Starting phenix.real_space_refine
on Fri Dec  8 19:36:18 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/12_2023/7vls_32025.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/12_2023/7vls_32025.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/12_2023/7vls_32025.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/12_2023/7vls_32025.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/12_2023/7vls_32025.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vls_32025/12_2023/7vls_32025.pdb"
  }
  resolution = 3.3
  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=   0.009 sd=   0.154
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: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      47      5.16       5
     C    5837      2.51       5
     N    1493      2.21       5
     O    1619      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 9003
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 9003
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1147, 9003
          Unusual residues: {' MG': 2, 'ADP': 1, 'ATP': 1, 'ESV': 1, 'Y01': 1}
          Classifications: {'peptide': 1141, 'undetermined': 6}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 33, 'TRANS': 1107, None: 6}
            Not linked:
              pdbres="MET A1545 "
              pdbres="Y01 A1601 "
            Not linked:
              pdbres="Y01 A1601 "
              pdbres="ADP A1602 "
            Not linked:
              pdbres="ADP A1602 "
              pdbres=" MG A1603 "
            Not linked:
              pdbres=" MG A1603 "
              pdbres=" MG A1604 "
            Not linked:
              pdbres=" MG A1604 "
              pdbres="ATP A1605 "
            Not linked:
              pdbres="ATP A1605 "
              pdbres="ESV A1606 "
          Chain breaks: 6
          Unresolved non-hydrogen bonds: 93
          Unresolved non-hydrogen angles: 115
          Unresolved non-hydrogen dihedrals: 74
          Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 6, 'GLU:plan': 7, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 79
  Time building chain proxies: 5.38, per 1000 atoms: 0.60
  Number of scatterers: 9003
  At special positions: 0
  Unit cell: (70.956, 90.666, 135.342, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      47     16.00
     P       5     15.00
     Mg      2     11.99
     O    1619      8.00
     N    1493      7.00
     C    5837      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  - 3.50
        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: 3.99
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2152

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 5 sheets defined
      72.7% alpha, 8.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.98
  Creating SS restraints...
    Processing helix  chain 'A' and resid 252 through 255
    Processing helix  chain 'A' and resid 256 through 278
      removed outlier: 3.520A  pdb=" N   ASN A 260 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   HIS A 278 " --> pdb=" O   LYS A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 312
      removed outlier: 3.575A  pdb=" N   ALA A 288 " --> pdb=" O   SER A 284 " (cutoff:3.500A)
      removed outlier: 5.838A  pdb=" N   ARG A 295 " --> pdb=" O   ARG A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
    Processing helix  chain 'A' and resid 312 through 327
      removed outlier: 4.020A  pdb=" N   LEU A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 395
    Processing helix  chain 'A' and resid 396 through 402
      removed outlier: 4.153A  pdb=" N   LEU A 400 " --> pdb=" O   SER A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 428
      removed outlier: 4.477A  pdb=" N   THR A 418 " --> pdb=" O   VAL A 414 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ASN A 419 " --> pdb=" O   ALA A 415 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   LEU A 427 " --> pdb=" O   TRP A 423 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 450
      Proline residue:  A 435  - end of helix
    Processing helix  chain 'A' and resid 450 through 462
      removed outlier: 4.233A  pdb=" N   LEU A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   VAL A 455 " --> pdb=" O   SER A 451 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLY A 456 " --> pdb=" O   SER A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 506
      removed outlier: 6.089A  pdb=" N   LYS A 500 " --> pdb=" O   LEU A 496 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   LEU A 501 " --> pdb=" O   LYS A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 507 through 559
      removed outlier: 3.603A  pdb=" N   SER A 514 " --> pdb=" O   ILE A 510 " (cutoff:3.500A)
      Proline residue:  A 544  - end of helix
    Processing helix  chain 'A' and resid 564 through 607
      Proline residue:  A 581  - end of helix
      removed outlier: 4.008A  pdb=" N   LEU A 584 " --> pdb=" O   THR A 580 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   SER A 586 " --> pdb=" O   LEU A 582 " (cutoff:3.500A)
      removed outlier: 5.224A  pdb=" N   THR A 587 " --> pdb=" O   PHE A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 715
    Processing helix  chain 'A' and resid 761 through 768
    Processing helix  chain 'A' and resid 773 through 784
    Processing helix  chain 'A' and resid 785 through 791
      removed outlier: 4.458A  pdb=" N   ASP A 789 " --> pdb=" O   SER A 785 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 824
    Processing helix  chain 'A' and resid 839 through 853
    Processing helix  chain 'A' and resid 853 through 858
      removed outlier: 3.548A  pdb=" N   ASP A 858 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 868 through 874
      removed outlier: 4.046A  pdb=" N   THR A 873 " --> pdb=" O   GLN A 870 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 899
    Processing helix  chain 'A' and resid 899 through 911
    Processing helix  chain 'A' and resid 976 through 984
    Processing helix  chain 'A' and resid 987 through 1017
      removed outlier: 3.626A  pdb=" N   PHE A 991 " --> pdb=" O   PHE A 987 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASP A1008 " --> pdb=" O   ILE A1004 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   GLU A1017 " --> pdb=" O   THR A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1029 through 1074
      removed outlier: 3.727A  pdb=" N   LEU A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR A1052 " --> pdb=" O   VAL A1048 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   VAL A1053 " --> pdb=" O   THR A1049 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   GLU A1054 " --> pdb=" O   SER A1050 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1076 through 1083
      removed outlier: 3.781A  pdb=" N   PHE A1080 " --> pdb=" O   PRO A1076 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1102
      removed outlier: 3.883A  pdb=" N   ILE A1088 " --> pdb=" O   PRO A1084 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   PHE A1092 " --> pdb=" O   ILE A1088 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   ASN A1097 " --> pdb=" O   SER A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1128
      removed outlier: 3.721A  pdb=" N   THR A1106 " --> pdb=" O   HIS A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1130 through 1176
      removed outlier: 3.732A  pdb=" N   ALA A1134 " --> pdb=" O   VAL A1130 " (cutoff:3.500A)
      Proline residue:  A1137  - end of helix
      removed outlier: 3.956A  pdb=" N   ASP A1155 " --> pdb=" O   VAL A1151 " (cutoff:3.500A)
      Proline residue:  A1166  - end of helix
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1186 through 1236
    Processing helix  chain 'A' and resid 1242 through 1282
      removed outlier: 3.809A  pdb=" N   LEU A1246 " --> pdb=" O   GLY A1242 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ALA A1251 " --> pdb=" O   GLY A1247 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   LEU A1252 " --> pdb=" O   LEU A1248 " (cutoff:3.500A)
      removed outlier: 4.444A  pdb=" N   THR A1253 " --> pdb=" O   LEU A1249 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   THR A1255 " --> pdb=" O   ALA A1251 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TRP A1260 " --> pdb=" O   ASN A1256 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LYS A1277 " --> pdb=" O   GLY A1273 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   VAL A1278 " --> pdb=" O   ALA A1274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1356
      removed outlier: 3.921A  pdb=" N   PHE A1355 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
      removed outlier: 4.185A  pdb=" N   PHE A1356 " --> pdb=" O   SER A1352 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1377 through 1384
    Processing helix  chain 'A' and resid 1399 through 1404
    Processing helix  chain 'A' and resid 1410 through 1421
    Processing helix  chain 'A' and resid 1423 through 1430
    Processing helix  chain 'A' and resid 1432 through 1435
    Processing helix  chain 'A' and resid 1439 through 1443
      removed outlier: 3.913A  pdb=" N   GLU A1443 " --> pdb=" O   GLU A1440 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1446 through 1460
    Processing helix  chain 'A' and resid 1476 through 1491
    Processing helix  chain 'A' and resid 1502 through 1509
      removed outlier: 4.130A  pdb=" N   THR A1508 " --> pdb=" O   THR A1505 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   ALA A1509 " --> pdb=" O   ILE A1506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1525 through 1532
    Processing helix  chain 'A' and resid 1535 through 1545
    Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 692
      removed outlier: 7.040A  pdb=" N   PHE A 675 " --> pdb=" O   THR A 683 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   SER A 685 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
      removed outlier: 6.633A  pdb=" N   GLY A 673 " --> pdb=" O   SER A 685 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   ILE A 687 " --> pdb=" O   THR A 671 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   THR A 671 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 6.766A  pdb=" N   ILE A 689 " --> pdb=" O   LYS A 669 " (cutoff:3.500A)
      removed outlier: 4.734A  pdb=" N   LYS A 669 " --> pdb=" O   ILE A 689 " (cutoff:3.500A)
      removed outlier: 6.821A  pdb=" N   ILE A 691 " --> pdb=" O   ALA A 667 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   GLY A 673 " --> pdb=" O   GLU A 722 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   GLU A 722 " --> pdb=" O   GLY A 673 " (cutoff:3.500A)
      removed outlier: 6.594A  pdb=" N   PHE A 675 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   THR A 720 " --> pdb=" O   PHE A 675 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 749 through 751
      removed outlier: 6.320A  pdb=" N   ALA A 749 " --> pdb=" O   PHE A 830 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   ASP A 832 " --> pdb=" O   ALA A 749 " (cutoff:3.500A)
      removed outlier: 6.608A  pdb=" N   ALA A 751 " --> pdb=" O   ASP A 832 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   LEU A 696 " --> pdb=" O   TRP A 877 " (cutoff:3.500A)
      removed outlier: 7.595A  pdb=" N   ILE A 879 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   MET A 698 " --> pdb=" O   ILE A 879 " (cutoff:3.500A)
      removed outlier: 7.415A  pdb=" N   MET A 881 " --> pdb=" O   MET A 698 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   VAL A 700 " --> pdb=" O   MET A 881 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   ARG A 888 " --> pdb=" O   ALA A 880 " (cutoff:3.500A)
      removed outlier: 6.064A  pdb=" N   LYS A 882 " --> pdb=" O   VAL A 886 " (cutoff:3.500A)
      removed outlier: 5.060A  pdb=" N   VAL A 886 " --> pdb=" O   LYS A 882 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1325 through 1332
      removed outlier: 6.910A  pdb=" N   LYS A1326 " --> pdb=" O   CYS A1314 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   CYS A1314 " --> pdb=" O   LYS A1326 " (cutoff:3.500A)
      removed outlier: 5.513A  pdb=" N   VAL A1328 " --> pdb=" O   ASP A1312 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   LEU A1313 " --> pdb=" O   ASP A1363 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   ASP A1363 " --> pdb=" O   LEU A1313 " (cutoff:3.500A)
      removed outlier: 6.842A  pdb=" N   VAL A1315 " --> pdb=" O   ILE A1361 " (cutoff:3.500A)
      removed outlier: 7.127A  pdb=" N   ILE A1361 " --> pdb=" O   VAL A1315 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1385 through 1388
      removed outlier: 6.416A  pdb=" N   LEU A1466 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   ILE A1499 " --> pdb=" O   LEU A1466 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   MET A1468 " --> pdb=" O   ILE A1499 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL A1338 " --> pdb=" O   THR A1498 " (cutoff:3.500A)
      removed outlier: 6.295A  pdb=" N   LYS A1337 " --> pdb=" O   LEU A1511 " (cutoff:3.500A)
      removed outlier: 7.874A  pdb=" N   ILE A1513 " --> pdb=" O   LYS A1337 " (cutoff:3.500A)
      removed outlier: 6.251A  pdb=" N   GLY A1339 " --> pdb=" O   ILE A1513 " (cutoff:3.500A)
      removed outlier: 7.571A  pdb=" N   MET A1515 " --> pdb=" O   GLY A1339 " (cutoff:3.500A)
      removed outlier: 6.632A  pdb=" N   CYS A1341 " --> pdb=" O   MET A1515 " (cutoff:3.500A)
      removed outlier: 6.775A  pdb=" N   VAL A1512 " --> pdb=" O   TYR A1523 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   TYR A1523 " --> pdb=" O   VAL A1512 " (cutoff:3.500A)
      removed outlier: 6.883A  pdb=" N   VAL A1514 " --> pdb=" O   LEU A1521 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1397 through 1398

    627 hydrogen bonds defined for protein.
    1845 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: 3.05

  Time building geometry restraints manager: 4.14 seconds

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

  Histogram of bond lengths:
        1.13 -     1.27: 1410
        1.27 -     1.41: 2219
        1.41 -     1.54: 5453
        1.54 -     1.68: 26
        1.68 -     1.82: 76
  Bond restraints: 9184
  Sorted by residual:
  bond pdb=" C17 ESV A1606 "
       pdb=" N3  ESV A1606 "
    ideal  model  delta    sigma   weight residual
    1.323  1.459 -0.136 2.00e-02 2.50e+03 4.65e+01
  bond pdb=" CAY Y01 A1601 "
       pdb=" OAW Y01 A1601 "
    ideal  model  delta    sigma   weight residual
    1.332  1.462 -0.130 2.00e-02 2.50e+03 4.25e+01
  bond pdb=" C11 ESV A1606 "
       pdb=" N2  ESV A1606 "
    ideal  model  delta    sigma   weight residual
    1.380  1.474 -0.094 2.00e-02 2.50e+03 2.22e+01
  bond pdb=" CAX Y01 A1601 "
       pdb=" OAH Y01 A1601 "
    ideal  model  delta    sigma   weight residual
    1.248  1.332 -0.084 2.00e-02 2.50e+03 1.77e+01
  bond pdb=" C12 ESV A1606 "
       pdb=" N2  ESV A1606 "
    ideal  model  delta    sigma   weight residual
    1.402  1.466 -0.064 2.00e-02 2.50e+03 1.01e+01
  ... (remaining 9179 not shown)

  Histogram of bond angle deviations from ideal:
      100.52 -   116.37: 6244
      116.37 -   132.22: 6216
      132.22 -   148.07: 24
      148.07 -   163.92: 0
      163.92 -   179.76: 1
  Bond angle restraints: 12485
  Sorted by residual:
  angle pdb=" N2  ESV A1606 "
        pdb=" C11 ESV A1606 "
        pdb=" N3  ESV A1606 "
      ideal   model   delta    sigma   weight residual
     112.24  125.48  -13.24 3.00e+00 1.11e-01 1.95e+01
  angle pdb=" CA  GLY A 701 "
        pdb=" C   GLY A 701 "
        pdb=" N   GLN A 702 "
      ideal   model   delta    sigma   weight residual
     114.58  117.31   -2.73 8.60e-01 1.35e+00 1.01e+01
  angle pdb=" C1' ATP A1605 "
        pdb=" C2' ATP A1605 "
        pdb=" C3' ATP A1605 "
      ideal   model   delta    sigma   weight residual
     101.56  105.17   -3.61 1.19e+00 7.05e-01 9.19e+00
  angle pdb=" C2' ATP A1605 "
        pdb=" C3' ATP A1605 "
        pdb=" C4' ATP A1605 "
      ideal   model   delta    sigma   weight residual
     102.49  105.44   -2.95 1.00e+00 1.00e+00 8.73e+00
  angle pdb=" CAJ Y01 A1601 "
        pdb=" CAO Y01 A1601 "
        pdb=" CBB Y01 A1601 "
      ideal   model   delta    sigma   weight residual
     115.08  106.36    8.72 3.00e+00 1.11e-01 8.46e+00
  ... (remaining 12480 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.64: 5346
       27.64 -    55.28: 150
       55.28 -    82.92: 18
       82.92 -   110.57: 0
      110.57 -   138.21: 1
  Dihedral angle restraints: 5515
    sinusoidal: 2194
      harmonic: 3321
  Sorted by residual:
  dihedral pdb=" O2A ADP A1602 "
           pdb=" O3A ADP A1602 "
           pdb=" PA  ADP A1602 "
           pdb=" PB  ADP A1602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   78.21 -138.21     1      2.00e+01 2.50e-03 4.19e+01
  dihedral pdb=" O1B ADP A1602 "
           pdb=" O3A ADP A1602 "
           pdb=" PB  ADP A1602 "
           pdb=" PA  ADP A1602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   14.54  -74.54     1      2.00e+01 2.50e-03 1.76e+01
  dihedral pdb=" CA  PHE A 795 "
           pdb=" C   PHE A 795 "
           pdb=" N   GLY A 796 "
           pdb=" CA  GLY A 796 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.40  -16.60     0      5.00e+00 4.00e-02 1.10e+01
  ... (remaining 5512 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1247
       0.049 -    0.099: 193
       0.099 -    0.148: 45
       0.148 -    0.198: 5
       0.198 -    0.247: 1
  Chirality restraints: 1491
  Sorted by residual:
  chirality pdb=" CBB Y01 A1601 "
            pdb=" CAC Y01 A1601 "
            pdb=" CAO Y01 A1601 "
            pdb=" CBE Y01 A1601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.58    2.33    0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" C2' ATP A1605 "
            pdb=" C1' ATP A1605 "
            pdb=" C3' ATP A1605 "
            pdb=" O2' ATP A1605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.87    0.19 2.00e-01 2.50e+01 8.79e-01
  chirality pdb=" C3' ATP A1605 "
            pdb=" C2' ATP A1605 "
            pdb=" C4' ATP A1605 "
            pdb=" O3' ATP A1605 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.82    0.18 2.00e-01 2.50e+01 8.15e-01
  ... (remaining 1488 not shown)

  Planarity restraints: 1524
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A1092 "   -0.013 2.00e-02 2.50e+03   2.68e-02 7.19e+00
        pdb=" C   PHE A1092 "    0.046 2.00e-02 2.50e+03
        pdb=" O   PHE A1092 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   SER A1093 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 580 "   -0.039 5.00e-02 4.00e+02   5.99e-02 5.73e+00
        pdb=" N   PRO A 581 "    0.104 5.00e-02 4.00e+02
        pdb=" CA  PRO A 581 "   -0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 581 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 847 "   -0.012 2.00e-02 2.50e+03   2.39e-02 5.71e+00
        pdb=" C   MET A 847 "    0.041 2.00e-02 2.50e+03
        pdb=" O   MET A 847 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   GLN A 848 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1521 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 10
        2.52 -     3.12: 7233
        3.12 -     3.71: 13971
        3.71 -     4.31: 20045
        4.31 -     4.90: 33770
  Nonbonded interactions: 75029
  Sorted by model distance:
  nonbonded pdb=" OE1 GLN A 753 "
            pdb="MG    MG A1603 "
     model   vdw
     1.926 2.170
  nonbonded pdb=" O1B ADP A1602 "
            pdb="MG    MG A1604 "
     model   vdw
     2.149 2.170
  nonbonded pdb=" OG  SER A1349 "
            pdb="MG    MG A1604 "
     model   vdw
     2.219 2.170
  nonbonded pdb=" OG  SER A 708 "
            pdb="MG    MG A1603 "
     model   vdw
     2.272 2.170
  nonbonded pdb=" OE2 GLU A 717 "
            pdb=" NH2 ARG A1182 "
     model   vdw
     2.300 2.520
  ... (remaining 75024 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.400
  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:          2.190
  Check model and map are aligned:         0.120
  Set scattering table:                    0.080
  Process input model:                     27.670
  Find NCS groups from input model:        0.230
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.136   9184  Z= 0.262
  Angle     :  0.619  13.240  12485  Z= 0.314
  Chirality :  0.040   0.247   1491
  Planarity :  0.005   0.060   1524
  Dihedral  : 13.156 138.207   3363
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 2.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  :  4.49 %
    Favored  : 94.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.24 (0.25), residues: 1127
  helix:  0.34 (0.19), residues: 743
  sheet: -0.64 (0.58), residues: 69
  loop : -1.00 (0.35), residues: 315

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A 727 
   HIS   0.004   0.001   HIS A1001 
   PHE   0.010   0.001   PHE A 552 
   TYR   0.011   0.001   TYR A 290 
   ARG   0.002   0.000   ARG A1461 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 189
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 4
  residues processed: 200
  average time/residue: 0.2705
  time to fit residues: 71.5177
Evaluate side-chains
  104 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 100
  time to evaluate  : 1.041 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0953
  time to fit residues: 2.0895
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 47 optimal weight:    0.1980
   chunk 29 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 89 optimal weight:    0.3980
   chunk 34 optimal weight:    0.6980
   chunk 54 optimal weight:    1.9990
   chunk 66 optimal weight:    5.9990
   chunk 103 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
A 702 GLN
A 719 GLN
A1102 HIS
A1379 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9184  Z= 0.192
  Angle     :  0.561   8.802  12485  Z= 0.282
  Chirality :  0.040   0.176   1491
  Planarity :  0.005   0.053   1524
  Dihedral  :  8.330 136.078   1337
  Min Nonbonded Distance : 1.997

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  2.09 %
    Allowed  : 10.86 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  1.75 (0.25), residues: 1127
  helix:  1.94 (0.19), residues: 754
  sheet: -0.37 (0.60), residues: 69
  loop : -0.40 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A1260 
   HIS   0.004   0.001   HIS A 576 
   PHE   0.016   0.001   PHE A1149 
   TYR   0.010   0.001   TYR A1317 
   ARG   0.005   0.000   ARG A1150 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
  outliers start: 20
  outliers final: 12
  residues processed: 120
  average time/residue: 0.2337
  time to fit residues: 38.9382
Evaluate side-chains
  98 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 1.013 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 0
  residues processed: 12
  average time/residue: 0.0922
  time to fit residues: 3.4631
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 32 optimal weight:    0.7980
   chunk 86 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 103 optimal weight:    0.4980
   chunk 112 optimal weight:    9.9990
   chunk 92 optimal weight:    7.9990
   chunk 102 optimal weight:    0.0030
   chunk 35 optimal weight:    7.9990
   chunk 83 optimal weight:    1.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
A 509 HIS
A1311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9184  Z= 0.173
  Angle     :  0.529   8.369  12485  Z= 0.261
  Chirality :  0.039   0.193   1491
  Planarity :  0.004   0.046   1524
  Dihedral  :  8.381 139.463   1337
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 13.36 %
    Favored  : 85.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.44 (0.25), residues: 1127
  helix:  2.59 (0.19), residues: 747
  sheet: -0.10 (0.63), residues: 69
  loop : -0.45 (0.35), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A1260 
   HIS   0.003   0.001   HIS A 576 
   PHE   0.014   0.001   PHE A 356 
   TYR   0.015   0.001   TYR A1317 
   ARG   0.004   0.000   ARG A1150 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 1.114 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 106
  average time/residue: 0.3561
  time to fit residues: 51.4531
Evaluate side-chains
  88 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 85
  time to evaluate  : 1.110 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1055
  time to fit residues: 2.2696
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 77 optimal weight:    0.6980
   chunk 53 optimal weight:    4.9990
   chunk 11 optimal weight:    0.7980
   chunk 49 optimal weight:    3.9990
   chunk 69 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 437 GLN
A 911 ASN
A1311 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9184  Z= 0.228
  Angle     :  0.548   8.731  12485  Z= 0.268
  Chirality :  0.040   0.181   1491
  Planarity :  0.004   0.046   1524
  Dihedral  :  8.426 150.841   1337
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 14.30 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.45 (0.25), residues: 1127
  helix:  2.58 (0.19), residues: 751
  sheet: -0.05 (0.63), residues: 69
  loop : -0.44 (0.35), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP A1302 
   HIS   0.005   0.001   HIS A1001 
   PHE   0.011   0.001   PHE A 356 
   TYR   0.009   0.001   TYR A1257 
   ARG   0.003   0.000   ARG A 590 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 1.078 
Fit side-chains
   revert: symmetry clash
  outliers start: 19
  outliers final: 9
  residues processed: 114
  average time/residue: 0.2193
  time to fit residues: 35.1429
Evaluate side-chains
  96 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.968 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0811
  time to fit residues: 2.6775
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 91 optimal weight:    6.9990
   chunk 62 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   chunk 82 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0670
   chunk 98 optimal weight:    0.1980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.5320

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

Flipped N/Q/H residues before XYZ refinement:
A 807 ASN
A1065 HIS
A1186 HIS
A1311 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.3522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9184  Z= 0.165
  Angle     :  0.503   8.282  12485  Z= 0.248
  Chirality :  0.039   0.190   1491
  Planarity :  0.004   0.044   1524
  Dihedral  :  8.257 154.736   1337
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 14.51 %
    Favored  : 84.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.64 (0.26), residues: 1127
  helix:  2.74 (0.19), residues: 752
  sheet: -0.07 (0.63), residues: 69
  loop : -0.41 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A1260 
   HIS   0.003   0.001   HIS A1065 
   PHE   0.014   0.001   PHE A 356 
   TYR   0.009   0.001   TYR A1257 
   ARG   0.005   0.000   ARG A1150 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 1.017 
Fit side-chains
   revert: symmetry clash
  outliers start: 12
  outliers final: 7
  residues processed: 107
  average time/residue: 0.2366
  time to fit residues: 35.1258
Evaluate side-chains
  93 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 1.026 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.1051
  time to fit residues: 2.7634
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 37 optimal weight:    0.8980
   chunk 99 optimal weight:    3.9990
   chunk 21 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 27 optimal weight:    0.6980
   chunk 110 optimal weight:    2.9990
   chunk 91 optimal weight:    0.3980
   chunk 51 optimal weight:    0.9980
   chunk 9 optimal weight:    0.6980
   chunk 36 optimal weight:    0.8980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9184  Z= 0.180
  Angle     :  0.510   9.002  12485  Z= 0.249
  Chirality :  0.039   0.185   1491
  Planarity :  0.004   0.044   1524
  Dihedral  :  8.206 159.557   1337
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.94 %
    Allowed  : 15.66 %
    Favored  : 83.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.64 (0.25), residues: 1127
  helix:  2.73 (0.19), residues: 756
  sheet: -0.01 (0.63), residues: 69
  loop : -0.41 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A1260 
   HIS   0.004   0.001   HIS A1065 
   PHE   0.009   0.001   PHE A 356 
   TYR   0.010   0.001   TYR A1257 
   ARG   0.005   0.000   ARG A1150 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 93
  time to evaluate  : 1.147 
Fit side-chains
  outliers start: 9
  outliers final: 6
  residues processed: 99
  average time/residue: 0.2582
  time to fit residues: 35.5641
Evaluate side-chains
  93 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 87
  time to evaluate  : 1.040 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0894
  time to fit residues: 2.4198
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9990
   chunk 62 optimal weight:    0.4980
   chunk 80 optimal weight:    3.9990
   chunk 92 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 109 optimal weight:    0.7980
   chunk 68 optimal weight:    0.2980
   chunk 66 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 347 ASN
A1311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.3787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9184  Z= 0.168
  Angle     :  0.504   8.268  12485  Z= 0.247
  Chirality :  0.039   0.187   1491
  Planarity :  0.004   0.044   1524
  Dihedral  :  8.149 163.419   1337
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.69 %
    Favored  : 98.31 %
  Rotamer:
    Outliers :  0.73 %
    Allowed  : 14.93 %
    Favored  : 84.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.70 (0.26), residues: 1127
  helix:  2.77 (0.19), residues: 757
  sheet:  0.05 (0.63), residues: 69
  loop : -0.42 (0.35), residues: 301

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.006   0.001   TRP A1260 
   HIS   0.003   0.001   HIS A1001 
   PHE   0.015   0.001   PHE A 356 
   TYR   0.008   0.001   TYR A1257 
   ARG   0.006   0.000   ARG A1078 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 92
  time to evaluate  : 1.016 
Fit side-chains
  outliers start: 7
  outliers final: 3
  residues processed: 96
  average time/residue: 0.2183
  time to fit residues: 29.8811
Evaluate side-chains
  89 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 86
  time to evaluate  : 1.018 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1041
  time to fit residues: 1.9437
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 69 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 54 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 99 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
A1311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.3793

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9184  Z= 0.255
  Angle     :  0.551   9.406  12485  Z= 0.270
  Chirality :  0.041   0.186   1491
  Planarity :  0.004   0.044   1524
  Dihedral  :  8.445 174.118   1337
  Min Nonbonded Distance : 1.915

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 15.24 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.49 (0.25), residues: 1127
  helix:  2.59 (0.19), residues: 758
  sheet: -0.05 (0.63), residues: 69
  loop : -0.43 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.005   0.001   TRP A1260 
   HIS   0.004   0.001   HIS A1001 
   PHE   0.011   0.001   PHE A 356 
   TYR   0.007   0.001   TYR A1257 
   ARG   0.004   0.000   ARG A1078 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 91
  time to evaluate  : 0.964 
Fit side-chains
  outliers start: 10
  outliers final: 7
  residues processed: 98
  average time/residue: 0.2288
  time to fit residues: 31.9693
Evaluate side-chains
  94 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 1.037 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0880
  time to fit residues: 2.5653
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 102 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 80 optimal weight:    2.9990
   chunk 31 optimal weight:    0.7980
   chunk 92 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 420 GLN
A1311 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9184  Z= 0.191
  Angle     :  0.534   9.378  12485  Z= 0.261
  Chirality :  0.040   0.195   1491
  Planarity :  0.004   0.044   1524
  Dihedral  :  8.436 175.357   1337
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 5.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  : 15.97 %
    Favored  : 83.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.57 (0.25), residues: 1127
  helix:  2.64 (0.19), residues: 756
  sheet:  0.01 (0.64), residues: 69
  loop : -0.33 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A1302 
   HIS   0.003   0.001   HIS A1065 
   PHE   0.016   0.001   PHE A 356 
   TYR   0.010   0.001   TYR A1257 
   ARG   0.007   0.000   ARG A1078 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.976 
Fit side-chains
  outliers start: 3
  outliers final: 2
  residues processed: 90
  average time/residue: 0.2256
  time to fit residues: 29.3276
Evaluate side-chains
  87 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 85
  time to evaluate  : 1.009 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0924
  time to fit residues: 1.8774
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 104 optimal weight:    0.9980
   chunk 90 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 69 optimal weight:    0.7980
   chunk 55 optimal weight:    0.3980
   chunk 71 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A1311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9184  Z= 0.191
  Angle     :  0.534   9.378  12485  Z= 0.261
  Chirality :  0.040   0.195   1491
  Planarity :  0.004   0.044   1524
  Dihedral  :  8.436 175.357   1337
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.70 %
    Favored  : 83.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  2.57 (0.25), residues: 1127
  helix:  2.64 (0.19), residues: 756
  sheet:  0.01 (0.64), residues: 69
  loop : -0.33 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A1302 
   HIS   0.003   0.001   HIS A1065 
   PHE   0.016   0.001   PHE A 356 
   TYR   0.010   0.001   TYR A1257 
   ARG   0.007   0.000   ARG A1078 

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

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

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2254 Ramachandran restraints generated.
    1127 Oldfield, 0 Emsley, 1127 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.909 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2207
  time to fit residues: 27.5797
Evaluate side-chains
  84 residues out of total 983 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 1.011 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4245
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 83 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 79 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A1311 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.134582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.110490 restraints weight = 11631.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3162 rms_B_bonded: 2.04
r_work: 0.3032 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3844

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9184  Z= 0.191
  Angle     :  0.534   9.378  12485  Z= 0.261
  Chirality :  0.040   0.195   1491
  Planarity :  0.004   0.044   1524
  Dihedral  :  8.436 175.357   1337
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 16.91 %
    Favored  : 83.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  2.57 (0.25), residues: 1127
  helix:  2.64 (0.19), residues: 756
  sheet:  0.01 (0.64), residues: 69
  loop : -0.33 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP A1302 
   HIS   0.003   0.001   HIS A1065 
   PHE   0.016   0.001   PHE A 356 
   TYR   0.010   0.001   TYR A1257 
   ARG   0.007   0.000   ARG A1078 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1942.16 seconds
wall clock time: 35 minutes 58.86 seconds (2158.86 seconds total)