Starting phenix.real_space_refine
on Fri Sep 11 17:53:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/25xl_80447/09_2026/25xl_80447.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/25xl_80447/09_2026/25xl_80447.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/25xl_80447/09_2026/25xl_80447.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/25xl_80447/09_2026/25xl_80447.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/25xl_80447/09_2026/25xl_80447.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/25xl_80447/09_2026/25xl_80447.map"
  }
  resolution = 2.88
  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=   0.015
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      71      5.16       5
     C    6468      2.51       5
     N    1775      2.21       5
     O    1836      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10152
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10149
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1363, 10138
          Classifications: {'peptide': 1363}
          Incomplete info: {'truncation_to_alanine': 227}
          Link IDs: {'PTRANS': 41, 'TRANS': 1321}
          Chain breaks: 15
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 786
          Unresolved non-hydrogen angles: 966
          Unresolved non-hydrogen dihedrals: 637
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'ASP:plan': 28, 'GLU:plan': 50, 'GLN:plan1': 13, 'ARG:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 475
      Conformer: "B"
        Number of residues, atoms: 1363, 10138
          Classifications: {'peptide': 1363}
          Incomplete info: {'truncation_to_alanine': 227}
          Link IDs: {'PTRANS': 41, 'TRANS': 1321}
          Chain breaks: 15
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 786
          Unresolved non-hydrogen angles: 966
          Unresolved non-hydrogen dihedrals: 637
          Unresolved non-hydrogen chiralities: 40
          Planarities with less than four sites: {'ASP:plan': 28, 'GLU:plan': 50, 'GLN:plan1': 13, 'ARG:plan': 7, 'PHE:plan': 4, 'ASN:plan1': 15, 'TRP:plan': 2, 'HIS:plan': 2, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 475
          bond proxies already assigned to first conformer: 10299
    Chain: "A"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2, 'water': 1}
          Link IDs: {None: 2}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    738  SG  CYS A1028      50.334  86.260  91.858  1.00152.29           S
  ATOM    757  SG  CYS A1031      46.566  86.822  92.134  1.00177.65           S
  ATOM   1000  SG  CYS A1062      48.682  89.631  90.842  1.00150.39           S
  ATOM   1020  SG  CYS A1065      48.278  86.704  88.681  1.00152.12           S
  ATOM   1601  SG  CYS A1294      43.181  73.046  41.562  1.00128.31           S

  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  APHE A2641 " occ=0.40
      ... (20 atoms not shown)
      pdb=" CZ BPHE A2641 " occ=0.60
  Time building chain proxies: 4.13, per 1000 atoms: 0.41
  Number of scatterers: 10152
  At special positions: 0
  Unit cell: (88.35, 102.6, 121.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      71     16.00
     O    1836      8.00
     N    1775      7.00
     C    6468      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1766 " - pdb=" SG  CYS A2558 " distance=2.03

  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: 0.82
  Conformation dependent library (CDL) restraints added in 839.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A4001 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1062 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1065 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1031 "
        pdb="ZN    ZN A4001 " - pdb=" SG  CYS A1028 "
      pdb="  ZN A4002 "
        pdb="ZN    ZN A4002 " - pdb=" ND1 HIS A1365 "
        pdb="ZN    ZN A4002 " - pdb=" SG  CYS A1294 "
        pdb="ZN    ZN A4002 " - pdb=" NE2 HIS A1090 "
      Number of angles added : 6


  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2622

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 10 sheets defined
      63.8% alpha, 5.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 930 through 947
      removed outlier: 4.881A  pdb=" N   GLU A 943 " --> pdb=" O   GLU A 939 " (cutoff:3.500A)
      removed outlier: 5.525A  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 1025
      removed outlier: 3.708A  pdb=" N   SER A1025 " --> pdb=" O   GLU A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1028 through 1042
      removed outlier: 4.154A  pdb=" N   GLU A1041 " --> pdb=" O   LYS A1037 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   THR A1042 " --> pdb=" O   THR A1038 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1044 through 1057
    Processing helix  chain 'A' and resid 1076 through 1081
    Processing helix  chain 'A' and resid 1224 through 1232
    Processing helix  chain 'A' and resid 1266 through 1281
      removed outlier: 3.618A  pdb=" N   CYS A1273 " --> pdb=" O   GLU A1269 " (cutoff:3.500A)
      removed outlier: 4.471A  pdb=" N   PHE A1279 " --> pdb=" O   ASP A1275 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   LYS A1280 " --> pdb=" O   VAL A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1291 through 1296
      removed outlier: 3.653A  pdb=" N   ILE A1295 " --> pdb=" O   GLN A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1307
    Processing helix  chain 'A' and resid 1315 through 1328
    Processing helix  chain 'A' and resid 1330 through 1351
    Processing helix  chain 'A' and resid 1401 through 1410
      removed outlier: 3.753A  pdb=" N   LEU A1407 " --> pdb=" O   ARG A1403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1426
    Processing helix  chain 'A' and resid 1430 through 1435
      removed outlier: 3.701A  pdb=" N   ASN A1433 " --> pdb=" O   GLU A1430 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   VAL A1435 " --> pdb=" O   ILE A1432 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1436 through 1464
    Processing helix  chain 'A' and resid 1465 through 1481
    Processing helix  chain 'A' and resid 1487 through 1505
      removed outlier: 3.528A  pdb=" N   SER A1494 " --> pdb=" O   ASP A1490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1507 through 1514
      removed outlier: 3.959A  pdb=" N   ASN A1514 " --> pdb=" O   ASN A1510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1524
    Processing helix  chain 'A' and resid 1524 through 1530
      removed outlier: 3.656A  pdb=" N   LEU A1530 " --> pdb=" O   ARG A1526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1531 through 1534
    Processing helix  chain 'A' and resid 1538 through 1546
      removed outlier: 3.734A  pdb=" N   LYS A1544 " --> pdb=" O   ASN A1540 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS A1545 " --> pdb=" O   GLU A1541 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   PHE A1546 " --> pdb=" O   LEU A1542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1552 through 1570
    Processing helix  chain 'A' and resid 1572 through 1583
      removed outlier: 4.294A  pdb=" N   LYS A1578 " --> pdb=" O   GLU A1574 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   LYS A1581 " --> pdb=" O   VAL A1577 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   GLN A1582 " --> pdb=" O   LYS A1578 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG A1583 " --> pdb=" O   HIS A1579 " (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 1632 through 1651
    Processing helix  chain 'A' and resid 1658 through 1666
    Processing helix  chain 'A' and resid 1758 through 1773
    Processing helix  chain 'A' and resid 1780 through 1791
    Processing helix  chain 'A' and resid 1792 through 1795
    Processing helix  chain 'A' and resid 1796 through 1805
    Processing helix  chain 'A' and resid 1806 through 1810
    Processing helix  chain 'A' and resid 2295 through 2306
      removed outlier: 3.599A  pdb=" N   THR A2306 " --> pdb=" O   ASN A2302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2316 through 2336
      removed outlier: 3.879A  pdb=" N   LEU A2322 " --> pdb=" O   LYS A2318 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ASP A2336 " --> pdb=" O   MET A2332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2367 through 2379
      removed outlier: 3.507A  pdb=" N   GLY A2373 " --> pdb=" O   SER A2369 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2382 through 2397
      removed outlier: 3.802A  pdb=" N   PHE A2388 " --> pdb=" O   ASP A2384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2448 through 2457
    Processing helix  chain 'A' and resid 2476 through 2503
      removed outlier: 3.725A  pdb=" N   LEU A2483 " --> pdb=" O   THR A2479 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   VAL A2489 " --> pdb=" O   SER A2485 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   LEU A2490 " --> pdb=" O   LEU A2486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2530 through 2559
      removed outlier: 3.577A  pdb=" N   GLN A2536 " --> pdb=" O   GLU A2532 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   THR A2540 " --> pdb=" O   GLN A2536 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   TRP A2542 " --> pdb=" O   ASP A2538 " (cutoff:3.500A)
      removed outlier: 5.311A  pdb=" N   LYS A2543 " --> pdb=" O   GLU A2539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2589 through 2594
      removed outlier: 3.505A  pdb=" N   MET A2594 " --> pdb=" O   ILE A2591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2595 through 2600
    Processing helix  chain 'A' and resid 2605 through 2623
      removed outlier: 3.594A  pdb=" N   ASN A2623 " --> pdb=" O   GLN A2619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2626 through 2645
      removed outlier: 3.648A  pdb=" N  APHE A2641 " --> pdb=" O   ARG A2637 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   HIS A2644 " --> pdb=" O   ILE A2640 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   VAL A2645 " --> pdb=" O  APHE A2641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2645 through 2653
    Processing helix  chain 'A' and resid 2660 through 2664
    Processing helix  chain 'A' and resid 2670 through 2675
    Processing helix  chain 'A' and resid 2678 through 2697
    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 2815
    Processing helix  chain 'A' and resid 2816 through 2837
      removed outlier: 3.607A  pdb=" N   VAL A2827 " --> pdb=" O   ARG A2823 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ARG A2837 " --> pdb=" O   ALA A2833 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2899 through 2909
    Processing helix  chain 'A' and resid 2993 through 3003
    Processing helix  chain 'A' and resid 3043 through 3060
      removed outlier: 3.516A  pdb=" N   VAL A3048 " --> pdb=" O   SER A3044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3062 through 3072
    Processing helix  chain 'A' and resid 3093 through 3100
      removed outlier: 3.927A  pdb=" N   GLU A3097 " --> pdb=" O   PHE A3093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3104 through 3114
      removed outlier: 3.792A  pdb=" N   MET A3109 " --> pdb=" O   PRO A3105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3114 through 3121
      removed outlier: 4.034A  pdb=" N   ILE A3118 " --> pdb=" O   ASP A3114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3127 through 3129
      No H-bonds generated for 'chain 'A' and resid 3127 through 3129'
    Processing helix  chain 'A' and resid 3130 through 3142
      removed outlier: 3.540A  pdb=" N   PHE A3136 " --> pdb=" O   LEU A3132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3142 through 3163
    Processing helix  chain 'A' and resid 3167 through 3185
      removed outlier: 3.893A  pdb=" N   LEU A3180 " --> pdb=" O   ASN A3176 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   LEU A3181 " --> pdb=" O   HIS A3177 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   MET A3184 " --> pdb=" O   LEU A3180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3208 through 3217
      removed outlier: 3.543A  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: 6.738A  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: 4.196A  pdb=" N   LEU A1383 " --> pdb=" O   LYS A1373 " (cutoff:3.500A)
      removed outlier: 5.464A  pdb=" N   LEU A1386 " --> pdb=" O   GLY A1396 " (cutoff:3.500A)
      removed outlier: 5.972A  pdb=" N   GLY A1396 " --> pdb=" O   LEU A1386 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 2347 through 2348
    Processing sheet with id=AA5, first strand: chain 'A' and resid 2508 through 2514
    Processing sheet with id=AA6, first strand: chain 'A' and resid 2399 through 2400
    Processing sheet with id=AA7, first strand: chain 'A' and resid 2574 through 2576
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3005 through 3009
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3078 through 3081
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3086 through 3089

    618 hydrogen bonds defined for protein.
    1786 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.09

  Time building geometry restraints manager: 1.11 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3315
        1.34 -     1.46: 2400
        1.46 -     1.58: 4511
        1.58 -     1.70: 0
        1.70 -     1.82: 99
  Bond restraints: 10325
  Sorted by residual:
  bond pdb=" CB  ASN A1390 "
       pdb=" CG  ASN A1390 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 2.50e-02 1.60e+03 1.06e+00
  bond pdb=" SD  MET A2374 "
       pdb=" CE  MET A2374 "
    ideal  model  delta    sigma   weight residual
    1.791  1.767  0.024 2.50e-02 1.60e+03 9.51e-01
  bond pdb=" CB  MET A 983 "
       pdb=" CG  MET A 983 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 7.04e-01
  bond pdb=" CA  VAL A2586 "
       pdb=" CB  VAL A2586 "
    ideal  model  delta    sigma   weight residual
    1.530  1.539 -0.009 1.05e-02 9.07e+03 6.58e-01
  bond pdb=" CG  ARG A3025 "
       pdb=" CD  ARG A3025 "
    ideal  model  delta    sigma   weight residual
    1.520  1.544 -0.024 3.00e-02 1.11e+03 6.15e-01
  ... (remaining 10320 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.02: 13904
        2.02 -     4.04: 101
        4.04 -     6.07: 13
        6.07 -     8.09: 3
        8.09 -    10.11: 4
  Bond angle restraints: 14025
  Sorted by residual:
  angle pdb=" CB  MET A2582 "
        pdb=" CG  MET A2582 "
        pdb=" SD  MET A2582 "
      ideal   model   delta    sigma   weight residual
     112.70  122.81  -10.11 3.00e+00 1.11e-01 1.14e+01
  angle pdb=" CB  MET A1792 "
        pdb=" CG  MET A1792 "
        pdb=" SD  MET A1792 "
      ideal   model   delta    sigma   weight residual
     112.70  122.67   -9.97 3.00e+00 1.11e-01 1.11e+01
  angle pdb=" CB  MET A1524 "
        pdb=" CG  MET A1524 "
        pdb=" SD  MET A1524 "
      ideal   model   delta    sigma   weight residual
     112.70  121.99   -9.29 3.00e+00 1.11e-01 9.59e+00
  angle pdb=" CB  MET A2375 "
        pdb=" CG  MET A2375 "
        pdb=" SD  MET A2375 "
      ideal   model   delta    sigma   weight residual
     112.70  121.21   -8.51 3.00e+00 1.11e-01 8.05e+00
  angle pdb=" N   ILE A1008 "
        pdb=" CA  ILE A1008 "
        pdb=" C   ILE A1008 "
      ideal   model   delta    sigma   weight residual
     112.96  110.13    2.83 1.00e+00 1.00e+00 8.01e+00
  ... (remaining 14020 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.98: 5476
       17.98 -    35.95: 571
       35.95 -    53.93: 123
       53.93 -    71.90: 22
       71.90 -    89.88: 11
  Dihedral angle restraints: 6203
    sinusoidal: 2192
      harmonic: 4011
  Sorted by residual:
  dihedral pdb=" CB  CYS A1766 "
           pdb=" SG  CYS A1766 "
           pdb=" SG  CYS A2558 "
           pdb=" CB  CYS A2558 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  170.15  -77.15     1      1.00e+01 1.00e-02 7.47e+01
  dihedral pdb=" CB  GLU A2819 "
           pdb=" CG  GLU A2819 "
           pdb=" CD  GLU A2819 "
           pdb=" OE1 GLU A2819 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.88   89.88     1      3.00e+01 1.11e-03 1.06e+01
  dihedral pdb=" CB  GLU A1444 "
           pdb=" CG  GLU A1444 "
           pdb=" CD  GLU A1444 "
           pdb=" OE1 GLU A1444 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -88.94   88.94     1      3.00e+01 1.11e-03 1.05e+01
  ... (remaining 6200 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1111
       0.028 -    0.056: 385
       0.056 -    0.084: 124
       0.084 -    0.112: 62
       0.112 -    0.140: 8
  Chirality restraints: 1690
  Sorted by residual:
  chirality pdb=" CG  LEU A1641 "
            pdb=" CB  LEU A1641 "
            pdb=" CD1 LEU A1641 "
            pdb=" CD2 LEU A1641 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.45   -0.14 2.00e-01 2.50e+01 4.90e-01
  chirality pdb=" CA  ASN A1390 "
            pdb=" N   ASN A1390 "
            pdb=" C   ASN A1390 "
            pdb=" CB  ASN A1390 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.20e-01
  chirality pdb=" CA  ILE A1591 "
            pdb=" N   ILE A1591 "
            pdb=" C   ILE A1591 "
            pdb=" CB  ILE A1591 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.93e-01
  ... (remaining 1687 not shown)

  Planarity restraints: 1774
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A3021 "    0.027 5.00e-02 4.00e+02   4.08e-02 2.66e+00
        pdb=" N   PRO A3022 "   -0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A3022 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A3022 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A3025 "   -0.123 9.50e-02 1.11e+02   5.53e-02 2.37e+00
        pdb=" NE  ARG A3025 "    0.012 2.00e-02 2.50e+03
        pdb=" CZ  ARG A3025 "   -0.011 2.00e-02 2.50e+03
        pdb=" NH1 ARG A3025 "    0.005 2.00e-02 2.50e+03
        pdb=" NH2 ARG A3025 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 954 "    0.021 5.00e-02 4.00e+02   3.25e-02 1.69e+00
        pdb=" N   PRO A 955 "   -0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 955 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 955 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1771 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.72: 273
        2.72 -     3.26: 10845
        3.26 -     3.81: 17158
        3.81 -     4.35: 21565
        4.35 -     4.90: 36024
  Nonbonded interactions: 85865
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A2788 "
            pdb="ZN    ZN A4002 "
     model   vdw
     2.171 2.230
  nonbonded pdb=" OD2 ASP A1604 "
            pdb=" NH1 ARG A2585 "
     model   vdw
     2.335 3.120
  nonbonded pdb=" OH  TYR A1419 "
            pdb=" OD1 ASN A1500 "
     model   vdw
     2.344 3.040
  nonbonded pdb=" OH  TYR A1612 "
            pdb=" O   SER A2578 "
     model   vdw
     2.380 3.040
  nonbonded pdb=" O   ILE A3070 "
            pdb=" OG  SER A3073 "
     model   vdw
     2.383 3.040
  ... (remaining 85860 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=0.40 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:             4.280
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.390
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  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:6.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.160
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
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   0.032  10333  Z= 0.080
  Angle     :  0.464  10.110  14033  Z= 0.226
  Chirality :  0.036   0.140   1690
  Planarity :  0.003   0.055   1774
  Dihedral  : 15.549  89.878   3578
  Min Nonbonded Distance : 2.171

Molprobity Statistics.
  All-atom Clashscore : 4.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 24.93 %
    Favored  : 74.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.23), residues: 1334
  helix:  1.49 (0.19), residues: 777
  sheet: -0.54 (0.60), residues: 83
  loop : -0.61 (0.28), residues: 474

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A3025 
 TYR   0.012   0.001   TYR A1612 
 PHE   0.010   0.001   PHE A2633 
 TRP   0.007   0.001   TRP A2542 
 HIS   0.002   0.001   HIS A1776 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00177 /  0.08 (10325)
  covalent geometry    : angle       0.45985 /  0.23 (14025)
  SS BOND              : bond        0.00186 /  0.12 (    1)
  SS BOND              : angle       0.37726 /  0.20 (    2)
  hydrogen bonds       : bond        0.24098 / 16.64 (  618)
  hydrogen bonds       : angle       6.91561 /  4.97 ( 1786)
  metal coordination   : bond        0.00390 /  0.20 (    7)
  metal coordination   : angle       3.09044 /  2.11 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 61
  time to evaluate  : 0.408 
Fit side-chains
REVERT: A 1618 ASN cc_start: 0.8474 (t0) cc_final: 0.8103 (t0)
  outliers start: 1
  outliers final: 1
  residues processed: 62
  average time/residue: 0.4734
  time to fit residues: 32.5483
Evaluate side-chains
  52 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 51
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1641 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1055 ASN
A1613 ASN
A2323 ASN
A2348 ASN
A2623 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.078351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.060986 restraints weight = 38900.161|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 3.40
r_work: 0.2713 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2712
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2712 r_free = 0.2712    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2712
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8397
moved from start:          0.1253

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10333  Z= 0.164
  Angle     :  0.534   7.640  14033  Z= 0.274
  Chirality :  0.040   0.152   1690
  Planarity :  0.003   0.041   1774
  Dihedral  :  3.518  27.615   1453
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 21.82 %
    Favored  : 75.95 %
  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:  1.15 (0.23), residues: 1334
  helix:  1.77 (0.18), residues: 795
  sheet: -0.47 (0.58), residues: 83
  loop : -0.78 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A3025 
 TYR   0.008   0.001   TYR A2622 
 PHE   0.015   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.005   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00367 /  0.16 (10325)
  covalent geometry    : angle       0.52851 /  0.27 (14025)
  SS BOND              : bond        0.00501 /  0.33 (    1)
  SS BOND              : angle       1.65854 /  0.90 (    2)
  hydrogen bonds       : bond        0.04737 /  3.34 (  618)
  hydrogen bonds       : angle       4.62333 /  3.28 ( 1786)
  metal coordination   : bond        0.00816 /  0.42 (    7)
  metal coordination   : angle       3.59255 /  2.57 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 55
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A 1040 ASP cc_start: 0.9109 (m-30) cc_final: 0.8821 (m-30)
REVERT: A 1641 LEU cc_start: 0.9642 (OUTLIER) cc_final: 0.9411 (mm)
REVERT: A 3113 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8769 (tp)
REVERT: A 3184 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8525 (mtp)
  outliers start: 23
  outliers final: 5
  residues processed: 73
  average time/residue: 0.3941
  time to fit residues: 32.3892
Evaluate side-chains
  53 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1635 THR
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 3113 LEU
Chi-restraints excluded: chain A residue 3138 ILE
Chi-restraints excluded: chain A residue 3184 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 117 optimal weight:    4.9990
   chunk 45 optimal weight:    0.5980
   chunk 104 optimal weight:    0.4980
   chunk 75 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 68 optimal weight:    0.0980
   chunk 88 optimal weight:    0.5980
   chunk 80 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.5580

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.078628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2880 r_free = 0.2880 target = 0.061372 restraints weight = 37947.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.2868 rms_B_bonded: 3.38
r_work: 0.2730 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2729
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2729 r_free = 0.2729    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2729
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8382
moved from start:          0.1521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10333  Z= 0.123
  Angle     :  0.482   7.859  14033  Z= 0.246
  Chirality :  0.039   0.147   1690
  Planarity :  0.003   0.031   1774
  Dihedral  :  3.442  29.989   1453
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 21.63 %
    Favored  : 76.72 %
  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: 1334
  helix:  1.97 (0.18), residues: 795
  sheet: -0.38 (0.57), residues: 83
  loop : -0.76 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A3025 
 TYR   0.010   0.001   TYR A1503 
 PHE   0.014   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00279 /  0.12 (10325)
  covalent geometry    : angle       0.47798 /  0.25 (14025)
  SS BOND              : bond        0.00377 /  0.25 (    1)
  SS BOND              : angle       1.13930 /  0.60 (    2)
  hydrogen bonds       : bond        0.03890 /  2.72 (  618)
  hydrogen bonds       : angle       4.23811 /  3.01 ( 1786)
  metal coordination   : bond        0.00588 /  0.31 (    7)
  metal coordination   : angle       3.05328 /  2.21 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  70 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 53
  time to evaluate  : 0.421 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9014 (tppt) cc_final: 0.8687 (tppt)
REVERT: A 1040 ASP cc_start: 0.9124 (m-30) cc_final: 0.8778 (m-30)
REVERT: A 1581 LYS cc_start: 0.9162 (OUTLIER) cc_final: 0.8904 (mttp)
REVERT: A 1612 TYR cc_start: 0.9132 (m-80) cc_final: 0.8890 (m-80)
REVERT: A 1641 LEU cc_start: 0.9660 (OUTLIER) cc_final: 0.9408 (mm)
REVERT: A 2581 MET cc_start: 0.8792 (tmm) cc_final: 0.8465 (tmm)
REVERT: A 3113 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8790 (tp)
  outliers start: 17
  outliers final: 3
  residues processed: 64
  average time/residue: 0.5001
  time to fit residues: 35.2714
Evaluate side-chains
  53 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1581 LYS
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2864 MET
Chi-restraints excluded: chain A residue 3113 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 46 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 107 optimal weight:    0.9990
   chunk 80 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 16 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9990
   chunk 127 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A1424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.078264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2866 r_free = 0.2866 target = 0.060651 restraints weight = 48680.755|
|-----------------------------------------------------------------------------|
r_work (start): 0.2844 rms_B_bonded: 3.82
r_work: 0.2692 rms_B_bonded: 4.20 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2688
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2688 r_free = 0.2688    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2688
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8402
moved from start:          0.1693

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10333  Z= 0.142
  Angle     :  0.472   6.662  14033  Z= 0.242
  Chirality :  0.039   0.148   1690
  Planarity :  0.003   0.030   1774
  Dihedral  :  3.444  31.859   1453
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.84 %
    Allowed  : 21.44 %
    Favored  : 76.72 %
  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:  1.49 (0.23), residues: 1334
  helix:  2.09 (0.18), residues: 795
  sheet: -0.37 (0.57), residues: 83
  loop : -0.74 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A3100 
 TYR   0.012   0.001   TYR A3111 
 PHE   0.016   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00330 /  0.14 (10325)
  covalent geometry    : angle       0.46826 /  0.24 (14025)
  SS BOND              : bond        0.00356 /  0.24 (    1)
  SS BOND              : angle       1.05286 /  0.59 (    2)
  hydrogen bonds       : bond        0.03582 /  2.51 (  618)
  hydrogen bonds       : angle       4.09916 /  2.90 ( 1786)
  metal coordination   : bond        0.00704 /  0.38 (    7)
  metal coordination   : angle       2.84729 /  2.11 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 48
  time to evaluate  : 0.382 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9011 (tppt) cc_final: 0.8702 (tppt)
REVERT: A 1040 ASP cc_start: 0.9130 (m-30) cc_final: 0.8825 (m-30)
REVERT: A 1581 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8681 (mttt)
REVERT: A 1641 LEU cc_start: 0.9648 (OUTLIER) cc_final: 0.9390 (mm)
  outliers start: 19
  outliers final: 7
  residues processed: 62
  average time/residue: 0.4073
  time to fit residues: 28.1244
Evaluate side-chains
  55 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1549 SER
Chi-restraints excluded: chain A residue 1581 LYS
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2749 ASN
Chi-restraints excluded: chain A residue 2864 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 88 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 135 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 48 optimal weight:    0.5980
   chunk 55 optimal weight:    0.5980
   chunk 83 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 95 optimal weight:    0.7980
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1424 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.078365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2867 r_free = 0.2867 target = 0.060733 restraints weight = 45829.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.2854 rms_B_bonded: 3.70
r_work: 0.2705 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2704
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2704 r_free = 0.2704    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2704
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
moved from start:          0.1766

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10333  Z= 0.128
  Angle     :  0.466   7.520  14033  Z= 0.236
  Chirality :  0.038   0.146   1690
  Planarity :  0.003   0.030   1774
  Dihedral  :  3.439  32.612   1453
  Min Nonbonded Distance : 2.036

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 21.92 %
    Favored  : 76.53 %
  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:  1.57 (0.23), residues: 1334
  helix:  2.16 (0.18), residues: 793
  sheet: -0.28 (0.57), residues: 83
  loop : -0.72 (0.28), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A3100 
 TYR   0.016   0.001   TYR A3111 
 PHE   0.015   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.13 (10325)
  covalent geometry    : angle       0.46281 /  0.24 (14025)
  SS BOND              : bond        0.00322 /  0.21 (    1)
  SS BOND              : angle       0.94314 /  0.57 (    2)
  hydrogen bonds       : bond        0.03417 /  2.39 (  618)
  hydrogen bonds       : angle       4.01587 /  2.84 ( 1786)
  metal coordination   : bond        0.00620 /  0.33 (    7)
  metal coordination   : angle       2.65788 /  1.96 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 51
  time to evaluate  : 0.329 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9014 (tppt) cc_final: 0.8680 (tppt)
REVERT: A 1040 ASP cc_start: 0.9138 (m-30) cc_final: 0.8758 (m-30)
REVERT: A 1524 MET cc_start: 0.9172 (tpp) cc_final: 0.8849 (mmm)
REVERT: A 1581 LYS cc_start: 0.9182 (OUTLIER) cc_final: 0.8665 (mttt)
REVERT: A 2493 GLU cc_start: 0.9474 (tp30) cc_final: 0.9205 (tp30)
REVERT: A 2581 MET cc_start: 0.8720 (tmm) cc_final: 0.7633 (tmm)
  outliers start: 16
  outliers final: 6
  residues processed: 64
  average time/residue: 0.4679
  time to fit residues: 33.1352
Evaluate side-chains
  54 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1581 LYS
Chi-restraints excluded: chain A residue 1665 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2749 ASN
Chi-restraints excluded: chain A residue 2864 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 91 optimal weight:    0.7980
   chunk 26 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   chunk 49 optimal weight:    0.7980
   chunk 3 optimal weight:    0.6980
   chunk 66 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.6980

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.078093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2873 r_free = 0.2873 target = 0.061169 restraints weight = 32754.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 3.13
r_work: 0.2734 rms_B_bonded: 3.60 restraints_weight: 0.5000
r_work (final): 0.2734
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2731
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2731 r_free = 0.2731    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2731
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8385
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10333  Z= 0.133
  Angle     :  0.474   8.705  14033  Z= 0.238
  Chirality :  0.038   0.145   1690
  Planarity :  0.003   0.031   1774
  Dihedral  :  3.339  16.986   1451
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 22.70 %
    Favored  : 75.95 %
  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:  1.59 (0.23), residues: 1334
  helix:  2.18 (0.18), residues: 794
  sheet: -0.20 (0.57), residues: 83
  loop : -0.73 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A3100 
 TYR   0.011   0.001   TYR A3111 
 PHE   0.015   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00310 /  0.13 (10325)
  covalent geometry    : angle       0.47076 /  0.24 (14025)
  SS BOND              : bond        0.00261 /  0.17 (    1)
  SS BOND              : angle       0.92707 /  0.59 (    2)
  hydrogen bonds       : bond        0.03362 /  2.35 (  618)
  hydrogen bonds       : angle       3.97923 /  2.81 ( 1786)
  metal coordination   : bond        0.00639 /  0.34 (    7)
  metal coordination   : angle       2.60716 /  1.95 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.433 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9004 (tppt) cc_final: 0.8670 (tppt)
REVERT: A 1040 ASP cc_start: 0.9106 (m-30) cc_final: 0.8761 (m-30)
REVERT: A 1524 MET cc_start: 0.9131 (tpp) cc_final: 0.8839 (mmm)
REVERT: A 2493 GLU cc_start: 0.9459 (tp30) cc_final: 0.9194 (tp30)
  outliers start: 14
  outliers final: 8
  residues processed: 59
  average time/residue: 0.5122
  time to fit residues: 33.5354
Evaluate side-chains
  55 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 47
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1549 SER
Chi-restraints excluded: chain A residue 1665 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2749 ASN
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2864 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 47 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 2 optimal weight:    0.7980
   chunk 79 optimal weight:    0.8980
   chunk 97 optimal weight:    0.6980
   chunk 124 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 135 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A2794 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.077734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.059763 restraints weight = 56082.990|
|-----------------------------------------------------------------------------|
r_work (start): 0.2835 rms_B_bonded: 4.05
r_work: 0.2679 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.2679
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2674
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2674 r_free = 0.2674    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2674
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.1893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  10333  Z= 0.144
  Angle     :  0.491   9.412  14033  Z= 0.242
  Chirality :  0.038   0.145   1690
  Planarity :  0.003   0.031   1774
  Dihedral  :  3.362  17.291   1451
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  : 22.89 %
    Favored  : 75.85 %
  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:  1.63 (0.23), residues: 1334
  helix:  2.22 (0.18), residues: 794
  sheet: -0.19 (0.56), residues: 83
  loop : -0.72 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A3100 
 TYR   0.012   0.001   TYR A3111 
 PHE   0.016   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.14 (10325)
  covalent geometry    : angle       0.48762 /  0.24 (14025)
  SS BOND              : bond        0.00266 /  0.18 (    1)
  SS BOND              : angle       0.97211 /  0.63 (    2)
  hydrogen bonds       : bond        0.03381 /  2.36 (  618)
  hydrogen bonds       : angle       3.95497 /  2.80 ( 1786)
  metal coordination   : bond        0.00716 /  0.38 (    7)
  metal coordination   : angle       2.60111 /  1.98 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.438 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9018 (tppt) cc_final: 0.8530 (tppt)
REVERT: A 1040 ASP cc_start: 0.9156 (m-30) cc_final: 0.8706 (m-30)
REVERT: A 1524 MET cc_start: 0.9188 (tpp) cc_final: 0.8848 (mmm)
REVERT: A 1581 LYS cc_start: 0.9217 (OUTLIER) cc_final: 0.8819 (mttp)
REVERT: A 2493 GLU cc_start: 0.9494 (tp30) cc_final: 0.9225 (tp30)
  outliers start: 13
  outliers final: 5
  residues processed: 59
  average time/residue: 0.5443
  time to fit residues: 35.4636
Evaluate side-chains
  53 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1549 SER
Chi-restraints excluded: chain A residue 1581 LYS
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2749 ASN
Chi-restraints excluded: chain A residue 2864 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 86 optimal weight:    0.9980
   chunk 118 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 125 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 85 optimal weight:    1.9990
   chunk 72 optimal weight:    0.7980
   chunk 30 optimal weight:    0.8980
   chunk 49 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 9 optimal weight:    0.9980
   overall best weight:    0.8380

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.077732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2854 r_free = 0.2854 target = 0.060022 restraints weight = 51906.954|
|-----------------------------------------------------------------------------|
r_work (start): 0.2836 rms_B_bonded: 3.92
r_work: 0.2684 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.2684
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2678
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2678 r_free = 0.2678    target_work(ls_wunit_k1) = 0.053         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2678
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8405
moved from start:          0.1948

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10333  Z= 0.150
  Angle     :  0.501  11.095  14033  Z= 0.246
  Chirality :  0.039   0.157   1690
  Planarity :  0.003   0.030   1774
  Dihedral  :  3.384  17.463   1451
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 23.08 %
    Favored  : 75.85 %
  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:  1.61 (0.23), residues: 1334
  helix:  2.21 (0.18), residues: 794
  sheet: -0.33 (0.57), residues: 83
  loop : -0.73 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A3100 
 TYR   0.009   0.001   TYR A3111 
 PHE   0.016   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00347 /  0.15 (10325)
  covalent geometry    : angle       0.49760 /  0.25 (14025)
  SS BOND              : bond        0.00290 /  0.19 (    1)
  SS BOND              : angle       1.00353 /  0.66 (    2)
  hydrogen bonds       : bond        0.03378 /  2.36 (  618)
  hydrogen bonds       : angle       3.93050 /  2.77 ( 1786)
  metal coordination   : bond        0.00753 /  0.40 (    7)
  metal coordination   : angle       2.65341 /  2.03 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.510 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9012 (tppt) cc_final: 0.8533 (tppt)
REVERT: A 1040 ASP cc_start: 0.9158 (m-30) cc_final: 0.8714 (m-30)
REVERT: A 1641 LEU cc_start: 0.9645 (OUTLIER) cc_final: 0.9394 (mm)
REVERT: A 2493 GLU cc_start: 0.9497 (tp30) cc_final: 0.9219 (tp30)
  outliers start: 11
  outliers final: 6
  residues processed: 56
  average time/residue: 0.5120
  time to fit residues: 31.9065
Evaluate side-chains
  54 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 47
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1549 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2749 ASN
Chi-restraints excluded: chain A residue 2864 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 8 optimal weight:    0.9980
   chunk 13 optimal weight:    0.9990
   chunk 121 optimal weight:    4.9990
   chunk 123 optimal weight:    4.9990
   chunk 116 optimal weight:    3.9990
   chunk 1 optimal weight:    0.9980
   chunk 84 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.9182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.077450 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2845 r_free = 0.2845 target = 0.059553 restraints weight = 58164.411|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 4.11
r_work: 0.2666 rms_B_bonded: 4.44 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2661
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2661 r_free = 0.2661    target_work(ls_wunit_k1) = 0.052         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2661
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8413
moved from start:          0.1964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10333  Z= 0.161
  Angle     :  0.510  10.612  14033  Z= 0.250
  Chirality :  0.039   0.176   1690
  Planarity :  0.003   0.030   1774
  Dihedral  :  3.423  17.716   1451
  Min Nonbonded Distance : 2.004

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.87 %
    Allowed  : 22.79 %
    Favored  : 76.33 %
  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:  1.58 (0.23), residues: 1334
  helix:  2.20 (0.18), residues: 795
  sheet: -0.44 (0.56), residues: 83
  loop : -0.76 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A3100 
 TYR   0.009   0.001   TYR A3111 
 PHE   0.016   0.001   PHE A2633 
 TRP   0.016   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.16 (10325)
  covalent geometry    : angle       0.50650 /  0.25 (14025)
  SS BOND              : bond        0.00253 /  0.17 (    1)
  SS BOND              : angle       1.06208 /  0.70 (    2)
  hydrogen bonds       : bond        0.03425 /  2.40 (  618)
  hydrogen bonds       : angle       3.94457 /  2.78 ( 1786)
  metal coordination   : bond        0.00817 /  0.43 (    7)
  metal coordination   : angle       2.81212 /  2.16 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.446 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9017 (tppt) cc_final: 0.8565 (tppt)
REVERT: A 1040 ASP cc_start: 0.9161 (m-30) cc_final: 0.8774 (m-30)
REVERT: A 1641 LEU cc_start: 0.9651 (OUTLIER) cc_final: 0.9395 (mm)
REVERT: A 2493 GLU cc_start: 0.9510 (tp30) cc_final: 0.9243 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 56
  average time/residue: 0.5109
  time to fit residues: 31.7399
Evaluate side-chains
  56 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 48
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1549 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2749 ASN
Chi-restraints excluded: chain A residue 2859 ILE
Chi-restraints excluded: chain A residue 2864 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   chunk 38 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 74 optimal weight:    7.9990
   chunk 26 optimal weight:    0.7980
   chunk 108 optimal weight:    2.9990
   overall best weight:    0.8782

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.077366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.060303 restraints weight = 35809.141|
|-----------------------------------------------------------------------------|
r_work (start): 0.2845 rms_B_bonded: 3.26
r_work: 0.2710 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.2710
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2707
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2707 r_free = 0.2707    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2707
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  10333  Z= 0.157
  Angle     :  0.519  10.997  14033  Z= 0.254
  Chirality :  0.039   0.173   1690
  Planarity :  0.003   0.030   1774
  Dihedral  :  3.456  17.671   1451
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 22.89 %
    Favored  : 76.14 %
  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:  1.57 (0.23), residues: 1334
  helix:  2.18 (0.18), residues: 795
  sheet: -0.41 (0.55), residues: 83
  loop : -0.76 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A3100 
 TYR   0.009   0.001   TYR A3111 
 PHE   0.016   0.001   PHE A2633 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.16 (10325)
  covalent geometry    : angle       0.51596 /  0.25 (14025)
  SS BOND              : bond        0.00245 /  0.16 (    1)
  SS BOND              : angle       1.06186 /  0.70 (    2)
  hydrogen bonds       : bond        0.03406 /  2.38 (  618)
  hydrogen bonds       : angle       3.93334 /  2.77 ( 1786)
  metal coordination   : bond        0.00801 /  0.43 (    7)
  metal coordination   : angle       2.75360 /  2.10 (    6)

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

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

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2668 Ramachandran restraints generated.
    1334 Oldfield, 0 Emsley, 1334 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 48
  time to evaluate  : 0.452 
Fit side-chains
REVERT: A 1036 LYS cc_start: 0.9012 (tppt) cc_final: 0.8542 (tppt)
REVERT: A 1040 ASP cc_start: 0.9112 (m-30) cc_final: 0.8700 (m-30)
REVERT: A 1641 LEU cc_start: 0.9650 (OUTLIER) cc_final: 0.9405 (mm)
REVERT: A 2493 GLU cc_start: 0.9480 (tp30) cc_final: 0.9228 (tp30)
  outliers start: 10
  outliers final: 7
  residues processed: 56
  average time/residue: 0.5187
  time to fit residues: 32.2419
Evaluate side-chains
  57 residues out of total 1256 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 49
  time to evaluate  : 0.450 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1026 SER
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1391 MET
Chi-restraints excluded: chain A residue 1549 SER
Chi-restraints excluded: chain A residue 1641 LEU
Chi-restraints excluded: chain A residue 1766 CYS
Chi-restraints excluded: chain A residue 2749 ASN
Chi-restraints excluded: chain A residue 2864 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 72 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 76 optimal weight:    4.9990
   chunk 108 optimal weight:    0.6980
   chunk 127 optimal weight:    0.7980
   chunk 120 optimal weight:    0.2980
   chunk 13 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 117 optimal weight:    3.9990
   chunk 129 optimal weight:   20.0000
   overall best weight:    0.7582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.077773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2859 r_free = 0.2859 target = 0.060446 restraints weight = 40964.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 3.50
r_work: 0.2707 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.2707
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2702
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2702 r_free = 0.2702    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.45   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (3 function evaluations)
r_final: 0.2702
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8396
moved from start:          0.2017

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10333  Z= 0.141
  Angle     :  0.511  12.014  14033  Z= 0.249
  Chirality :  0.039   0.191   1690
  Planarity :  0.003   0.030   1774
  Dihedral  :  3.422  17.392   1451
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  1.07 %
    Allowed  : 22.89 %
    Favored  : 76.04 %
  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:  1.58 (0.23), residues: 1334
  helix:  2.19 (0.18), residues: 795
  sheet: -0.45 (0.55), residues: 83
  loop : -0.73 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A3100 
 TYR   0.009   0.001   TYR A1612 
 PHE   0.038   0.001   PHE A1230 
 TRP   0.015   0.001   TRP A2542 
 HIS   0.004   0.001   HIS A1615 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00327 /  0.14 (10325)
  covalent geometry    : angle       0.50759 /  0.25 (14025)
  SS BOND              : bond        0.00255 /  0.17 (    1)
  SS BOND              : angle       1.01873 /  0.68 (    2)
  hydrogen bonds       : bond        0.03328 /  2.33 (  618)
  hydrogen bonds       : angle       3.89973 /  2.75 ( 1786)
  metal coordination   : bond        0.00729 /  0.39 (    7)
  metal coordination   : angle       2.71374 /  2.05 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2838.58 seconds
wall clock time: 49 minutes 37.56 seconds (2977.56 seconds total)