Starting phenix.real_space_refine
on Sat Feb 17 11:51:53 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/02_2024/8sxb_40830_trim_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/02_2024/8sxb_40830.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/02_2024/8sxb_40830.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/02_2024/8sxb_40830.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/02_2024/8sxb_40830_trim_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sxb_40830/02_2024/8sxb_40830_trim_updated.pdb"
  }
  resolution = 2.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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=   0.002 sd=   0.066
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      35      5.16       5
     C    5971      2.51       5
     N    1544      2.21       5
     O    1649      1.98       5
     H    9405      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE 2497": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib"
  Total number of atoms: 18604
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 18576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1152, 18576
          Classifications: {'peptide': 1152}
          Link IDs: {'PCIS': 1, 'PTRANS': 33, 'TRANS': 1117}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'P2E': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Time building chain proxies: 8.44, per 1000 atoms: 0.45
  Number of scatterers: 18604
  At special positions: 0
  Unit cell: (81.83, 96.025, 144.455, 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      35     16.00
     O    1649      8.00
     N    1544      7.00
     C    5971      6.00
     H    9405      1.00
    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  - 3.50
        Amino acid           : False - 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: 15.75
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2176

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      48 helices and 4 sheets defined
      67.2% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.65
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1369 through 1371
      No H-bonds generated for 'chain 'A' and resid 1369 through 1371'
    Processing helix  chain 'A' and resid 1373 through 1393
      removed outlier: 4.085A  pdb=" N   LEU A1380 " --> pdb=" O   LEU A1376 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   TYR A1383 " --> pdb=" O   GLU A1379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1400 through 1441
      removed outlier: 5.867A  pdb=" N   LYS A1410 " --> pdb=" O   LYS A1406 " (cutoff:3.500A)
      removed outlier: 5.796A  pdb=" N   SER A1411 " --> pdb=" O   CYS A1407 " (cutoff:3.500A)
      removed outlier: 4.252A  pdb=" N   VAL A1414 " --> pdb=" O   LYS A1410 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   LEU A1415 " --> pdb=" O   SER A1411 " (cutoff:3.500A)
      removed outlier: 4.007A  pdb=" N   GLY A1416 " --> pdb=" O   TYR A1412 " (cutoff:3.500A)
      removed outlier: 4.341A  pdb=" N   ILE A1417 " --> pdb=" O   VAL A1413 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   PHE A1418 " --> pdb=" O   VAL A1414 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   THR A1419 " --> pdb=" O   LEU A1415 " (cutoff:3.500A)
      Proline residue:  A1430  - end of helix
      removed outlier: 3.578A  pdb=" N   TYR A1439 " --> pdb=" O   LYS A1435 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   PHE A1440 " --> pdb=" O   ILE A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1448 through 1500
      removed outlier: 4.103A  pdb=" N   ARG A1500 " --> pdb=" O   ARG A1496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1505 through 1508
      removed outlier: 3.661A  pdb=" N   LYS A1508 " --> pdb=" O   ALA A1505 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1505 through 1508'
    Processing helix  chain 'A' and resid 1511 through 1520
      removed outlier: 3.542A  pdb=" N   LEU A1517 " --> pdb=" O   GLN A1513 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LEU A1518 " --> pdb=" O   ILE A1514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1522 through 1530
      removed outlier: 4.096A  pdb=" N   ASP A1526 " --> pdb=" O   ASN A1523 " (cutoff:3.500A)
      removed outlier: 4.363A  pdb=" N   THR A1529 " --> pdb=" O   ASP A1526 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1532 through 1601
      removed outlier: 3.749A  pdb=" N   ALA A1537 " --> pdb=" O   PHE A1534 " (cutoff:3.500A)
      removed outlier: 5.129A  pdb=" N   GLY A1538 " --> pdb=" O   LEU A1535 " (cutoff:3.500A)
      Proline residue:  A1539  - end of helix
      removed outlier: 3.520A  pdb=" N   VAL A1545 " --> pdb=" O   ALA A1542 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A1549 " --> pdb=" O   THR A1546 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   ILE A1553 " --> pdb=" O   TRP A1550 " (cutoff:3.500A)
      removed outlier: 5.239A  pdb=" N   GLY A1554 " --> pdb=" O   MET A1551 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   ILE A1555 " --> pdb=" O   GLU A1552 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   SER A1556 " --> pdb=" O   ILE A1553 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A1562 " --> pdb=" O   ALA A1559 " (cutoff:3.500A)
      removed outlier: 4.452A  pdb=" N   LEU A1568 " --> pdb=" O   ILE A1565 " (cutoff:3.500A)
      Proline residue:  A1569  - end of helix
      removed outlier: 3.604A  pdb=" N   ILE A1574 " --> pdb=" O   GLN A1571 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   PHE A1578 " --> pdb=" O   GLY A1575 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ALA A1587 " --> pdb=" O   LYS A1584 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   ASP A1590 " --> pdb=" O   ALA A1587 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ILE A1600 " --> pdb=" O   ASN A1597 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   THR A1601 " --> pdb=" O   GLU A1598 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1603 through 1608
    Processing helix  chain 'A' and resid 1611 through 1661
      removed outlier: 3.591A  pdb=" N   ALA A1616 " --> pdb=" O   LYS A1613 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A1619 " --> pdb=" O   ALA A1616 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN A1621 " --> pdb=" O   LEU A1618 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   ILE A1627 " --> pdb=" O   ARG A1624 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER A1633 " --> pdb=" O   ILE A1630 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   LEU A1641 " --> pdb=" O   GLY A1638 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA A1642 " --> pdb=" O   MET A1639 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   ALA A1647 " --> pdb=" O   PHE A1644 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   SER A1648 " --> pdb=" O   PHE A1645 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   VAL A1652 " --> pdb=" O   LYS A1649 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL A1654 " --> pdb=" O   ILE A1651 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A1655 " --> pdb=" O   VAL A1652 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   PHE A1656 " --> pdb=" O   PHE A1653 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR A1657 " --> pdb=" O   VAL A1654 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR A1659 " --> pdb=" O   PHE A1656 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL A1660 " --> pdb=" O   THR A1657 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1668 through 1684
    Processing helix  chain 'A' and resid 1688 through 1710
      removed outlier: 3.540A  pdb=" N   VAL A1701 " --> pdb=" O   SER A1697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1771 through 1778
    Processing helix  chain 'A' and resid 1809 through 1814
    Processing helix  chain 'A' and resid 1821 through 1830
      removed outlier: 3.797A  pdb=" N   LYS A1826 " --> pdb=" O   GLU A1822 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1834 through 1839
    Processing helix  chain 'A' and resid 1843 through 1845
      No H-bonds generated for 'chain 'A' and resid 1843 through 1845'
    Processing helix  chain 'A' and resid 1857 through 1871
      removed outlier: 3.601A  pdb=" N   ALA A1868 " --> pdb=" O   ASN A1864 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLN A1871 " --> pdb=" O   ARG A1867 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1881 through 1884
    Processing helix  chain 'A' and resid 1887 through 1896
    Processing helix  chain 'A' and resid 1914 through 1919
      removed outlier: 4.778A  pdb=" N   LYS A1918 " --> pdb=" O   GLN A1915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2018 through 2026
    Processing helix  chain 'A' and resid 2031 through 2064
      removed outlier: 3.575A  pdb=" N   ASP A2052 " --> pdb=" O   TYR A2048 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2081 through 2127
      removed outlier: 3.657A  pdb=" N   PHE A2107 " --> pdb=" O   SER A2103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2130 through 2135
      removed outlier: 3.525A  pdb=" N   ARG A2135 " --> pdb=" O   PHE A2132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2138 through 2153
      removed outlier: 3.974A  pdb=" N   ARG A2144 " --> pdb=" O   ARG A2140 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE A2145 " --> pdb=" O   ILE A2141 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   ILE A2149 " --> pdb=" O   PHE A2145 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2155 through 2180
      removed outlier: 3.631A  pdb=" N   GLN A2169 " --> pdb=" O   GLN A2165 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2182 through 2229
      Proline residue:  A2187  - end of helix
      Proline residue:  A2190  - end of helix
      removed outlier: 3.735A  pdb=" N   VAL A2194 " --> pdb=" O   LEU A2191 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   ARG A2199 " --> pdb=" O   PHE A2196 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   LEU A2203 " --> pdb=" O   ARG A2200 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU A2204 " --> pdb=" O   TYR A2201 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   ARG A2207 " --> pdb=" O   GLU A2204 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   LYS A2210 " --> pdb=" O   ARG A2207 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   GLU A2213 " --> pdb=" O   LYS A2210 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER A2218 " --> pdb=" O   THR A2215 " (cutoff:3.500A)
      Proline residue:  A2219  - end of helix
      removed outlier: 3.833A  pdb=" N   SER A2225 " --> pdb=" O   SER A2222 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   LEU A2228 " --> pdb=" O   SER A2225 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   GLN A2229 " --> pdb=" O   SER A2226 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2231 through 2234
      No H-bonds generated for 'chain 'A' and resid 2231 through 2234'
    Processing helix  chain 'A' and resid 2240 through 2289
      removed outlier: 3.603A  pdb=" N   PHE A2247 " --> pdb=" O   PHE A2243 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ARG A2271 " --> pdb=" O   TRP A2267 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   LEU A2288 " --> pdb=" O   ALA A2284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2291 through 2293
      No H-bonds generated for 'chain 'A' and resid 2291 through 2293'
    Processing helix  chain 'A' and resid 2296 through 2334
      removed outlier: 3.626A  pdb=" N   LEU A2309 " --> pdb=" O   TYR A2305 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   MET A2310 " --> pdb=" O   ALA A2306 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   GLY A2311 " --> pdb=" O   LEU A2307 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   MET A2312 " --> pdb=" O   THR A2308 " (cutoff:3.500A)
      removed outlier: 4.673A  pdb=" N   GLN A2314 " --> pdb=" O   MET A2310 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   TRP A2315 " --> pdb=" O   GLY A2311 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ALA A2321 " --> pdb=" O   VAL A2317 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   ILE A2328 " --> pdb=" O   GLU A2324 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   SER A2329 " --> pdb=" O   ASN A2325 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   VAL A2330 " --> pdb=" O   MET A2326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2336 through 2338
      No H-bonds generated for 'chain 'A' and resid 2336 through 2338'
    Processing helix  chain 'A' and resid 2401 through 2408
      removed outlier: 3.978A  pdb=" N   ILE A2405 " --> pdb=" O   LYS A2401 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2425 through 2427
      No H-bonds generated for 'chain 'A' and resid 2425 through 2427'
    Processing helix  chain 'A' and resid 2430 through 2435
    Processing helix  chain 'A' and resid 2451 through 2455
    Processing helix  chain 'A' and resid 2463 through 2472
    Processing helix  chain 'A' and resid 2476 through 2480
    Processing helix  chain 'A' and resid 2485 through 2487
      No H-bonds generated for 'chain 'A' and resid 2485 through 2487'
    Processing helix  chain 'A' and resid 2492 through 2494
      No H-bonds generated for 'chain 'A' and resid 2492 through 2494'
    Processing helix  chain 'A' and resid 2499 through 2512
      removed outlier: 3.798A  pdb=" N   VAL A2505 " --> pdb=" O   GLN A2501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2524 through 2526
      No H-bonds generated for 'chain 'A' and resid 2524 through 2526'
    Processing helix  chain 'A' and resid 2529 through 2542
      removed outlier: 4.737A  pdb=" N   LEU A2534 " --> pdb=" O   ARG A2530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 2555 through 2557
      No H-bonds generated for 'chain 'A' and resid 2555 through 2557'
    Processing helix  chain 'A' and resid 2578 through 2583
    Processing helix  chain 'A' and resid 2588 through 2596
    Processing helix  chain 'A' and resid 2598 through 2617
    Processing sheet with id=  A, first strand: chain 'A' and resid 1753 through 1755
    Processing sheet with id=  B, first strand: chain 'A' and resid 1930 through 1935
      removed outlier: 7.086A  pdb=" N   ILE A1925 " --> pdb=" O   VAL A1932 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LYS A1934 " --> pdb=" O   ILE A1923 " (cutoff:3.500A)
      removed outlier: 6.641A  pdb=" N   ILE A1923 " --> pdb=" O   LYS A1934 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   ARG A1907 " --> pdb=" O   LEU A1761 " (cutoff:3.500A)
      removed outlier: 7.138A  pdb=" N   VAL A1763 " --> pdb=" O   ARG A1907 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU A1909 " --> pdb=" O   VAL A1763 " (cutoff:3.500A)
      removed outlier: 8.508A  pdb=" N   GLY A1765 " --> pdb=" O   LEU A1909 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'A' and resid 2383 through 2385
    Processing sheet with id=  D, first strand: chain 'A' and resid 2572 through 2576
      removed outlier: 6.805A  pdb=" N   VAL A2566 " --> pdb=" O   LYS A2573 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   TYR A2575 " --> pdb=" O   ILE A2564 " (cutoff:3.500A)
      removed outlier: 6.262A  pdb=" N   ILE A2564 " --> pdb=" O   TYR A2575 " (cutoff:3.500A)
      removed outlier: 6.175A  pdb=" N   VAL A2548 " --> pdb=" O   VAL A2391 " (cutoff:3.500A)
      removed outlier: 7.581A  pdb=" N   ILE A2393 " --> pdb=" O   VAL A2548 " (cutoff:3.500A)
      removed outlier: 6.653A  pdb=" N   THR A2550 " --> pdb=" O   ILE A2393 " (cutoff:3.500A)
      removed outlier: 8.711A  pdb=" N   GLY A2395 " --> pdb=" O   THR A2550 " (cutoff:3.500A)
      removed outlier: 6.321A  pdb=" N   SER A2438 " --> pdb=" O   ILE A2519 " (cutoff:3.500A)
      removed outlier: 7.511A  pdb=" N   ASP A2521 " --> pdb=" O   SER A2438 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   ILE A2440 " --> pdb=" O   ASP A2521 " (cutoff:3.500A)

    534 hydrogen bonds defined for protein.
    1242 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: 7.17

  Time building geometry restraints manager: 16.13 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 9392
        1.03 -     1.23: 37
        1.23 -     1.42: 3862
        1.42 -     1.62: 5447
        1.62 -     1.81: 57
  Bond restraints: 18795
  Sorted by residual:
  bond pdb=" C1  P2E A2701 "
       pdb=" O1  P2E A2701 "
    ideal  model  delta    sigma   weight residual
    1.247  1.209  0.038 2.00e-02 2.50e+03 3.67e+00
  bond pdb=" C1  P2E A2701 "
       pdb=" O2  P2E A2701 "
    ideal  model  delta    sigma   weight residual
    1.250  1.212  0.038 2.00e-02 2.50e+03 3.56e+00
  bond pdb=" CB  THR A1686 "
       pdb=" CG2 THR A1686 "
    ideal  model  delta    sigma   weight residual
    1.521  1.470  0.051 3.30e-02 9.18e+02 2.43e+00
  bond pdb=" C   ALA A2343 "
       pdb=" N   PRO A2344 "
    ideal  model  delta    sigma   weight residual
    1.331  1.349 -0.018 1.21e-02 6.83e+03 2.13e+00
  bond pdb=" C2  P2E A2701 "
       pdb=" C3  P2E A2701 "
    ideal  model  delta    sigma   weight residual
    1.519  1.545 -0.026 2.00e-02 2.50e+03 1.72e+00
  ... (remaining 18790 not shown)

  Histogram of bond angle deviations from ideal:
       99.75 -   106.64: 302
      106.64 -   113.53: 22321
      113.53 -   120.41: 6408
      120.41 -   127.30: 4891
      127.30 -   134.19: 107
  Bond angle restraints: 34029
  Sorted by residual:
  angle pdb=" N   HIS A1478 "
        pdb=" CA  HIS A1478 "
        pdb=" C   HIS A1478 "
      ideal   model   delta    sigma   weight residual
     111.36  115.11   -3.75 1.09e+00 8.42e-01 1.18e+01
  angle pdb=" N   TRP A2345 "
        pdb=" CA  TRP A2345 "
        pdb=" C   TRP A2345 "
      ideal   model   delta    sigma   weight residual
     111.36  114.64   -3.28 1.09e+00 8.42e-01 9.06e+00
  angle pdb=" N   GLY A2175 "
        pdb=" CA  GLY A2175 "
        pdb=" C   GLY A2175 "
      ideal   model   delta    sigma   weight residual
     112.50  115.88   -3.38 1.16e+00 7.43e-01 8.50e+00
  angle pdb=" N   GLY A2172 "
        pdb=" CA  GLY A2172 "
        pdb=" C   GLY A2172 "
      ideal   model   delta    sigma   weight residual
     112.73  116.06   -3.33 1.20e+00 6.94e-01 7.69e+00
  angle pdb=" CA  HIS A1473 "
        pdb=" CB  HIS A1473 "
        pdb=" CG  HIS A1473 "
      ideal   model   delta    sigma   weight residual
     113.80  111.09    2.71 1.00e+00 1.00e+00 7.35e+00
  ... (remaining 34024 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 8083
       17.93 -    35.85: 371
       35.85 -    53.78: 149
       53.78 -    71.71: 155
       71.71 -    89.64: 10
  Dihedral angle restraints: 8768
    sinusoidal: 4763
      harmonic: 4005
  Sorted by residual:
  dihedral pdb=" CA  ALA A2343 "
           pdb=" C   ALA A2343 "
           pdb=" N   PRO A2344 "
           pdb=" CA  PRO A2344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.98  -26.02     0      5.00e+00 4.00e-02 2.71e+01
  dihedral pdb=" CA  CYS A2546 "
           pdb=" C   CYS A2546 "
           pdb=" N   THR A2547 "
           pdb=" CA  THR A2547 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.01   24.99     0      5.00e+00 4.00e-02 2.50e+01
  dihedral pdb=" CA  GLU A2522 "
           pdb=" C   GLU A2522 "
           pdb=" N   ALA A2523 "
           pdb=" CA  ALA A2523 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.53  -24.47     0      5.00e+00 4.00e-02 2.39e+01
  ... (remaining 8765 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.056: 1066
       0.056 -    0.113: 323
       0.113 -    0.169: 76
       0.169 -    0.225: 12
       0.225 -    0.282: 3
  Chirality restraints: 1480
  Sorted by residual:
  chirality pdb=" CA  PHE A1656 "
            pdb=" N   PHE A1656 "
            pdb=" C   PHE A1656 "
            pdb=" CB  PHE A1656 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.98e+00
  chirality pdb=" C15 P2E A2701 "
            pdb=" C14 P2E A2701 "
            pdb=" C16 P2E A2701 "
            pdb=" O5  P2E A2701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.23    2.49   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" CA  PHE A1672 "
            pdb=" N   PHE A1672 "
            pdb=" C   PHE A1672 "
            pdb=" CB  PHE A1672 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.50e+00
  ... (remaining 1477 not shown)

  Planarity restraints: 2698
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1794 "   -0.097 9.50e-02 1.11e+02   4.91e-02 3.17e+01
        pdb=" NE  ARG A1794 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1794 "   -0.006 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1794 "   -0.043 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1794 "    0.063 2.00e-02 2.50e+03
        pdb="HH11 ARG A1794 "    0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A1794 "    0.049 2.00e-02 2.50e+03
        pdb="HH21 ARG A1794 "    0.002 2.00e-02 2.50e+03
        pdb="HH22 ARG A1794 "   -0.063 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS A1473 "   -0.037 2.00e-02 2.50e+03   3.44e-02 2.67e+01
        pdb=" CG  HIS A1473 "    0.066 2.00e-02 2.50e+03
        pdb=" ND1 HIS A1473 "    0.020 2.00e-02 2.50e+03
        pdb=" CD2 HIS A1473 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 HIS A1473 "    0.038 2.00e-02 2.50e+03
        pdb=" NE2 HIS A1473 "   -0.010 2.00e-02 2.50e+03
        pdb=" HD1 HIS A1473 "   -0.023 2.00e-02 2.50e+03
        pdb=" HD2 HIS A1473 "   -0.028 2.00e-02 2.50e+03
        pdb=" HE1 HIS A1473 "   -0.039 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1500 "    0.221 9.50e-02 1.11e+02   7.95e-02 2.56e+01
        pdb=" NE  ARG A1500 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1500 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1500 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1500 "   -0.063 2.00e-02 2.50e+03
        pdb="HH11 ARG A1500 "   -0.000 2.00e-02 2.50e+03
        pdb="HH12 ARG A1500 "   -0.018 2.00e-02 2.50e+03
        pdb="HH21 ARG A1500 "   -0.001 2.00e-02 2.50e+03
        pdb="HH22 ARG A1500 "    0.061 2.00e-02 2.50e+03
  ... (remaining 2695 not shown)

  Histogram of nonbonded interaction distances:
        1.54 -     2.15: 747
        2.15 -     2.76: 35437
        2.76 -     3.38: 52933
        3.38 -     3.99: 66026
        3.99 -     4.60: 105984
  Nonbonded interactions: 261127
  Sorted by model distance:
  nonbonded pdb="HH21 ARG A2127 "
            pdb=" O   GLU A2342 "
     model   vdw
     1.540 1.850
  nonbonded pdb=" HZ1 LYS A1497 "
            pdb=" OE1 GLU A1714 "
     model   vdw
     1.554 1.850
  nonbonded pdb=" HG1 THR A1589 "
            pdb=" OE2 GLU A1626 "
     model   vdw
     1.564 1.850
  nonbonded pdb=" O   ALA A1616 "
            pdb=" HG1 THR A1620 "
     model   vdw
     1.564 1.850
  nonbonded pdb=" OD2 ASP A2052 "
            pdb=" HH  TYR A2305 "
     model   vdw
     1.580 1.850
  ... (remaining 261122 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.260
  Extract box with map and model:          6.570
  Check model and map are aligned:         0.250
  Set scattering table:                    0.150
  Process input model:                     61.610
  Find NCS groups from input model:        0.320
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:12.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   83.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
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      :  0.006   0.051   9390  Z= 0.372
  Angle     :  0.833   6.103  12724  Z= 0.528
  Chirality :  0.058   0.282   1480
  Planarity :  0.009   0.109   1584
  Dihedral  : 12.608  89.636   3441
  Min Nonbonded Distance : 2.288

Molprobity Statistics.
  All-atom Clashscore : 0.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.22), residues: 1144
  helix: -0.90 (0.16), residues: 750
  sheet:  0.48 (0.56), residues: 78
  loop :  0.57 (0.36), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.005   TRP A2054 
 HIS   0.025   0.003   HIS A1473 
 PHE   0.020   0.003   PHE A1805 
 TYR   0.027   0.006   TYR A1412 
 ARG   0.025   0.002   ARG A1670 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 143
  time to evaluate  : 1.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7530 (mtt-85) cc_final: 0.7013 (mmt180)
REVERT: A 2451 MET cc_start: 0.7417 (tpt) cc_final: 0.7205 (mmm)
REVERT: A 2542 LYS cc_start: 0.7886 (mmmt) cc_final: 0.7682 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 143
  average time/residue: 2.4578
  time to fit residues: 378.2523
Evaluate side-chains
  79 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 1.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 97 optimal weight:    0.0980
   chunk 87 optimal weight:    3.9990
   chunk 48 optimal weight:   10.0000
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:    5.9990
   chunk 34 optimal weight:    2.9990
   chunk 54 optimal weight:    9.9990
   chunk 67 optimal weight:    1.9990
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.9984

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

Flipped N/Q/H residues before XYZ refinement:
A2254 HIS
A2442 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7944
moved from start:          0.2187

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9390  Z= 0.192
  Angle     :  0.539   5.038  12724  Z= 0.300
  Chirality :  0.039   0.155   1480
  Planarity :  0.005   0.058   1584
  Dihedral  :  5.508  46.690   1277
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  :  6.91 %
    Favored  : 91.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.46 (0.24), residues: 1144
  helix:  0.24 (0.18), residues: 739
  sheet:  0.31 (0.55), residues: 78
  loop :  0.91 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.008   0.002   HIS A1473 
 PHE   0.017   0.002   PHE A1672 
 TYR   0.015   0.002   TYR A2590 
 ARG   0.008   0.001   ARG A2502 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 1.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1442 ASN cc_start: 0.7187 (m110) cc_final: 0.6925 (t0)
REVERT: A 1596 MET cc_start: 0.7813 (tpt) cc_final: 0.7575 (tpt)
REVERT: A 1632 ARG cc_start: 0.7344 (mtt-85) cc_final: 0.6807 (mmt180)
REVERT: A 2217 ARG cc_start: 0.8157 (ttm170) cc_final: 0.7900 (ttm-80)
REVERT: A 2229 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6954 (mp10)
REVERT: A 2259 PHE cc_start: 0.7304 (OUTLIER) cc_final: 0.6959 (t80)
REVERT: A 2402 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7826 (p)
REVERT: A 2421 ASP cc_start: 0.7910 (t0) cc_final: 0.6781 (t0)
REVERT: A 2485 LYS cc_start: 0.7520 (mtmt) cc_final: 0.6991 (pttt)
REVERT: A 2502 ARG cc_start: 0.6656 (mtm-85) cc_final: 0.6190 (mtt90)
  outliers start: 11
  outliers final: 3
  residues processed: 91
  average time/residue: 2.1994
  time to fit residues: 218.1753
Evaluate side-chains
  72 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 1.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2402 SER
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 58 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 86 optimal weight:    2.9990
   chunk 71 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9990
   chunk 104 optimal weight:    4.9990
   chunk 113 optimal weight:    0.6980
   chunk 93 optimal weight:    7.9990
   chunk 103 optimal weight:    2.9990
   chunk 35 optimal weight:   30.0000
   chunk 83 optimal weight:    2.9990
   overall best weight:    1.3388

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

Flipped N/Q/H residues before XYZ refinement:
A2442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.2784

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9390  Z= 0.207
  Angle     :  0.497   4.950  12724  Z= 0.275
  Chirality :  0.038   0.149   1480
  Planarity :  0.004   0.039   1584
  Dihedral  :  5.063  33.240   1277
  Min Nonbonded Distance : 1.852

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  :  8.31 %
    Favored  : 90.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.24), residues: 1144
  helix:  0.44 (0.19), residues: 747
  sheet:  0.19 (0.51), residues: 85
  loop :  0.96 (0.37), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A2053 
 HIS   0.011   0.002   HIS A2357 
 PHE   0.017   0.001   PHE A1672 
 TYR   0.011   0.001   TYR A2590 
 ARG   0.005   0.000   ARG A2502 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 1.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1596 MET cc_start: 0.7956 (tpt) cc_final: 0.7582 (tpp)
REVERT: A 1632 ARG cc_start: 0.7386 (mtt-85) cc_final: 0.6800 (mmt180)
REVERT: A 2016 VAL cc_start: 0.7420 (OUTLIER) cc_final: 0.7175 (m)
REVERT: A 2229 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7042 (mp10)
REVERT: A 2259 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.6977 (t80)
REVERT: A 2402 SER cc_start: 0.8108 (OUTLIER) cc_final: 0.7899 (p)
REVERT: A 2485 LYS cc_start: 0.7458 (mtmt) cc_final: 0.6892 (pptt)
REVERT: A 2502 ARG cc_start: 0.6592 (mtm-85) cc_final: 0.6099 (mtt90)
  outliers start: 13
  outliers final: 4
  residues processed: 81
  average time/residue: 1.9844
  time to fit residues: 177.8223
Evaluate side-chains
  77 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 69
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1513 GLN
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2402 SER
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.2980
   chunk 78 optimal weight:    2.9990
   chunk 54 optimal weight:   30.0000
   chunk 11 optimal weight:    1.9990
   chunk 49 optimal weight:   20.0000
   chunk 70 optimal weight:    0.9990
   chunk 104 optimal weight:    3.9990
   chunk 111 optimal weight:   10.0000
   chunk 99 optimal weight:    7.9990
   chunk 29 optimal weight:    0.6980
   chunk 92 optimal weight:    6.9990
   overall best weight:    1.3986

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9390  Z= 0.203
  Angle     :  0.478   6.002  12724  Z= 0.262
  Chirality :  0.037   0.142   1480
  Planarity :  0.004   0.038   1584
  Dihedral  :  4.927  34.871   1277
  Min Nonbonded Distance : 1.846

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  8.11 %
    Favored  : 90.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.73 (0.25), residues: 1144
  helix:  0.53 (0.19), residues: 753
  sheet:  0.26 (0.51), residues: 85
  loop :  0.89 (0.36), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.010   0.001   HIS A1473 
 PHE   0.016   0.001   PHE A1672 
 TYR   0.009   0.001   TYR A2590 
 ARG   0.008   0.000   ARG A2217 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 1.414 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7400 (mtt-85) cc_final: 0.6793 (mmt180)
REVERT: A 2016 VAL cc_start: 0.7513 (OUTLIER) cc_final: 0.7254 (m)
REVERT: A 2259 PHE cc_start: 0.7416 (OUTLIER) cc_final: 0.6926 (t80)
REVERT: A 2485 LYS cc_start: 0.7428 (mtmt) cc_final: 0.6876 (pptt)
REVERT: A 2502 ARG cc_start: 0.6489 (mtm-85) cc_final: 0.6203 (mtt90)
  outliers start: 16
  outliers final: 5
  residues processed: 76
  average time/residue: 2.1679
  time to fit residues: 180.6640
Evaluate side-chains
  69 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 1.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 63 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 45 optimal weight:   10.0000
   chunk 94 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 99 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
A1442 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.3358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9390  Z= 0.223
  Angle     :  0.475   5.871  12724  Z= 0.261
  Chirality :  0.038   0.139   1480
  Planarity :  0.004   0.039   1584
  Dihedral  :  4.976  37.520   1277
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 3.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  :  8.91 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.25), residues: 1144
  helix:  0.53 (0.19), residues: 752
  sheet:  0.61 (0.54), residues: 78
  loop :  0.80 (0.35), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.009   0.001   HIS A1473 
 PHE   0.018   0.001   PHE A1672 
 TYR   0.008   0.001   TYR A2305 
 ARG   0.003   0.000   ARG A2502 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 1.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7445 (mtt-85) cc_final: 0.6803 (mmt180)
REVERT: A 1704 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.7585 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7498 (OUTLIER) cc_final: 0.7282 (m)
REVERT: A 2259 PHE cc_start: 0.7384 (OUTLIER) cc_final: 0.6897 (t80)
REVERT: A 2502 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.6231 (mtt90)
  outliers start: 16
  outliers final: 6
  residues processed: 75
  average time/residue: 2.1583
  time to fit residues: 177.8435
Evaluate side-chains
  73 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1660 VAL
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2298 GLN
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 100 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 65 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 111 optimal weight:    9.9990
   chunk 92 optimal weight:    9.9990
   chunk 51 optimal weight:    9.9990
   chunk 9 optimal weight:    0.0870
   chunk 36 optimal weight:   20.0000
   chunk 58 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   overall best weight:    2.0166

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

Flipped N/Q/H residues before XYZ refinement:
A2442 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.3580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9390  Z= 0.268
  Angle     :  0.505   6.239  12724  Z= 0.278
  Chirality :  0.038   0.138   1480
  Planarity :  0.004   0.042   1584
  Dihedral  :  5.737  56.642   1277
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  :  9.21 %
    Favored  : 88.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1144
  helix:  0.35 (0.19), residues: 757
  sheet:  0.34 (0.52), residues: 85
  loop :  0.49 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A2053 
 HIS   0.012   0.002   HIS A1473 
 PHE   0.019   0.002   PHE A1672 
 TYR   0.010   0.002   TYR A2305 
 ARG   0.003   0.000   ARG A2332 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 71
  time to evaluate  : 1.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7441 (mtt-85) cc_final: 0.6756 (mmt180)
REVERT: A 1704 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7540 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7659 (OUTLIER) cc_final: 0.7371 (m)
REVERT: A 2259 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6878 (t80)
REVERT: A 2502 ARG cc_start: 0.6577 (mtm-85) cc_final: 0.6366 (mtt90)
REVERT: A 2513 ARG cc_start: 0.6449 (mtp-110) cc_final: 0.6244 (mmm-85)
  outliers start: 19
  outliers final: 8
  residues processed: 81
  average time/residue: 2.3891
  time to fit residues: 211.3886
Evaluate side-chains
  79 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 1.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1660 VAL
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2402 SER
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2486 MET
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 12 optimal weight:    1.9990
   chunk 63 optimal weight:    0.7980
   chunk 81 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 93 optimal weight:    6.9990
   chunk 110 optimal weight:   10.0000
   chunk 69 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 51 optimal weight:   20.0000
   chunk 68 optimal weight:    0.5980
   chunk 44 optimal weight:    3.9990
   overall best weight:    1.0784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7998
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9390  Z= 0.165
  Angle     :  0.454   5.858  12724  Z= 0.246
  Chirality :  0.037   0.136   1480
  Planarity :  0.004   0.037   1584
  Dihedral  :  4.756  37.909   1277
  Min Nonbonded Distance : 1.856

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.01 %
    Favored  : 88.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1144
  helix:  0.52 (0.19), residues: 758
  sheet:  0.43 (0.53), residues: 85
  loop :  0.59 (0.36), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.006   0.001   HIS A1473 
 PHE   0.016   0.001   PHE A2018 
 TYR   0.008   0.001   TYR A1609 
 ARG   0.005   0.000   ARG A2271 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 1.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7477 (mtt-85) cc_final: 0.6781 (mmt180)
REVERT: A 1704 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7552 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7655 (OUTLIER) cc_final: 0.7361 (m)
REVERT: A 2259 PHE cc_start: 0.7333 (OUTLIER) cc_final: 0.6816 (t80)
  outliers start: 13
  outliers final: 4
  residues processed: 74
  average time/residue: 2.1856
  time to fit residues: 176.8164
Evaluate side-chains
  72 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 65
  time to evaluate  : 1.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   chunk 75 optimal weight:    2.9990
   chunk 54 optimal weight:   30.0000
   chunk 10 optimal weight:    1.9990
   chunk 87 optimal weight:    2.9990
   chunk 100 optimal weight:    8.9990
   chunk 106 optimal weight:    7.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    1.5186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.3816

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9390  Z= 0.211
  Angle     :  0.467   5.938  12724  Z= 0.254
  Chirality :  0.037   0.135   1480
  Planarity :  0.004   0.039   1584
  Dihedral  :  4.650  36.517   1277
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 10.51 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.25), residues: 1144
  helix:  0.46 (0.19), residues: 764
  sheet:  0.49 (0.53), residues: 85
  loop :  0.61 (0.36), residues: 295

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.009   0.001   HIS A1473 
 PHE   0.018   0.001   PHE A1672 
 TYR   0.008   0.001   TYR A2057 
 ARG   0.002   0.000   ARG A2271 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 1.356 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7505 (mtt-85) cc_final: 0.6795 (mmt180)
REVERT: A 1704 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7554 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7684 (OUTLIER) cc_final: 0.7389 (m)
REVERT: A 2259 PHE cc_start: 0.7337 (OUTLIER) cc_final: 0.6820 (t80)
  outliers start: 10
  outliers final: 5
  residues processed: 71
  average time/residue: 2.2140
  time to fit residues: 172.5215
Evaluate side-chains
  71 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 1.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2402 SER
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 106 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 93 optimal weight:    7.9990
   chunk 97 optimal weight:    2.9990
   chunk 102 optimal weight:    9.9990
   chunk 67 optimal weight:    1.9990
   chunk 109 optimal weight:   10.0000
   overall best weight:    1.3788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.3925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9390  Z= 0.193
  Angle     :  0.457   5.450  12724  Z= 0.248
  Chirality :  0.037   0.133   1480
  Planarity :  0.004   0.038   1584
  Dihedral  :  4.578  35.870   1277
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 3.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.30 %
    Allowed  : 10.31 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.64 (0.25), residues: 1144
  helix:  0.51 (0.19), residues: 765
  sheet:  0.51 (0.53), residues: 85
  loop :  0.62 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.008   0.001   HIS A1473 
 PHE   0.016   0.001   PHE A2018 
 TYR   0.008   0.001   TYR A2057 
 ARG   0.002   0.000   ARG A2502 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 65
  time to evaluate  : 1.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7515 (mtt-85) cc_final: 0.6800 (mmt180)
REVERT: A 1704 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7542 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7685 (OUTLIER) cc_final: 0.7392 (m)
REVERT: A 2259 PHE cc_start: 0.7336 (OUTLIER) cc_final: 0.6807 (t80)
  outliers start: 13
  outliers final: 6
  residues processed: 71
  average time/residue: 2.0844
  time to fit residues: 163.3557
Evaluate side-chains
  73 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.520 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2206 SER
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2402 SER
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 51 optimal weight:    5.9990
   chunk 75 optimal weight:    2.9990
   chunk 114 optimal weight:   10.0000
   chunk 105 optimal weight:    4.9990
   chunk 91 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 55 optimal weight:   10.0000
   chunk 72 optimal weight:    0.2980
   chunk 97 optimal weight:    0.9980
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.4006

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9390  Z= 0.166
  Angle     :  0.445   5.356  12724  Z= 0.241
  Chirality :  0.037   0.133   1480
  Planarity :  0.004   0.037   1584
  Dihedral  :  4.440  32.944   1277
  Min Nonbonded Distance : 1.864

Molprobity Statistics.
  All-atom Clashscore : 4.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 10.71 %
    Favored  : 88.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.25), residues: 1144
  helix:  0.62 (0.19), residues: 759
  sheet:  0.58 (0.53), residues: 85
  loop :  0.58 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.007   0.001   HIS A1473 
 PHE   0.016   0.001   PHE A2018 
 TYR   0.007   0.001   TYR A2057 
 ARG   0.002   0.000   ARG A2502 

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

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

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2288 Ramachandran restraints generated.
    1144 Oldfield, 0 Emsley, 1144 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 1.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1632 ARG cc_start: 0.7513 (mtt-85) cc_final: 0.6795 (mmt180)
REVERT: A 1704 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7527 (mtm180)
REVERT: A 2016 VAL cc_start: 0.7710 (OUTLIER) cc_final: 0.7436 (m)
REVERT: A 2259 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6771 (t80)
  outliers start: 9
  outliers final: 6
  residues processed: 68
  average time/residue: 2.2299
  time to fit residues: 166.2844
Evaluate side-chains
  71 residues out of total 999 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 1.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1442 ASN
Chi-restraints excluded: chain A residue 1643 SER
Chi-restraints excluded: chain A residue 1704 ARG
Chi-restraints excluded: chain A residue 2016 VAL
Chi-restraints excluded: chain A residue 2229 GLN
Chi-restraints excluded: chain A residue 2259 PHE
Chi-restraints excluded: chain A residue 2402 SER
Chi-restraints excluded: chain A residue 2445 VAL
Chi-restraints excluded: chain A residue 2503 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 115
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 84 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 93 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 5 optimal weight:    0.4980
   overall best weight:    1.2584

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

Flipped N/Q/H residues before XYZ refinement:
A1513 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4408 r_free = 0.4408 target = 0.202506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.146095 restraints weight = 33316.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.3762 rms_B_bonded: 2.16
r_work: 0.3544 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.3434 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7933
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9390  Z= 0.186
  Angle     :  0.452   5.479  12724  Z= 0.245
  Chirality :  0.037   0.131   1480
  Planarity :  0.004   0.038   1584
  Dihedral  :  4.459  35.287   1277
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  1.10 %
    Allowed  : 10.81 %
    Favored  : 88.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.94 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.68 (0.25), residues: 1144
  helix:  0.55 (0.19), residues: 765
  sheet:  0.69 (0.55), residues: 85
  loop :  0.51 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A2053 
 HIS   0.008   0.001   HIS A1473 
 PHE   0.017   0.001   PHE A1672 
 TYR   0.008   0.001   TYR A2305 
 ARG   0.002   0.000   ARG A2502 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5604.78 seconds
wall clock time: 99 minutes 2.36 seconds (5942.36 seconds total)