Starting phenix.real_space_refine
on Tue Jan 13 19:24:09 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8fo7_29340/01_2026/8fo7_29340.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8fo7_29340/01_2026/8fo7_29340.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.52
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8fo7_29340/01_2026/8fo7_29340.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8fo7_29340/01_2026/8fo7_29340.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8fo7_29340/01_2026/8fo7_29340.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8fo7_29340/01_2026/8fo7_29340.map"
  }
  resolution = 3.52
  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=   0.069
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 42 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      50      5.16       5
     C    5451      2.51       5
     N    1441      2.21       5
     O    1511      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8455
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 8385
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1141, 8385
          Classifications: {'peptide': 1141}
          Incomplete info: {'truncation_to_alanine': 194}
          Link IDs: {'PTRANS': 50, 'TRANS': 1090}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 755
          Unresolved non-hydrogen angles: 914
          Unresolved non-hydrogen dihedrals: 619
          Unresolved non-hydrogen chiralities: 23
          Planarities with less than four sites: {'ASN:plan1': 18, 'GLN:plan1': 15, 'ASP:plan': 23, 'ARG:plan': 24, 'GLU:plan': 33, 'TYR:plan': 3, 'PHE:plan': 4, 'HIS:plan': 3}
          Unresolved non-hydrogen planarities: 495
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 28
          Unusual residues: {'GDP': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 42
          Unusual residues: {'4K4': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.23, per 1000 atoms: 0.26
  Number of scatterers: 8455
  At special positions: 0
  Unit cell: (78.116, 95.328, 142.992, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     P       2     15.00
     O    1511      8.00
     N    1441      7.00
     C    5451      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.80
  Conformation dependent library (CDL) restraints added in 389.1 milliseconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2162

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 19 sheets defined
      31.9% alpha, 17.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'C' and resid 1346 through 1356
    Processing helix  chain 'C' and resid 1398 through 1404
      removed outlier: 3.599A  pdb=" N   TYR C1402 " --> pdb=" O   GLU C1399 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   SER C1403 " --> pdb=" O   GLU C1400 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR C1404 " --> pdb=" O   PHE C1401 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1405 through 1409
    Processing helix  chain 'C' and resid 1425 through 1431
      removed outlier: 3.724A  pdb=" N   ASP C1429 " --> pdb=" O   GLN C1425 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1431 through 1442
      removed outlier: 3.513A  pdb=" N   LYS C1439 " --> pdb=" O   LEU C1435 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1459 through 1472
    Processing helix  chain 'C' and resid 1494 through 1511
      removed outlier: 3.892A  pdb=" N   ALA C1498 " --> pdb=" O   SER C1494 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1524 through 1539
      removed outlier: 3.746A  pdb=" N   VAL C1528 " --> pdb=" O   PRO C1524 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   LYS C1539 " --> pdb=" O   LEU C1535 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1549 through 1561
    Processing helix  chain 'C' and resid 1568 through 1580
    Processing helix  chain 'C' and resid 1599 through 1604
      removed outlier: 3.558A  pdb=" N   LEU C1603 " --> pdb=" O   GLU C1599 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   CYS C1604 " --> pdb=" O   PRO C1600 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1599 through 1604'
    Processing helix  chain 'C' and resid 1605 through 1612
    Processing helix  chain 'C' and resid 1628 through 1634
    Processing helix  chain 'C' and resid 1644 through 1650
      removed outlier: 3.700A  pdb=" N   GLN C1648 " --> pdb=" O   ASN C1644 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   TYR C1649 " --> pdb=" O   TYR C1645 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1669 through 1673
      removed outlier: 3.517A  pdb=" N   SER C1672 " --> pdb=" O   VAL C1669 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   LEU C1673 " --> pdb=" O   PRO C1670 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1669 through 1673'
    Processing helix  chain 'C' and resid 1703 through 1712
      removed outlier: 3.564A  pdb=" N   ARG C1707 " --> pdb=" O   GLY C1703 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1719 through 1723
      removed outlier: 3.643A  pdb=" N   GLY C1722 " --> pdb=" O   MET C1719 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1770 through 1791
      removed outlier: 3.614A  pdb=" N   ASP C1782 " --> pdb=" O   GLY C1778 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1827 through 1837
      removed outlier: 3.515A  pdb=" N   GLU C1836 " --> pdb=" O   LYS C1832 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1852 through 1856
    Processing helix  chain 'C' and resid 1913 through 1925
      removed outlier: 3.638A  pdb=" N   LEU C1917 " --> pdb=" O   SER C1913 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLU C1920 " --> pdb=" O   LEU C1916 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   VAL C1923 " --> pdb=" O   GLN C1919 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1954 through 1962
      removed outlier: 3.659A  pdb=" N   LEU C1958 " --> pdb=" O   SER C1954 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1969 through 1988
    Processing helix  chain 'C' and resid 2040 through 2045
    Processing helix  chain 'C' and resid 2053 through 2068
      removed outlier: 3.890A  pdb=" N   TYR C2057 " --> pdb=" O   GLN C2053 " (cutoff:3.500A)
      removed outlier: 3.833A  pdb=" N   SER C2058 " --> pdb=" O   ALA C2054 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2070 through 2079
      removed outlier: 3.573A  pdb=" N   VAL C2074 " --> pdb=" O   GLY C2070 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   LYS C2078 " --> pdb=" O   VAL C2074 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   PHE C2079 " --> pdb=" O   GLU C2075 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2079 through 2090
    Processing helix  chain 'C' and resid 2094 through 2099
    Processing helix  chain 'C' and resid 2107 through 2114
    Processing helix  chain 'C' and resid 2118 through 2122
    Processing helix  chain 'C' and resid 2124 through 2133
      removed outlier: 3.603A  pdb=" N   PHE C2129 " --> pdb=" O   SER C2125 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ASP C2130 " --> pdb=" O   ALA C2126 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2134 through 2138
      removed outlier: 3.662A  pdb=" N   VAL C2138 " --> pdb=" O   ALA C2135 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 2208 through 2211
    Processing helix  chain 'C' and resid 2278 through 2280
      No H-bonds generated for 'chain 'C' and resid 2278 through 2280'
    Processing helix  chain 'C' and resid 2389 through 2394
    Processing helix  chain 'C' and resid 2499 through 2527
      removed outlier: 3.871A  pdb=" N   GLN C2505 " --> pdb=" O   PRO C2501 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   GLU C2508 " --> pdb=" O   VAL C2504 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 1334 through 1339
    Processing sheet with id=AA2, first strand: chain 'C' and resid 1418 through 1419
    Processing sheet with id=AA3, first strand: chain 'C' and resid 1512 through 1513
    Processing sheet with id=AA4, first strand: chain 'C' and resid 1690 through 1692
    Processing sheet with id=AA5, first strand: chain 'C' and resid 1695 through 1696
      removed outlier: 3.586A  pdb=" N   TYR C1814 " --> pdb=" O   GLN C1823 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 1733 through 1734
      removed outlier: 4.337A  pdb=" N   TRP C1734 " --> pdb=" O   GLY C1737 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   GLY C1737 " --> pdb=" O   TRP C1734 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'C' and resid 1741 through 1743
    Processing sheet with id=AA8, first strand: chain 'C' and resid 1751 through 1753
      removed outlier: 3.586A  pdb=" N   GLU C1753 " --> pdb=" O   PHE C1762 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 1839 through 1841
      removed outlier: 3.552A  pdb=" N   ILE C1850 " --> pdb=" O   LEU C1840 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 1875 through 1877
      removed outlier: 3.726A  pdb=" N   ALA C1937 " --> pdb=" O   VAL C1946 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 2000 through 2002
    Processing sheet with id=AB3, first strand: chain 'C' and resid 2140 through 2145
      removed outlier: 3.503A  pdb=" N   ARG C2142 " --> pdb=" O   VAL C2495 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   LYS C2467 " --> pdb=" O   LEU C2463 " (cutoff:3.500A)
      removed outlier: 5.677A  pdb=" N   LEU C2463 " --> pdb=" O   LYS C2467 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   VAL C2469 " --> pdb=" O   ALA C2461 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL C2457 " --> pdb=" O   LEU C2473 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   TYR C2475 " --> pdb=" O   VAL C2455 " (cutoff:3.500A)
      removed outlier: 6.187A  pdb=" N   VAL C2455 " --> pdb=" O   TYR C2475 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 2152 through 2157
      removed outlier: 4.150A  pdb=" N   CYS C2154 " --> pdb=" O   GLY C2170 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   GLN C2178 " --> pdb=" O   CYS C2171 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 2199 through 2207
      removed outlier: 6.781A  pdb=" N   GLY C2218 " --> pdb=" O   LEU C2200 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   LEU C2202 " --> pdb=" O   VAL C2216 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   VAL C2216 " --> pdb=" O   LEU C2202 " (cutoff:3.500A)
      removed outlier: 4.907A  pdb=" N   LEU C2204 " --> pdb=" O   TRP C2214 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   TRP C2214 " --> pdb=" O   LEU C2204 " (cutoff:3.500A)
      removed outlier: 5.114A  pdb=" N   HIS C2206 " --> pdb=" O   GLU C2212 " (cutoff:3.500A)
      removed outlier: 7.236A  pdb=" N   GLU C2212 " --> pdb=" O   HIS C2206 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 2245 through 2247
      removed outlier: 3.518A  pdb=" N   THR C2267 " --> pdb=" O   LYS C2271 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LYS C2271 " --> pdb=" O   THR C2267 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 2245 through 2247
      removed outlier: 3.518A  pdb=" N   THR C2267 " --> pdb=" O   LYS C2271 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   LYS C2271 " --> pdb=" O   THR C2267 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE C2274 " --> pdb=" O   LYS C2289 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   LYS C2289 " --> pdb=" O   ILE C2274 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'C' and resid 2317 through 2319
    Processing sheet with id=AB9, first strand: chain 'C' and resid 2354 through 2359
      removed outlier: 6.780A  pdb=" N   ALA C2366 " --> pdb=" O   ILE C2355 " (cutoff:3.500A)
      removed outlier: 4.223A  pdb=" N   VAL C2357 " --> pdb=" O   TYR C2364 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   TYR C2364 " --> pdb=" O   VAL C2357 " (cutoff:3.500A)
      removed outlier: 5.050A  pdb=" N   LYS C2367 " --> pdb=" O   VAL C2372 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   VAL C2372 " --> pdb=" O   LYS C2367 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 2416 through 2419
      removed outlier: 3.539A  pdb=" N   THR C2416 " --> pdb=" O   GLY C2428 " (cutoff:3.500A)
      removed outlier: 6.392A  pdb=" N   ILE C2434 " --> pdb=" O   VAL C2447 " (cutoff:3.500A)
      removed outlier: 4.480A  pdb=" N   VAL C2447 " --> pdb=" O   ILE C2434 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   LEU C2436 " --> pdb=" O   ILE C2445 " (cutoff:3.500A)

    301 hydrogen bonds defined for protein.
    837 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.48

  Time building geometry restraints manager: 1.04 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: 2724
        1.34 -     1.46: 1826
        1.46 -     1.58: 4001
        1.58 -     1.70: 3
        1.70 -     1.81: 75
  Bond restraints: 8629
  Sorted by residual:
  bond pdb=" CBA 4K4 C2602 "
       pdb=" CBB 4K4 C2602 "
    ideal  model  delta    sigma   weight residual
    1.493  1.432  0.061 2.00e-02 2.50e+03 9.31e+00
  bond pdb=" CBF 4K4 C2602 "
       pdb=" NBO 4K4 C2602 "
    ideal  model  delta    sigma   weight residual
    1.356  1.412 -0.056 2.00e-02 2.50e+03 7.94e+00
  bond pdb=" CAU 4K4 C2602 "
       pdb=" NBN 4K4 C2602 "
    ideal  model  delta    sigma   weight residual
    1.458  1.503 -0.045 2.00e-02 2.50e+03 5.06e+00
  bond pdb=" CAS 4K4 C2602 "
       pdb=" NBL 4K4 C2602 "
    ideal  model  delta    sigma   weight residual
    1.450  1.495 -0.045 2.00e-02 2.50e+03 4.96e+00
  bond pdb=" C5  4K4 C2602 "
       pdb=" C6  4K4 C2602 "
    ideal  model  delta    sigma   weight residual
    1.380  1.420 -0.040 2.00e-02 2.50e+03 4.05e+00
  ... (remaining 8624 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.15: 11563
        2.15 -     4.29: 188
        4.29 -     6.44: 26
        6.44 -     8.58: 10
        8.58 -    10.73: 3
  Bond angle restraints: 11790
  Sorted by residual:
  angle pdb=" CA  LEU C2383 "
        pdb=" CB  LEU C2383 "
        pdb=" CG  LEU C2383 "
      ideal   model   delta    sigma   weight residual
     116.30  127.03  -10.73 3.50e+00 8.16e-02 9.39e+00
  angle pdb=" CBB 4K4 C2602 "
        pdb=" CBA 4K4 C2602 "
        pdb=" NBM 4K4 C2602 "
      ideal   model   delta    sigma   weight residual
     117.77  126.79   -9.02 3.00e+00 1.11e-01 9.04e+00
  angle pdb=" CA  MET C2106 "
        pdb=" CB  MET C2106 "
        pdb=" CG  MET C2106 "
      ideal   model   delta    sigma   weight residual
     114.10  119.59   -5.49 2.00e+00 2.50e-01 7.53e+00
  angle pdb=" N3  4K4 C2602 "
        pdb=" C2  4K4 C2602 "
        pdb=" NAY 4K4 C2602 "
      ideal   model   delta    sigma   weight residual
     113.98  122.00   -8.02 3.00e+00 1.11e-01 7.14e+00
  angle pdb=" CA  LEU C1749 "
        pdb=" CB  LEU C1749 "
        pdb=" CG  LEU C1749 "
      ideal   model   delta    sigma   weight residual
     116.30  125.18   -8.88 3.50e+00 8.16e-02 6.44e+00
  ... (remaining 11785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.06: 5008
       31.06 -    62.13: 119
       62.13 -    93.19: 11
       93.19 -   124.26: 1
      124.26 -   155.32: 1
  Dihedral angle restraints: 5140
    sinusoidal: 1814
      harmonic: 3326
  Sorted by residual:
  dihedral pdb=" O4' GDP C2601 "
           pdb=" C1' GDP C2601 "
           pdb=" N9  GDP C2601 "
           pdb=" C8  GDP C2601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      27.02 -177.66 -155.32     1      2.00e+01 2.50e-03 4.58e+01
  dihedral pdb=" CA  MET C2106 "
           pdb=" C   MET C2106 "
           pdb=" N   VAL C2107 "
           pdb=" CA  VAL C2107 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.90   31.10     0      5.00e+00 4.00e-02 3.87e+01
  dihedral pdb=" O2B GDP C2601 "
           pdb=" O3A GDP C2601 "
           pdb=" PB  GDP C2601 "
           pdb=" PA  GDP C2601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00  -60.01 -119.99     1      2.00e+01 2.50e-03 3.60e+01
  ... (remaining 5137 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.978: 1426
       0.978 -    1.955: 0
       1.955 -    2.933: 0
       2.933 -    3.910: 0
       3.910 -    4.888: 1
  Chirality restraints: 1427
  Sorted by residual:
  chirality pdb=" CBK 4K4 C2602 "
            pdb=" CAO 4K4 C2602 "
            pdb=" CAP 4K4 C2602 "
            pdb=" NBN 4K4 C2602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.50   -2.38    4.89 2.00e-01 2.50e+01 5.97e+02
  chirality pdb=" CB  ILE C1482 "
            pdb=" CA  ILE C1482 "
            pdb=" CG1 ILE C1482 "
            pdb=" CG2 ILE C1482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.71e-01
  chirality pdb=" CA  MET C2106 "
            pdb=" N   MET C2106 "
            pdb=" C   MET C2106 "
            pdb=" CB  MET C2106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.50e-01
  ... (remaining 1424 not shown)

  Planarity restraints: 1476
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU C1749 "   -0.011 2.00e-02 2.50e+03   2.23e-02 4.98e+00
        pdb=" C   LEU C1749 "    0.039 2.00e-02 2.50e+03
        pdb=" O   LEU C1749 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   VAL C1750 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG C1693 "   -0.011 2.00e-02 2.50e+03   2.18e-02 4.75e+00
        pdb=" C   ARG C1693 "    0.038 2.00e-02 2.50e+03
        pdb=" O   ARG C1693 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU C1694 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C1734 "   -0.020 2.00e-02 2.50e+03   1.36e-02 4.60e+00
        pdb=" CG  TRP C1734 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TRP C1734 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP C1734 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C1734 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP C1734 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP C1734 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C1734 "   -0.005 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C1734 "    0.000 2.00e-02 2.50e+03
        pdb=" CH2 TRP C1734 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 1473 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1603
        2.78 -     3.31: 7658
        3.31 -     3.84: 12897
        3.84 -     4.37: 15035
        4.37 -     4.90: 26300
  Nonbonded interactions: 63493
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C1992 "
            pdb=" O   ALA C2016 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OG1 THR C1348 "
            pdb=" OG1 THR C1368 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" O   PRO C1433 "
            pdb=" ND2 ASN C1437 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" O   THR C1410 "
            pdb=" OH  TYR C1415 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" O   LEU C1982 "
            pdb=" ND1 HIS C1986 "
     model   vdw
     2.342 3.120
  ... (remaining 63488 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.610
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     9.860
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   8629  Z= 0.166
  Angle     :  0.710  10.727  11790  Z= 0.343
  Chirality :  0.138   4.888   1427
  Planarity :  0.005   0.052   1476
  Dihedral  : 13.851 155.320   2978
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  0.24 %
    Favored  : 99.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.24), residues: 1123
  helix: -0.42 (0.28), residues: 319
  sheet: -1.21 (0.33), residues: 258
  loop : -1.62 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C1771 
 TYR   0.015   0.001   TYR C2475 
 PHE   0.011   0.001   PHE C2326 
 TRP   0.036   0.002   TRP C1734 
 HIS   0.006   0.001   HIS C2433 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8629)
  covalent geometry    : angle       0.71016 (11790)
  hydrogen bonds       : bond        0.26718 (  299)
  hydrogen bonds       : angle       8.92921 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 97
  time to evaluate  : 0.346 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 98
  average time/residue: 0.0875
  time to fit residues: 12.2906
Evaluate side-chains
  77 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    5.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.3980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 100 optimal weight:    0.0020
   overall best weight:    0.5188

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
C2391 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.156985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.123123 restraints weight = 12073.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.124044 restraints weight = 6802.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.125454 restraints weight = 5872.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.126272 restraints weight = 5026.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.126379 restraints weight = 4648.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7368
moved from start:          0.1367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8629  Z= 0.137
  Angle     :  0.592   8.022  11790  Z= 0.295
  Chirality :  0.044   0.166   1427
  Planarity :  0.005   0.073   1476
  Dihedral  :  7.383 155.846   1242
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.97 %
    Favored  : 94.03 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  :  7.63 %
    Favored  : 91.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.41 (0.25), residues: 1123
  helix:  0.50 (0.30), residues: 329
  sheet: -1.35 (0.32), residues: 256
  loop : -1.60 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C1771 
 TYR   0.013   0.001   TYR C2475 
 PHE   0.011   0.001   PHE C2181 
 TRP   0.025   0.001   TRP C1734 
 HIS   0.009   0.001   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 ( 8629)
  covalent geometry    : angle       0.59189 (11790)
  hydrogen bonds       : bond        0.04044 (  299)
  hydrogen bonds       : angle       5.69115 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.329 
Fit side-chains
REVERT: C 2029 ILE cc_start: 0.8971 (tt) cc_final: 0.8607 (tt)
REVERT: C 2249 TYR cc_start: 0.7504 (t80) cc_final: 0.7142 (t80)
REVERT: C 2519 GLU cc_start: 0.7796 (mm-30) cc_final: 0.7523 (mm-30)
  outliers start: 10
  outliers final: 5
  residues processed: 86
  average time/residue: 0.0895
  time to fit residues: 10.9510
Evaluate side-chains
  76 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 71
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1646 MET
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 57 optimal weight:    0.9980
   chunk 112 optimal weight:    0.5980
   chunk 48 optimal weight:    0.0370
   chunk 104 optimal weight:    0.9990
   chunk 90 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 10 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 95 optimal weight:    0.0470
   chunk 92 optimal weight:    1.9990
   overall best weight:    0.4956

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

Flipped N/Q/H residues before XYZ refinement:
C2391 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.156179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.119720 restraints weight = 11906.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.122434 restraints weight = 8375.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.124892 restraints weight = 6066.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.126228 restraints weight = 4890.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3546 r_free = 0.3546 target = 0.126567 restraints weight = 4635.811|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8629  Z= 0.127
  Angle     :  0.559   7.429  11790  Z= 0.277
  Chirality :  0.044   0.168   1427
  Planarity :  0.004   0.059   1476
  Dihedral  :  7.042 154.481   1242
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 11.99 %
    Favored  : 86.44 %
  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: -1.17 (0.26), residues: 1123
  helix:  0.84 (0.31), residues: 323
  sheet: -1.29 (0.32), residues: 268
  loop : -1.48 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C1771 
 TYR   0.011   0.001   TYR C2475 
 PHE   0.010   0.001   PHE C2181 
 TRP   0.022   0.001   TRP C1734 
 HIS   0.008   0.001   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 8629)
  covalent geometry    : angle       0.55870 (11790)
  hydrogen bonds       : bond        0.03354 (  299)
  hydrogen bonds       : angle       5.05860 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 77
  time to evaluate  : 0.353 
Fit side-chains
REVERT: C 1596 TYR cc_start: 0.7447 (m-80) cc_final: 0.7138 (m-10)
REVERT: C 2151 ILE cc_start: 0.8878 (mm) cc_final: 0.8449 (pt)
REVERT: C 2198 ARG cc_start: 0.7577 (mtm-85) cc_final: 0.7036 (mtm-85)
REVERT: C 2249 TYR cc_start: 0.7308 (t80) cc_final: 0.6945 (t80)
REVERT: C 2519 GLU cc_start: 0.7841 (mm-30) cc_final: 0.7509 (mm-30)
  outliers start: 13
  outliers final: 7
  residues processed: 84
  average time/residue: 0.0856
  time to fit residues: 10.5127
Evaluate side-chains
  79 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2449 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    0.0060
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 52 optimal weight:    0.0770
   chunk 88 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 8 optimal weight:    1.9990
   chunk 35 optimal weight:    0.2980
   overall best weight:    0.6556

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
C1779 GLN
C2053 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.153698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.117667 restraints weight = 12354.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.119762 restraints weight = 8779.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.122446 restraints weight = 6288.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.123107 restraints weight = 4948.027|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.123489 restraints weight = 4647.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3517
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   8629  Z= 0.150
  Angle     :  0.577   7.343  11790  Z= 0.287
  Chirality :  0.045   0.168   1427
  Planarity :  0.004   0.057   1476
  Dihedral  :  6.913 153.239   1242
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 14.29 %
    Favored  : 83.66 %
  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: -1.19 (0.26), residues: 1123
  helix:  0.88 (0.31), residues: 328
  sheet: -1.33 (0.32), residues: 262
  loop : -1.55 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2339 
 TYR   0.011   0.001   TYR C2475 
 PHE   0.011   0.001   PHE C2181 
 TRP   0.022   0.001   TRP C1734 
 HIS   0.009   0.002   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 8629)
  covalent geometry    : angle       0.57665 (11790)
  hydrogen bonds       : bond        0.03264 (  299)
  hydrogen bonds       : angle       4.91263 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.386 
Fit side-chains
REVERT: C 1596 TYR cc_start: 0.7409 (m-80) cc_final: 0.7108 (m-10)
REVERT: C 2151 ILE cc_start: 0.8797 (mm) cc_final: 0.8455 (pt)
REVERT: C 2198 ARG cc_start: 0.7582 (mtm-85) cc_final: 0.7093 (mtm-85)
REVERT: C 2249 TYR cc_start: 0.7360 (t80) cc_final: 0.6977 (t80)
REVERT: C 2519 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7537 (mm-30)
  outliers start: 17
  outliers final: 9
  residues processed: 94
  average time/residue: 0.0846
  time to fit residues: 11.5423
Evaluate side-chains
  87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2053 GLN
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2449 TYR
Chi-restraints excluded: chain C residue 2459 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    1.9990
   chunk 34 optimal weight:    0.4980
   chunk 104 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 84 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 65 optimal weight:    0.9990
   chunk 26 optimal weight:    0.6980
   chunk 69 optimal weight:    0.5980
   chunk 7 optimal weight:    0.9990
   overall best weight:    0.5358

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
C2391 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.154925 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.121782 restraints weight = 11591.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.122796 restraints weight = 9083.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.125008 restraints weight = 7084.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.126073 restraints weight = 5624.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.126532 restraints weight = 5209.604|
|-----------------------------------------------------------------------------|
r_work (final): 0.3529
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8629  Z= 0.132
  Angle     :  0.563   7.265  11790  Z= 0.277
  Chirality :  0.044   0.154   1427
  Planarity :  0.004   0.053   1476
  Dihedral  :  6.723 152.811   1242
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.34 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 15.86 %
    Favored  : 82.45 %
  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: -1.13 (0.26), residues: 1123
  helix:  0.97 (0.31), residues: 322
  sheet: -1.28 (0.32), residues: 268
  loop : -1.52 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C2072 
 TYR   0.011   0.001   TYR C1419 
 PHE   0.011   0.001   PHE C2181 
 TRP   0.020   0.001   TRP C1734 
 HIS   0.008   0.001   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 8629)
  covalent geometry    : angle       0.56289 (11790)
  hydrogen bonds       : bond        0.03027 (  299)
  hydrogen bonds       : angle       4.79256 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.341 
Fit side-chains
REVERT: C 1431 MET cc_start: 0.7426 (ttm) cc_final: 0.7193 (ttm)
REVERT: C 1441 ARG cc_start: 0.7056 (OUTLIER) cc_final: 0.6343 (mmp80)
REVERT: C 2047 ASN cc_start: 0.7887 (p0) cc_final: 0.7675 (p0)
REVERT: C 2151 ILE cc_start: 0.8607 (mm) cc_final: 0.8239 (pt)
REVERT: C 2198 ARG cc_start: 0.7572 (mtm-85) cc_final: 0.7052 (mtm-85)
REVERT: C 2249 TYR cc_start: 0.7331 (t80) cc_final: 0.6923 (t80)
  outliers start: 14
  outliers final: 9
  residues processed: 87
  average time/residue: 0.0923
  time to fit residues: 11.5074
Evaluate side-chains
  87 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 77
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1441 ARG
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2393 LEU
Chi-restraints excluded: chain C residue 2449 TYR
Chi-restraints excluded: chain C residue 2459 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 22 optimal weight:    9.9990
   chunk 61 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0000
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.7784

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
C2053 GLN
C2391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.153214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.119863 restraints weight = 11641.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.120795 restraints weight = 9234.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.122729 restraints weight = 7197.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.123828 restraints weight = 5982.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124264 restraints weight = 5474.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3496
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7321
moved from start:          0.2280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   8629  Z= 0.170
  Angle     :  0.596   7.198  11790  Z= 0.295
  Chirality :  0.045   0.163   1427
  Planarity :  0.004   0.056   1476
  Dihedral  :  6.690 150.616   1242
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.59 %
    Favored  : 93.41 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.86 %
    Favored  : 81.72 %
  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: -1.23 (0.25), residues: 1123
  helix:  0.88 (0.31), residues: 323
  sheet: -1.30 (0.32), residues: 253
  loop : -1.62 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2072 
 TYR   0.013   0.001   TYR C1695 
 PHE   0.013   0.001   PHE C2181 
 TRP   0.022   0.001   TRP C1734 
 HIS   0.009   0.002   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 ( 8629)
  covalent geometry    : angle       0.59606 (11790)
  hydrogen bonds       : bond        0.03290 (  299)
  hydrogen bonds       : angle       4.85421 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.319 
Fit side-chains
REVERT: C 1431 MET cc_start: 0.7585 (ttm) cc_final: 0.7303 (ttm)
REVERT: C 1441 ARG cc_start: 0.7195 (OUTLIER) cc_final: 0.6297 (mmp80)
REVERT: C 1596 TYR cc_start: 0.7269 (m-80) cc_final: 0.7035 (m-10)
REVERT: C 2151 ILE cc_start: 0.8679 (mm) cc_final: 0.8359 (pt)
REVERT: C 2249 TYR cc_start: 0.7376 (t80) cc_final: 0.6961 (t80)
REVERT: C 2321 THR cc_start: 0.7246 (OUTLIER) cc_final: 0.6913 (m)
REVERT: C 2519 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7583 (mm-30)
  outliers start: 20
  outliers final: 13
  residues processed: 92
  average time/residue: 0.0846
  time to fit residues: 11.3082
Evaluate side-chains
  91 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 76
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1441 ARG
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1916 LEU
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2107 VAL
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2246 THR
Chi-restraints excluded: chain C residue 2321 THR
Chi-restraints excluded: chain C residue 2373 VAL
Chi-restraints excluded: chain C residue 2393 LEU
Chi-restraints excluded: chain C residue 2449 TYR
Chi-restraints excluded: chain C residue 2459 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 50 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 18 optimal weight:    0.0470
   chunk 45 optimal weight:    1.9990
   chunk 12 optimal weight:    5.9990
   chunk 13 optimal weight:    0.3980
   chunk 28 optimal weight:    4.9990
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5478

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
C2391 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.153263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.117590 restraints weight = 12328.239|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.119552 restraints weight = 8908.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.121689 restraints weight = 6508.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.122313 restraints weight = 5235.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.122749 restraints weight = 4915.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3513
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2371

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8629  Z= 0.135
  Angle     :  0.568   7.232  11790  Z= 0.280
  Chirality :  0.044   0.156   1427
  Planarity :  0.004   0.050   1476
  Dihedral  :  6.539 150.164   1242
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.52 %
    Favored  : 94.48 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.34 %
    Favored  : 81.23 %
  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: -1.17 (0.25), residues: 1123
  helix:  0.99 (0.31), residues: 323
  sheet: -1.31 (0.32), residues: 254
  loop : -1.59 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2339 
 TYR   0.012   0.001   TYR C1596 
 PHE   0.011   0.001   PHE C2181 
 TRP   0.021   0.001   TRP C1734 
 HIS   0.010   0.001   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 8629)
  covalent geometry    : angle       0.56831 (11790)
  hydrogen bonds       : bond        0.02942 (  299)
  hydrogen bonds       : angle       4.72348 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 76
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: C 1431 MET cc_start: 0.7509 (ttm) cc_final: 0.7239 (ttm)
REVERT: C 1441 ARG cc_start: 0.7208 (OUTLIER) cc_final: 0.6287 (mmp80)
REVERT: C 1523 ILE cc_start: 0.9052 (tp) cc_final: 0.8836 (tp)
REVERT: C 1596 TYR cc_start: 0.7441 (m-80) cc_final: 0.7192 (m-10)
REVERT: C 2151 ILE cc_start: 0.8675 (mm) cc_final: 0.8351 (pt)
REVERT: C 2249 TYR cc_start: 0.7315 (t80) cc_final: 0.6973 (t80)
REVERT: C 2321 THR cc_start: 0.7406 (OUTLIER) cc_final: 0.7075 (m)
  outliers start: 20
  outliers final: 14
  residues processed: 90
  average time/residue: 0.0807
  time to fit residues: 10.7805
Evaluate side-chains
  91 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1441 ARG
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1822 HIS
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1907 ILE
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2107 VAL
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2246 THR
Chi-restraints excluded: chain C residue 2321 THR
Chi-restraints excluded: chain C residue 2373 VAL
Chi-restraints excluded: chain C residue 2449 TYR
Chi-restraints excluded: chain C residue 2459 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0870
   chunk 79 optimal weight:    0.9980
   chunk 29 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 102 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 105 optimal weight:    0.9980
   chunk 26 optimal weight:    0.0000
   chunk 72 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   overall best weight:    0.4362

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
C2053 GLN
C2391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.155907 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.124368 restraints weight = 11637.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.126192 restraints weight = 8326.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.128037 restraints weight = 6719.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.128452 restraints weight = 5268.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.128714 restraints weight = 4908.313|
|-----------------------------------------------------------------------------|
r_work (final): 0.3551
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7250
moved from start:          0.2443

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8629  Z= 0.118
  Angle     :  0.554   7.109  11790  Z= 0.273
  Chirality :  0.044   0.157   1427
  Planarity :  0.004   0.054   1476
  Dihedral  :  6.370 148.864   1242
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 16.59 %
    Favored  : 80.87 %
  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: -1.06 (0.25), residues: 1123
  helix:  1.09 (0.31), residues: 323
  sheet: -1.17 (0.32), residues: 256
  loop : -1.57 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2072 
 TYR   0.010   0.001   TYR C1596 
 PHE   0.010   0.001   PHE C2181 
 TRP   0.019   0.001   TRP C1734 
 HIS   0.011   0.001   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 8629)
  covalent geometry    : angle       0.55354 (11790)
  hydrogen bonds       : bond        0.02744 (  299)
  hydrogen bonds       : angle       4.60410 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 80
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: C 1431 MET cc_start: 0.7543 (ttm) cc_final: 0.7286 (ttm)
REVERT: C 1441 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6440 (mmp80)
REVERT: C 1596 TYR cc_start: 0.7322 (m-80) cc_final: 0.7036 (m-10)
REVERT: C 1607 MET cc_start: 0.7943 (tmm) cc_final: 0.5326 (mmm)
REVERT: C 2151 ILE cc_start: 0.8651 (mm) cc_final: 0.8327 (pt)
REVERT: C 2249 TYR cc_start: 0.7299 (t80) cc_final: 0.6908 (t80)
REVERT: C 2321 THR cc_start: 0.7366 (OUTLIER) cc_final: 0.7045 (m)
  outliers start: 21
  outliers final: 17
  residues processed: 95
  average time/residue: 0.0784
  time to fit residues: 11.1875
Evaluate side-chains
  98 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1441 ARG
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1822 HIS
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1907 ILE
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2053 GLN
Chi-restraints excluded: chain C residue 2107 VAL
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2246 THR
Chi-restraints excluded: chain C residue 2321 THR
Chi-restraints excluded: chain C residue 2373 VAL
Chi-restraints excluded: chain C residue 2391 HIS
Chi-restraints excluded: chain C residue 2393 LEU
Chi-restraints excluded: chain C residue 2449 TYR
Chi-restraints excluded: chain C residue 2459 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 68 optimal weight:    0.6980
   chunk 98 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 15 optimal weight:    7.9990
   chunk 39 optimal weight:    0.6980
   chunk 94 optimal weight:   10.0000
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
** C1842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C2053 GLN
C2391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.152019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.119202 restraints weight = 11826.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.120112 restraints weight = 9362.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.121394 restraints weight = 7426.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.121920 restraints weight = 6100.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.123793 restraints weight = 5817.551|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7334
moved from start:          0.2545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   8629  Z= 0.204
  Angle     :  0.624   7.010  11790  Z= 0.309
  Chirality :  0.046   0.169   1427
  Planarity :  0.005   0.053   1476
  Dihedral  :  6.567 148.778   1242
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.12 %
    Favored  : 92.88 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 17.07 %
    Favored  : 80.27 %
  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: -1.27 (0.25), residues: 1123
  helix:  0.86 (0.31), residues: 323
  sheet: -1.36 (0.31), residues: 257
  loop : -1.62 (0.25), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2072 
 TYR   0.021   0.002   TYR C1402 
 PHE   0.014   0.001   PHE C2181 
 TRP   0.021   0.002   TRP C1734 
 HIS   0.016   0.002   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00497 ( 8629)
  covalent geometry    : angle       0.62432 (11790)
  hydrogen bonds       : bond        0.03420 (  299)
  hydrogen bonds       : angle       4.81407 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.322 
Fit side-chains
REVERT: C 1431 MET cc_start: 0.7657 (ttm) cc_final: 0.7367 (ttm)
REVERT: C 1441 ARG cc_start: 0.7273 (OUTLIER) cc_final: 0.6331 (mmp80)
REVERT: C 1523 ILE cc_start: 0.9059 (tp) cc_final: 0.8858 (tp)
REVERT: C 1596 TYR cc_start: 0.7445 (m-80) cc_final: 0.7160 (m-10)
REVERT: C 1718 TYR cc_start: 0.6841 (m-10) cc_final: 0.6631 (m-80)
REVERT: C 2151 ILE cc_start: 0.8580 (mm) cc_final: 0.8252 (pt)
REVERT: C 2198 ARG cc_start: 0.7783 (mtt90) cc_final: 0.7502 (mtt90)
REVERT: C 2249 TYR cc_start: 0.7404 (t80) cc_final: 0.6980 (t80)
REVERT: C 2321 THR cc_start: 0.7466 (OUTLIER) cc_final: 0.7135 (m)
  outliers start: 22
  outliers final: 18
  residues processed: 91
  average time/residue: 0.0794
  time to fit residues: 10.6876
Evaluate side-chains
  97 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1441 ARG
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1822 HIS
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1907 ILE
Chi-restraints excluded: chain C residue 1916 LEU
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2029 ILE
Chi-restraints excluded: chain C residue 2053 GLN
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2246 THR
Chi-restraints excluded: chain C residue 2321 THR
Chi-restraints excluded: chain C residue 2373 VAL
Chi-restraints excluded: chain C residue 2391 HIS
Chi-restraints excluded: chain C residue 2393 LEU
Chi-restraints excluded: chain C residue 2449 TYR
Chi-restraints excluded: chain C residue 2459 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 16 optimal weight:    0.6980
   chunk 1 optimal weight:    0.2980
   chunk 97 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 64 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 105 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
** C1842 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C2053 GLN
C2391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.153111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.121451 restraints weight = 11666.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.122988 restraints weight = 8814.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.124413 restraints weight = 6930.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.124956 restraints weight = 5688.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.125491 restraints weight = 5357.577|
|-----------------------------------------------------------------------------|
r_work (final): 0.3514
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8629  Z= 0.164
  Angle     :  0.595   7.156  11790  Z= 0.294
  Chirality :  0.045   0.161   1427
  Planarity :  0.004   0.051   1476
  Dihedral  :  6.530 148.902   1242
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.31 %
    Favored  : 80.15 %
  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: -1.22 (0.25), residues: 1123
  helix:  0.91 (0.31), residues: 323
  sheet: -1.25 (0.32), residues: 253
  loop : -1.65 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2072 
 TYR   0.018   0.001   TYR C1402 
 PHE   0.013   0.001   PHE C2181 
 TRP   0.021   0.001   TRP C1734 
 HIS   0.015   0.002   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00400 ( 8629)
  covalent geometry    : angle       0.59483 (11790)
  hydrogen bonds       : bond        0.03153 (  299)
  hydrogen bonds       : angle       4.76684 (  837)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 77
  time to evaluate  : 0.320 
Fit side-chains
REVERT: C 1431 MET cc_start: 0.7691 (ttm) cc_final: 0.7433 (ttm)
REVERT: C 1441 ARG cc_start: 0.7236 (OUTLIER) cc_final: 0.6314 (mmp80)
REVERT: C 1523 ILE cc_start: 0.9011 (tp) cc_final: 0.8805 (tp)
REVERT: C 1596 TYR cc_start: 0.7468 (m-80) cc_final: 0.7205 (m-10)
REVERT: C 2151 ILE cc_start: 0.8584 (mm) cc_final: 0.8238 (pt)
REVERT: C 2249 TYR cc_start: 0.7410 (t80) cc_final: 0.7012 (t80)
REVERT: C 2321 THR cc_start: 0.7432 (OUTLIER) cc_final: 0.7076 (m)
  outliers start: 21
  outliers final: 17
  residues processed: 90
  average time/residue: 0.0709
  time to fit residues: 9.8197
Evaluate side-chains
  95 residues out of total 1020 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 76
  time to evaluate  : 0.310 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1441 ARG
Chi-restraints excluded: chain C residue 1454 LEU
Chi-restraints excluded: chain C residue 1509 LEU
Chi-restraints excluded: chain C residue 1763 LEU
Chi-restraints excluded: chain C residue 1822 HIS
Chi-restraints excluded: chain C residue 1826 LEU
Chi-restraints excluded: chain C residue 1864 LEU
Chi-restraints excluded: chain C residue 1907 ILE
Chi-restraints excluded: chain C residue 1923 VAL
Chi-restraints excluded: chain C residue 2029 ILE
Chi-restraints excluded: chain C residue 2053 GLN
Chi-restraints excluded: chain C residue 2201 CYS
Chi-restraints excluded: chain C residue 2215 ILE
Chi-restraints excluded: chain C residue 2246 THR
Chi-restraints excluded: chain C residue 2321 THR
Chi-restraints excluded: chain C residue 2373 VAL
Chi-restraints excluded: chain C residue 2393 LEU
Chi-restraints excluded: chain C residue 2449 TYR
Chi-restraints excluded: chain C residue 2459 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 98 optimal weight:    0.5980
   chunk 106 optimal weight:    0.0470
   chunk 96 optimal weight:    0.0270
   chunk 53 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 74 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 82 optimal weight:    0.5980
   chunk 81 optimal weight:    3.9990
   overall best weight:    0.3936

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

Flipped N/Q/H residues before XYZ refinement:
C1571 HIS
C2053 GLN
C2391 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.155541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.123948 restraints weight = 11667.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.125785 restraints weight = 8490.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.127033 restraints weight = 6719.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127741 restraints weight = 5501.424|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.128301 restraints weight = 5161.452|
|-----------------------------------------------------------------------------|
r_work (final): 0.3547
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7268
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8629  Z= 0.114
  Angle     :  0.551   7.249  11790  Z= 0.272
  Chirality :  0.044   0.155   1427
  Planarity :  0.004   0.051   1476
  Dihedral  :  6.380 148.361   1242
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.70 %
    Favored  : 94.30 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 17.68 %
    Favored  : 79.78 %
  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: -1.09 (0.25), residues: 1123
  helix:  1.10 (0.31), residues: 323
  sheet: -1.21 (0.32), residues: 256
  loop : -1.60 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C2072 
 TYR   0.012   0.001   TYR C1402 
 PHE   0.010   0.001   PHE C2181 
 TRP   0.019   0.001   TRP C1734 
 HIS   0.012   0.001   HIS C2391 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 8629)
  covalent geometry    : angle       0.55061 (11790)
  hydrogen bonds       : bond        0.02720 (  299)
  hydrogen bonds       : angle       4.60588 (  837)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1306.27 seconds
wall clock time: 23 minutes 15.65 seconds (1395.65 seconds total)