Starting phenix.real_space_refine
on Wed Mar  4 00:46:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9zjz_74347/03_2026/9zjz_74347.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9zjz_74347/03_2026/9zjz_74347.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9zjz_74347/03_2026/9zjz_74347.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9zjz_74347/03_2026/9zjz_74347.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9zjz_74347/03_2026/9zjz_74347.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9zjz_74347/03_2026/9zjz_74347.map"
  }
  resolution = 2.87
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.044
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       3      5.49       5
     Mg      1      5.21       5
     S      43      5.16       5
     C    5933      2.51       5
     N    1522      2.21       5
     O    1709      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9211
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1121, 9179
          Classifications: {'peptide': 1121}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 39, 'TRANS': 1081}
          Chain breaks: 11
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.95, per 1000 atoms: 0.21
  Number of scatterers: 9211
  At special positions: 0
  Unit cell: (93.72, 93.72, 133.98, 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      43     16.00
     P       3     15.00
     Mg      1     11.99
     O    1709      8.00
     N    1522      7.00
     C    5933      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 362.4 milliseconds
  

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 6 sheets defined
      61.6% alpha, 10.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 4.126A  pdb=" N   LYS A 393 " --> pdb=" O   ARG A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
    Processing helix  chain 'A' and resid 429 through 433
    Processing helix  chain 'A' and resid 445 through 450
      removed outlier: 3.505A  pdb=" N   ASN A 449 " --> pdb=" O   GLU A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 450 through 456
      removed outlier: 3.516A  pdb=" N   ALA A 454 " --> pdb=" O   GLY A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 465 through 470
    Processing helix  chain 'A' and resid 476 through 483
    Processing helix  chain 'A' and resid 509 through 517
    Processing helix  chain 'A' and resid 517 through 529
    Processing helix  chain 'A' and resid 554 through 568
    Processing helix  chain 'A' and resid 579 through 594
    Processing helix  chain 'A' and resid 601 through 603
      No H-bonds generated for 'chain 'A' and resid 601 through 603'
    Processing helix  chain 'A' and resid 610 through 620
      removed outlier: 3.573A  pdb=" N   LYS A 620 " --> pdb=" O   GLY A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 647
    Processing helix  chain 'A' and resid 664 through 667
    Processing helix  chain 'A' and resid 668 through 685
    Processing helix  chain 'A' and resid 690 through 699
      removed outlier: 4.007A  pdb=" N   PHE A 694 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   SER A 697 " --> pdb=" O   ASN A 693 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 723
      removed outlier: 3.593A  pdb=" N   ASP A 723 " --> pdb=" O   GLN A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 754
      removed outlier: 3.541A  pdb=" N   LEU A 746 " --> pdb=" O   GLY A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 782
    Processing helix  chain 'A' and resid 804 through 822
      removed outlier: 4.242A  pdb=" N   TYR A 808 " --> pdb=" O   GLN A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 845
    Processing helix  chain 'A' and resid 858 through 876
      removed outlier: 3.816A  pdb=" N   GLU A 874 " --> pdb=" O   LYS A 870 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   GLN A 875 " --> pdb=" O   GLU A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 878 through 881
    Processing helix  chain 'A' and resid 882 through 890
    Processing helix  chain 'A' and resid 893 through 906
    Processing helix  chain 'A' and resid 912 through 928
    Processing helix  chain 'A' and resid 935 through 943
    Processing helix  chain 'A' and resid 956 through 961
    Processing helix  chain 'A' and resid 962 through 965
      removed outlier: 3.794A  pdb=" N   THR A 965 " --> pdb=" O   THR A 962 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 962 through 965'
    Processing helix  chain 'A' and resid 985 through 1000
    Processing helix  chain 'A' and resid 1003 through 1012
    Processing helix  chain 'A' and resid 1014 through 1020
      removed outlier: 4.098A  pdb=" N   PHE A1018 " --> pdb=" O   GLU A1014 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   THR A1020 " --> pdb=" O   LEU A1016 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1023 through 1036
    Processing helix  chain 'A' and resid 1052 through 1062
    Processing helix  chain 'A' and resid 1063 through 1078
      removed outlier: 3.790A  pdb=" N   VAL A1067 " --> pdb=" O   GLY A1063 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1081 through 1095
      removed outlier: 3.728A  pdb=" N   CYS A1085 " --> pdb=" O   ASN A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1098 through 1113
    Processing helix  chain 'A' and resid 1116 through 1139
      removed outlier: 3.910A  pdb=" N   LYS A1130 " --> pdb=" O   VAL A1126 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   ILE A1131 " --> pdb=" O   TYR A1127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1172
      removed outlier: 3.778A  pdb=" N   ILE A1150 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA A1151 " --> pdb=" O   ASP A1147 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1194 through 1212
      removed outlier: 3.667A  pdb=" N   GLN A1198 " --> pdb=" O   ILE A1194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1213 through 1218
      removed outlier: 6.218A  pdb=" N   PHE A1216 " --> pdb=" O   LEU A1213 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ASP A1218 " --> pdb=" O   PRO A1215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1233
    Processing helix  chain 'A' and resid 1244 through 1251
    Processing helix  chain 'A' and resid 1253 through 1258
    Processing helix  chain 'A' and resid 1259 through 1277
    Processing helix  chain 'A' and resid 1285 through 1308
      removed outlier: 3.852A  pdb=" N   GLU A1289 " --> pdb=" O   LYS A1285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1325 through 1339
    Processing helix  chain 'A' and resid 1343 through 1349
    Processing helix  chain 'A' and resid 1350 through 1353
      removed outlier: 3.884A  pdb=" N   LYS A1353 " --> pdb=" O   TYR A1350 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1350 through 1353'
    Processing helix  chain 'A' and resid 1354 through 1375
    Processing helix  chain 'A' and resid 1381 through 1399
    Processing helix  chain 'A' and resid 1407 through 1423
      Proline residue:  A1421  - end of helix
    Processing helix  chain 'A' and resid 1429 through 1439
    Processing helix  chain 'A' and resid 1449 through 1451
      No H-bonds generated for 'chain 'A' and resid 1449 through 1451'
    Processing helix  chain 'A' and resid 1452 through 1468
    Processing helix  chain 'A' and resid 1487 through 1490
    Processing helix  chain 'A' and resid 1495 through 1501
    Processing helix  chain 'A' and resid 1516 through 1519
    Processing helix  chain 'A' and resid 1520 through 1525
      removed outlier: 3.533A  pdb=" N   GLN A1524 " --> pdb=" O   GLU A1520 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 462 through 464
      removed outlier: 7.188A  pdb=" N   TYR A 413 " --> pdb=" O   ALA A 438 " (cutoff:3.500A)
      removed outlier: 8.755A  pdb=" N   LEU A 440 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
      removed outlier: 6.894A  pdb=" N   LEU A 415 " --> pdb=" O   LEU A 440 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   GLN A 412 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
      removed outlier: 7.886A  pdb=" N   VAL A 542 " --> pdb=" O   GLN A 412 " (cutoff:3.500A)
      removed outlier: 6.372A  pdb=" N   ILE A 414 " --> pdb=" O   VAL A 542 " (cutoff:3.500A)
      removed outlier: 7.288A  pdb=" N   LEU A 544 " --> pdb=" O   ILE A 414 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   VAL A 416 " --> pdb=" O   LEU A 544 " (cutoff:3.500A)
      removed outlier: 8.034A  pdb=" N   LEU A 574 " --> pdb=" O   PHE A 539 " (cutoff:3.500A)
      removed outlier: 6.150A  pdb=" N   VAL A 541 " --> pdb=" O   LEU A 574 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ILE A 576 " --> pdb=" O   VAL A 541 " (cutoff:3.500A)
      removed outlier: 6.245A  pdb=" N   PHE A 543 " --> pdb=" O   ILE A 576 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 631 through 632
    Processing sheet with id=AA3, first strand: chain 'A' and resid 652 through 655
      removed outlier: 4.136A  pdb=" N   CYS A 760 " --> pdb=" O   ILE A 655 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   ASP A 799 " --> pdb=" O   LEU A 763 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   VAL A 794 " --> pdb=" O   ILE A 831 " (cutoff:3.500A)
      removed outlier: 7.434A  pdb=" N   LEU A 833 " --> pdb=" O   VAL A 794 " (cutoff:3.500A)
      removed outlier: 6.581A  pdb=" N   LEU A 796 " --> pdb=" O   LEU A 833 " (cutoff:3.500A)
      removed outlier: 7.625A  pdb=" N   CYS A 835 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL A 798 " --> pdb=" O   CYS A 835 " (cutoff:3.500A)
      removed outlier: 8.619A  pdb=" N   ARG A 837 " --> pdb=" O   VAL A 798 " (cutoff:3.500A)
      removed outlier: 8.857A  pdb=" N   ILE A 851 " --> pdb=" O   ILE A 732 " (cutoff:3.500A)
      removed outlier: 6.553A  pdb=" N   HIS A 734 " --> pdb=" O   ILE A 851 " (cutoff:3.500A)
      removed outlier: 7.920A  pdb=" N   VAL A 853 " --> pdb=" O   HIS A 734 " (cutoff:3.500A)
      removed outlier: 6.575A  pdb=" N   TYR A 736 " --> pdb=" O   VAL A 853 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 933 through 934
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1278 through 1280
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1492 through 1494
      removed outlier: 3.736A  pdb=" N   PHE A1481 " --> pdb=" O   PHE A1576 " (cutoff:3.500A)
      removed outlier: 5.426A  pdb=" N   LEU A1574 " --> pdb=" O   LEU A1483 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   TYR A1573 " --> pdb=" O   ASP A1585 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   ASP A1585 " --> pdb=" O   TYR A1573 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   GLY A1575 " --> pdb=" O   ALA A1583 " (cutoff:3.500A)
      removed outlier: 5.121A  pdb=" N   ALA A1583 " --> pdb=" O   GLY A1575 " (cutoff:3.500A)
      removed outlier: 6.229A  pdb=" N   SER A1577 " --> pdb=" O   PRO A1581 " (cutoff:3.500A)
      removed outlier: 8.273A  pdb=" N   ALA A1583 " --> pdb=" O   PRO A1552 " (cutoff:3.500A)
      removed outlier: 7.384A  pdb=" N   THR A1554 " --> pdb=" O   ALA A1583 " (cutoff:3.500A)
      removed outlier: 9.382A  pdb=" N   ASP A1585 " --> pdb=" O   THR A1554 " (cutoff:3.500A)
      removed outlier: 5.475A  pdb=" N   GLU A1542 " --> pdb=" O   GLN A1531 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   GLN A1531 " --> pdb=" O   GLU A1542 " (cutoff:3.500A)

    485 hydrogen bonds defined for protein.
    1407 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.26

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2916
        1.34 -     1.46: 2099
        1.46 -     1.58: 4325
        1.58 -     1.70: 4
        1.70 -     1.82: 61
  Bond restraints: 9405
  Sorted by residual:
  bond pdb=" N   ASN A1143 "
       pdb=" CA  ASN A1143 "
    ideal  model  delta    sigma   weight residual
    1.454  1.489 -0.035 1.17e-02 7.31e+03 8.94e+00
  bond pdb=" N   LEU A1012 "
       pdb=" CA  LEU A1012 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.037 1.32e-02 5.74e+03 7.88e+00
  bond pdb=" N   LYS A 419 "
       pdb=" CA  LYS A 419 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.22e-02 6.72e+03 7.82e+00
  bond pdb=" N   ILE A1144 "
       pdb=" CA  ILE A1144 "
    ideal  model  delta    sigma   weight residual
    1.459  1.492 -0.033 1.19e-02 7.06e+03 7.55e+00
  bond pdb=" N   TYR A1253 "
       pdb=" CA  TYR A1253 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.16e-02 7.43e+03 7.52e+00
  ... (remaining 9400 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 12433
        2.08 -     4.15: 222
        4.15 -     6.23: 23
        6.23 -     8.31: 0
        8.31 -    10.39: 2
  Bond angle restraints: 12680
  Sorted by residual:
  angle pdb=" N   ASP A1148 "
        pdb=" CA  ASP A1148 "
        pdb=" C   ASP A1148 "
      ideal   model   delta    sigma   weight residual
     112.89  106.87    6.02 1.24e+00 6.50e-01 2.36e+01
  angle pdb=" N   ASP A1154 "
        pdb=" CA  ASP A1154 "
        pdb=" C   ASP A1154 "
      ideal   model   delta    sigma   weight residual
     112.90  107.15    5.75 1.31e+00 5.83e-01 1.93e+01
  angle pdb=" N   GLN A 424 "
        pdb=" CA  GLN A 424 "
        pdb=" C   GLN A 424 "
      ideal   model   delta    sigma   weight residual
     113.72  108.22    5.50 1.30e+00 5.92e-01 1.79e+01
  angle pdb=" N   ASP A1147 "
        pdb=" CA  ASP A1147 "
        pdb=" C   ASP A1147 "
      ideal   model   delta    sigma   weight residual
     113.88  109.10    4.78 1.23e+00 6.61e-01 1.51e+01
  angle pdb=" N   LEU A1016 "
        pdb=" CA  LEU A1016 "
        pdb=" CB  LEU A1016 "
      ideal   model   delta    sigma   weight residual
     110.12  104.63    5.49 1.47e+00 4.63e-01 1.39e+01
  ... (remaining 12675 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.66: 4798
       17.66 -    35.31: 647
       35.31 -    52.97: 204
       52.97 -    70.62: 53
       70.62 -    88.28: 10
  Dihedral angle restraints: 5712
    sinusoidal: 2407
      harmonic: 3305
  Sorted by residual:
  dihedral pdb=" CA  ASP A 499 "
           pdb=" CB  ASP A 499 "
           pdb=" CG  ASP A 499 "
           pdb=" OD1 ASP A 499 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.22   56.22     1      2.00e+01 2.50e-03 1.07e+01
  dihedral pdb=" CG  ARG A1491 "
           pdb=" CD  ARG A1491 "
           pdb=" NE  ARG A1491 "
           pdb=" CZ  ARG A1491 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  136.76   43.24     2      1.50e+01 4.44e-03 1.00e+01
  dihedral pdb=" CG  ARG A 837 "
           pdb=" CD  ARG A 837 "
           pdb=" NE  ARG A 837 "
           pdb=" CZ  ARG A 837 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.12  -42.12     2      1.50e+01 4.44e-03 9.60e+00
  ... (remaining 5709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1113
       0.051 -    0.101: 210
       0.101 -    0.152: 53
       0.152 -    0.202: 13
       0.202 -    0.253: 1
  Chirality restraints: 1390
  Sorted by residual:
  chirality pdb=" CB  VAL A 689 "
            pdb=" CA  VAL A 689 "
            pdb=" CG1 VAL A 689 "
            pdb=" CG2 VAL A 689 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.60e+00
  chirality pdb=" CA  LEU A1016 "
            pdb=" N   LEU A1016 "
            pdb=" C   LEU A1016 "
            pdb=" CB  LEU A1016 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  ILE A1422 "
            pdb=" CA  ILE A1422 "
            pdb=" CG1 ILE A1422 "
            pdb=" CG2 ILE A1422 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.57e-01
  ... (remaining 1387 not shown)

  Planarity restraints: 1600
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 683 "   -0.013 2.00e-02 2.50e+03   2.49e-02 6.18e+00
        pdb=" C   PHE A 683 "    0.043 2.00e-02 2.50e+03
        pdb=" O   PHE A 683 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   TYR A 684 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1250 "    0.011 2.00e-02 2.50e+03   2.18e-02 4.77e+00
        pdb=" C   LEU A1250 "   -0.038 2.00e-02 2.50e+03
        pdb=" O   LEU A1250 "    0.014 2.00e-02 2.50e+03
        pdb=" N   LYS A1251 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A1152 "   -0.010 2.00e-02 2.50e+03   2.09e-02 4.38e+00
        pdb=" C   LEU A1152 "    0.036 2.00e-02 2.50e+03
        pdb=" O   LEU A1152 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   LEU A1153 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1597 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 65
        2.62 -     3.19: 7561
        3.19 -     3.76: 13975
        3.76 -     4.33: 19853
        4.33 -     4.90: 33484
  Nonbonded interactions: 74938
  Sorted by model distance:
  nonbonded pdb=" O2B ATP A1601 "
            pdb="MG    MG A1602 "
     model   vdw
     2.048 2.170
  nonbonded pdb=" OG1 THR A 744 "
            pdb="MG    MG A1602 "
     model   vdw
     2.056 2.170
  nonbonded pdb=" OD1 ASP A1121 "
            pdb=" OG  SER A1166 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OD2 ASP A1272 "
            pdb=" NZ  LYS A1343 "
     model   vdw
     2.201 3.120
  nonbonded pdb=" OD2 ASP A1098 "
            pdb=" ND2 ASN A1101 "
     model   vdw
     2.249 3.120
  ... (remaining 74933 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:             8.740
  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:          0.220
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     8.330
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
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   0.038   9405  Z= 0.252
  Angle     :  0.625  10.387  12680  Z= 0.384
  Chirality :  0.045   0.253   1390
  Planarity :  0.004   0.041   1600
  Dihedral  : 18.351  88.280   3566
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.82 %
    Favored  : 98.18 %
  Rotamer:
    Outliers :  2.64 %
    Allowed  : 24.44 %
    Favored  : 72.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.90 (0.26), residues: 1097
  helix:  1.96 (0.21), residues: 610
  sheet:  1.01 (0.52), residues: 115
  loop :  0.25 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1473 
 TYR   0.021   0.002   TYR A1426 
 PHE   0.010   0.001   PHE A 683 
 TRP   0.011   0.001   TRP A1105 
 HIS   0.003   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 9405)
  covalent geometry    : angle       0.62480 (12680)
  hydrogen bonds       : bond        0.14718 (  485)
  hydrogen bonds       : angle       5.65956 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 97
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  419 LYS cc_start: 0.7866 (ttpt) cc_final: 0.7236 (tttp)
REVERT: A  514 GLN cc_start: 0.7301 (OUTLIER) cc_final: 0.6009 (mp10)
REVERT: A  553 ARG cc_start: 0.7417 (mtm110) cc_final: 0.6261 (mtp85)
REVERT: A  757 LYS cc_start: 0.8719 (mttt) cc_final: 0.7997 (mmtm)
REVERT: A  786 MET cc_start: 0.6218 (mmm) cc_final: 0.4384 (ppp)
REVERT: A  994 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7203 (mp0)
REVERT: A 1137 GLU cc_start: 0.6626 (OUTLIER) cc_final: 0.6148 (mm-30)
REVERT: A 1187 ARG cc_start: 0.5759 (mmm160) cc_final: 0.5110 (mtp85)
REVERT: A 1375 GLN cc_start: 0.6414 (OUTLIER) cc_final: 0.6141 (pp30)
REVERT: A 1396 SER cc_start: 0.8135 (t) cc_final: 0.7832 (m)
REVERT: A 1416 ARG cc_start: 0.6890 (mtp180) cc_final: 0.6411 (ttp80)
  outliers start: 27
  outliers final: 19
  residues processed: 119
  average time/residue: 0.6443
  time to fit residues: 81.2790
Evaluate side-chains
  118 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 95
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  782 THR
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue  866 GLU
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1113 GLU
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1258 THR
Chi-restraints excluded: chain A residue 1375 GLN
Chi-restraints excluded: chain A residue 1401 THR
Chi-restraints excluded: chain A residue 1417 GLU
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1554 THR
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0050
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    1.4998

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

Flipped N/Q/H residues before XYZ refinement:
A 626 GLN
A1198 GLN
A1414 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.147138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.121147 restraints weight = 11831.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.3401 rms_B_bonded: 2.27
r_work: 0.3286 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.3158 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.0981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9405  Z= 0.185
  Angle     :  0.520   8.663  12680  Z= 0.271
  Chirality :  0.043   0.155   1390
  Planarity :  0.004   0.043   1600
  Dihedral  :  9.076  71.117   1281
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  6.26 %
    Allowed  : 20.23 %
    Favored  : 73.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.63 (0.26), residues: 1097
  helix:  1.83 (0.21), residues: 621
  sheet:  0.80 (0.49), residues: 111
  loop : -0.05 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1529 
 TYR   0.017   0.002   TYR A1093 
 PHE   0.012   0.001   PHE A1083 
 TRP   0.011   0.001   TRP A1105 
 HIS   0.004   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 ( 9405)
  covalent geometry    : angle       0.51980 (12680)
  hydrogen bonds       : bond        0.04972 (  485)
  hydrogen bonds       : angle       4.49378 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 105
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  419 LYS cc_start: 0.7798 (ttpt) cc_final: 0.7092 (ttmt)
REVERT: A  553 ARG cc_start: 0.7261 (mtm110) cc_final: 0.6583 (mtp85)
REVERT: A  584 GLN cc_start: 0.7330 (OUTLIER) cc_final: 0.6572 (mp10)
REVERT: A  613 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.7028 (mm-30)
REVERT: A  664 LEU cc_start: 0.8203 (OUTLIER) cc_final: 0.7886 (mp)
REVERT: A  757 LYS cc_start: 0.8747 (mttt) cc_final: 0.8001 (mmtm)
REVERT: A 1062 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7281 (mt-10)
REVERT: A 1222 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.5115 (tm-30)
REVERT: A 1228 MET cc_start: 0.7559 (OUTLIER) cc_final: 0.6326 (tpp)
REVERT: A 1291 LYS cc_start: 0.8350 (OUTLIER) cc_final: 0.7866 (tttt)
REVERT: A 1396 SER cc_start: 0.8145 (t) cc_final: 0.7795 (m)
REVERT: A 1404 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7875 (mt)
REVERT: A 1465 LYS cc_start: 0.8166 (ttpp) cc_final: 0.7847 (mmtm)
REVERT: A 1487 LYS cc_start: 0.6352 (mttt) cc_final: 0.5863 (mptt)
REVERT: A 1570 VAL cc_start: 0.7299 (t) cc_final: 0.6926 (m)
  outliers start: 64
  outliers final: 21
  residues processed: 144
  average time/residue: 0.6416
  time to fit residues: 98.0680
Evaluate side-chains
  127 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 98
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1404 LEU
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1528 LEU
Chi-restraints excluded: chain A residue 1554 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 106 optimal weight:    0.6980
   chunk 21 optimal weight:    0.5980
   chunk 40 optimal weight:    4.9990
   chunk 79 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 78 optimal weight:    3.9990
   chunk 52 optimal weight:    0.9980
   chunk 46 optimal weight:    3.9990
   chunk 82 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   overall best weight:    0.8720

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

Flipped N/Q/H residues before XYZ refinement:
A 581 HIS
A 626 GLN
A 840 ASN
A1076 HIS
A1209 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.149427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.123491 restraints weight = 11721.957|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.27
r_work: 0.3303 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3174 rms_B_bonded: 4.82 restraints_weight: 0.2500
r_work (final): 0.3174
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.1281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9405  Z= 0.126
  Angle     :  0.462   7.860  12680  Z= 0.240
  Chirality :  0.041   0.140   1390
  Planarity :  0.003   0.041   1600
  Dihedral  :  7.653  61.248   1254
  Min Nonbonded Distance : 2.067

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 20.72 %
    Favored  : 73.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.80 (0.26), residues: 1097
  helix:  2.01 (0.21), residues: 617
  sheet:  0.57 (0.48), residues: 111
  loop :  0.08 (0.33), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1403 
 TYR   0.016   0.001   TYR A1093 
 PHE   0.009   0.001   PHE A 675 
 TRP   0.011   0.001   TRP A 586 
 HIS   0.002   0.001   HIS A 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 9405)
  covalent geometry    : angle       0.46196 (12680)
  hydrogen bonds       : bond        0.04148 (  485)
  hydrogen bonds       : angle       4.23861 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 103
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  419 LYS cc_start: 0.7783 (ttpt) cc_final: 0.7084 (tttp)
REVERT: A  514 GLN cc_start: 0.7305 (OUTLIER) cc_final: 0.5934 (mp10)
REVERT: A  553 ARG cc_start: 0.7235 (mtm110) cc_final: 0.6149 (mtp85)
REVERT: A  613 GLU cc_start: 0.7671 (OUTLIER) cc_final: 0.7073 (mm-30)
REVERT: A  645 GLU cc_start: 0.8552 (OUTLIER) cc_final: 0.7961 (mt-10)
REVERT: A  664 LEU cc_start: 0.8170 (tp) cc_final: 0.7866 (mp)
REVERT: A  731 LYS cc_start: 0.7612 (OUTLIER) cc_final: 0.7338 (ptpt)
REVERT: A  757 LYS cc_start: 0.8804 (mttt) cc_final: 0.8058 (mmtm)
REVERT: A 1062 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7317 (mt-10)
REVERT: A 1137 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6065 (mm-30)
REVERT: A 1222 GLU cc_start: 0.7286 (OUTLIER) cc_final: 0.5177 (tm-30)
REVERT: A 1228 MET cc_start: 0.7541 (OUTLIER) cc_final: 0.6370 (tpp)
REVERT: A 1291 LYS cc_start: 0.8271 (OUTLIER) cc_final: 0.7803 (tttt)
REVERT: A 1377 THR cc_start: 0.5342 (OUTLIER) cc_final: 0.5100 (m)
REVERT: A 1396 SER cc_start: 0.8191 (t) cc_final: 0.7799 (p)
REVERT: A 1399 GLN cc_start: 0.7676 (OUTLIER) cc_final: 0.7376 (mt0)
REVERT: A 1416 ARG cc_start: 0.6824 (mtp-110) cc_final: 0.6212 (mtp180)
REVERT: A 1465 LYS cc_start: 0.8159 (ttpp) cc_final: 0.7751 (tppt)
REVERT: A 1487 LYS cc_start: 0.6296 (mttt) cc_final: 0.5779 (mptt)
REVERT: A 1570 VAL cc_start: 0.7366 (t) cc_final: 0.7047 (m)
  outliers start: 58
  outliers final: 26
  residues processed: 140
  average time/residue: 0.6307
  time to fit residues: 93.7451
Evaluate side-chains
  132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 95
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  570 MET
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  645 GLU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  851 ILE
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1377 THR
Chi-restraints excluded: chain A residue 1399 GLN
Chi-restraints excluded: chain A residue 1402 SER
Chi-restraints excluded: chain A residue 1404 LEU
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1554 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 101 optimal weight:    3.9990
   chunk 61 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   chunk 81 optimal weight:    0.5980
   chunk 70 optimal weight:    0.6980
   chunk 110 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 98 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.6586

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

Flipped N/Q/H residues before XYZ refinement:
A 626 GLN
A 840 ASN
A1167 GLN
A1209 GLN
A1414 GLN
A1448 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.143227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.117265 restraints weight = 11963.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 2.30
r_work: 0.3259 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work: 0.3131 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.1558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.033   9405  Z= 0.201
  Angle     :  0.516   7.778  12680  Z= 0.269
  Chirality :  0.043   0.138   1390
  Planarity :  0.004   0.043   1600
  Dihedral  :  7.910  66.279   1254
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.37 %
    Favored  : 97.63 %
  Rotamer:
    Outliers :  5.67 %
    Allowed  : 21.51 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.36 (0.25), residues: 1097
  helix:  1.74 (0.21), residues: 627
  sheet:  0.34 (0.48), residues: 111
  loop : -0.34 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1473 
 TYR   0.016   0.002   TYR A1093 
 PHE   0.015   0.002   PHE A1083 
 TRP   0.012   0.001   TRP A1105 
 HIS   0.004   0.001   HIS A 530 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 ( 9405)
  covalent geometry    : angle       0.51618 (12680)
  hydrogen bonds       : bond        0.05040 (  485)
  hydrogen bonds       : angle       4.37858 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 103
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
REVERT: A  419 LYS cc_start: 0.7870 (ttpt) cc_final: 0.7192 (tttp)
REVERT: A  553 ARG cc_start: 0.7147 (mtm110) cc_final: 0.6380 (mtp85)
REVERT: A  558 GLU cc_start: 0.7482 (tp30) cc_final: 0.7261 (tp30)
REVERT: A  613 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7134 (mm-30)
REVERT: A  731 LYS cc_start: 0.7807 (OUTLIER) cc_final: 0.7513 (ptpt)
REVERT: A  757 LYS cc_start: 0.8837 (mttt) cc_final: 0.8095 (mmtm)
REVERT: A  846 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7223 (mtt-85)
REVERT: A 1062 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7385 (mt-10)
REVERT: A 1137 GLU cc_start: 0.6497 (OUTLIER) cc_final: 0.6118 (mm-30)
REVERT: A 1222 GLU cc_start: 0.7371 (OUTLIER) cc_final: 0.5301 (tm-30)
REVERT: A 1223 LEU cc_start: 0.7837 (mm) cc_final: 0.7532 (mt)
REVERT: A 1228 MET cc_start: 0.7776 (OUTLIER) cc_final: 0.6681 (tpp)
REVERT: A 1266 LYS cc_start: 0.8283 (OUTLIER) cc_final: 0.7793 (mtmm)
REVERT: A 1291 LYS cc_start: 0.8416 (OUTLIER) cc_final: 0.7934 (tttt)
REVERT: A 1377 THR cc_start: 0.5329 (OUTLIER) cc_final: 0.5045 (m)
REVERT: A 1396 SER cc_start: 0.8274 (t) cc_final: 0.7974 (m)
REVERT: A 1399 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7467 (mt0)
REVERT: A 1416 ARG cc_start: 0.6910 (mtp-110) cc_final: 0.6314 (mtp180)
REVERT: A 1465 LYS cc_start: 0.8261 (ttpp) cc_final: 0.7827 (tppt)
REVERT: A 1487 LYS cc_start: 0.6342 (mttt) cc_final: 0.5774 (mptt)
REVERT: A 1531 GLN cc_start: 0.7164 (mt0) cc_final: 0.6802 (tp40)
  outliers start: 58
  outliers final: 29
  residues processed: 142
  average time/residue: 0.6476
  time to fit residues: 97.6151
Evaluate side-chains
  132 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 92
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 GLU
Chi-restraints excluded: chain A residue  399 THR
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  536 ARG
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  846 ARG
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1266 LYS
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1377 THR
Chi-restraints excluded: chain A residue 1399 GLN
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1429 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1528 LEU
Chi-restraints excluded: chain A residue 1533 ARG
Chi-restraints excluded: chain A residue 1554 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    2.9990
   chunk 38 optimal weight:    7.9990
   chunk 18 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 110 optimal weight:    3.9990
   chunk 71 optimal weight:    0.1980
   chunk 96 optimal weight:    4.9990
   chunk 84 optimal weight:    3.9990
   chunk 68 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   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 626 GLN
A 840 ASN
A 876 HIS
A1414 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.149551 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.123722 restraints weight = 11810.430|
|-----------------------------------------------------------------------------|
r_work (start): 0.3427 rms_B_bonded: 2.28
r_work: 0.3312 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3184 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   9405  Z= 0.100
  Angle     :  0.432   8.713  12680  Z= 0.226
  Chirality :  0.040   0.133   1390
  Planarity :  0.003   0.040   1600
  Dihedral  :  7.463  60.070   1252
  Min Nonbonded Distance : 2.068

Molprobity Statistics.
  All-atom Clashscore : 4.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  4.59 %
    Allowed  : 22.58 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.76 (0.26), residues: 1097
  helix:  2.05 (0.21), residues: 623
  sheet:  0.41 (0.48), residues: 110
  loop : -0.09 (0.33), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1403 
 TYR   0.017   0.001   TYR A1093 
 PHE   0.008   0.001   PHE A 675 
 TRP   0.010   0.001   TRP A 586 
 HIS   0.002   0.001   HIS A1059 

Details of bonding type rmsd
  covalent geometry    : bond        0.00221 ( 9405)
  covalent geometry    : angle       0.43179 (12680)
  hydrogen bonds       : bond        0.03651 (  485)
  hydrogen bonds       : angle       4.07262 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 106
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: A  419 LYS cc_start: 0.7842 (ttpt) cc_final: 0.7112 (tppt)
REVERT: A  514 GLN cc_start: 0.7286 (OUTLIER) cc_final: 0.5945 (mp10)
REVERT: A  553 ARG cc_start: 0.7091 (mtm110) cc_final: 0.5839 (mtp85)
REVERT: A  584 GLN cc_start: 0.7349 (OUTLIER) cc_final: 0.6633 (mp10)
REVERT: A  613 GLU cc_start: 0.7654 (OUTLIER) cc_final: 0.7086 (mm-30)
REVERT: A  731 LYS cc_start: 0.7628 (OUTLIER) cc_final: 0.7341 (ptpt)
REVERT: A  757 LYS cc_start: 0.8819 (mttt) cc_final: 0.8061 (mmtm)
REVERT: A  998 LYS cc_start: 0.8006 (mppt) cc_final: 0.7451 (tttp)
REVERT: A 1062 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7231 (mt-10)
REVERT: A 1121 ASP cc_start: 0.8188 (m-30) cc_final: 0.7956 (m-30)
REVERT: A 1137 GLU cc_start: 0.6421 (OUTLIER) cc_final: 0.6058 (mm-30)
REVERT: A 1222 GLU cc_start: 0.7363 (OUTLIER) cc_final: 0.5263 (tm-30)
REVERT: A 1223 LEU cc_start: 0.7776 (mm) cc_final: 0.7461 (mt)
REVERT: A 1228 MET cc_start: 0.7520 (OUTLIER) cc_final: 0.6363 (tpp)
REVERT: A 1291 LYS cc_start: 0.8339 (mttp) cc_final: 0.7871 (tttt)
REVERT: A 1396 SER cc_start: 0.8215 (t) cc_final: 0.7804 (p)
REVERT: A 1416 ARG cc_start: 0.6953 (mtp-110) cc_final: 0.6535 (ttp80)
REVERT: A 1447 ASP cc_start: 0.6861 (t70) cc_final: 0.6579 (t0)
REVERT: A 1465 LYS cc_start: 0.8115 (ttpp) cc_final: 0.7691 (tppt)
REVERT: A 1531 GLN cc_start: 0.7124 (mt0) cc_final: 0.6753 (tp40)
  outliers start: 47
  outliers final: 25
  residues processed: 141
  average time/residue: 0.6398
  time to fit residues: 95.4979
Evaluate side-chains
  135 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 102
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1088 LEU
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1426 TYR
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1528 LEU
Chi-restraints excluded: chain A residue 1533 ARG
Chi-restraints excluded: chain A residue 1554 THR
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 80 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 14 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 16 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 840 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.148143 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.122312 restraints weight = 11825.818|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.27
r_work: 0.3292 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   9405  Z= 0.125
  Angle     :  0.448   8.988  12680  Z= 0.233
  Chirality :  0.041   0.131   1390
  Planarity :  0.003   0.040   1600
  Dihedral  :  7.412  62.586   1251
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 4.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 21.90 %
    Favored  : 73.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.83 (0.26), residues: 1097
  helix:  2.14 (0.21), residues: 617
  sheet:  0.35 (0.48), residues: 110
  loop : -0.04 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 788 
 TYR   0.017   0.001   TYR A1093 
 PHE   0.011   0.001   PHE A1083 
 TRP   0.010   0.001   TRP A1105 
 HIS   0.002   0.001   HIS A 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 9405)
  covalent geometry    : angle       0.44830 (12680)
  hydrogen bonds       : bond        0.04011 (  485)
  hydrogen bonds       : angle       4.09700 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 102
  time to evaluate  : 0.366 
Fit side-chains
REVERT: A  419 LYS cc_start: 0.7862 (ttpt) cc_final: 0.7139 (tppt)
REVERT: A  514 GLN cc_start: 0.7276 (OUTLIER) cc_final: 0.5918 (mp10)
REVERT: A  553 ARG cc_start: 0.7257 (mtm110) cc_final: 0.6012 (mtp85)
REVERT: A  584 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.6545 (mp10)
REVERT: A  613 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7128 (mm-30)
REVERT: A  731 LYS cc_start: 0.7647 (OUTLIER) cc_final: 0.7354 (ptpt)
REVERT: A  757 LYS cc_start: 0.8824 (mttt) cc_final: 0.8062 (mmtm)
REVERT: A  870 LYS cc_start: 0.7834 (OUTLIER) cc_final: 0.7631 (mtpt)
REVERT: A  998 LYS cc_start: 0.8019 (mppt) cc_final: 0.7446 (tttp)
REVERT: A 1062 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7297 (mt-10)
REVERT: A 1121 ASP cc_start: 0.8202 (m-30) cc_final: 0.7977 (m-30)
REVERT: A 1137 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6047 (mm-30)
REVERT: A 1150 ILE cc_start: 0.7589 (mm) cc_final: 0.7383 (mm)
REVERT: A 1222 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.5286 (tm-30)
REVERT: A 1223 LEU cc_start: 0.7787 (mm) cc_final: 0.7475 (mt)
REVERT: A 1228 MET cc_start: 0.7545 (OUTLIER) cc_final: 0.6417 (tpp)
REVERT: A 1291 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7901 (tttt)
REVERT: A 1396 SER cc_start: 0.8222 (t) cc_final: 0.7838 (p)
REVERT: A 1416 ARG cc_start: 0.6951 (OUTLIER) cc_final: 0.6553 (ttp80)
REVERT: A 1447 ASP cc_start: 0.6961 (t70) cc_final: 0.6668 (t0)
REVERT: A 1465 LYS cc_start: 0.8132 (ttpp) cc_final: 0.7731 (tppt)
REVERT: A 1531 GLN cc_start: 0.7072 (mt0) cc_final: 0.6707 (tp40)
  outliers start: 52
  outliers final: 30
  residues processed: 140
  average time/residue: 0.6308
  time to fit residues: 93.7213
Evaluate side-chains
  137 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 96
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  870 LYS
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1416 ARG
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1426 TYR
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1450 SER
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1528 LEU
Chi-restraints excluded: chain A residue 1533 ARG
Chi-restraints excluded: chain A residue 1554 THR
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 82 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 28 optimal weight:    0.4980
   chunk 20 optimal weight:    6.9990
   chunk 104 optimal weight:    0.0370
   chunk 31 optimal weight:    0.7980
   chunk 38 optimal weight:    2.9990
   overall best weight:    0.8662

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

Flipped N/Q/H residues before XYZ refinement:
A 840 ASN
A 899 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.148493 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.122546 restraints weight = 11915.087|
|-----------------------------------------------------------------------------|
r_work (start): 0.3409 rms_B_bonded: 2.29
r_work: 0.3291 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3165 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9405  Z= 0.121
  Angle     :  0.449  10.099  12680  Z= 0.233
  Chirality :  0.040   0.132   1390
  Planarity :  0.003   0.040   1600
  Dihedral  :  7.330  62.390   1251
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 4.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  5.47 %
    Allowed  : 22.09 %
    Favored  : 72.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.85 (0.26), residues: 1097
  helix:  2.15 (0.21), residues: 617
  sheet:  0.36 (0.48), residues: 110
  loop : -0.02 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1226 
 TYR   0.017   0.001   TYR A1093 
 PHE   0.010   0.001   PHE A1083 
 TRP   0.010   0.001   TRP A1105 
 HIS   0.002   0.001   HIS A 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 ( 9405)
  covalent geometry    : angle       0.44917 (12680)
  hydrogen bonds       : bond        0.03921 (  485)
  hydrogen bonds       : angle       4.06711 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 101
  time to evaluate  : 0.490 
Fit side-chains
REVERT: A  419 LYS cc_start: 0.7861 (ttpt) cc_final: 0.7137 (tppt)
REVERT: A  514 GLN cc_start: 0.7322 (OUTLIER) cc_final: 0.5994 (mp10)
REVERT: A  553 ARG cc_start: 0.7238 (OUTLIER) cc_final: 0.5898 (mtp85)
REVERT: A  584 GLN cc_start: 0.7292 (OUTLIER) cc_final: 0.6548 (mp10)
REVERT: A  613 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7113 (mm-30)
REVERT: A  731 LYS cc_start: 0.7622 (OUTLIER) cc_final: 0.7329 (ptpt)
REVERT: A  757 LYS cc_start: 0.8826 (mttt) cc_final: 0.8061 (mmtm)
REVERT: A  870 LYS cc_start: 0.7840 (OUTLIER) cc_final: 0.7636 (mtpt)
REVERT: A  994 GLU cc_start: 0.7638 (OUTLIER) cc_final: 0.7023 (mp0)
REVERT: A  998 LYS cc_start: 0.8009 (mppt) cc_final: 0.7471 (tttp)
REVERT: A 1062 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7303 (mt-10)
REVERT: A 1121 ASP cc_start: 0.8223 (m-30) cc_final: 0.7998 (m-30)
REVERT: A 1137 GLU cc_start: 0.6463 (OUTLIER) cc_final: 0.6099 (mm-30)
REVERT: A 1222 GLU cc_start: 0.7326 (OUTLIER) cc_final: 0.5283 (tm-30)
REVERT: A 1223 LEU cc_start: 0.7798 (mm) cc_final: 0.7472 (mt)
REVERT: A 1228 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.6437 (tpp)
REVERT: A 1266 LYS cc_start: 0.8211 (OUTLIER) cc_final: 0.7741 (mtmm)
REVERT: A 1291 LYS cc_start: 0.8368 (OUTLIER) cc_final: 0.7898 (tttt)
REVERT: A 1396 SER cc_start: 0.8248 (t) cc_final: 0.7856 (p)
REVERT: A 1416 ARG cc_start: 0.6911 (OUTLIER) cc_final: 0.6524 (ttp80)
REVERT: A 1447 ASP cc_start: 0.6917 (t70) cc_final: 0.6580 (t0)
REVERT: A 1465 LYS cc_start: 0.8121 (ttpp) cc_final: 0.7722 (tppt)
REVERT: A 1531 GLN cc_start: 0.7045 (mt0) cc_final: 0.6666 (tp40)
  outliers start: 56
  outliers final: 30
  residues processed: 141
  average time/residue: 0.6202
  time to fit residues: 92.6748
Evaluate side-chains
  142 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 GLU
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  417 THR
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  870 LYS
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1266 LYS
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1416 ARG
Chi-restraints excluded: chain A residue 1424 LEU
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1429 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1528 LEU
Chi-restraints excluded: chain A residue 1533 ARG
Chi-restraints excluded: chain A residue 1554 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 108 optimal weight:    0.8980
   chunk 96 optimal weight:    3.9990
   chunk 100 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 6 optimal weight:    3.9990
   chunk 58 optimal weight:    0.5980
   chunk 90 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 840 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.148439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.123076 restraints weight = 11863.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.3417 rms_B_bonded: 2.25
r_work: 0.3290 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3157 rms_B_bonded: 4.90 restraints_weight: 0.2500
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8151
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9405  Z= 0.115
  Angle     :  0.444  10.899  12680  Z= 0.230
  Chirality :  0.040   0.131   1390
  Planarity :  0.003   0.040   1600
  Dihedral  :  7.179  62.186   1251
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 4.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  5.08 %
    Allowed  : 22.87 %
    Favored  : 72.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.91 (0.26), residues: 1097
  helix:  2.19 (0.21), residues: 617
  sheet:  0.47 (0.48), residues: 109
  loop : -0.01 (0.33), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 788 
 TYR   0.017   0.001   TYR A1093 
 PHE   0.009   0.001   PHE A1083 
 TRP   0.010   0.001   TRP A1105 
 HIS   0.002   0.001   HIS A1494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 9405)
  covalent geometry    : angle       0.44404 (12680)
  hydrogen bonds       : bond        0.03800 (  485)
  hydrogen bonds       : angle       4.02650 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 101
  time to evaluate  : 0.296 
Fit side-chains
REVERT: A  419 LYS cc_start: 0.7973 (ttpt) cc_final: 0.7282 (tppt)
REVERT: A  514 GLN cc_start: 0.7373 (OUTLIER) cc_final: 0.6044 (mp10)
REVERT: A  553 ARG cc_start: 0.7264 (OUTLIER) cc_final: 0.5924 (mtp85)
REVERT: A  584 GLN cc_start: 0.7500 (OUTLIER) cc_final: 0.6751 (mp10)
REVERT: A  613 GLU cc_start: 0.7675 (OUTLIER) cc_final: 0.7105 (mm-30)
REVERT: A  731 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.7388 (ptpt)
REVERT: A  757 LYS cc_start: 0.8825 (mttt) cc_final: 0.8084 (mmtm)
REVERT: A  870 LYS cc_start: 0.7883 (OUTLIER) cc_final: 0.7663 (mtpt)
REVERT: A  994 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7141 (mp0)
REVERT: A  998 LYS cc_start: 0.8057 (mppt) cc_final: 0.7500 (tttp)
REVERT: A 1062 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7288 (mt-10)
REVERT: A 1121 ASP cc_start: 0.8233 (m-30) cc_final: 0.8020 (m-30)
REVERT: A 1137 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6196 (mm-30)
REVERT: A 1200 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8258 (tt0)
REVERT: A 1222 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.5312 (tm-30)
REVERT: A 1223 LEU cc_start: 0.7826 (mm) cc_final: 0.7505 (mt)
REVERT: A 1228 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.6615 (tpp)
REVERT: A 1291 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7965 (tttt)
REVERT: A 1396 SER cc_start: 0.8283 (t) cc_final: 0.7876 (p)
REVERT: A 1416 ARG cc_start: 0.6983 (OUTLIER) cc_final: 0.6600 (ttp80)
REVERT: A 1447 ASP cc_start: 0.6961 (t70) cc_final: 0.6593 (t0)
REVERT: A 1465 LYS cc_start: 0.8191 (ttpp) cc_final: 0.7809 (tppt)
REVERT: A 1471 MET cc_start: 0.7827 (OUTLIER) cc_final: 0.6738 (mmt)
REVERT: A 1531 GLN cc_start: 0.7064 (mt0) cc_final: 0.6728 (mm110)
REVERT: A 1570 VAL cc_start: 0.7588 (t) cc_final: 0.7279 (m)
  outliers start: 52
  outliers final: 26
  residues processed: 138
  average time/residue: 0.6315
  time to fit residues: 92.4722
Evaluate side-chains
  138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 97
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  390 GLU
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  478 GLU
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue  870 LYS
Chi-restraints excluded: chain A residue  994 GLU
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1200 GLU
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1416 ARG
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1429 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1471 MET
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1533 ARG
Chi-restraints excluded: chain A residue 1554 THR
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 38 optimal weight:    8.9990
   chunk 52 optimal weight:    0.0030
   chunk 69 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 84 optimal weight:    4.9990
   chunk 90 optimal weight:    3.9990
   chunk 13 optimal weight:    2.9990
   chunk 2 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 106 optimal weight:    3.9990
   overall best weight:    1.1194

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

Flipped N/Q/H residues before XYZ refinement:
A 424 GLN
A 840 ASN
A1193 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.147204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.121882 restraints weight = 11910.295|
|-----------------------------------------------------------------------------|
r_work (start): 0.3398 rms_B_bonded: 2.24
r_work: 0.3271 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work: 0.3139 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.3139
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8170
moved from start:          0.1998

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9405  Z= 0.146
  Angle     :  0.477  11.515  12680  Z= 0.247
  Chirality :  0.041   0.148   1390
  Planarity :  0.004   0.040   1600
  Dihedral  :  7.234  64.249   1250
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 4.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 23.26 %
    Favored  : 71.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.78 (0.26), residues: 1097
  helix:  2.10 (0.21), residues: 617
  sheet:  0.39 (0.48), residues: 109
  loop : -0.08 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 788 
 TYR   0.016   0.001   TYR A1093 
 PHE   0.012   0.001   PHE A1083 
 TRP   0.011   0.001   TRP A1105 
 HIS   0.003   0.001   HIS A 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 ( 9405)
  covalent geometry    : angle       0.47662 (12680)
  hydrogen bonds       : bond        0.04224 (  485)
  hydrogen bonds       : angle       4.11244 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 99
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  419 LYS cc_start: 0.7966 (ttpt) cc_final: 0.7347 (tttp)
REVERT: A  514 GLN cc_start: 0.7427 (OUTLIER) cc_final: 0.6009 (mp10)
REVERT: A  553 ARG cc_start: 0.7287 (OUTLIER) cc_final: 0.5928 (mtp85)
REVERT: A  584 GLN cc_start: 0.7461 (OUTLIER) cc_final: 0.6713 (mp10)
REVERT: A  613 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7102 (mm-30)
REVERT: A  731 LYS cc_start: 0.7734 (OUTLIER) cc_final: 0.7459 (ptpt)
REVERT: A  757 LYS cc_start: 0.8843 (mttt) cc_final: 0.8089 (mmtm)
REVERT: A  998 LYS cc_start: 0.8070 (mppt) cc_final: 0.7513 (tttp)
REVERT: A 1062 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7309 (mt-10)
REVERT: A 1121 ASP cc_start: 0.8236 (m-30) cc_final: 0.8024 (m-30)
REVERT: A 1137 GLU cc_start: 0.6541 (OUTLIER) cc_final: 0.6142 (mm-30)
REVERT: A 1222 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.5292 (tm-30)
REVERT: A 1223 LEU cc_start: 0.7825 (mm) cc_final: 0.7535 (mt)
REVERT: A 1228 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6665 (tpp)
REVERT: A 1266 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7855 (mtmm)
REVERT: A 1291 LYS cc_start: 0.8444 (OUTLIER) cc_final: 0.7974 (tttt)
REVERT: A 1396 SER cc_start: 0.8300 (t) cc_final: 0.7897 (p)
REVERT: A 1416 ARG cc_start: 0.7000 (OUTLIER) cc_final: 0.6640 (ttp80)
REVERT: A 1447 ASP cc_start: 0.6973 (t70) cc_final: 0.6625 (t0)
REVERT: A 1465 LYS cc_start: 0.8218 (ttpp) cc_final: 0.7792 (tppt)
REVERT: A 1531 GLN cc_start: 0.7045 (mt0) cc_final: 0.6692 (mm110)
  outliers start: 49
  outliers final: 24
  residues processed: 132
  average time/residue: 0.6579
  time to fit residues: 92.0739
Evaluate side-chains
  133 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 97
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  403 ASP
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  584 GLN
Chi-restraints excluded: chain A residue  613 GLU
Chi-restraints excluded: chain A residue  634 SER
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1266 LYS
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1416 ARG
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1429 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1469 LYS
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1533 ARG
Chi-restraints excluded: chain A residue 1554 THR
Chi-restraints excluded: chain A residue 1558 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 44 optimal weight:    0.0570
   chunk 49 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 52 optimal weight:    0.9980
   chunk 5 optimal weight:    0.5980
   chunk 98 optimal weight:    0.6980
   chunk 74 optimal weight:    0.9990
   chunk 92 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 87 optimal weight:    3.9990
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 840 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.150443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.124645 restraints weight = 11778.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3422 rms_B_bonded: 2.27
r_work: 0.3306 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.3179 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8031
moved from start:          0.2128

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   9405  Z= 0.093
  Angle     :  0.436  12.069  12680  Z= 0.225
  Chirality :  0.040   0.138   1390
  Planarity :  0.003   0.040   1600
  Dihedral  :  6.801  59.979   1247
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 24.54 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.06 (0.26), residues: 1097
  helix:  2.32 (0.21), residues: 617
  sheet:  0.42 (0.48), residues: 110
  loop :  0.09 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1173 
 TYR   0.017   0.001   TYR A1093 
 PHE   0.009   0.001   PHE A1216 
 TRP   0.009   0.001   TRP A1105 
 HIS   0.002   0.001   HIS A1059 

Details of bonding type rmsd
  covalent geometry    : bond        0.00206 ( 9405)
  covalent geometry    : angle       0.43605 (12680)
  hydrogen bonds       : bond        0.03385 (  485)
  hydrogen bonds       : angle       3.93150 ( 1407)

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

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

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2194 Ramachandran restraints generated.
    1097 Oldfield, 0 Emsley, 1097 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 101
  time to evaluate  : 0.384 
Fit side-chains
REVERT: A  419 LYS cc_start: 0.7837 (ttpt) cc_final: 0.7118 (tppt)
REVERT: A  514 GLN cc_start: 0.7166 (OUTLIER) cc_final: 0.5960 (mp10)
REVERT: A  553 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.5775 (mtp85)
REVERT: A  731 LYS cc_start: 0.7515 (OUTLIER) cc_final: 0.7246 (ptpt)
REVERT: A  757 LYS cc_start: 0.8815 (mttt) cc_final: 0.8040 (mmtm)
REVERT: A  998 LYS cc_start: 0.7983 (mppt) cc_final: 0.7425 (tttp)
REVERT: A 1062 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7223 (mt-10)
REVERT: A 1121 ASP cc_start: 0.8217 (m-30) cc_final: 0.7998 (m-30)
REVERT: A 1137 GLU cc_start: 0.6498 (OUTLIER) cc_final: 0.6082 (mm-30)
REVERT: A 1157 GLU cc_start: 0.7806 (tt0) cc_final: 0.7568 (tt0)
REVERT: A 1222 GLU cc_start: 0.7213 (OUTLIER) cc_final: 0.5233 (tm-30)
REVERT: A 1223 LEU cc_start: 0.7758 (mm) cc_final: 0.7471 (mt)
REVERT: A 1228 MET cc_start: 0.7483 (OUTLIER) cc_final: 0.6404 (tpp)
REVERT: A 1272 ASP cc_start: 0.7703 (m-30) cc_final: 0.7472 (m-30)
REVERT: A 1291 LYS cc_start: 0.8354 (OUTLIER) cc_final: 0.7891 (tttt)
REVERT: A 1396 SER cc_start: 0.8259 (t) cc_final: 0.7812 (p)
REVERT: A 1416 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6463 (ttp80)
REVERT: A 1447 ASP cc_start: 0.6940 (t70) cc_final: 0.6551 (t0)
REVERT: A 1465 LYS cc_start: 0.8079 (ttpp) cc_final: 0.7674 (tppt)
REVERT: A 1531 GLN cc_start: 0.7046 (mt0) cc_final: 0.6659 (mm110)
REVERT: A 1584 TYR cc_start: 0.7467 (m-80) cc_final: 0.7191 (m-80)
  outliers start: 37
  outliers final: 20
  residues processed: 128
  average time/residue: 0.6342
  time to fit residues: 86.2799
Evaluate side-chains
  130 residues out of total 1023 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  500 LEU
Chi-restraints excluded: chain A residue  514 GLN
Chi-restraints excluded: chain A residue  526 SER
Chi-restraints excluded: chain A residue  553 ARG
Chi-restraints excluded: chain A residue  678 SER
Chi-restraints excluded: chain A residue  731 LYS
Chi-restraints excluded: chain A residue  751 LEU
Chi-restraints excluded: chain A residue  801 PHE
Chi-restraints excluded: chain A residue  847 ILE
Chi-restraints excluded: chain A residue 1011 MET
Chi-restraints excluded: chain A residue 1020 THR
Chi-restraints excluded: chain A residue 1062 GLU
Chi-restraints excluded: chain A residue 1137 GLU
Chi-restraints excluded: chain A residue 1160 SER
Chi-restraints excluded: chain A residue 1191 THR
Chi-restraints excluded: chain A residue 1222 GLU
Chi-restraints excluded: chain A residue 1228 MET
Chi-restraints excluded: chain A residue 1291 LYS
Chi-restraints excluded: chain A residue 1345 SER
Chi-restraints excluded: chain A residue 1355 GLN
Chi-restraints excluded: chain A residue 1416 ARG
Chi-restraints excluded: chain A residue 1427 GLN
Chi-restraints excluded: chain A residue 1429 SER
Chi-restraints excluded: chain A residue 1436 SER
Chi-restraints excluded: chain A residue 1517 VAL
Chi-restraints excluded: chain A residue 1526 LEU
Chi-restraints excluded: chain A residue 1533 ARG
Chi-restraints excluded: chain A residue 1554 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 42 optimal weight:    0.9980
   chunk 45 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 30 optimal weight:    0.6980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 840 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.148730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.123007 restraints weight = 11698.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3415 rms_B_bonded: 2.25
r_work: 0.3301 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3175 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3175
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9405  Z= 0.122
  Angle     :  0.461  11.937  12680  Z= 0.238
  Chirality :  0.041   0.135   1390
  Planarity :  0.003   0.040   1600
  Dihedral  :  6.865  63.252   1246
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 24.83 %
    Favored  : 71.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.97 (0.26), residues: 1097
  helix:  2.25 (0.21), residues: 617
  sheet:  0.34 (0.48), residues: 110
  loop :  0.05 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 788 
 TYR   0.016   0.001   TYR A1093 
 PHE   0.011   0.001   PHE A1083 
 TRP   0.010   0.001   TRP A1105 
 HIS   0.002   0.001   HIS A 737 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 9405)
  covalent geometry    : angle       0.46095 (12680)
  hydrogen bonds       : bond        0.03888 (  485)
  hydrogen bonds       : angle       4.01138 ( 1407)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3397.17 seconds
wall clock time: 58 minutes 37.16 seconds (3517.16 seconds total)