: 1496
  helix:  1.47 (0.18), residues: 858
  sheet:  0.50 (0.60), residues: 75
  loop : -1.33 (0.25), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1348 
 TYR   0.011   0.001   TYR A1130 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.006   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00340 /  0.15 (12515)
  covalent geometry    : angle       0.51798 /  0.27 (16905)
  hydrogen bonds       : bond        0.03570 /  2.33 (  650)
  hydrogen bonds       : angle       4.03028 /  2.92 ( 1881)
  metal coordination   : bond        0.00440 /  0.21 (    4)
  metal coordination   : angle       3.68554 /  2.27 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  355 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 328
  time to evaluate  : 0.429 
Fit side-chains
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7419 (t0) cc_final: 0.7144 (t0)
REVERT: A  962 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8282 (mtm)
REVERT: A 1037 LYS cc_start: 0.8406 (tttt) cc_final: 0.8154 (mtpp)
REVERT: A 1079 CYS cc_start: 0.8040 (t) cc_final: 0.7616 (m)
REVERT: A 1086 GLU cc_start: 0.7743 (mp0) cc_final: 0.7435 (mp0)
REVERT: A 1094 LYS cc_start: 0.8208 (mttt) cc_final: 0.7942 (mttm)
REVERT: A 1104 THR cc_start: 0.7977 (OUTLIER) cc_final: 0.7724 (t)
REVERT: A 1117 LYS cc_start: 0.8341 (tmtt) cc_final: 0.8103 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7284 (tp30) cc_final: 0.6845 (tp30)
REVERT: A 1134 LEU cc_start: 0.8490 (mt) cc_final: 0.8215 (mp)
REVERT: A 1181 ASP cc_start: 0.7604 (t0) cc_final: 0.7317 (t0)
REVERT: A 1213 GLN cc_start: 0.7895 (mm-40) cc_final: 0.7280 (mt0)
REVERT: A 1380 GLU cc_start: 0.7848 (tt0) cc_final: 0.7426 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8053 (ttmm) cc_final: 0.7756 (ttmm)
REVERT: A 1578 LYS cc_start: 0.8538 (tttt) cc_final: 0.8317 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7772 (ttm110) cc_final: 0.7316 (ttm-80)
REVERT: A 1640 MET cc_start: 0.8133 (ttp) cc_final: 0.7850 (ttm)
REVERT: A 1647 MET cc_start: 0.8361 (ttp) cc_final: 0.8043 (ttp)
REVERT: A 1648 ASN cc_start: 0.8219 (m-40) cc_final: 0.7962 (m-40)
REVERT: A 1764 LYS cc_start: 0.8307 (mtpp) cc_final: 0.8074 (mtpp)
REVERT: A 1792 MET cc_start: 0.8583 (mmp) cc_final: 0.8365 (mmm)
REVERT: A 2301 ARG cc_start: 0.8429 (ttm110) cc_final: 0.8058 (ttm110)
REVERT: A 2302 ASN cc_start: 0.8646 (m-40) cc_final: 0.8321 (m-40)
REVERT: A 2318 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7956 (ttpp)
REVERT: A 2358 ASP cc_start: 0.6608 (m-30) cc_final: 0.6363 (m-30)
REVERT: A 2471 MET cc_start: 0.6838 (OUTLIER) cc_final: 0.6507 (mmm)
REVERT: A 2511 GLU cc_start: 0.7982 (mm-30) cc_final: 0.7761 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8310 (ptmt) cc_final: 0.8043 (ttpp)
REVERT: A 2575 GLU cc_start: 0.7017 (pp20) cc_final: 0.6511 (tm-30)
REVERT: A 2675 VAL cc_start: 0.8069 (t) cc_final: 0.7828 (m)
REVERT: A 2802 MET cc_start: 0.8650 (ttm) cc_final: 0.8349 (ttm)
REVERT: A 2902 LEU cc_start: 0.8235 (mt) cc_final: 0.7976 (mt)
REVERT: A 2905 LYS cc_start: 0.8328 (mttt) cc_final: 0.7845 (mttt)
REVERT: A 2966 LEU cc_start: 0.8593 (mt) cc_final: 0.8364 (mt)
REVERT: A 3014 VAL cc_start: 0.8881 (t) cc_final: 0.8651 (p)
REVERT: A 3088 VAL cc_start: 0.8470 (m) cc_final: 0.8246 (p)
REVERT: A 3199 LYS cc_start: 0.8607 (tttt) cc_final: 0.8379 (tttt)
REVERT: A 3203 MET cc_start: 0.6203 (mpp) cc_final: 0.5594 (mpp)
  outliers start: 27
  outliers final: 15
  residues processed: 338
  average time/residue: 0.6261
  time to fit residues: 227.4996
Evaluate side-chains
  332 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 314
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  975 GLU
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1196 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1614 VAL
Chi-restraints excluded: chain A residue 2471 MET
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2861 GLU
Chi-restraints excluded: chain A residue 3029 LEU
Chi-restraints excluded: chain A residue 3135 ARG
Chi-restraints excluded: chain A residue 3140 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 55 optimal weight:    0.0270
   chunk 60 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9990
   chunk 126 optimal weight:    0.5980
   chunk 90 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 20 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9980
   chunk 98 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.6638

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A1064 ASN
A1100 ASN
A1401 ASN
A2477 HIS
A2536 GLN
** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN
A2695 GLN
A2777 ASN
** A2911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.123469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.109579 restraints weight = 16911.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 1.64
r_work: 0.3353 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3214 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12519  Z= 0.148
  Angle     :  0.526   7.904  16911  Z= 0.268
  Chirality :  0.040   0.155   1953
  Planarity :  0.004   0.044   2114
  Dihedral  :  8.697 172.804   1740
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.21 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 18.03 %
    Favored  : 80.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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 (0.22), residues: 1496
  helix:  1.51 (0.18), residues: 856
  sheet:  0.50 (0.60), residues: 75
  loop : -1.26 (0.25), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1348 
 TYR   0.014   0.001   TYR A1130 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.007   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (12515)
  covalent geometry    : angle       0.52128 /  0.27 (16905)
  hydrogen bonds       : bond        0.03562 /  2.32 (  650)
  hydrogen bonds       : angle       4.02024 /  2.91 ( 1881)
  metal coordination   : bond        0.00439 /  0.20 (    4)
  metal coordination   : angle       3.74120 /  2.32 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 322
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7406 (t0) cc_final: 0.7126 (t0)
REVERT: A  962 MET cc_start: 0.8642 (OUTLIER) cc_final: 0.8317 (mtm)
REVERT: A 1037 LYS cc_start: 0.8426 (tttt) cc_final: 0.8174 (mtpp)
REVERT: A 1079 CYS cc_start: 0.8023 (t) cc_final: 0.7631 (m)
REVERT: A 1086 GLU cc_start: 0.7744 (mp0) cc_final: 0.7438 (mp0)
REVERT: A 1094 LYS cc_start: 0.8200 (mttt) cc_final: 0.7938 (mttm)
REVERT: A 1104 THR cc_start: 0.8000 (OUTLIER) cc_final: 0.7758 (t)
REVERT: A 1117 LYS cc_start: 0.8341 (tmtt) cc_final: 0.8111 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7267 (tp30) cc_final: 0.6845 (tp30)
REVERT: A 1134 LEU cc_start: 0.8501 (mt) cc_final: 0.8226 (mp)
REVERT: A 1181 ASP cc_start: 0.7624 (t0) cc_final: 0.7325 (t0)
REVERT: A 1213 GLN cc_start: 0.7820 (mm-40) cc_final: 0.7288 (mt0)
REVERT: A 1380 GLU cc_start: 0.7816 (tt0) cc_final: 0.7420 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8058 (ttmm) cc_final: 0.7767 (ttmm)
REVERT: A 1578 LYS cc_start: 0.8543 (tttt) cc_final: 0.8322 (ttpp)
REVERT: A 1605 ARG cc_start: 0.8135 (mmm160) cc_final: 0.7916 (ttt180)
REVERT: A 1638 ARG cc_start: 0.7802 (ttm110) cc_final: 0.7349 (ttm-80)
REVERT: A 1640 MET cc_start: 0.8142 (ttp) cc_final: 0.7806 (ttm)
REVERT: A 1647 MET cc_start: 0.8369 (ttp) cc_final: 0.8059 (ttp)
REVERT: A 1648 ASN cc_start: 0.8227 (m-40) cc_final: 0.7968 (m-40)
REVERT: A 1764 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8099 (mtpp)
REVERT: A 2301 ARG cc_start: 0.8430 (ttm110) cc_final: 0.8065 (ttm110)
REVERT: A 2302 ASN cc_start: 0.8633 (m-40) cc_final: 0.8310 (m-40)
REVERT: A 2358 ASP cc_start: 0.6608 (m-30) cc_final: 0.6358 (m-30)
REVERT: A 2511 GLU cc_start: 0.7963 (mm-30) cc_final: 0.7748 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8328 (ptmt) cc_final: 0.8059 (ttpp)
REVERT: A 2575 GLU cc_start: 0.7007 (pp20) cc_final: 0.6585 (tm-30)
REVERT: A 2675 VAL cc_start: 0.8068 (t) cc_final: 0.7827 (m)
REVERT: A 2802 MET cc_start: 0.8645 (ttm) cc_final: 0.8344 (ttm)
REVERT: A 2902 LEU cc_start: 0.8238 (mt) cc_final: 0.7991 (mt)
REVERT: A 2905 LYS cc_start: 0.8339 (mttt) cc_final: 0.7860 (mttt)
REVERT: A 2966 LEU cc_start: 0.8594 (mt) cc_final: 0.8362 (mt)
REVERT: A 3014 VAL cc_start: 0.8888 (t) cc_final: 0.8647 (p)
REVERT: A 3088 VAL cc_start: 0.8474 (m) cc_final: 0.8246 (p)
REVERT: A 3199 LYS cc_start: 0.8592 (tttt) cc_final: 0.8371 (tttt)
REVERT: A 3203 MET cc_start: 0.6199 (mpp) cc_final: 0.5595 (mpp)
  outliers start: 24
  outliers final: 15
  residues processed: 332
  average time/residue: 0.6313
  time to fit residues: 225.4590
Evaluate side-chains
  331 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 314
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  975 GLU
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1196 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 2779 ILE
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2861 GLU
Chi-restraints excluded: chain A residue 3029 LEU
Chi-restraints excluded: chain A residue 3135 ARG
Chi-restraints excluded: chain A residue 3140 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 85 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 129 optimal weight:    1.9990
   chunk 17 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 64 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 122 optimal weight:    1.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 944 HIS
A 960 GLN
A1064 ASN
A1100 ASN
A1401 ASN
A2477 HIS
A2536 GLN
** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN
A2777 ASN
** A2911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.122929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.109129 restraints weight = 16798.274|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 1.63
r_work: 0.3350 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.2546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12519  Z= 0.178
  Angle     :  0.557   7.742  16911  Z= 0.284
  Chirality :  0.041   0.161   1953
  Planarity :  0.004   0.044   2114
  Dihedral  :  8.715 172.913   1740
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.65
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  4.21 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 18.24 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  0.62 (0.21), residues: 1496
  helix:  1.49 (0.18), residues: 859
  sheet:  0.44 (0.59), residues: 75
  loop : -1.32 (0.25), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1348 
 TYR   0.013   0.001   TYR A1617 
 PHE   0.028   0.002   PHE A2633 
 TRP   0.014   0.001   TRP A2542 
 HIS   0.008   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00422 /  0.18 (12515)
  covalent geometry    : angle       0.55213 /  0.28 (16905)
  hydrogen bonds       : bond        0.03712 /  2.42 (  650)
  hydrogen bonds       : angle       4.03873 /  2.92 ( 1881)
  metal coordination   : bond        0.00568 /  0.27 (    4)
  metal coordination   : angle       3.92881 /  2.44 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  352 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 323
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  933 ASP cc_start: 0.7426 (t0) cc_final: 0.7141 (t0)
REVERT: A  962 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8282 (mtm)
REVERT: A  964 LYS cc_start: 0.8008 (ttmt) cc_final: 0.7802 (ttmt)
REVERT: A  968 GLU cc_start: 0.7837 (mp0) cc_final: 0.7336 (mp0)
REVERT: A 1037 LYS cc_start: 0.8421 (tttt) cc_final: 0.8171 (mtpp)
REVERT: A 1079 CYS cc_start: 0.8042 (t) cc_final: 0.7645 (m)
REVERT: A 1086 GLU cc_start: 0.7750 (mp0) cc_final: 0.7442 (mp0)
REVERT: A 1094 LYS cc_start: 0.8251 (mttt) cc_final: 0.7990 (mttm)
REVERT: A 1104 THR cc_start: 0.8055 (OUTLIER) cc_final: 0.7805 (t)
REVERT: A 1117 LYS cc_start: 0.8368 (tmtt) cc_final: 0.8127 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7295 (tp30) cc_final: 0.6864 (tp30)
REVERT: A 1134 LEU cc_start: 0.8513 (mt) cc_final: 0.8222 (mp)
REVERT: A 1181 ASP cc_start: 0.7634 (t0) cc_final: 0.7331 (t0)
REVERT: A 1213 GLN cc_start: 0.7782 (mm-40) cc_final: 0.7323 (mt0)
REVERT: A 1380 GLU cc_start: 0.7834 (tt0) cc_final: 0.7476 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8062 (ttmm) cc_final: 0.7769 (ttmm)
REVERT: A 1578 LYS cc_start: 0.8540 (tttt) cc_final: 0.8317 (ttpp)
REVERT: A 1638 ARG cc_start: 0.7780 (ttm110) cc_final: 0.7316 (ttm-80)
REVERT: A 1640 MET cc_start: 0.8135 (ttp) cc_final: 0.7798 (ttm)
REVERT: A 1647 MET cc_start: 0.8386 (ttp) cc_final: 0.8134 (ttp)
REVERT: A 1648 ASN cc_start: 0.8234 (m-40) cc_final: 0.7961 (m-40)
REVERT: A 1764 LYS cc_start: 0.8334 (mtpp) cc_final: 0.8106 (mtpp)
REVERT: A 2301 ARG cc_start: 0.8425 (ttm110) cc_final: 0.8064 (ttm110)
REVERT: A 2302 ASN cc_start: 0.8635 (m-40) cc_final: 0.8331 (m-40)
REVERT: A 2358 ASP cc_start: 0.6601 (m-30) cc_final: 0.6375 (m-30)
REVERT: A 2511 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7758 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8322 (ptmt) cc_final: 0.8053 (ttpp)
REVERT: A 2575 GLU cc_start: 0.6992 (pp20) cc_final: 0.6490 (tm-30)
REVERT: A 2675 VAL cc_start: 0.8095 (t) cc_final: 0.7857 (m)
REVERT: A 2902 LEU cc_start: 0.8265 (mt) cc_final: 0.8022 (mt)
REVERT: A 2905 LYS cc_start: 0.8333 (mttt) cc_final: 0.7859 (mttt)
REVERT: A 2966 LEU cc_start: 0.8591 (mt) cc_final: 0.8364 (mt)
REVERT: A 3014 VAL cc_start: 0.8888 (t) cc_final: 0.8652 (p)
REVERT: A 3088 VAL cc_start: 0.8464 (m) cc_final: 0.8237 (p)
REVERT: A 3199 LYS cc_start: 0.8598 (tttt) cc_final: 0.8365 (tttt)
REVERT: A 3203 MET cc_start: 0.6190 (mpp) cc_final: 0.5569 (mpp)
  outliers start: 29
  outliers final: 18
  residues processed: 333
  average time/residue: 0.6249
  time to fit residues: 223.5022
Evaluate side-chains
  338 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 318
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  975 GLU
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1196 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1454 SER
Chi-restraints excluded: chain A residue 1529 MET
Chi-restraints excluded: chain A residue 1801 ASP
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 2761 LYS
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2861 GLU
Chi-restraints excluded: chain A residue 3029 LEU
Chi-restraints excluded: chain A residue 3101 LEU
Chi-restraints excluded: chain A residue 3135 ARG
Chi-restraints excluded: chain A residue 3140 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 1 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0770
   chunk 24 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 12 optimal weight:    0.0470
   chunk 47 optimal weight:    1.9990
   chunk 139 optimal weight:    1.9990
   chunk 44 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 130 optimal weight:    0.1980
   chunk 52 optimal weight:    0.7980
   overall best weight:    0.3836

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
A1064 ASN
A1100 ASN
A1401 ASN
A1514 ASN
A2366 HIS
A2477 HIS
A2536 GLN
** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2692 GLN
A2695 GLN
A2777 ASN
** A2911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.124097 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.110210 restraints weight = 16886.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3480 rms_B_bonded: 1.65
r_work: 0.3373 rms_B_bonded: 2.11 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 3.73 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8362
moved from start:          0.2583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  12519  Z= 0.119
  Angle     :  0.539   7.895  16911  Z= 0.276
  Chirality :  0.039   0.153   1953
  Planarity :  0.004   0.042   2114
  Dihedral  :  8.694 173.828   1740
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.94 %
    Favored  : 95.99 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 19.31 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  0.74 (0.22), residues: 1496
  helix:  1.63 (0.18), residues: 858
  sheet:  0.31 (0.59), residues: 75
  loop : -1.30 (0.25), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1348 
 TYR   0.009   0.001   TYR A1617 
 PHE   0.023   0.001   PHE A2633 
 TRP   0.018   0.001   TRP A2542 
 HIS   0.007   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00275 /  0.12 (12515)
  covalent geometry    : angle       0.53523 /  0.28 (16905)
  hydrogen bonds       : bond        0.03366 /  2.21 (  650)
  hydrogen bonds       : angle       3.97057 /  2.87 ( 1881)
  metal coordination   : bond        0.00279 /  0.13 (    4)
  metal coordination   : angle       3.60071 /  2.21 (    6)

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

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

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2992 Ramachandran restraints generated.
    1496 Oldfield, 0 Emsley, 1496 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  346 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 326
  time to evaluate  : 0.372 
Fit side-chains
   revert: symmetry clash
REVERT: A  962 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8302 (mtm)
REVERT: A 1037 LYS cc_start: 0.8431 (tttt) cc_final: 0.8171 (mtpp)
REVERT: A 1079 CYS cc_start: 0.8025 (t) cc_final: 0.7631 (m)
REVERT: A 1094 LYS cc_start: 0.8232 (mttt) cc_final: 0.7957 (mttm)
REVERT: A 1104 THR cc_start: 0.8006 (OUTLIER) cc_final: 0.7788 (t)
REVERT: A 1117 LYS cc_start: 0.8340 (tmtt) cc_final: 0.8108 (tmtt)
REVERT: A 1119 GLU cc_start: 0.7263 (tp30) cc_final: 0.6838 (tp30)
REVERT: A 1134 LEU cc_start: 0.8469 (mt) cc_final: 0.8203 (mp)
REVERT: A 1181 ASP cc_start: 0.7625 (t0) cc_final: 0.7320 (t0)
REVERT: A 1213 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7268 (mt0)
REVERT: A 1380 GLU cc_start: 0.7739 (tt0) cc_final: 0.7355 (mt-10)
REVERT: A 1438 LYS cc_start: 0.8040 (ttmm) cc_final: 0.7752 (ttmm)
REVERT: A 1578 LYS cc_start: 0.8535 (tttt) cc_final: 0.8291 (ttpp)
REVERT: A 1605 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7900 (ttt180)
REVERT: A 1638 ARG cc_start: 0.7784 (ttm110) cc_final: 0.7075 (ttm110)
REVERT: A 1640 MET cc_start: 0.8108 (ttp) cc_final: 0.7863 (ttm)
REVERT: A 1647 MET cc_start: 0.8302 (ttp) cc_final: 0.8043 (ttp)
REVERT: A 1648 ASN cc_start: 0.8250 (m-40) cc_final: 0.8037 (m-40)
REVERT: A 2301 ARG cc_start: 0.8427 (ttm110) cc_final: 0.8072 (ttm110)
REVERT: A 2302 ASN cc_start: 0.8618 (m-40) cc_final: 0.8299 (m-40)
REVERT: A 2358 ASP cc_start: 0.6607 (m-30) cc_final: 0.6377 (m-30)
REVERT: A 2511 GLU cc_start: 0.7964 (mm-30) cc_final: 0.7750 (mm-30)
REVERT: A 2543 LYS cc_start: 0.8319 (ptmt) cc_final: 0.8062 (ttpp)
REVERT: A 2575 GLU cc_start: 0.7085 (pp20) cc_final: 0.6602 (tm-30)
REVERT: A 2802 MET cc_start: 0.8648 (ttm) cc_final: 0.8380 (ttm)
REVERT: A 2902 LEU cc_start: 0.8259 (mt) cc_final: 0.8014 (mt)
REVERT: A 2905 LYS cc_start: 0.8332 (mttt) cc_final: 0.7857 (mttt)
REVERT: A 2966 LEU cc_start: 0.8588 (mt) cc_final: 0.8362 (mt)
REVERT: A 3014 VAL cc_start: 0.8881 (t) cc_final: 0.8641 (p)
REVERT: A 3088 VAL cc_start: 0.8464 (m) cc_final: 0.8225 (p)
REVERT: A 3150 LYS cc_start: 0.7945 (mmpt) cc_final: 0.7731 (mmpt)
REVERT: A 3199 LYS cc_start: 0.8576 (tttt) cc_final: 0.8354 (tttt)
REVERT: A 3203 MET cc_start: 0.6200 (mpp) cc_final: 0.5579 (mpp)
  outliers start: 20
  outliers final: 12
  residues processed: 334
  average time/residue: 0.6258
  time to fit residues: 224.8568
Evaluate side-chains
  328 residues out of total 1398 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 314
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  983 MET
Chi-restraints excluded: chain A residue 1044 ASN
Chi-restraints excluded: chain A residue 1099 SER
Chi-restraints excluded: chain A residue 1104 THR
Chi-restraints excluded: chain A residue 1196 SER
Chi-restraints excluded: chain A residue 1614 VAL
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2760 ILE
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2861 GLU
Chi-restraints excluded: chain A residue 3029 LEU
Chi-restraints excluded: chain A residue 3135 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 152
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 149 optimal weight:    0.0060
   chunk 53 optimal weight:    0.5980
   chunk 111 optimal weight:    0.5980
   chunk 141 optimal weight:    0.6980
   chunk 9 optimal weight:    0.9990
   chunk 69 optimal weight:    0.2980
   chunk 88 optimal weight:    0.3980
   chunk 22 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 87 optimal weight:    0.2980
   overall best weight:    0.3196

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
A1064 ASN
A1100 ASN
A1401 ASN
A1514 ASN
A2477 HIS
A2536 GLN
** A2607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A2638 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A2695 GLN
A2777 ASN
** A2911 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.124579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.110688 restraints weight = 16729.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3484 rms_B_bonded: 1.64
r_work: 0.3377 rms_B_bonded: 2.10 restraints_weight: 0.5000
r_work: 0.3240 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3240
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8352
moved from start:          0.2663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  12519  Z= 0.114
  Angle     :  0.539   7.740  16911  Z= 0.275
  Chirality :  0.039   0.153   1953
  Planarity :  0.004   0.040   2114
  Dihedral  :  8.667 174.131   1740
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.88 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 19.31 %
    Favored  : 79.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.13 %
    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:  0.80 (0.22), residues: 1496
  helix:  1.67 (0.18), residues: 858
  sheet:  0.38 (0.60), residues: 75
  loop : -1.29 (0.25), residues: 563

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1348 
 TYR   0.009   0.001   TYR A1503 
 PHE   0.023   0.001   PHE A2633 
 TRP   0.018   0.001   TRP A2542 
 HIS   0.007   0.001   HIS A2512 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.11 (12515)
  covalent geometry    : angle       0.53505 /  0.27 (16905)
  hydrogen bonds       : bond        0.03282 /  2.16 (  650)
  hydrogen bonds       : angle       3.92959 /  2.84 ( 1881)
  metal coordination   : bond        0.00291 /  0.13 (    4)
  metal coordination   : angle       3.51678 /  2.15 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5329.53 seconds
wall clock time: 91 minutes 23.65 seconds (5483.65 seconds total)