Starting phenix.real_space_refine
on Wed Feb 12 14:08:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ftk_29439/02_2025/8ftk_29439.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ftk_29439/02_2025/8ftk_29439.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ftk_29439/02_2025/8ftk_29439.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ftk_29439/02_2025/8ftk_29439.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ftk_29439/02_2025/8ftk_29439.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ftk_29439/02_2025/8ftk_29439.cif"
  }
  resolution = 4.56
  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=   0.000 sd=   0.013
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: 3
    Type Number    sf(0)   Gaussians
     C    4672      2.51       5
     N    1584      2.21       5
     O    1584      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7840
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7840
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1584, 7840
          Classifications: {'peptide': 1584}
          Incomplete info: {'truncation_to_alanine': 1377}
          Link IDs: {'PCIS': 1, 'PTRANS': 66, 'TRANS': 1516}
          Chain breaks: 6
          Unresolved chain link angles: 67
          Unresolved non-hydrogen bonds: 5043
          Unresolved non-hydrogen angles: 6424
          Unresolved non-hydrogen dihedrals: 4199
          Unresolved non-hydrogen chiralities: 442
          Planarities with less than four sites: {'GLN:plan1': 85, 'HIS:plan': 28, 'TYR:plan': 41, 'ASN:plan1': 51, 'TRP:plan': 25, 'ASP:plan': 103, 'PHE:plan': 58, 'GLU:plan': 112, 'ARG:plan': 101}
          Unresolved non-hydrogen planarities: 2755
  Time building chain proxies: 5.97, per 1000 atoms: 0.76
  Number of scatterers: 7840
  At special positions: 0
  Unit cell: (91.504, 90.44, 205.352, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 3
    Type Number    sf(0)
     O    1584      8.00
     N    1584      7.00
     C    4672      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: 2.63
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3008

  Finding SS restraints...
    Secondary structure from input PDB file:
      77 helices and 5 sheets defined
      67.2% alpha, 3.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.47
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 19
    Processing helix  chain 'A' and resid 51 through 72
    Processing helix  chain 'A' and resid 72 through 77
    Processing helix  chain 'A' and resid 79 through 84
    Processing helix  chain 'A' and resid 84 through 98
      removed outlier: 4.185A  pdb=" N   ASP A  88 " --> pdb=" O   GLY A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 101 through 119
      removed outlier: 3.801A  pdb=" N   ASP A 113 " --> pdb=" O   HIS A 109 " (cutoff:3.500A)
      Proline residue:  A 114  - end of helix
    Processing helix  chain 'A' and resid 122 through 156
    Processing helix  chain 'A' and resid 159 through 180
      removed outlier: 7.526A  pdb=" N   SER A 169 " --> pdb=" O   ASP A 165 " (cutoff:3.500A)
      removed outlier: 6.753A  pdb=" N   ALA A 170 " --> pdb=" O   HIS A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 186
    Processing helix  chain 'A' and resid 189 through 202
      removed outlier: 3.609A  pdb=" N   ARG A 202 " --> pdb=" O   GLU A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 222
      removed outlier: 4.292A  pdb=" N   THR A 217 " --> pdb=" O   ILE A 213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 236
    Processing helix  chain 'A' and resid 244 through 252
    Processing helix  chain 'A' and resid 252 through 263
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 273 through 289
    Processing helix  chain 'A' and resid 292 through 298
    Processing helix  chain 'A' and resid 308 through 317
    Processing helix  chain 'A' and resid 321 through 339
      removed outlier: 3.522A  pdb=" N   SER A 339 " --> pdb=" O   LEU A 335 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 347
    Processing helix  chain 'A' and resid 351 through 361
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 3.952A  pdb=" N   LEU A 369 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ASN A 370 " --> pdb=" O   ARG A 366 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   LYS A 371 " --> pdb=" O   PRO A 367 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ARG A 374 " --> pdb=" O   ASN A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 400
      removed outlier: 3.895A  pdb=" N   ALA A 391 " --> pdb=" O   PRO A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 417
      removed outlier: 4.079A  pdb=" N   SER A 406 " --> pdb=" O   SER A 402 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ASP A 407 " --> pdb=" O   THR A 403 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 408 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 451
    Processing helix  chain 'A' and resid 459 through 474
    Processing helix  chain 'A' and resid 476 through 482
    Processing helix  chain 'A' and resid 493 through 523
      removed outlier: 3.544A  pdb=" N   ALA A 497 " --> pdb=" O   GLY A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 545
      removed outlier: 4.014A  pdb=" N   MET A 544 " --> pdb=" O   THR A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 564
      removed outlier: 3.853A  pdb=" N   LEU A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 569
      removed outlier: 4.200A  pdb=" N   SER A 568 " --> pdb=" O   ARG A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 581 through 607
    Processing helix  chain 'A' and resid 609 through 617
    Processing helix  chain 'A' and resid 624 through 634
    Processing helix  chain 'A' and resid 636 through 652
    Processing helix  chain 'A' and resid 655 through 684
      removed outlier: 3.505A  pdb=" N   PHE A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
      removed outlier: 8.120A  pdb=" N   THR A 669 " --> pdb=" O   GLU A 665 " (cutoff:3.500A)
      Proline residue:  A 670  - end of helix
    Processing helix  chain 'A' and resid 694 through 710
    Processing helix  chain 'A' and resid 715 through 720
    Processing helix  chain 'A' and resid 723 through 751
    Processing helix  chain 'A' and resid 752 through 754
      No H-bonds generated for 'chain 'A' and resid 752 through 754'
    Processing helix  chain 'A' and resid 756 through 785
      removed outlier: 4.541A  pdb=" N   GLY A 779 " --> pdb=" O   LEU A 775 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 790 through 808
      Proline residue:  A 804  - end of helix
    Processing helix  chain 'A' and resid 808 through 816
    Processing helix  chain 'A' and resid 820 through 841
    Processing helix  chain 'A' and resid 846 through 858
    Processing helix  chain 'A' and resid 876 through 888
      removed outlier: 3.738A  pdb=" N   LEU A 887 " --> pdb=" O   LEU A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 897
    Processing helix  chain 'A' and resid 1107 through 1117
    Processing helix  chain 'A' and resid 1141 through 1166
      removed outlier: 3.998A  pdb=" N   LYS A1146 " --> pdb=" O   PRO A1142 " (cutoff:3.500A)
      Proline residue:  A1151  - end of helix
      removed outlier: 3.781A  pdb=" N   ASP A1166 " --> pdb=" O   VAL A1162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1202
    Processing helix  chain 'A' and resid 1216 through 1220
      removed outlier: 3.563A  pdb=" N   GLN A1220 " --> pdb=" O   PRO A1217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1271 through 1284
    Processing helix  chain 'A' and resid 1285 through 1287
      No H-bonds generated for 'chain 'A' and resid 1285 through 1287'
    Processing helix  chain 'A' and resid 1289 through 1294
    Processing helix  chain 'A' and resid 1308 through 1317
    Processing helix  chain 'A' and resid 1319 through 1330
      removed outlier: 3.829A  pdb=" N   ALA A1325 " --> pdb=" O   GLY A1321 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE A1326 " --> pdb=" O   GLN A1322 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   ASN A1328 " --> pdb=" O   ARG A1324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1344
    Processing helix  chain 'A' and resid 1345 through 1362
    Processing helix  chain 'A' and resid 1395 through 1408
    Processing helix  chain 'A' and resid 1432 through 1439
      removed outlier: 3.938A  pdb=" N   VAL A1435 " --> pdb=" O   ASN A1432 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ASP A1437 " --> pdb=" O   ALA A1434 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR A1439 " --> pdb=" O   LYS A1436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1440 through 1452
    Processing helix  chain 'A' and resid 1462 through 1487
      Proline residue:  A1480  - end of helix
      removed outlier: 3.964A  pdb=" N   LEU A1487 " --> pdb=" O   ASP A1483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1490 through 1543
      removed outlier: 3.879A  pdb=" N   GLY A1522 " --> pdb=" O   ASP A1518 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   ASN A1523 " --> pdb=" O   LYS A1519 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   THR A1524 " --> pdb=" O   ALA A1520 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LYS A1543 " --> pdb=" O   GLU A1539 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1551 through 1556
      removed outlier: 3.731A  pdb=" N   HIS A1556 " --> pdb=" O   GLY A1553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1557 through 1562
      removed outlier: 4.018A  pdb=" N   ASN A1561 " --> pdb=" O   GLU A1557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1573 through 1577
      removed outlier: 3.692A  pdb=" N   CYS A1577 " --> pdb=" O   ALA A1574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1578 through 1583
      removed outlier: 3.610A  pdb=" N   LEU A1583 " --> pdb=" O   GLU A1579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1584 through 1587
    Processing helix  chain 'A' and resid 1620 through 1628
    Processing helix  chain 'A' and resid 1642 through 1653
      removed outlier: 4.265A  pdb=" N   PHE A1648 " --> pdb=" O   GLU A1644 " (cutoff:3.500A)
      Proline residue:  A1649  - end of helix
    Processing helix  chain 'A' and resid 1670 through 1675
    Processing helix  chain 'A' and resid 1701 through 1717
    Processing helix  chain 'A' and resid 1734 through 1749
    Processing helix  chain 'A' and resid 1750 through 1755
      removed outlier: 3.816A  pdb=" N   GLU A1755 " --> pdb=" O   SER A1752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1792 through 1802
    Processing helix  chain 'A' and resid 1818 through 1832
      removed outlier: 3.757A  pdb=" N   ALA A1822 " --> pdb=" O   GLY A1818 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1838 through 1844
      removed outlier: 4.234A  pdb=" N   LEU A1842 " --> pdb=" O   ASN A1838 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 379 through 381
    Processing sheet with id=AA2, first strand: chain 'A' and resid 859 through 861
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1186 through 1193
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1225 through 1229
      removed outlier: 6.906A  pdb=" N   ILE A1208 " --> pdb=" O   ILE A1268 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1422 through 1424
      removed outlier: 6.494A  pdb=" N   LEU A1423 " --> pdb=" O   CYS A1548 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   LEU A1389 " --> pdb=" O   LEU A1547 " (cutoff:3.500A)
      removed outlier: 7.419A  pdb=" N   ALA A1549 " --> pdb=" O   LEU A1389 " (cutoff:3.500A)
      removed outlier: 5.862A  pdb=" N   VAL A1391 " --> pdb=" O   ALA A1549 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   LEU A1390 " --> pdb=" O   ILE A1570 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   GLY A1334 " --> pdb=" O   CYS A1593 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   LEU A1595 " --> pdb=" O   GLY A1334 " (cutoff:3.500A)
      removed outlier: 6.109A  pdb=" N   THR A1336 " --> pdb=" O   LEU A1595 " (cutoff:3.500A)
      removed outlier: 4.791A  pdb=" N   HIS A1633 " --> pdb=" O   LEU A1337 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   GLN A1339 " --> pdb=" O   HIS A1633 " (cutoff:3.500A)

    734 hydrogen bonds defined for protein.
    2154 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: 3.92

  Time building geometry restraints manager: 2.68 seconds

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

  Histogram of bond lengths:
        1.23 -     1.29: 1584
        1.29 -     1.36: 1577
        1.36 -     1.42: 0
        1.42 -     1.49: 1584
        1.49 -     1.55: 3088
  Bond restraints: 7833
  Sorted by residual:
  bond pdb=" N   ILE A1773 "
       pdb=" CA  ILE A1773 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.018 1.57e-02 4.06e+03 1.29e+00
  bond pdb=" N   VAL A1430 "
       pdb=" CA  VAL A1430 "
    ideal  model  delta    sigma   weight residual
    1.474  1.457  0.017 1.57e-02 4.06e+03 1.22e+00
  bond pdb=" N   TYR A1139 "
       pdb=" CA  TYR A1139 "
    ideal  model  delta    sigma   weight residual
    1.454  1.464 -0.010 1.29e-02 6.01e+03 6.44e-01
  bond pdb=" CA  LYS A1411 "
       pdb=" CB  LYS A1411 "
    ideal  model  delta    sigma   weight residual
    1.523  1.534 -0.011 1.35e-02 5.49e+03 6.28e-01
  bond pdb=" CA  LEU A1678 "
       pdb=" C   LEU A1678 "
    ideal  model  delta    sigma   weight residual
    1.530  1.521  0.009 1.14e-02 7.69e+03 6.11e-01
  ... (remaining 7828 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.17: 10351
        1.17 -     2.33: 473
        2.33 -     3.50: 71
        3.50 -     4.66: 9
        4.66 -     5.83: 3
  Bond angle restraints: 10907
  Sorted by residual:
  angle pdb=" N   VAL A1135 "
        pdb=" CA  VAL A1135 "
        pdb=" C   VAL A1135 "
      ideal   model   delta    sigma   weight residual
     113.53  108.68    4.85 9.80e-01 1.04e+00 2.45e+01
  angle pdb=" C   LEU A1294 "
        pdb=" N   LYS A1295 "
        pdb=" CA  LYS A1295 "
      ideal   model   delta    sigma   weight residual
     121.90  116.44    5.46 1.26e+00 6.30e-01 1.88e+01
  angle pdb=" C   TYR A1639 "
        pdb=" N   ARG A1640 "
        pdb=" CA  ARG A1640 "
      ideal   model   delta    sigma   weight residual
     122.74  127.38   -4.64 1.44e+00 4.82e-01 1.04e+01
  angle pdb=" N   GLY A 779 "
        pdb=" CA  GLY A 779 "
        pdb=" C   GLY A 779 "
      ideal   model   delta    sigma   weight residual
     112.77  108.79    3.98 1.28e+00 6.10e-01 9.67e+00
  angle pdb=" C   LYS A1146 "
        pdb=" N   GLN A1147 "
        pdb=" CA  GLN A1147 "
      ideal   model   delta    sigma   weight residual
     120.38  124.89   -4.51 1.46e+00 4.69e-01 9.53e+00
  ... (remaining 10902 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -     8.14: 4478
        8.14 -    16.29: 100
       16.29 -    24.43: 3
       24.43 -    32.57: 3
       32.57 -    40.71: 1
  Dihedral angle restraints: 4585
    sinusoidal: 0
      harmonic: 4585
  Sorted by residual:
  dihedral pdb=" CA  VAL A1700 "
           pdb=" C   VAL A1700 "
           pdb=" N   ASN A1701 "
           pdb=" CA  ASN A1701 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  139.29   40.71     0      5.00e+00 4.00e-02 6.63e+01
  dihedral pdb=" CA  ARG A 480 "
           pdb=" C   ARG A 480 "
           pdb=" N   ALA A 481 "
           pdb=" CA  ALA A 481 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.17   31.83     0      5.00e+00 4.00e-02 4.05e+01
  dihedral pdb=" CA  ASP A1718 "
           pdb=" C   ASP A1718 "
           pdb=" N   TYR A1719 "
           pdb=" CA  TYR A1719 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.91   26.09     0      5.00e+00 4.00e-02 2.72e+01
  ... (remaining 4582 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.030: 950
       0.030 -    0.060: 381
       0.060 -    0.091: 109
       0.091 -    0.121: 62
       0.121 -    0.151: 2
  Chirality restraints: 1504
  Sorted by residual:
  chirality pdb=" CA  ILE A1431 "
            pdb=" N   ILE A1431 "
            pdb=" C   ILE A1431 "
            pdb=" CB  ILE A1431 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.70e-01
  chirality pdb=" CA  ILE A1420 "
            pdb=" N   ILE A1420 "
            pdb=" C   ILE A1420 "
            pdb=" CB  ILE A1420 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.62e-01
  chirality pdb=" CA  PRO A1140 "
            pdb=" N   PRO A1140 "
            pdb=" C   PRO A1140 "
            pdb=" CB  PRO A1140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.60    0.12 2.00e-01 2.50e+01 3.44e-01
  ... (remaining 1501 not shown)

  Planarity restraints: 1577
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 476 "    0.009 2.00e-02 2.50e+03   1.83e-02 3.35e+00
        pdb=" C   GLU A 476 "   -0.032 2.00e-02 2.50e+03
        pdb=" O   GLU A 476 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ILE A 477 "    0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A1146 "   -0.009 2.00e-02 2.50e+03   1.75e-02 3.05e+00
        pdb=" C   LYS A1146 "    0.030 2.00e-02 2.50e+03
        pdb=" O   LYS A1146 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   GLN A1147 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1745 "    0.007 2.00e-02 2.50e+03   1.31e-02 1.71e+00
        pdb=" C   PHE A1745 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   PHE A1745 "    0.008 2.00e-02 2.50e+03
        pdb=" N   VAL A1746 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1574 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 101
        2.68 -     3.24: 8355
        3.24 -     3.79: 12356
        3.79 -     4.35: 13071
        4.35 -     4.90: 20921
  Nonbonded interactions: 54804
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 802 "
            pdb=" N   ARG A 806 "
     model   vdw
     2.125 3.120
  nonbonded pdb=" O   PHE A1149 "
            pdb=" N   LEU A1153 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" O   ASP A1663 "
            pdb=" N   LEU A1667 "
     model   vdw
     2.270 3.120
  nonbonded pdb=" O   ILE A1478 "
            pdb=" N   LEU A1482 "
     model   vdw
     2.295 3.120
  nonbonded pdb=" O   ASN A 111 "
            pdb=" N   TYR A 115 "
     model   vdw
     2.333 3.120
  ... (remaining 54799 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:             1.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     25.340
  Find NCS groups from input model:        0.130
  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:3.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8093
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.018   7833  Z= 0.141
  Angle     :  0.575   5.830  10907  Z= 0.404
  Chirality :  0.039   0.151   1504
  Planarity :  0.002   0.018   1577
  Dihedral  :  4.661  40.713   1577
  Min Nonbonded Distance : 2.125

Molprobity Statistics.
  All-atom Clashscore : 4.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.86 %
    Favored  : 94.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.74 (0.23), residues: 1570
  helix:  1.83 (0.18), residues: 929
  sheet: -1.80 (0.62), residues: 66
  loop : -1.52 (0.27), residues: 575

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.886 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0742
  time to fit residues: 7.9759
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.858 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 133 optimal weight:   20.0000
   chunk 119 optimal weight:   30.0000
   chunk 66 optimal weight:    0.1980
   chunk 40 optimal weight:    7.9990
   chunk 80 optimal weight:    2.9990
   chunk 63 optimal weight:    9.9990
   chunk 123 optimal weight:    6.9990
   chunk 47 optimal weight:    6.9990
   chunk 75 optimal weight:    0.5980
   chunk 92 optimal weight:    6.9990
   chunk 143 optimal weight:    0.4980
   overall best weight:    2.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.041205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.030895 restraints weight = 112328.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.031178 restraints weight = 97170.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.031322 restraints weight = 86666.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.0914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.017   7833  Z= 0.145
  Angle     :  0.413   5.529  10907  Z= 0.269
  Chirality :  0.039   0.143   1504
  Planarity :  0.003   0.018   1577
  Dihedral  :  4.443  37.952   1577
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.79 (0.23), residues: 1570
  helix:  1.91 (0.17), residues: 952
  sheet: -1.93 (0.57), residues: 77
  loop : -1.70 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.979 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0810
  time to fit residues: 8.9250
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.885 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 109 optimal weight:   20.0000
   chunk 4 optimal weight:    0.3980
   chunk 116 optimal weight:   40.0000
   chunk 157 optimal weight:   50.0000
   chunk 86 optimal weight:    8.9990
   chunk 59 optimal weight:    8.9990
   chunk 8 optimal weight:   20.0000
   chunk 22 optimal weight:    4.9990
   chunk 147 optimal weight:   30.0000
   chunk 72 optimal weight:    1.9990
   chunk 15 optimal weight:   30.0000
   overall best weight:    5.0788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.039455 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.029307 restraints weight = 118035.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2739 r_free = 0.2739 target = 0.029523 restraints weight = 101698.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.029760 restraints weight = 91467.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7833  Z= 0.237
  Angle     :  0.525   7.114  10907  Z= 0.349
  Chirality :  0.041   0.166   1504
  Planarity :  0.003   0.026   1577
  Dihedral  :  5.285  36.267   1577
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 3.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -0.30 (0.22), residues: 1570
  helix:  0.96 (0.17), residues: 957
  sheet: -1.94 (0.61), residues: 72
  loop : -2.09 (0.28), residues: 541

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.859 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0792
  time to fit residues: 8.6363
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.836 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 28 optimal weight:    5.9990
   chunk 106 optimal weight:   20.0000
   chunk 36 optimal weight:    4.9990
   chunk 134 optimal weight:    0.6980
   chunk 23 optimal weight:    9.9990
   chunk 52 optimal weight:    5.9990
   chunk 120 optimal weight:    0.0980
   chunk 87 optimal weight:   10.0000
   chunk 30 optimal weight:    9.9990
   chunk 56 optimal weight:    0.6980
   chunk 157 optimal weight:   50.0000
   overall best weight:    2.4984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.040012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.029711 restraints weight = 115266.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.029957 restraints weight = 99623.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2769 r_free = 0.2769 target = 0.030168 restraints weight = 89412.769|
|-----------------------------------------------------------------------------|
r_work (final): 0.2741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.019   7833  Z= 0.127
  Angle     :  0.394   5.620  10907  Z= 0.255
  Chirality :  0.039   0.158   1504
  Planarity :  0.002   0.023   1577
  Dihedral  :  4.480  30.824   1577
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 1.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  0.65 (0.23), residues: 1570
  helix:  1.91 (0.17), residues: 951
  sheet: -1.84 (0.61), residues: 70
  loop : -2.04 (0.27), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.853 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0780
  time to fit residues: 8.5003
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 83 optimal weight:    5.9990
   chunk 32 optimal weight:    5.9990
   chunk 117 optimal weight:    0.6980
   chunk 127 optimal weight:    5.9990
   chunk 85 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 71 optimal weight:   20.0000
   chunk 84 optimal weight:    0.9980
   chunk 135 optimal weight:    8.9990
   chunk 21 optimal weight:   20.0000
   overall best weight:    0.8380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.040933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.030570 restraints weight = 112610.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.030879 restraints weight = 101002.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.030879 restraints weight = 83026.482|
|-----------------------------------------------------------------------------|
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.001   0.010   7833  Z= 0.076
  Angle     :  0.341   4.950  10907  Z= 0.216
  Chirality :  0.038   0.151   1504
  Planarity :  0.002   0.022   1577
  Dihedral  :  3.868  26.962   1577
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 1.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    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:  1.53 (0.23), residues: 1570
  helix:  2.62 (0.17), residues: 953
  sheet: -1.35 (0.63), residues: 70
  loop : -1.73 (0.28), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.890 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0799
  time to fit residues: 8.6089
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.942 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 154 optimal weight:   40.0000
   chunk 120 optimal weight:    0.0010
   chunk 0 optimal weight:   30.0000
   chunk 140 optimal weight:   30.0000
   chunk 73 optimal weight:    6.9990
   chunk 70 optimal weight:    0.9990
   chunk 128 optimal weight:    9.9990
   chunk 28 optimal weight:    6.9990
   chunk 54 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 31 optimal weight:    9.9990
   overall best weight:    4.1994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.039371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2751 r_free = 0.2751 target = 0.029816 restraints weight = 116398.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2747 r_free = 0.2747 target = 0.029611 restraints weight = 110404.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.029514 restraints weight = 102846.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.2712
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.3271

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   7833  Z= 0.204
  Angle     :  0.442   5.569  10907  Z= 0.297
  Chirality :  0.039   0.159   1504
  Planarity :  0.002   0.019   1577
  Dihedral  :  4.301  30.429   1577
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 2.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.96 %
    Favored  : 92.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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:  1.15 (0.23), residues: 1570
  helix:  2.30 (0.17), residues: 960
  sheet: -1.43 (0.62), residues: 71
  loop : -1.91 (0.28), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.865 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0782
  time to fit residues: 9.0948
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.861 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 113 optimal weight:    5.9990
   chunk 145 optimal weight:    6.9990
   chunk 131 optimal weight:   20.0000
   chunk 147 optimal weight:   40.0000
   chunk 144 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 3 optimal weight:   50.0000
   chunk 152 optimal weight:   20.0000
   chunk 75 optimal weight:    0.3980
   chunk 124 optimal weight:    8.9990
   overall best weight:    4.6788

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.036837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2576 r_free = 0.2576 target = 0.025999 restraints weight = 134963.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2585 r_free = 0.2585 target = 0.026215 restraints weight = 117815.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2592 r_free = 0.2592 target = 0.026392 restraints weight = 105805.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.2567
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6852
moved from start:          0.4308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   7833  Z= 0.217
  Angle     :  0.466   5.951  10907  Z= 0.310
  Chirality :  0.040   0.168   1504
  Planarity :  0.003   0.017   1577
  Dihedral  :  4.899  31.011   1577
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.54 %
    Favored  : 91.46 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

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:  0.33 (0.22), residues: 1570
  helix:  1.57 (0.17), residues: 956
  sheet: -1.90 (0.59), residues: 71
  loop : -2.03 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.904 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0696
  time to fit residues: 7.6665
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 93 optimal weight:   30.0000
   chunk 100 optimal weight:   30.0000
   chunk 16 optimal weight:   10.0000
   chunk 70 optimal weight:   10.0000
   chunk 28 optimal weight:    5.9990
   chunk 153 optimal weight:    4.9990
   chunk 72 optimal weight:    9.9990
   chunk 92 optimal weight:    0.0170
   chunk 71 optimal weight:    4.9990
   chunk 6 optimal weight:    7.9990
   chunk 15 optimal weight:    6.9990
   overall best weight:    4.6026

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.038754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2735 r_free = 0.2735 target = 0.029311 restraints weight = 116909.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2732 r_free = 0.2732 target = 0.029173 restraints weight = 105887.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2731 r_free = 0.2731 target = 0.029160 restraints weight = 98939.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.2704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   7833  Z= 0.212
  Angle     :  0.448   5.253  10907  Z= 0.300
  Chirality :  0.039   0.156   1504
  Planarity :  0.003   0.014   1577
  Dihedral  :  4.680  29.450   1577
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 2.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.34 %
    Favored  : 91.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    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:  0.44 (0.22), residues: 1570
  helix:  1.69 (0.17), residues: 960
  sheet: -2.08 (0.58), residues: 71
  loop : -2.04 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.794 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0786
  time to fit residues: 8.4205
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 119 optimal weight:    0.0020
   chunk 109 optimal weight:   10.0000
   chunk 155 optimal weight:    6.9990
   chunk 129 optimal weight:    5.9990
   chunk 23 optimal weight:   20.0000
   chunk 154 optimal weight:   20.0000
   chunk 142 optimal weight:    7.9990
   chunk 48 optimal weight:    8.9990
   chunk 65 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 81 optimal weight:    9.9990
   overall best weight:    4.1996

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.038712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2711 r_free = 0.2711 target = 0.028665 restraints weight = 118885.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.028927 restraints weight = 102180.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.2729 r_free = 0.2729 target = 0.029088 restraints weight = 91368.892|
|-----------------------------------------------------------------------------|
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.5008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7833  Z= 0.192
  Angle     :  0.435   5.361  10907  Z= 0.290
  Chirality :  0.039   0.170   1504
  Planarity :  0.002   0.013   1577
  Dihedral  :  4.597  29.682   1577
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 2.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    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:  0.62 (0.22), residues: 1570
  helix:  1.87 (0.17), residues: 962
  sheet: -2.11 (0.57), residues: 71
  loop : -2.05 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 1.023 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0730
  time to fit residues: 8.1226
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.964 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 91 optimal weight:   20.0000
   chunk 22 optimal weight:   10.0000
   chunk 14 optimal weight:    6.9990
   chunk 35 optimal weight:   10.0000
   chunk 15 optimal weight:    8.9990
   chunk 50 optimal weight:    1.9990
   chunk 105 optimal weight:   30.0000
   chunk 123 optimal weight:    0.9990
   chunk 147 optimal weight:    7.9990
   chunk 139 optimal weight:   40.0000
   chunk 36 optimal weight:    6.9990
   overall best weight:    4.9990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.038213 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2696 r_free = 0.2696 target = 0.028321 restraints weight = 119469.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2707 r_free = 0.2707 target = 0.028568 restraints weight = 103017.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2715 r_free = 0.2715 target = 0.028772 restraints weight = 91850.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.2691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.5540

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   7833  Z= 0.231
  Angle     :  0.471   5.170  10907  Z= 0.317
  Chirality :  0.039   0.142   1504
  Planarity :  0.003   0.014   1577
  Dihedral  :  4.867  28.926   1577
  Min Nonbonded Distance : 2.326

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    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:  0.18 (0.22), residues: 1570
  helix:  1.43 (0.17), residues: 967
  sheet: -2.48 (0.55), residues: 76
  loop : -2.03 (0.28), residues: 527

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 

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

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

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3140 Ramachandran restraints generated.
    1570 Oldfield, 0 Emsley, 1570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.858 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 50
  average time/residue: 0.0756
  time to fit residues: 8.4310
Evaluate side-chains
  50 residues out of total 1377 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 158
   random chunks:
   chunk 91 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 132 optimal weight:   10.0000
   chunk 68 optimal weight:    1.9990
   chunk 112 optimal weight:    9.9990
   chunk 37 optimal weight:   20.0000
   chunk 157 optimal weight:    1.9990
   chunk 104 optimal weight:   40.0000
   chunk 147 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 127 optimal weight:    8.9990
   overall best weight:    5.3990

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.038132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.2693 r_free = 0.2693 target = 0.028265 restraints weight = 119054.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.2704 r_free = 0.2704 target = 0.028513 restraints weight = 101984.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.028708 restraints weight = 91073.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.5964

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   7833  Z= 0.240
  Angle     :  0.482   5.355  10907  Z= 0.325
  Chirality :  0.039   0.135   1504
  Planarity :  0.003   0.014   1577
  Dihedral  :  4.948  28.396   1577
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 2.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.49 %
    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: -0.04 (0.22), residues: 1570
  helix:  1.24 (0.17), residues: 975
  sheet: -2.35 (0.57), residues: 70
  loop : -2.17 (0.28), residues: 525

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.000   0.000   TRP A  13 
 PHE   0.000   0.000   PHE A  17 
 TYR   0.000   0.000   TYR A   7 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2632.62 seconds
wall clock time: 47 minutes 7.95 seconds (2827.95 seconds total)