Starting phenix.real_space_refine
on Fri Oct 23 19:39:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/22te_68655/10_2026/22te_68655.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/22te_68655/10_2026/22te_68655.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/22te_68655/10_2026/22te_68655.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/22te_68655/10_2026/22te_68655.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/22te_68655/10_2026/22te_68655.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/22te_68655/10_2026/22te_68655.map"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
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: 7
    Type Number    sf(0)   Gaussians
     Mn      1      7.51       5
     Zn      2      6.06       5
     Mg      1      5.21       5
     S      78      5.16       5
     C    6684      2.51       5
     N    1817      2.21       5
     O    1963      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10546
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1351, 10542
          Classifications: {'peptide': 1351}
          Incomplete info: {'truncation_to_alanine': 70}
          Link IDs: {'PTRANS': 40, 'TRANS': 1310}
          Chain breaks: 12
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 243
          Unresolved non-hydrogen angles: 291
          Unresolved non-hydrogen dihedrals: 196
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'GLU:plan': 19, 'ARG:plan': 3, 'ASN:plan1': 3, 'GLN:plan1': 5, 'ASP:plan': 4}
          Unresolved non-hydrogen planarities: 132
    Chain: "A"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Unusual residues: {' MG': 1, ' MN': 1, ' ZN': 2}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    788  SG  CYS A1028      25.931  18.191  91.804  1.00 78.53           S
  ATOM    803  SG  CYS A1031      28.976  15.972  91.563  1.00 82.12           S
  ATOM   1038  SG  CYS A1062      25.613  14.632  90.408  1.00 87.50           S
  ATOM   1058  SG  CYS A1065      27.357  17.320  88.385  1.00 94.61           S
  ATOM   1575  SG  CYS A1294      38.617  26.971  40.912  1.00 65.62           S

  Time building chain proxies: 2.40, per 1000 atoms: 0.23
  Number of scatterers: 10546
  At special positions: 0
  Unit cell: (95.63, 107.31, 121.91, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     Mn      1     24.99
     S      78     16.00
     Mg      1     11.99
     O    1963      8.00
     N    1817      7.00
     C    6684      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 248.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A4001 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1031 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1065 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1028 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1062 "
      pdb="  ZN A4002 "
        pdb="ZN    ZN A4002 " - pdb=" SG  CYS A1294 "
        pdb="ZN    ZN A4002 " - pdb=" NE2 HIS A1090 "
      Number of angles added : 6


  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2592

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 10 sheets defined
      63.6% alpha, 7.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 930 through 946
      removed outlier: 3.544A  pdb=" N   VAL A 934 " --> pdb=" O   SER A 930 " (cutoff:3.500A)
      removed outlier: 5.658A  pdb=" N   GLU A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      removed outlier: 5.314A  pdb=" N   HIS A 944 " --> pdb=" O   LYS A 940 " (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 1042
      removed outlier: 3.859A  pdb=" N   THR A1042 " --> pdb=" O   ALA A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1057
      removed outlier: 3.610A  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 1062 through 1066
      removed outlier: 3.578A  pdb=" N   HIS A1066 " --> pdb=" O   SER A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1088
      removed outlier: 3.570A  pdb=" N   VAL A1088 " --> pdb=" O   ILE A1085 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1279
      removed outlier: 4.006A  pdb=" N   PHE A1279 " --> pdb=" O   ASP A1275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1296
      removed outlier: 3.645A  pdb=" N   ILE A1295 " --> pdb=" O   GLN A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1309
    Processing helix  chain 'A' and resid 1315 through 1329
    Processing helix  chain 'A' and resid 1330 through 1350
    Processing helix  chain 'A' and resid 1401 through 1426
      removed outlier: 4.253A  pdb=" N   LEU A1412 " --> pdb=" O   GLY A1408 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   TYR A1413 " --> pdb=" O   SER A1409 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A1416 " --> pdb=" O   LEU A1412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1430 through 1435
      removed outlier: 3.543A  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: 3.672A  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: 3.670A  pdb=" N   ASN A1514 " --> pdb=" O   ASN A1510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1531
      removed outlier: 4.043A  pdb=" N   ARG A1526 " --> pdb=" O   LEU A1522 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   PHE A1527 " --> pdb=" O   GLN A1523 " (cutoff:3.500A)
    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 1538 through 1547
      removed outlier: 3.668A  pdb=" N   SER A1547 " --> pdb=" O   GLY A1543 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1552 through 1571
    Processing helix  chain 'A' and resid 1572 through 1581
      removed outlier: 3.903A  pdb=" N   LYS A1581 " --> pdb=" O   VAL A1577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1612
    Processing helix  chain 'A' and resid 1613 through 1616
    Processing helix  chain 'A' and resid 1631 through 1651
    Processing helix  chain 'A' and resid 1659 through 1666
    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 2307
      removed outlier: 3.684A  pdb=" N   THR A2306 " --> pdb=" O   ASN A2302 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   THR A2307 " --> pdb=" O   LEU A2303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2316 through 2336
    Processing helix  chain 'A' and resid 2367 through 2379
    Processing helix  chain 'A' and resid 2382 through 2397
    Processing helix  chain 'A' and resid 2448 through 2457
    Processing helix  chain 'A' and resid 2476 through 2503
      removed outlier: 3.796A  pdb=" N   VAL A2489 " --> pdb=" O   SER A2485 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   LEU A2490 " --> pdb=" O   LEU A2486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2559
      removed outlier: 4.806A  pdb=" N   TRP A2542 " --> pdb=" O   ASP A2538 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   LYS A2543 " --> pdb=" O   GLU A2539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2589 through 2594
      removed outlier: 3.525A  pdb=" N   MET A2594 " --> pdb=" O   ILE A2591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2595 through 2600
      removed outlier: 3.803A  pdb=" N   ASN A2600 " --> pdb=" O   THR A2596 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2605 through 2623
    Processing helix  chain 'A' and resid 2626 through 2645
      removed outlier: 3.702A  pdb=" N   PHE A2641 " --> pdb=" O   ARG A2637 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   HIS A2644 " --> pdb=" O   ILE A2640 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   VAL A2645 " --> pdb=" O   PHE A2641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2645 through 2657
      removed outlier: 6.671A  pdb=" N   ILE A2654 " --> pdb=" O   ARG A2650 " (cutoff:3.500A)
      removed outlier: 6.661A  pdb=" N   LEU A2655 " --> pdb=" O   ARG A2651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2660 through 2664
      removed outlier: 3.665A  pdb=" N   GLY A2664 " --> pdb=" O   SER A2661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2678 through 2697
    Processing helix  chain 'A' and resid 2698 through 2701
    Processing helix  chain 'A' and resid 2753 through 2765
    Processing helix  chain 'A' and resid 2770 through 2783
    Processing helix  chain 'A' and resid 2806 through 2816
    Processing helix  chain 'A' and resid 2816 through 2836
    Processing helix  chain 'A' and resid 2899 through 2911
    Processing helix  chain 'A' and resid 2993 through 3003
    Processing helix  chain 'A' and resid 3043 through 3060
    Processing helix  chain 'A' and resid 3062 through 3072
    Processing helix  chain 'A' and resid 3093 through 3099
    Processing helix  chain 'A' and resid 3104 through 3114
    Processing helix  chain 'A' and resid 3114 through 3122
      removed outlier: 4.305A  pdb=" N   ILE A3118 " --> pdb=" O   ASP A3114 " (cutoff:3.500A)
      removed outlier: 4.313A  pdb=" N   SER A3119 " --> pdb=" O   GLU A3115 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3130 through 3141
      removed outlier: 3.668A  pdb=" N   GLN A3140 " --> pdb=" O   PHE A3136 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   PHE A3141 " --> pdb=" O   LYS A3137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3142 through 3163
      removed outlier: 3.514A  pdb=" N   PHE A3146 " --> pdb=" O   PHE A3142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3167 through 3172
    Processing helix  chain 'A' and resid 3174 through 3185
    Processing helix  chain 'A' and resid 3208 through 3217
      removed outlier: 3.732A  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: 6.739A  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 1357 through 1362
      removed outlier: 3.853A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
      removed outlier: 6.060A  pdb=" N   MET A1382 " --> pdb=" O   PHE A1398 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   PHE A1398 " --> pdb=" O   MET A1382 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   CYS A1384 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      removed outlier: 6.218A  pdb=" N   GLY A1396 " --> pdb=" O   CYS A1384 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   LEU A1386 " --> pdb=" O   LEU A1394 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2338 through 2339
      removed outlier: 4.154A  pdb=" N   LYS A2338 " --> pdb=" O   ASN A2348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2338 through 2339
      removed outlier: 4.154A  pdb=" N   LYS A2338 " --> pdb=" O   ASN A2348 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2399 through 2402
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576
      removed outlier: 4.548A  pdb=" N   PHE A2580 " --> pdb=" O   THR A2587 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3005 through 3009
      removed outlier: 6.337A  pdb=" N   SER A3005 " --> pdb=" O   LEU A3039 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   VAL A3041 " --> pdb=" O   SER A3005 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   SER A3007 " --> pdb=" O   VAL A3041 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3079 through 3080
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3086 through 3089

    629 hydrogen bonds defined for protein.
    1824 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.80

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3441
        1.34 -     1.46: 2036
        1.46 -     1.58: 5135
        1.58 -     1.70: 0
        1.70 -     1.81: 111
  Bond restraints: 10723
  Sorted by residual:
  bond pdb=" C   VAL A1288 "
       pdb=" N   PRO A1289 "
    ideal  model  delta    sigma   weight residual
    1.335  1.358 -0.023 1.30e-02 5.92e+03 3.13e+00
  bond pdb=" CA  THR A1595 "
       pdb=" C   THR A1595 "
    ideal  model  delta    sigma   weight residual
    1.524  1.507  0.017 1.32e-02 5.74e+03 1.66e+00
  bond pdb=" CG1 ILE A1432 "
       pdb=" CD1 ILE A1432 "
    ideal  model  delta    sigma   weight residual
    1.513  1.471  0.042 3.90e-02 6.57e+02 1.18e+00
  bond pdb=" C   THR A1595 "
       pdb=" O   THR A1595 "
    ideal  model  delta    sigma   weight residual
    1.236  1.223  0.013 1.22e-02 6.72e+03 1.12e+00
  bond pdb=" N   THR A1595 "
       pdb=" CA  THR A1595 "
    ideal  model  delta    sigma   weight residual
    1.458  1.471 -0.012 1.26e-02 6.30e+03 9.08e-01
  ... (remaining 10718 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 14299
        1.64 -     3.28: 164
        3.28 -     4.92: 30
        4.92 -     6.56: 3
        6.56 -     8.20: 3
  Bond angle restraints: 14499
  Sorted by residual:
  angle pdb=" CA  THR A1595 "
        pdb=" CB  THR A1595 "
        pdb=" OG1 THR A1595 "
      ideal   model   delta    sigma   weight residual
     109.60  104.57    5.03 1.50e+00 4.44e-01 1.13e+01
  angle pdb=" CA  MET A3151 "
        pdb=" CB  MET A3151 "
        pdb=" CG  MET A3151 "
      ideal   model   delta    sigma   weight residual
     114.10  119.09   -4.99 2.00e+00 2.50e-01 6.23e+00
  angle pdb=" CA  LEU A3152 "
        pdb=" CB  LEU A3152 "
        pdb=" CG  LEU A3152 "
      ideal   model   delta    sigma   weight residual
     116.30  124.50   -8.20 3.50e+00 8.16e-02 5.49e+00
  angle pdb=" CA  LEU A1644 "
        pdb=" CB  LEU A1644 "
        pdb=" CG  LEU A1644 "
      ideal   model   delta    sigma   weight residual
     116.30  124.45   -8.15 3.50e+00 8.16e-02 5.42e+00
  angle pdb=" CA  VAL A1570 "
        pdb=" CB  VAL A1570 "
        pdb=" CG2 VAL A1570 "
      ideal   model   delta    sigma   weight residual
     110.40  114.12   -3.72 1.70e+00 3.46e-01 4.78e+00
  ... (remaining 14494 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 5575
       17.99 -    35.97: 706
       35.97 -    53.96: 190
       53.96 -    71.95: 30
       71.95 -    89.94: 9
  Dihedral angle restraints: 6510
    sinusoidal: 2540
      harmonic: 3970
  Sorted by residual:
  dihedral pdb=" CA  MET A1391 "
           pdb=" C   MET A1391 "
           pdb=" N   GLU A1392 "
           pdb=" CA  GLU A1392 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.87   18.13     0      5.00e+00 4.00e-02 1.32e+01
  dihedral pdb=" CA  LEU A3202 "
           pdb=" C   LEU A3202 "
           pdb=" N   MET A3203 "
           pdb=" CA  MET A3203 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.36   16.64     0      5.00e+00 4.00e-02 1.11e+01
  dihedral pdb=" CB  GLU A3038 "
           pdb=" CG  GLU A3038 "
           pdb=" CD  GLU A3038 "
           pdb=" OE1 GLU A3038 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.94   89.94     1      3.00e+01 1.11e-03 1.07e+01
  ... (remaining 6507 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1350
       0.044 -    0.089: 272
       0.089 -    0.133: 69
       0.133 -    0.177: 2
       0.177 -    0.222: 1
  Chirality restraints: 1694
  Sorted by residual:
  chirality pdb=" CB  VAL A1570 "
            pdb=" CA  VAL A1570 "
            pdb=" CG1 VAL A1570 "
            pdb=" CG2 VAL A1570 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ILE A2353 "
            pdb=" N   ILE A2353 "
            pdb=" C   ILE A2353 "
            pdb=" CB  ILE A2353 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.11e-01
  chirality pdb=" CA  ILE A2528 "
            pdb=" N   ILE A2528 "
            pdb=" C   ILE A2528 "
            pdb=" CB  ILE A2528 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.44e-01
  ... (remaining 1691 not shown)

  Planarity restraints: 1841
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A1286 "    0.011 2.00e-02 2.50e+03   2.10e-02 4.41e+00
        pdb=" C   GLN A1286 "   -0.036 2.00e-02 2.50e+03
        pdb=" O   GLN A1286 "    0.014 2.00e-02 2.50e+03
        pdb=" N   PRO A1287 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A3021 "    0.026 5.00e-02 4.00e+02   4.05e-02 2.62e+00
        pdb=" N   PRO A3022 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO A3022 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A3022 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A1286 "   -0.026 5.00e-02 4.00e+02   3.96e-02 2.51e+00
        pdb=" N   PRO A1287 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A1287 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A1287 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1838 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 118
        2.59 -     3.17: 8704
        3.17 -     3.74: 17747
        3.74 -     4.32: 24094
        4.32 -     4.90: 40067
  Nonbonded interactions: 90730
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A3081 "
            pdb="MG    MG A4004 "
     model   vdw
     2.010 2.170
  nonbonded pdb=" OE2 GLU A2788 "
            pdb="ZN    ZN A4002 "
     model   vdw
     2.080 2.230
  nonbonded pdb=" OE1 GLU A2575 "
            pdb="MN    MN A4003 "
     model   vdw
     2.100 2.320
  nonbonded pdb=" OD2 ASP A2518 "
            pdb="MN    MN A4003 "
     model   vdw
     2.103 2.320
  nonbonded pdb=" OD1 ASP A2518 "
            pdb="MN    MN A4003 "
     model   vdw
     2.153 2.320
  ... (remaining 90725 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             4.600
  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:             0.020
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.580
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.560
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
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      :  0.002   0.046  10729  Z= 0.097
  Angle     :  0.466   8.202  14505  Z= 0.251
  Chirality :  0.037   0.222   1694
  Planarity :  0.003   0.040   1841
  Dihedral  : 16.993  89.935   3918
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.11 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 23.65 %
    Favored  : 76.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.00 (0.24), residues: 1325
  helix:  2.42 (0.19), residues: 788
  sheet:  1.25 (0.65), residues: 73
  loop : -0.63 (0.29), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A1465 
 TYR   0.009   0.001   TYR A1054 
 PHE   0.018   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.003   0.000   HIS A3177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00203 /  0.10 (10723)
  covalent geometry    : angle       0.46615 /  0.25 (14499)
  hydrogen bonds       : bond        0.10312 /  6.53 (  628)
  hydrogen bonds       : angle       4.55250 /  3.26 ( 1824)
  metal coordination   : bond        0.00113 /  0.07 (    6)
  metal coordination   : angle       0.80437 /  0.44 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 166
  time to evaluate  : 0.474 
Fit side-chains
REVERT: A  952 LEU cc_start: 0.7489 (tt) cc_final: 0.7234 (tp)
REVERT: A  974 LYS cc_start: 0.7601 (tptt) cc_final: 0.7382 (tmtt)
REVERT: A 1047 GLU cc_start: 0.7517 (mt-10) cc_final: 0.7144 (mt-10)
REVERT: A 1059 THR cc_start: 0.7851 (p) cc_final: 0.7448 (t)
REVERT: A 1323 LEU cc_start: 0.8389 (tp) cc_final: 0.8102 (tp)
REVERT: A 1374 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6772 (mt)
REVERT: A 1390 ASN cc_start: 0.6789 (m-40) cc_final: 0.6462 (m110)
REVERT: A 1403 ARG cc_start: 0.7833 (ptm160) cc_final: 0.7594 (ptm160)
REVERT: A 1438 LYS cc_start: 0.8133 (tppt) cc_final: 0.7419 (tptp)
REVERT: A 1520 LYS cc_start: 0.7625 (mtmt) cc_final: 0.6872 (mmtt)
REVERT: A 1620 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6736 (pt0)
REVERT: A 2319 GLU cc_start: 0.7872 (tt0) cc_final: 0.7202 (mp0)
REVERT: A 3077 GLU cc_start: 0.7636 (mt-10) cc_final: 0.7194 (mm-30)
REVERT: A 3203 MET cc_start: 0.4992 (pmm) cc_final: 0.3063 (mmm)
  outliers start: 3
  outliers final: 2
  residues processed: 167
  average time/residue: 0.5777
  time to fit residues: 103.9940
Evaluate side-chains
  152 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 149
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1374 LEU
Chi-restraints excluded: chain A residue 1401 ASN
Chi-restraints excluded: chain A residue 3012 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 55]
   chunk 98 optimal weight:    5.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    5.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1799 ASN
A2396 ASN
A3009 ASN
** A3103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.149534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114274 restraints weight = 11654.521|
|-----------------------------------------------------------------------------|
r_work (start): 0.3303 rms_B_bonded: 1.80
r_work: 0.3189 rms_B_bonded: 2.36 restraints_weight: 0.5000
r_work: 0.3071 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8417
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.060  10729  Z= 0.233
  Angle     :  0.577   8.606  14505  Z= 0.305
  Chirality :  0.044   0.234   1694
  Planarity :  0.004   0.054   1841
  Dihedral  :  4.252  37.290   1449
  Min Nonbonded Distance : 1.880

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.72 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.26 %
    Favored  : 74.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.23 (0.23), residues: 1325
  helix:  1.76 (0.18), residues: 787
  sheet:  1.22 (0.65), residues: 72
  loop : -0.90 (0.27), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A2750 
 TYR   0.013   0.002   TYR A2584 
 PHE   0.024   0.002   PHE A2633 
 TRP   0.017   0.001   TRP A2542 
 HIS   0.006   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00566 /  0.23 (10723)
  covalent geometry    : angle       0.57622 /  0.31 (14499)
  hydrogen bonds       : bond        0.04465 /  2.95 (  628)
  hydrogen bonds       : angle       4.22341 /  3.06 ( 1824)
  metal coordination   : bond        0.00532 /  0.34 (    6)
  metal coordination   : angle       1.80836 /  1.06 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 138
  time to evaluate  : 0.314 
Fit side-chains
REVERT: A  974 LYS cc_start: 0.7666 (tptt) cc_final: 0.7358 (tptt)
REVERT: A 1001 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8424 (pttp)
REVERT: A 1047 GLU cc_start: 0.7690 (mt-10) cc_final: 0.7261 (mt-10)
REVERT: A 1350 CYS cc_start: 0.7511 (m) cc_final: 0.7194 (t)
REVERT: A 1438 LYS cc_start: 0.8109 (tppt) cc_final: 0.7264 (tptt)
REVERT: A 1465 ARG cc_start: 0.8070 (mtm110) cc_final: 0.7838 (mtm110)
REVERT: A 1509 ASP cc_start: 0.8302 (m-30) cc_final: 0.8062 (m-30)
REVERT: A 1520 LYS cc_start: 0.7767 (mtmt) cc_final: 0.6944 (mmtt)
REVERT: A 1620 GLU cc_start: 0.7186 (mm-30) cc_final: 0.6793 (pt0)
REVERT: A 1758 ASN cc_start: 0.7989 (t0) cc_final: 0.7730 (t0)
REVERT: A 1804 ARG cc_start: 0.5889 (OUTLIER) cc_final: 0.4948 (ttm170)
REVERT: A 2529 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7470 (pp)
REVERT: A 3077 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7297 (mm-30)
REVERT: A 3112 LEU cc_start: 0.7065 (OUTLIER) cc_final: 0.6771 (mp)
REVERT: A 3221 ARG cc_start: 0.8503 (OUTLIER) cc_final: 0.6198 (mmp-170)
  outliers start: 45
  outliers final: 20
  residues processed: 170
  average time/residue: 0.5194
  time to fit residues: 95.5466
Evaluate side-chains
  159 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.385 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  934 VAL
Chi-restraints excluded: chain A residue 1001 LYS
Chi-restraints excluded: chain A residue 1025 SER
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1382 MET
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 1660 THR
Chi-restraints excluded: chain A residue 1804 ARG
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2391 LEU
Chi-restraints excluded: chain A residue 2507 THR
Chi-restraints excluded: chain A residue 2516 SER
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2766 LEU
Chi-restraints excluded: chain A residue 2796 VAL
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3014 VAL
Chi-restraints excluded: chain A residue 3112 LEU
Chi-restraints excluded: chain A residue 3171 VAL
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [110, 111, 71, 72, 32, 6, 61, 34, 127, 52, 126]
   chunk 110 optimal weight:    0.7980
   chunk 111 optimal weight:    0.4980
   chunk 71 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 32 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   chunk 34 optimal weight:    2.9990
   chunk 127 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 126 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 GLN
A1799 ASN
A3103 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.152847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.117638 restraints weight = 11696.554|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 1.81
r_work: 0.3234 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8372
moved from start:          0.1277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10729  Z= 0.119
  Angle     :  0.466   7.461  14505  Z= 0.250
  Chirality :  0.039   0.186   1694
  Planarity :  0.003   0.049   1841
  Dihedral  :  3.871  23.923   1445
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.26 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 22.63 %
    Favored  : 74.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.23), residues: 1325
  helix:  1.91 (0.18), residues: 792
  sheet:  1.23 (0.64), residues: 72
  loop : -0.96 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1465 
 TYR   0.015   0.001   TYR A1054 
 PHE   0.024   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 (10723)
  covalent geometry    : angle       0.46518 /  0.25 (14499)
  hydrogen bonds       : bond        0.03539 /  2.33 (  628)
  hydrogen bonds       : angle       3.93722 /  2.86 ( 1824)
  metal coordination   : bond        0.00302 /  0.18 (    6)
  metal coordination   : angle       1.25939 /  0.71 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 144
  time to evaluate  : 0.420 
Fit side-chains
REVERT: A  962 MET cc_start: 0.8319 (OUTLIER) cc_final: 0.8059 (mtp)
REVERT: A  974 LYS cc_start: 0.7768 (tptt) cc_final: 0.7346 (tptt)
REVERT: A 1266 SER cc_start: 0.8122 (p) cc_final: 0.7894 (m)
REVERT: A 1350 CYS cc_start: 0.7526 (m) cc_final: 0.7223 (t)
REVERT: A 1438 LYS cc_start: 0.8087 (tppt) cc_final: 0.7227 (tptt)
REVERT: A 1516 GLN cc_start: 0.7599 (mt0) cc_final: 0.7127 (mm110)
REVERT: A 1620 GLU cc_start: 0.7194 (mm-30) cc_final: 0.6827 (pt0)
REVERT: A 1804 ARG cc_start: 0.5921 (OUTLIER) cc_final: 0.5717 (ttt180)
REVERT: A 2395 LYS cc_start: 0.7932 (mtpp) cc_final: 0.7414 (mtmt)
REVERT: A 2458 ILE cc_start: 0.4169 (OUTLIER) cc_final: 0.3870 (pp)
REVERT: A 2529 LEU cc_start: 0.7802 (OUTLIER) cc_final: 0.7487 (pp)
REVERT: A 3023 ASN cc_start: 0.7289 (t0) cc_final: 0.7089 (t0)
REVERT: A 3077 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7273 (mm-30)
REVERT: A 3180 LEU cc_start: 0.5417 (tp) cc_final: 0.5186 (mp)
REVERT: A 3186 GLN cc_start: 0.5009 (OUTLIER) cc_final: 0.4687 (tp40)
REVERT: A 3211 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7366 (mp0)
  outliers start: 35
  outliers final: 12
  residues processed: 166
  average time/residue: 0.5296
  time to fit residues: 94.9555
Evaluate side-chains
  152 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 134
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1385 CYS
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 1660 THR
Chi-restraints excluded: chain A residue 1804 ARG
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2458 ILE
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2796 VAL
Chi-restraints excluded: chain A residue 3014 VAL
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3211 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [123, 83, 122, 127, 8, 92, 134, 94, 112, 31, 38]
   chunk 123 optimal weight:   10.0000
   chunk 83 optimal weight:    0.7980
   chunk 122 optimal weight:    7.9990
   chunk 127 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   chunk 92 optimal weight:    0.8980
   chunk 134 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 112 optimal weight:    3.9990
   chunk 31 optimal weight:    3.9990
   chunk 38 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1799 ASN
A2348 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.152383 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.117202 restraints weight = 11839.941|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.81
r_work: 0.3230 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.1390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10729  Z= 0.126
  Angle     :  0.464   7.765  14505  Z= 0.248
  Chirality :  0.039   0.179   1694
  Planarity :  0.003   0.051   1841
  Dihedral  :  3.805  19.972   1444
  Min Nonbonded Distance : 1.946

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 22.20 %
    Favored  : 74.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.41 (0.23), residues: 1325
  helix:  1.95 (0.18), residues: 792
  sheet:  1.23 (0.64), residues: 72
  loop : -0.94 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1465 
 TYR   0.010   0.001   TYR A1503 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00294 /  0.13 (10723)
  covalent geometry    : angle       0.46285 /  0.25 (14499)
  hydrogen bonds       : bond        0.03520 /  2.32 (  628)
  hydrogen bonds       : angle       3.89499 /  2.82 ( 1824)
  metal coordination   : bond        0.00287 /  0.19 (    6)
  metal coordination   : angle       1.35916 /  0.77 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 136
  time to evaluate  : 0.306 
Fit side-chains
REVERT: A  962 MET cc_start: 0.8303 (OUTLIER) cc_final: 0.8051 (mtp)
REVERT: A  974 LYS cc_start: 0.7734 (tptt) cc_final: 0.7338 (tptt)
REVERT: A 1266 SER cc_start: 0.8165 (p) cc_final: 0.7945 (m)
REVERT: A 1350 CYS cc_start: 0.7590 (m) cc_final: 0.7291 (t)
REVERT: A 1438 LYS cc_start: 0.8069 (tppt) cc_final: 0.7200 (tptt)
REVERT: A 1465 ARG cc_start: 0.7976 (mtm110) cc_final: 0.7771 (mtm110)
REVERT: A 1509 ASP cc_start: 0.8237 (m-30) cc_final: 0.8031 (m-30)
REVERT: A 1516 GLN cc_start: 0.7612 (mt0) cc_final: 0.7139 (mm110)
REVERT: A 1620 GLU cc_start: 0.7218 (mm-30) cc_final: 0.6825 (pt0)
REVERT: A 2395 LYS cc_start: 0.7888 (mtpp) cc_final: 0.7394 (mtmt)
REVERT: A 2458 ILE cc_start: 0.4163 (OUTLIER) cc_final: 0.3854 (pp)
REVERT: A 2529 LEU cc_start: 0.7805 (OUTLIER) cc_final: 0.7475 (pp)
REVERT: A 2696 MET cc_start: 0.8501 (mtp) cc_final: 0.8195 (ttm)
REVERT: A 3023 ASN cc_start: 0.7298 (t0) cc_final: 0.7076 (t0)
REVERT: A 3077 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7321 (mm-30)
REVERT: A 3180 LEU cc_start: 0.5487 (tp) cc_final: 0.5266 (mp)
REVERT: A 3186 GLN cc_start: 0.4926 (OUTLIER) cc_final: 0.4659 (tp40)
REVERT: A 3211 GLU cc_start: 0.7814 (OUTLIER) cc_final: 0.7377 (mp0)
REVERT: A 3221 ARG cc_start: 0.8464 (OUTLIER) cc_final: 0.5708 (mmp-170)
  outliers start: 39
  outliers final: 19
  residues processed: 161
  average time/residue: 0.5535
  time to fit residues: 96.2717
Evaluate side-chains
  159 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1003 GLU
Chi-restraints excluded: chain A residue 1025 SER
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1385 CYS
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 1660 THR
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2458 ILE
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2507 THR
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2796 VAL
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3014 VAL
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3198 LEU
Chi-restraints excluded: chain A residue 3211 GLU
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [85, 83, 76, 24, 32, 1, 134, 91, 100, 122, 40]
   chunk 85 optimal weight:    2.9990
   chunk 83 optimal weight:    0.6980
   chunk 76 optimal weight:    3.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 134 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 100 optimal weight:    0.0370
   chunk 122 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.6658

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1799 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.153575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.118519 restraints weight = 11717.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3358 rms_B_bonded: 1.81
r_work: 0.3246 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.3130 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8353
moved from start:          0.1409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10729  Z= 0.108
  Angle     :  0.442   7.463  14505  Z= 0.237
  Chirality :  0.038   0.166   1694
  Planarity :  0.003   0.048   1841
  Dihedral  :  3.730  19.396   1444
  Min Nonbonded Distance : 1.971

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 23.48 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.23), residues: 1325
  helix:  2.04 (0.18), residues: 793
  sheet:  1.21 (0.64), residues: 72
  loop : -0.94 (0.27), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1465 
 TYR   0.014   0.001   TYR A1054 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A3177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00245 /  0.11 (10723)
  covalent geometry    : angle       0.44114 /  0.24 (14499)
  hydrogen bonds       : bond        0.03290 /  2.17 (  628)
  hydrogen bonds       : angle       3.80244 /  2.75 ( 1824)
  metal coordination   : bond        0.00235 /  0.15 (    6)
  metal coordination   : angle       1.31249 /  0.74 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.401 
Fit side-chains
   revert: symmetry clash
REVERT: A  962 MET cc_start: 0.8274 (OUTLIER) cc_final: 0.8038 (mtp)
REVERT: A  974 LYS cc_start: 0.7726 (tptt) cc_final: 0.7288 (tptt)
REVERT: A 1266 SER cc_start: 0.8151 (p) cc_final: 0.7949 (m)
REVERT: A 1350 CYS cc_start: 0.7572 (m) cc_final: 0.7278 (t)
REVERT: A 1438 LYS cc_start: 0.8069 (tppt) cc_final: 0.7204 (tptt)
REVERT: A 1465 ARG cc_start: 0.7956 (mtm110) cc_final: 0.7710 (mtm110)
REVERT: A 1509 ASP cc_start: 0.8190 (m-30) cc_final: 0.7985 (m-30)
REVERT: A 1620 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6789 (pt0)
REVERT: A 2395 LYS cc_start: 0.7853 (mtpp) cc_final: 0.7365 (mtmt)
REVERT: A 2529 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7483 (pp)
REVERT: A 2696 MET cc_start: 0.8501 (mtp) cc_final: 0.8195 (ttm)
REVERT: A 3023 ASN cc_start: 0.7319 (t0) cc_final: 0.7078 (t0)
REVERT: A 3077 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7267 (mm-30)
REVERT: A 3180 LEU cc_start: 0.5494 (tp) cc_final: 0.5285 (mp)
REVERT: A 3186 GLN cc_start: 0.5035 (OUTLIER) cc_final: 0.4738 (tp40)
REVERT: A 3211 GLU cc_start: 0.7771 (OUTLIER) cc_final: 0.7336 (mp0)
  outliers start: 34
  outliers final: 14
  residues processed: 159
  average time/residue: 0.5331
  time to fit residues: 91.6697
Evaluate side-chains
  150 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 132
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1059 THR
Chi-restraints excluded: chain A residue 1385 CYS
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3014 VAL
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3198 LEU
Chi-restraints excluded: chain A residue 3211 GLU
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [47, 46, 39, 132, 114, 25, 72, 96, 110, 50, 101]
   chunk 47 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 39 optimal weight:    0.6980
   chunk 132 optimal weight:    5.9990
   chunk 114 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 72 optimal weight:    7.9990
   chunk 96 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9980
   chunk 50 optimal weight:    3.9990
   chunk 101 optimal weight:    3.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 GLN
A1799 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.152780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.117683 restraints weight = 11741.482|
|-----------------------------------------------------------------------------|
r_work (start): 0.3348 rms_B_bonded: 1.81
r_work: 0.3236 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3120 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.3120
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10729  Z= 0.120
  Angle     :  0.452   7.832  14505  Z= 0.242
  Chirality :  0.039   0.155   1694
  Planarity :  0.003   0.050   1841
  Dihedral  :  3.755  19.727   1444
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.87 %
    Favored  : 97.13 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 22.72 %
    Favored  : 74.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.47 (0.23), residues: 1325
  helix:  2.01 (0.18), residues: 792
  sheet:  1.20 (0.64), residues: 72
  loop : -0.93 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1465 
 TYR   0.010   0.001   TYR A1503 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00280 /  0.12 (10723)
  covalent geometry    : angle       0.45173 /  0.24 (14499)
  hydrogen bonds       : bond        0.03386 /  2.24 (  628)
  hydrogen bonds       : angle       3.82154 /  2.77 ( 1824)
  metal coordination   : bond        0.00265 /  0.17 (    6)
  metal coordination   : angle       1.27391 /  0.72 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 138
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
REVERT: A  962 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8071 (mtp)
REVERT: A  974 LYS cc_start: 0.7762 (tptt) cc_final: 0.7354 (tptt)
REVERT: A 1001 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8347 (pttp)
REVERT: A 1266 SER cc_start: 0.8153 (p) cc_final: 0.7951 (m)
REVERT: A 1350 CYS cc_start: 0.7600 (m) cc_final: 0.7295 (t)
REVERT: A 1388 SER cc_start: 0.8009 (t) cc_final: 0.7317 (p)
REVERT: A 1438 LYS cc_start: 0.8069 (tppt) cc_final: 0.7201 (tptt)
REVERT: A 1620 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6802 (pt0)
REVERT: A 2395 LYS cc_start: 0.7854 (mtpp) cc_final: 0.7378 (mtmt)
REVERT: A 2458 ILE cc_start: 0.4135 (OUTLIER) cc_final: 0.3836 (pp)
REVERT: A 2529 LEU cc_start: 0.7790 (OUTLIER) cc_final: 0.7477 (pp)
REVERT: A 2696 MET cc_start: 0.8507 (mtp) cc_final: 0.8205 (ttm)
REVERT: A 3023 ASN cc_start: 0.7311 (t0) cc_final: 0.7063 (t0)
REVERT: A 3077 GLU cc_start: 0.7867 (mt-10) cc_final: 0.7361 (mm-30)
REVERT: A 3186 GLN cc_start: 0.5075 (OUTLIER) cc_final: 0.4797 (tp40)
REVERT: A 3211 GLU cc_start: 0.7791 (OUTLIER) cc_final: 0.7349 (mp0)
  outliers start: 38
  outliers final: 20
  residues processed: 166
  average time/residue: 0.5200
  time to fit residues: 93.5290
Evaluate side-chains
  162 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 136
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1001 LYS
Chi-restraints excluded: chain A residue 1025 SER
Chi-restraints excluded: chain A residue 1059 THR
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1385 CYS
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2458 ILE
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2507 THR
Chi-restraints excluded: chain A residue 2522 CYS
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2796 VAL
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3014 VAL
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3198 LEU
Chi-restraints excluded: chain A residue 3211 GLU
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [86, 90, 29, 11, 79, 91, 68, 57, 113, 28, 134]
   chunk 86 optimal weight:    0.7980
   chunk 90 optimal weight:    1.9990
   chunk 29 optimal weight:    0.3980
   chunk 11 optimal weight:    0.8980
   chunk 79 optimal weight:    4.9990
   chunk 91 optimal weight:    0.6980
   chunk 68 optimal weight:    0.0770
   chunk 57 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 134 optimal weight:    2.9990
   overall best weight:    0.5738

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 GLN
A1799 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.154175 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.119375 restraints weight = 11614.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.3367 rms_B_bonded: 1.79
r_work: 0.3252 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.3136 rms_B_bonded: 3.98 restraints_weight: 0.2500
r_work (final): 0.3136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10729  Z= 0.104
  Angle     :  0.442   7.518  14505  Z= 0.237
  Chirality :  0.038   0.150   1694
  Planarity :  0.003   0.047   1841
  Dihedral  :  3.704  19.186   1444
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.65 %
    Favored  : 73.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.23), residues: 1325
  helix:  2.09 (0.18), residues: 793
  sheet:  1.06 (0.63), residues: 74
  loop : -0.91 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1465 
 TYR   0.016   0.001   TYR A1054 
 PHE   0.026   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A3177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00233 /  0.10 (10723)
  covalent geometry    : angle       0.44077 /  0.24 (14499)
  hydrogen bonds       : bond        0.03200 /  2.11 (  628)
  hydrogen bonds       : angle       3.75980 /  2.72 ( 1824)
  metal coordination   : bond        0.00215 /  0.14 (    6)
  metal coordination   : angle       1.36482 /  0.77 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 139
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
REVERT: A  962 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.8054 (mtp)
REVERT: A  974 LYS cc_start: 0.7765 (tptt) cc_final: 0.7297 (tptt)
REVERT: A 1001 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8323 (pttp)
REVERT: A 1350 CYS cc_start: 0.7580 (m) cc_final: 0.7314 (t)
REVERT: A 1388 SER cc_start: 0.7977 (t) cc_final: 0.7326 (p)
REVERT: A 1438 LYS cc_start: 0.8071 (tppt) cc_final: 0.7210 (tptt)
REVERT: A 1478 ARG cc_start: 0.7945 (mtt-85) cc_final: 0.7488 (mtm110)
REVERT: A 1620 GLU cc_start: 0.7266 (mm-30) cc_final: 0.6766 (pt0)
REVERT: A 1759 LYS cc_start: 0.7306 (mtpp) cc_final: 0.6925 (mttm)
REVERT: A 2458 ILE cc_start: 0.4113 (OUTLIER) cc_final: 0.3825 (pp)
REVERT: A 2529 LEU cc_start: 0.7773 (OUTLIER) cc_final: 0.7481 (pp)
REVERT: A 2696 MET cc_start: 0.8492 (mtp) cc_final: 0.8194 (ttm)
REVERT: A 3023 ASN cc_start: 0.7320 (t0) cc_final: 0.7095 (t0)
REVERT: A 3077 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7303 (mm-30)
REVERT: A 3186 GLN cc_start: 0.5109 (OUTLIER) cc_final: 0.4811 (tp40)
REVERT: A 3211 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7307 (mp0)
  outliers start: 31
  outliers final: 19
  residues processed: 163
  average time/residue: 0.5232
  time to fit residues: 92.0988
Evaluate side-chains
  159 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1001 LYS
Chi-restraints excluded: chain A residue 1025 SER
Chi-restraints excluded: chain A residue 1051 LEU
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2458 ILE
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2507 THR
Chi-restraints excluded: chain A residue 2522 CYS
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2579 GLU
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3014 VAL
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3198 LEU
Chi-restraints excluded: chain A residue 3211 GLU
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [8, 1, 32, 101, 104, 87, 11, 80, 44, 25, 76]
   chunk 8 optimal weight:    0.6980
   chunk 1 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 101 optimal weight:    2.9990
   chunk 104 optimal weight:    4.9990
   chunk 87 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 25 optimal weight:    0.5980
   chunk 76 optimal weight:    3.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 GLN
A1799 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.152408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.117315 restraints weight = 11597.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.80
r_work: 0.3229 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10729  Z= 0.132
  Angle     :  0.476   7.848  14505  Z= 0.252
  Chirality :  0.039   0.154   1694
  Planarity :  0.003   0.049   1841
  Dihedral  :  3.789  20.235   1444
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 23.83 %
    Favored  : 73.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.23), residues: 1325
  helix:  2.01 (0.18), residues: 792
  sheet:  1.15 (0.64), residues: 72
  loop : -0.91 (0.27), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A1465 
 TYR   0.009   0.001   TYR A1503 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A3177 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00311 /  0.13 (10723)
  covalent geometry    : angle       0.47520 /  0.25 (14499)
  hydrogen bonds       : bond        0.03475 /  2.30 (  628)
  hydrogen bonds       : angle       3.83815 /  2.77 ( 1824)
  metal coordination   : bond        0.00279 /  0.18 (    6)
  metal coordination   : angle       1.36838 /  0.78 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 135
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  962 MET cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (mtp)
REVERT: A  974 LYS cc_start: 0.7772 (tptt) cc_final: 0.7306 (tptt)
REVERT: A 1001 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8347 (pttp)
REVERT: A 1350 CYS cc_start: 0.7589 (m) cc_final: 0.7339 (t)
REVERT: A 1388 SER cc_start: 0.8001 (t) cc_final: 0.7324 (p)
REVERT: A 1438 LYS cc_start: 0.8093 (tppt) cc_final: 0.7285 (tptp)
REVERT: A 1465 ARG cc_start: 0.7958 (mtm110) cc_final: 0.7705 (mtm110)
REVERT: A 1516 GLN cc_start: 0.7583 (mt0) cc_final: 0.7057 (mm110)
REVERT: A 1620 GLU cc_start: 0.7248 (mm-30) cc_final: 0.6771 (pt0)
REVERT: A 2458 ILE cc_start: 0.4185 (OUTLIER) cc_final: 0.3880 (pp)
REVERT: A 2529 LEU cc_start: 0.7786 (OUTLIER) cc_final: 0.7490 (pp)
REVERT: A 2696 MET cc_start: 0.8482 (mtp) cc_final: 0.8196 (ttm)
REVERT: A 3023 ASN cc_start: 0.7382 (t0) cc_final: 0.7158 (t0)
REVERT: A 3077 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7343 (mm-30)
REVERT: A 3186 GLN cc_start: 0.5176 (OUTLIER) cc_final: 0.4874 (tp40)
REVERT: A 3211 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7390 (mp0)
REVERT: A 3221 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.5855 (mmp-170)
  outliers start: 35
  outliers final: 18
  residues processed: 161
  average time/residue: 0.5337
  time to fit residues: 92.8854
Evaluate side-chains
  156 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1001 LYS
Chi-restraints excluded: chain A residue 1025 SER
Chi-restraints excluded: chain A residue 1059 THR
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1385 CYS
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2458 ILE
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2507 THR
Chi-restraints excluded: chain A residue 2522 CYS
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2796 VAL
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3198 LEU
Chi-restraints excluded: chain A residue 3211 GLU
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [109, 133, 54, 42, 108, 88, 82, 121, 105, 48, 70]
   chunk 109 optimal weight:    2.9990
   chunk 133 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9980
   chunk 108 optimal weight:    4.9990
   chunk 88 optimal weight:    0.7980
   chunk 82 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   chunk 105 optimal weight:    0.9990
   chunk 48 optimal weight:    1.9990
   chunk 70 optimal weight:    0.8980
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1799 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.152392 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.117413 restraints weight = 11709.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.3342 rms_B_bonded: 1.80
r_work: 0.3229 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8370
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10729  Z= 0.127
  Angle     :  0.471   7.809  14505  Z= 0.250
  Chirality :  0.039   0.153   1694
  Planarity :  0.003   0.049   1841
  Dihedral  :  3.802  20.592   1444
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 24.77 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.50 (0.23), residues: 1325
  helix:  2.02 (0.18), residues: 791
  sheet:  1.11 (0.64), residues: 72
  loop : -0.88 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A1465 
 TYR   0.018   0.001   TYR A1054 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.13 (10723)
  covalent geometry    : angle       0.47016 /  0.25 (14499)
  hydrogen bonds       : bond        0.03443 /  2.28 (  628)
  hydrogen bonds       : angle       3.83150 /  2.77 ( 1824)
  metal coordination   : bond        0.00258 /  0.17 (    6)
  metal coordination   : angle       1.34381 /  0.76 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 136
  time to evaluate  : 0.396 
Fit side-chains
REVERT: A  962 MET cc_start: 0.8299 (OUTLIER) cc_final: 0.8078 (mtp)
REVERT: A  974 LYS cc_start: 0.7773 (tptt) cc_final: 0.7311 (tptt)
REVERT: A 1001 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8353 (pttp)
REVERT: A 1350 CYS cc_start: 0.7627 (m) cc_final: 0.7395 (t)
REVERT: A 1388 SER cc_start: 0.7996 (t) cc_final: 0.7331 (p)
REVERT: A 1438 LYS cc_start: 0.8095 (tppt) cc_final: 0.7219 (tptt)
REVERT: A 1465 ARG cc_start: 0.7951 (mtm110) cc_final: 0.7671 (mtm110)
REVERT: A 1516 GLN cc_start: 0.7564 (mt0) cc_final: 0.7027 (mm110)
REVERT: A 1620 GLU cc_start: 0.7249 (mm-30) cc_final: 0.6768 (pt0)
REVERT: A 2458 ILE cc_start: 0.4290 (OUTLIER) cc_final: 0.3988 (pp)
REVERT: A 2529 LEU cc_start: 0.7784 (OUTLIER) cc_final: 0.7510 (pp)
REVERT: A 2655 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7923 (mp)
REVERT: A 2696 MET cc_start: 0.8481 (mtp) cc_final: 0.8218 (ttm)
REVERT: A 2993 LYS cc_start: 0.8259 (mtpt) cc_final: 0.7972 (ptpt)
REVERT: A 3023 ASN cc_start: 0.7429 (t0) cc_final: 0.7139 (t0)
REVERT: A 3077 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7487 (mm-30)
REVERT: A 3186 GLN cc_start: 0.5272 (OUTLIER) cc_final: 0.4971 (tp40)
REVERT: A 3211 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7380 (mp0)
REVERT: A 3221 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.5825 (mmp-170)
  outliers start: 29
  outliers final: 17
  residues processed: 159
  average time/residue: 0.5368
  time to fit residues: 92.2599
Evaluate side-chains
  156 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.409 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1001 LYS
Chi-restraints excluded: chain A residue 1025 SER
Chi-restraints excluded: chain A residue 1059 THR
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1385 CYS
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2458 ILE
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2507 THR
Chi-restraints excluded: chain A residue 2522 CYS
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2655 LEU
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3198 LEU
Chi-restraints excluded: chain A residue 3211 GLU
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [69, 93, 109, 54, 125, 116, 1, 41, 89, 62, 123]
   chunk 69 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 109 optimal weight:    0.9980
   chunk 54 optimal weight:    0.9990
   chunk 125 optimal weight:    7.9990
   chunk 116 optimal weight:    5.9990
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    3.9990
   chunk 89 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 123 optimal weight:    6.9990
   overall best weight:    0.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1523 GLN
A1799 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.152265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.117179 restraints weight = 11652.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 1.80
r_work: 0.3228 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.3114 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8371
moved from start:          0.1661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10729  Z= 0.129
  Angle     :  0.480   7.819  14505  Z= 0.254
  Chirality :  0.039   0.153   1694
  Planarity :  0.003   0.050   1841
  Dihedral  :  3.817  20.366   1444
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 7.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 25.11 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.48 (0.23), residues: 1325
  helix:  2.00 (0.18), residues: 791
  sheet:  1.10 (0.64), residues: 72
  loop : -0.88 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1465 
 TYR   0.009   0.001   TYR A1503 
 PHE   0.027   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 (10723)
  covalent geometry    : angle       0.47881 /  0.25 (14499)
  hydrogen bonds       : bond        0.03457 /  2.29 (  628)
  hydrogen bonds       : angle       3.87026 /  2.81 ( 1824)
  metal coordination   : bond        0.00278 /  0.18 (    6)
  metal coordination   : angle       1.36810 /  0.78 (    6)

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

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

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2650 Ramachandran restraints generated.
    1325 Oldfield, 0 Emsley, 1325 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 135
  time to evaluate  : 0.409 
Fit side-chains
REVERT: A  962 MET cc_start: 0.8297 (OUTLIER) cc_final: 0.8079 (mtp)
REVERT: A  974 LYS cc_start: 0.7768 (tptt) cc_final: 0.7309 (tptt)
REVERT: A 1001 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8355 (pttp)
REVERT: A 1350 CYS cc_start: 0.7644 (m) cc_final: 0.7416 (t)
REVERT: A 1388 SER cc_start: 0.7977 (t) cc_final: 0.7320 (p)
REVERT: A 1438 LYS cc_start: 0.8094 (tppt) cc_final: 0.7218 (tptt)
REVERT: A 1452 GLU cc_start: 0.7937 (OUTLIER) cc_final: 0.6918 (tm-30)
REVERT: A 1465 ARG cc_start: 0.7981 (mtm110) cc_final: 0.7684 (mtm110)
REVERT: A 1516 GLN cc_start: 0.7576 (mt0) cc_final: 0.7033 (mm110)
REVERT: A 1620 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6765 (pt0)
REVERT: A 2458 ILE cc_start: 0.4305 (OUTLIER) cc_final: 0.4003 (pp)
REVERT: A 2529 LEU cc_start: 0.7796 (OUTLIER) cc_final: 0.7541 (pp)
REVERT: A 2655 LEU cc_start: 0.8345 (OUTLIER) cc_final: 0.7940 (mp)
REVERT: A 2696 MET cc_start: 0.8469 (mtp) cc_final: 0.8217 (ttm)
REVERT: A 3023 ASN cc_start: 0.7375 (t0) cc_final: 0.7121 (t0)
REVERT: A 3077 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7469 (mm-30)
REVERT: A 3186 GLN cc_start: 0.5272 (OUTLIER) cc_final: 0.4991 (tp40)
REVERT: A 3211 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7394 (mp0)
REVERT: A 3221 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.5879 (mmp-170)
  outliers start: 29
  outliers final: 17
  residues processed: 159
  average time/residue: 0.5533
  time to fit residues: 94.8928
Evaluate side-chains
  158 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 132
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  962 MET
Chi-restraints excluded: chain A residue  977 SER
Chi-restraints excluded: chain A residue 1001 LYS
Chi-restraints excluded: chain A residue 1025 SER
Chi-restraints excluded: chain A residue 1059 THR
Chi-restraints excluded: chain A residue 1078 VAL
Chi-restraints excluded: chain A residue 1385 CYS
Chi-restraints excluded: chain A residue 1407 LEU
Chi-restraints excluded: chain A residue 1452 GLU
Chi-restraints excluded: chain A residue 1458 ILE
Chi-restraints excluded: chain A residue 1573 VAL
Chi-restraints excluded: chain A residue 2340 ILE
Chi-restraints excluded: chain A residue 2352 VAL
Chi-restraints excluded: chain A residue 2356 SER
Chi-restraints excluded: chain A residue 2458 ILE
Chi-restraints excluded: chain A residue 2485 SER
Chi-restraints excluded: chain A residue 2507 THR
Chi-restraints excluded: chain A residue 2522 CYS
Chi-restraints excluded: chain A residue 2529 LEU
Chi-restraints excluded: chain A residue 2655 LEU
Chi-restraints excluded: chain A residue 2796 VAL
Chi-restraints excluded: chain A residue 2830 ILE
Chi-restraints excluded: chain A residue 3012 THR
Chi-restraints excluded: chain A residue 3186 GLN
Chi-restraints excluded: chain A residue 3211 GLU
Chi-restraints excluded: chain A residue 3221 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks: [60, 23, 63, 99, 54, 90, 36, 130, 121, 77, 107]
   chunk 60 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0770
   chunk 99 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 90 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 130 optimal weight:    6.9990
   chunk 121 optimal weight:    6.9990
   chunk 77 optimal weight:    3.9990
   chunk 107 optimal weight:    2.9990
   overall best weight:    1.4142

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 960 GLN
** A1074 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1277 GLN
** A1284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1523 GLN
A1799 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.150508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115387 restraints weight = 11741.142|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 1.80
r_work: 0.3206 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3090 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.3090
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.1772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  10729  Z= 0.166
  Angle     :  0.511   9.007  14505  Z= 0.270
  Chirality :  0.041   0.155   1694
  Planarity :  0.003   0.051   1841
  Dihedral  :  3.960  21.637   1444
  Min Nonbonded Distance : 1.930

Molprobity Statistics.
  All-atom Clashscore : 7.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 24.85 %
    Favored  : 72.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.33 (0.23), residues: 1325
  helix:  1.87 (0.18), residues: 790
  sheet:  0.89 (0.63), residues: 74
  loop : -0.88 (0.28), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1465 
 TYR   0.022   0.002   TYR A1054 
 PHE   0.029   0.002   PHE A2633 
 TRP   0.014   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1491 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00396 /  0.17 (10723)
  covalent geometry    : angle       0.51020 /  0.27 (14499)
  hydrogen bonds       : bond        0.03772 /  2.51 (  628)
  hydrogen bonds       : angle       3.98314 /  2.89 ( 1824)
  metal coordination   : bond        0.00328 /  0.23 (    6)
  metal coordination   : angle       1.33252 /  0.76 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4014.32 seconds
wall clock time: 69 minutes 15.42 seconds (4155.42 seconds total)