Starting phenix.real_space_refine
on Wed Jun 11 05:21:23 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zeq_60043/06_2025/8zeq_60043.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zeq_60043/06_2025/8zeq_60043.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.36
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zeq_60043/06_2025/8zeq_60043.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zeq_60043/06_2025/8zeq_60043.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zeq_60043/06_2025/8zeq_60043.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zeq_60043/06_2025/8zeq_60043.cif"
  }
  resolution = 3.36
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.066
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      70      5.16       5
     C    7840      2.51       5
     N    2124      2.21       5
     O    2260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12294
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1532, 12294
          Classifications: {'peptide': 1532}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 85, 'TRANS': 1446}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1}
          Unresolved non-hydrogen planarities: 4
  Time building chain proxies: 7.35, per 1000 atoms: 0.60
  Number of scatterers: 12294
  At special positions: 0
  Unit cell: (82.8, 131.56, 158.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      70     16.00
     O    2260      8.00
     N    2124      7.00
     C    7840      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.78
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2872

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      38.7% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 40
      removed outlier: 4.004A  pdb=" N   GLN A  40 " --> pdb=" O   PRO A  37 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 138
      removed outlier: 3.603A  pdb=" N   GLY A 138 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 143 through 154
    Processing helix  chain 'A' and resid 193 through 209
    Processing helix  chain 'A' and resid 231 through 235
      removed outlier: 3.766A  pdb=" N   CYS A 234 " --> pdb=" O   HIS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 263
    Processing helix  chain 'A' and resid 279 through 296
      removed outlier: 3.626A  pdb=" N   SER A 283 " --> pdb=" O   HIS A 279 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ASP A 291 " --> pdb=" O   ILE A 287 " (cutoff:3.500A)
      Proline residue:  A 294  - end of helix
    Processing helix  chain 'A' and resid 297 through 316
    Processing helix  chain 'A' and resid 337 through 341
      removed outlier: 3.939A  pdb=" N   TYR A 341 " --> pdb=" O   ASP A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 350 through 357
    Processing helix  chain 'A' and resid 363 through 409
      removed outlier: 3.688A  pdb=" N   TYR A 391 " --> pdb=" O   ARG A 387 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   HIS A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 441 through 447
    Processing helix  chain 'A' and resid 448 through 454
      removed outlier: 4.054A  pdb=" N   PHE A 454 " --> pdb=" O   ASN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 482
    Processing helix  chain 'A' and resid 498 through 501
    Processing helix  chain 'A' and resid 502 through 520
    Processing helix  chain 'A' and resid 532 through 547
      removed outlier: 3.721A  pdb=" N   ALA A 536 " --> pdb=" O   PRO A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 572
      removed outlier: 4.275A  pdb=" N   ASP A 564 " --> pdb=" O   SER A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 596
    Processing helix  chain 'A' and resid 630 through 635
      removed outlier: 3.602A  pdb=" N   HIS A 634 " --> pdb=" O   CYS A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 636 through 638
      No H-bonds generated for 'chain 'A' and resid 636 through 638'
    Processing helix  chain 'A' and resid 639 through 649
      removed outlier: 3.621A  pdb=" N   MET A 649 " --> pdb=" O   THR A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 662
      removed outlier: 4.159A  pdb=" N   GLU A 662 " --> pdb=" O   ARG A 658 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 658 through 662'
    Processing helix  chain 'A' and resid 698 through 716
    Processing helix  chain 'A' and resid 853 through 855
      No H-bonds generated for 'chain 'A' and resid 853 through 855'
    Processing helix  chain 'A' and resid 856 through 869
    Processing helix  chain 'A' and resid 892 through 898
      removed outlier: 3.845A  pdb=" N   SER A 897 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG A 898 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 900 through 905
    Processing helix  chain 'A' and resid 912 through 918
    Processing helix  chain 'A' and resid 935 through 947
      removed outlier: 3.610A  pdb=" N   LEU A 939 " --> pdb=" O   GLY A 935 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   VAL A 942 " --> pdb=" O   GLY A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 963
      removed outlier: 3.871A  pdb=" N   GLY A 963 " --> pdb=" O   ASN A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 964 through 975
      removed outlier: 3.553A  pdb=" N   ASP A 968 " --> pdb=" O   ASP A 964 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 979 through 996
    Processing helix  chain 'A' and resid 1002 through 1025
      removed outlier: 3.876A  pdb=" N   TYR A1006 " --> pdb=" O   LEU A1002 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1048
      removed outlier: 3.620A  pdb=" N   LYS A1038 " --> pdb=" O   SER A1034 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   CYS A1048 " --> pdb=" O   SER A1044 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1114
    Processing helix  chain 'A' and resid 1116 through 1131
    Processing helix  chain 'A' and resid 1153 through 1168
    Processing helix  chain 'A' and resid 1170 through 1174
      removed outlier: 4.117A  pdb=" N   ASP A1173 " --> pdb=" O   ASN A1170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1199 through 1214
      removed outlier: 3.891A  pdb=" N   VAL A1203 " --> pdb=" O   PRO A1199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1284 through 1303
      removed outlier: 3.629A  pdb=" N   LYS A1303 " --> pdb=" O   GLU A1299 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1323 through 1339
      removed outlier: 3.597A  pdb=" N   TRP A1327 " --> pdb=" O   SER A1323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1381 through 1388
    Processing helix  chain 'A' and resid 1395 through 1405
    Processing helix  chain 'A' and resid 1456 through 1470
    Processing helix  chain 'A' and resid 1470 through 1494
      removed outlier: 3.712A  pdb=" N   THR A1474 " --> pdb=" O   GLY A1470 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ALA A1475 " --> pdb=" O   PRO A1471 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LYS A1476 " --> pdb=" O   GLU A1472 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A1494 " --> pdb=" O   VAL A1490 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1522 through 1532
    Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34
      removed outlier: 4.246A  pdb=" N   ARG A 610 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ILE A   9 " --> pdb=" O   ARG A 610 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 63 through 64
      removed outlier: 3.795A  pdb=" N   THR A  45 " --> pdb=" O   LEU A  96 " (cutoff:3.500A)
      removed outlier: 6.919A  pdb=" N   TYR A  93 " --> pdb=" O   GLY A 104 " (cutoff:3.500A)
      removed outlier: 4.764A  pdb=" N   GLY A 104 " --> pdb=" O   TYR A  93 " (cutoff:3.500A)
      removed outlier: 7.842A  pdb=" N   PHE A  95 " --> pdb=" O   SER A 102 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   SER A 102 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   GLU A 100 " --> pdb=" O   GLN A  97 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 114 through 115
      removed outlier: 3.767A  pdb=" N   VAL A 115 " --> pdb=" O   HIS A 120 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   HIS A 120 " --> pdb=" O   VAL A 115 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 211 through 213
      removed outlier: 5.984A  pdb=" N   THR A 128 " --> pdb=" O   MET A 157 " (cutoff:3.500A)
      removed outlier: 7.276A  pdb=" N   HIS A 159 " --> pdb=" O   THR A 128 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   GLN A 130 " --> pdb=" O   HIS A 159 " (cutoff:3.500A)
      removed outlier: 5.682A  pdb=" N   LEU A 129 " --> pdb=" O   SER A 656 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 430 through 431
      removed outlier: 4.208A  pdb=" N   THR A 431 " --> pdb=" O   MET A 456 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   MET A 456 " --> pdb=" O   THR A 431 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 522 through 524
      removed outlier: 3.732A  pdb=" N   VAL A 553 " --> pdb=" O   VAL A 523 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ILE A 577 " --> pdb=" O   ALA A 554 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   MET A 622 " --> pdb=" O   ARG A 578 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 599 through 600
      removed outlier: 5.525A  pdb=" N   GLU A 599 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 731 through 732
      removed outlier: 3.912A  pdb=" N   VAL A 732 " --> pdb=" O   ALA A 745 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   ALA A 745 " --> pdb=" O   VAL A 732 " (cutoff:3.500A)
      removed outlier: 7.242A  pdb=" N   ILE A 847 " --> pdb=" O   VAL A 775 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   VAL A 775 " --> pdb=" O   ILE A 847 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   ARG A 849 " --> pdb=" O   GLU A 773 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LYS A 771 " --> pdb=" O   SER A 851 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 767 through 769
      removed outlier: 6.607A  pdb=" N   GLU A 830 " --> pdb=" O   LYS A 826 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   LYS A 826 " --> pdb=" O   GLU A 830 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLY A 822 " --> pdb=" O   GLU A 834 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   GLU A 836 " --> pdb=" O   GLN A 820 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   GLN A 820 " --> pdb=" O   GLU A 836 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 780 through 783
      removed outlier: 3.745A  pdb=" N   ILE A 782 " --> pdb=" O   THR A 803 " (cutoff:3.500A)
      removed outlier: 4.268A  pdb=" N   THR A 803 " --> pdb=" O   ILE A 782 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1068 through 1070
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1314 through 1315

    414 hydrogen bonds defined for protein.
    1200 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: 4.24

  Time building geometry restraints manager: 3.36 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 4045
        1.35 -     1.46: 2908
        1.46 -     1.58: 5559
        1.58 -     1.70: 0
        1.70 -     1.82: 102
  Bond restraints: 12614
  Sorted by residual:
  bond pdb=" CA  ASN A1304 "
       pdb=" CB  ASN A1304 "
    ideal  model  delta    sigma   weight residual
    1.530  1.550 -0.020 1.69e-02 3.50e+03 1.40e+00
  bond pdb=" CB  ASN A1304 "
       pdb=" CG  ASN A1304 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 2.50e-02 1.60e+03 1.37e+00
  bond pdb=" CB  ASP A 184 "
       pdb=" CG  ASP A 184 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.83e-01
  bond pdb=" CB  MET A 350 "
       pdb=" CG  MET A 350 "
    ideal  model  delta    sigma   weight residual
    1.520  1.548 -0.028 3.00e-02 1.11e+03 8.59e-01
  bond pdb=" CB  ASP A 541 "
       pdb=" CG  ASP A 541 "
    ideal  model  delta    sigma   weight residual
    1.516  1.538 -0.022 2.50e-02 1.60e+03 7.51e-01
  ... (remaining 12609 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 16893
        1.70 -     3.41: 193
        3.41 -     5.11: 25
        5.11 -     6.82: 8
        6.82 -     8.52: 3
  Bond angle restraints: 17122
  Sorted by residual:
  angle pdb=" N   GLU A 674 "
        pdb=" CA  GLU A 674 "
        pdb=" C   GLU A 674 "
      ideal   model   delta    sigma   weight residual
     114.56  110.88    3.68 1.27e+00 6.20e-01 8.38e+00
  angle pdb=" CB  MET A 350 "
        pdb=" CG  MET A 350 "
        pdb=" SD  MET A 350 "
      ideal   model   delta    sigma   weight residual
     112.70  121.22   -8.52 3.00e+00 1.11e-01 8.07e+00
  angle pdb=" CA  MET A 350 "
        pdb=" CB  MET A 350 "
        pdb=" CG  MET A 350 "
      ideal   model   delta    sigma   weight residual
     114.10  119.20   -5.10 2.00e+00 2.50e-01 6.50e+00
  angle pdb=" CB  MET A 581 "
        pdb=" CG  MET A 581 "
        pdb=" SD  MET A 581 "
      ideal   model   delta    sigma   weight residual
     112.70  120.21   -7.51 3.00e+00 1.11e-01 6.26e+00
  angle pdb=" C   LYS A1303 "
        pdb=" N   ASN A1304 "
        pdb=" CA  ASN A1304 "
      ideal   model   delta    sigma   weight residual
     121.54  126.26   -4.72 1.91e+00 2.74e-01 6.12e+00
  ... (remaining 17117 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.14: 6137
       16.14 -    32.28: 934
       32.28 -    48.42: 362
       48.42 -    64.56: 81
       64.56 -    80.70: 31
  Dihedral angle restraints: 7545
    sinusoidal: 3079
      harmonic: 4466
  Sorted by residual:
  dihedral pdb=" CG  ARG A1315 "
           pdb=" CD  ARG A1315 "
           pdb=" NE  ARG A1315 "
           pdb=" CZ  ARG A1315 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.73   44.73     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" CA  ASP A1187 "
           pdb=" CB  ASP A1187 "
           pdb=" CG  ASP A1187 "
           pdb=" OD1 ASP A1187 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -84.47   54.47     1      2.00e+01 2.50e-03 1.01e+01
  dihedral pdb=" CA  ASP A1102 "
           pdb=" CB  ASP A1102 "
           pdb=" CG  ASP A1102 "
           pdb=" OD1 ASP A1102 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -83.69   53.69     1      2.00e+01 2.50e-03 9.79e+00
  ... (remaining 7542 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.033: 1269
       0.033 -    0.066: 380
       0.066 -    0.099: 121
       0.099 -    0.132: 66
       0.132 -    0.165: 1
  Chirality restraints: 1837
  Sorted by residual:
  chirality pdb=" CA  ASN A1304 "
            pdb=" N   ASN A1304 "
            pdb=" C   ASN A1304 "
            pdb=" CB  ASN A1304 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.80e-01
  chirality pdb=" CA  ILE A 768 "
            pdb=" N   ILE A 768 "
            pdb=" C   ILE A 768 "
            pdb=" CB  ILE A 768 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.91e-01
  chirality pdb=" CA  ILE A 358 "
            pdb=" N   ILE A 358 "
            pdb=" C   ILE A 358 "
            pdb=" CB  ILE A 358 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.84e-01
  ... (remaining 1834 not shown)

  Planarity restraints: 2226
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A1448 "   -0.034 5.00e-02 4.00e+02   5.14e-02 4.23e+00
        pdb=" N   PRO A1449 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A1449 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A1449 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 763 "    0.020 5.00e-02 4.00e+02   3.01e-02 1.45e+00
        pdb=" N   PRO A 764 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO A 764 "    0.015 5.00e-02 4.00e+02
        pdb=" CD  PRO A 764 "    0.017 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG A1220 "   -0.005 2.00e-02 2.50e+03   1.07e-02 1.15e+00
        pdb=" C   ARG A1220 "    0.019 2.00e-02 2.50e+03
        pdb=" O   ARG A1220 "   -0.007 2.00e-02 2.50e+03
        pdb=" N   ASN A1221 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 2223 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.78: 2622
        2.78 -     3.31: 10773
        3.31 -     3.84: 19597
        3.84 -     4.37: 19720
        4.37 -     4.90: 35867
  Nonbonded interactions: 88579
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1503 "
            pdb=" NE2 GLN A1509 "
     model   vdw
     2.255 3.120
  nonbonded pdb=" O   VAL A 647 "
            pdb=" OG  SER A 654 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" N   GLN A1031 "
            pdb=" OE1 GLN A1031 "
     model   vdw
     2.293 3.120
  nonbonded pdb=" OH  TYR A 155 "
            pdb=" OG  SER A 656 "
     model   vdw
     2.318 3.040
  nonbonded pdb=" ND2 ASN A 905 "
            pdb=" O   VAL A1045 "
     model   vdw
     2.319 3.120
  ... (remaining 88574 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:                  0.010
  Normalize map: mean=0, sd=1:             1.460
  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:          0.440
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     30.030
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.650
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.040
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5729
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  12614  Z= 0.082
  Angle     :  0.451   8.525  17122  Z= 0.224
  Chirality :  0.039   0.165   1837
  Planarity :  0.003   0.051   2226
  Dihedral  : 18.477  80.701   4673
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.99 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 33.28 %
    Favored  : 63.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.23), residues: 1530
  helix:  2.67 (0.24), residues: 518
  sheet:  1.81 (0.64), residues: 83
  loop : -0.51 (0.21), residues: 929

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.000   TRP A1398 
 HIS   0.003   0.000   HIS A1316 
 PHE   0.018   0.000   PHE A 993 
 TYR   0.009   0.000   TYR A 933 
 ARG   0.005   0.000   ARG A 898 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14942 (  414)
  hydrogen bonds       : angle       5.32569 ( 1200)
  covalent geometry    : bond        0.00170 (12614)
  covalent geometry    : angle       0.45144 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 124
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
REVERT: A  125 ASP cc_start: 0.7010 (t0) cc_final: 0.6718 (t0)
REVERT: A  137 LEU cc_start: 0.8100 (mt) cc_final: 0.7407 (mt)
REVERT: A  164 GLN cc_start: 0.7987 (OUTLIER) cc_final: 0.7343 (mm-40)
REVERT: A  220 HIS cc_start: 0.5082 (OUTLIER) cc_final: 0.4309 (p-80)
REVERT: A  281 MET cc_start: 0.2907 (OUTLIER) cc_final: 0.2242 (ppp)
REVERT: A  392 HIS cc_start: -0.1421 (OUTLIER) cc_final: -0.2172 (t70)
REVERT: A  423 HIS cc_start: 0.6935 (m90) cc_final: 0.6656 (m90)
REVERT: A  853 ASP cc_start: 0.4958 (OUTLIER) cc_final: 0.4743 (p0)
REVERT: A  933 TYR cc_start: 0.5389 (p90) cc_final: 0.4244 (p90)
REVERT: A 1230 MET cc_start: 0.4712 (tmm) cc_final: 0.2679 (pmm)
REVERT: A 1233 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5057 (pm20)
REVERT: A 1254 PHE cc_start: 0.6147 (p90) cc_final: 0.5403 (p90)
REVERT: A 1450 GLU cc_start: 0.4918 (mp0) cc_final: 0.4303 (pp20)
REVERT: A 1531 ASP cc_start: 0.7786 (t0) cc_final: 0.7570 (t0)
  outliers start: 46
  outliers final: 37
  residues processed: 165
  average time/residue: 0.2307
  time to fit residues: 58.8318
Evaluate side-chains
  164 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 121
  time to evaluate  : 1.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  164 GLN
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  341 TYR
Chi-restraints excluded: chain A residue  348 VAL
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  409 LEU
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  534 HIS
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  625 THR
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  718 ILE
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  818 VAL
Chi-restraints excluded: chain A residue  853 ASP
Chi-restraints excluded: chain A residue  882 ASP
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  901 LEU
Chi-restraints excluded: chain A residue  924 ASP
Chi-restraints excluded: chain A residue  960 LEU
Chi-restraints excluded: chain A residue 1005 CYS
Chi-restraints excluded: chain A residue 1099 TRP
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1125 LEU
Chi-restraints excluded: chain A residue 1140 LEU
Chi-restraints excluded: chain A residue 1191 LEU
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1233 GLU
Chi-restraints excluded: chain A residue 1248 VAL
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1322 VAL
Chi-restraints excluded: chain A residue 1350 GLU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 ASP
Chi-restraints excluded: chain A residue 1453 TRP
Chi-restraints excluded: chain A residue 1485 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 129 optimal weight:    3.9990
   chunk 115 optimal weight:    1.9990
   chunk 64 optimal weight:    3.9990
   chunk 39 optimal weight:    9.9990
   chunk 78 optimal weight:    7.9990
   chunk 61 optimal weight:    3.9990
   chunk 119 optimal weight:    0.0870
   chunk 46 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 89 optimal weight:    5.9990
   chunk 138 optimal weight:    0.9980
   overall best weight:    2.0164

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
A  84 ASN
A 159 HIS
A 280 HIS
** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1216 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4723 r_free = 0.4723 target = 0.232676 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4388 r_free = 0.4388 target = 0.191456 restraints weight = 18084.030|
|-----------------------------------------------------------------------------|
r_work (start): 0.4341 rms_B_bonded: 3.05
r_work: 0.4136 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.4136
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6665
moved from start:          0.3789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12614  Z= 0.226
  Angle     :  0.696  10.640  17122  Z= 0.361
  Chirality :  0.047   0.174   1837
  Planarity :  0.005   0.053   2226
  Dihedral  :  6.988  57.111   1759
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.34 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  7.18 %
    Allowed  : 28.50 %
    Favored  : 64.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.22), residues: 1530
  helix:  1.85 (0.23), residues: 517
  sheet:  0.70 (0.51), residues: 118
  loop : -0.94 (0.21), residues: 895

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP A1259 
 HIS   0.007   0.001   HIS A1211 
 PHE   0.031   0.002   PHE A1104 
 TYR   0.023   0.002   TYR A1006 
 ARG   0.007   0.001   ARG A  34 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05877 (  414)
  hydrogen bonds       : angle       4.44165 ( 1200)
  covalent geometry    : bond        0.00527 (12614)
  covalent geometry    : angle       0.69586 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 96
    poor density    : 136
  time to evaluate  : 1.317 
Fit side-chains
REVERT: A  125 ASP cc_start: 0.7501 (t0) cc_final: 0.6738 (t0)
REVERT: A  130 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7632 (tp40)
REVERT: A  281 MET cc_start: 0.2592 (OUTLIER) cc_final: 0.2034 (ppp)
REVERT: A  392 HIS cc_start: -0.1671 (OUTLIER) cc_final: -0.2369 (t70)
REVERT: A  469 ARG cc_start: 0.4961 (OUTLIER) cc_final: 0.4749 (ptt90)
REVERT: A  581 MET cc_start: 0.7401 (mmp) cc_final: 0.7001 (mmm)
REVERT: A  711 GLU cc_start: 0.7826 (tt0) cc_final: 0.7619 (tt0)
REVERT: A  757 SER cc_start: 0.6933 (OUTLIER) cc_final: 0.6516 (p)
REVERT: A  816 LYS cc_start: 0.2446 (OUTLIER) cc_final: 0.1176 (ptmm)
REVERT: A  933 TYR cc_start: 0.6930 (OUTLIER) cc_final: 0.6066 (p90)
REVERT: A 1183 TYR cc_start: 0.5043 (OUTLIER) cc_final: 0.4141 (t80)
REVERT: A 1200 LEU cc_start: 0.4842 (OUTLIER) cc_final: 0.4512 (pt)
REVERT: A 1230 MET cc_start: 0.5607 (tmm) cc_final: 0.2926 (ptt)
REVERT: A 1338 LEU cc_start: 0.5903 (tt) cc_final: 0.5497 (mp)
REVERT: A 1450 GLU cc_start: 0.6446 (mt-10) cc_final: 0.4426 (tp30)
REVERT: A 1485 LEU cc_start: 0.7794 (OUTLIER) cc_final: 0.7487 (mt)
REVERT: A 1531 ASP cc_start: 0.7837 (t0) cc_final: 0.7513 (t0)
  outliers start: 96
  outliers final: 45
  residues processed: 221
  average time/residue: 0.2246
  time to fit residues: 75.7577
Evaluate side-chains
  166 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 111
  time to evaluate  : 1.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   25 LEU
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  674 GLU
Chi-restraints excluded: chain A residue  698 ILE
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  804 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  960 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1082 VAL
Chi-restraints excluded: chain A residue 1104 PHE
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1162 GLN
Chi-restraints excluded: chain A residue 1183 TYR
Chi-restraints excluded: chain A residue 1191 LEU
Chi-restraints excluded: chain A residue 1200 LEU
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1290 SER
Chi-restraints excluded: chain A residue 1382 THR
Chi-restraints excluded: chain A residue 1386 VAL
Chi-restraints excluded: chain A residue 1473 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 105 optimal weight:    1.9990
   chunk 131 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 112 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 56 optimal weight:    0.6980
   chunk 37 optimal weight:   20.0000
   chunk 23 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9980
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
A 237 ASN
A 392 HIS
** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 906 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4720 r_free = 0.4720 target = 0.232103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4366 r_free = 0.4366 target = 0.189623 restraints weight = 17736.181|
|-----------------------------------------------------------------------------|
r_work (start): 0.4317 rms_B_bonded: 3.71
r_work: 0.4112 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.4112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.4281

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12614  Z= 0.134
  Angle     :  0.536   9.520  17122  Z= 0.273
  Chirality :  0.042   0.150   1837
  Planarity :  0.004   0.033   2226
  Dihedral  :  5.335  56.708   1707
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.62 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 29.24 %
    Favored  : 65.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.22), residues: 1530
  helix:  2.18 (0.23), residues: 512
  sheet:  0.72 (0.57), residues: 98
  loop : -0.90 (0.21), residues: 920

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1259 
 HIS   0.004   0.001   HIS A1316 
 PHE   0.014   0.001   PHE A1104 
 TYR   0.013   0.001   TYR A 933 
 ARG   0.003   0.000   ARG A 898 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04072 (  414)
  hydrogen bonds       : angle       4.03546 ( 1200)
  covalent geometry    : bond        0.00310 (12614)
  covalent geometry    : angle       0.53563 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 126
  time to evaluate  : 1.258 
Fit side-chains
REVERT: A   82 LYS cc_start: 0.7791 (mppt) cc_final: 0.7525 (mmmm)
REVERT: A  281 MET cc_start: 0.2475 (OUTLIER) cc_final: 0.1925 (ppp)
REVERT: A  392 HIS cc_start: -0.1638 (OUTLIER) cc_final: -0.2227 (t-170)
REVERT: A  469 ARG cc_start: 0.5027 (OUTLIER) cc_final: 0.4586 (ptt90)
REVERT: A  581 MET cc_start: 0.7702 (mmp) cc_final: 0.7232 (mmm)
REVERT: A  757 SER cc_start: 0.7098 (OUTLIER) cc_final: 0.6589 (p)
REVERT: A  783 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6698 (pm20)
REVERT: A  816 LYS cc_start: 0.3081 (OUTLIER) cc_final: 0.1737 (ptmm)
REVERT: A  933 TYR cc_start: 0.6792 (OUTLIER) cc_final: 0.5696 (p90)
REVERT: A  954 HIS cc_start: 0.4902 (OUTLIER) cc_final: 0.4539 (t-90)
REVERT: A 1183 TYR cc_start: 0.5117 (OUTLIER) cc_final: 0.4086 (t80)
REVERT: A 1212 MET cc_start: 0.8079 (tpt) cc_final: 0.7866 (tpt)
REVERT: A 1230 MET cc_start: 0.5447 (tmm) cc_final: 0.2830 (ptt)
REVERT: A 1338 LEU cc_start: 0.5725 (tt) cc_final: 0.5316 (mp)
REVERT: A 1406 LYS cc_start: 0.7093 (tptt) cc_final: 0.6569 (pttp)
REVERT: A 1450 GLU cc_start: 0.6746 (OUTLIER) cc_final: 0.4907 (tp30)
  outliers start: 75
  outliers final: 36
  residues processed: 191
  average time/residue: 0.2183
  time to fit residues: 63.1183
Evaluate side-chains
  150 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 104
  time to evaluate  : 1.288 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue   88 SER
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  783 GLU
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  954 HIS
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  960 LEU
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1047 LEU
Chi-restraints excluded: chain A residue 1104 PHE
Chi-restraints excluded: chain A residue 1114 THR
Chi-restraints excluded: chain A residue 1162 GLN
Chi-restraints excluded: chain A residue 1183 TYR
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1450 GLU
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 139 optimal weight:    8.9990
   chunk 59 optimal weight:    0.2980
   chunk 35 optimal weight:    9.9990
   chunk 110 optimal weight:    0.9980
   chunk 70 optimal weight:    2.9990
   chunk 14 optimal weight:    0.0970
   chunk 90 optimal weight:    3.9990
   chunk 36 optimal weight:    4.9990
   chunk 138 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
A   3 HIS
A 626 HIS
** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 906 GLN
A1133 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4670 r_free = 0.4670 target = 0.226682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4318 r_free = 0.4318 target = 0.184797 restraints weight = 18140.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.4268 rms_B_bonded: 3.46
r_work: 0.4066 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6772
moved from start:          0.5248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12614  Z= 0.151
  Angle     :  0.580  10.984  17122  Z= 0.297
  Chirality :  0.043   0.195   1837
  Planarity :  0.004   0.045   2226
  Dihedral  :  5.390  58.337   1702
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.86 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  6.21 %
    Allowed  : 28.50 %
    Favored  : 65.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.14 (0.22), residues: 1530
  helix:  2.05 (0.23), residues: 509
  sheet:  0.30 (0.56), residues: 102
  loop : -1.14 (0.20), residues: 919

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A1520 
 HIS   0.005   0.001   HIS A1340 
 PHE   0.020   0.001   PHE A1104 
 TYR   0.021   0.001   TYR A1530 
 ARG   0.004   0.000   ARG A1000 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04694 (  414)
  hydrogen bonds       : angle       4.11273 ( 1200)
  covalent geometry    : bond        0.00347 (12614)
  covalent geometry    : angle       0.58025 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 125
  time to evaluate  : 1.368 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.8273 (OUTLIER) cc_final: 0.7266 (mt0)
REVERT: A  220 HIS cc_start: 0.4685 (OUTLIER) cc_final: 0.3733 (p-80)
REVERT: A  281 MET cc_start: 0.2348 (OUTLIER) cc_final: 0.1829 (ppp)
REVERT: A  316 LEU cc_start: 0.5630 (OUTLIER) cc_final: 0.4795 (tt)
REVERT: A  392 HIS cc_start: -0.1591 (OUTLIER) cc_final: -0.2318 (t-170)
REVERT: A  469 ARG cc_start: 0.5508 (OUTLIER) cc_final: 0.5123 (ptt90)
REVERT: A  581 MET cc_start: 0.8100 (mmp) cc_final: 0.7704 (mmt)
REVERT: A  620 LEU cc_start: 0.8485 (OUTLIER) cc_final: 0.8138 (mp)
REVERT: A  757 SER cc_start: 0.7112 (OUTLIER) cc_final: 0.6560 (p)
REVERT: A  783 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7201 (pm20)
REVERT: A  816 LYS cc_start: 0.3857 (OUTLIER) cc_final: 0.2480 (ptmm)
REVERT: A  933 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.5708 (p90)
REVERT: A  954 HIS cc_start: 0.4955 (OUTLIER) cc_final: 0.4691 (t-90)
REVERT: A 1002 LEU cc_start: 0.4479 (OUTLIER) cc_final: 0.4267 (pp)
REVERT: A 1183 TYR cc_start: 0.5454 (OUTLIER) cc_final: 0.4043 (t80)
REVERT: A 1200 LEU cc_start: 0.5338 (OUTLIER) cc_final: 0.4812 (pt)
REVERT: A 1209 GLN cc_start: 0.6450 (tp40) cc_final: 0.6086 (mt0)
REVERT: A 1230 MET cc_start: 0.5778 (tmm) cc_final: 0.2869 (ptt)
REVERT: A 1338 LEU cc_start: 0.5635 (tt) cc_final: 0.5270 (mp)
REVERT: A 1406 LYS cc_start: 0.7110 (tptt) cc_final: 0.6609 (pttp)
REVERT: A 1531 ASP cc_start: 0.8089 (t0) cc_final: 0.7830 (t0)
  outliers start: 83
  outliers final: 53
  residues processed: 197
  average time/residue: 0.2248
  time to fit residues: 67.4134
Evaluate side-chains
  174 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 68
    poor density    : 106
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  533 LEU
Chi-restraints excluded: chain A residue  534 HIS
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  783 GLU
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  804 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  954 HIS
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  960 LEU
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1104 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1114 THR
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1183 TYR
Chi-restraints excluded: chain A residue 1200 LEU
Chi-restraints excluded: chain A residue 1211 HIS
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1256 CYS
Chi-restraints excluded: chain A residue 1282 SER
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 86 optimal weight:    5.9990
   chunk 113 optimal weight:    2.9990
   chunk 83 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 87 optimal weight:    0.0980
   chunk 70 optimal weight:    5.9990
   chunk 34 optimal weight:   10.0000
   chunk 58 optimal weight:    0.0170
   chunk 122 optimal weight:    0.5980
   chunk 79 optimal weight:    0.2980
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
A 626 HIS
A 857 GLN
** A 905 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1209 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4681 r_free = 0.4681 target = 0.227836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.185758 restraints weight = 18138.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.4281 rms_B_bonded: 3.76
r_work: 0.4073 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6753
moved from start:          0.5421

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  12614  Z= 0.115
  Angle     :  0.529   9.401  17122  Z= 0.267
  Chirality :  0.041   0.153   1837
  Planarity :  0.004   0.036   2226
  Dihedral  :  5.176  57.227   1702
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  5.88 %
    Favored  : 93.99 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 29.02 %
    Favored  : 65.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.22 (0.22), residues: 1530
  helix:  2.22 (0.23), residues: 509
  sheet:  0.14 (0.51), residues: 121
  loop : -1.16 (0.20), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1453 
 HIS   0.004   0.001   HIS A1316 
 PHE   0.022   0.001   PHE A1235 
 TYR   0.017   0.001   TYR A1530 
 ARG   0.003   0.000   ARG A1097 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03715 (  414)
  hydrogen bonds       : angle       3.91670 ( 1200)
  covalent geometry    : bond        0.00262 (12614)
  covalent geometry    : angle       0.52864 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 109
  time to evaluate  : 1.416 
Fit side-chains
REVERT: A  220 HIS cc_start: 0.4673 (OUTLIER) cc_final: 0.3764 (p-80)
REVERT: A  237 ASN cc_start: 0.6800 (OUTLIER) cc_final: 0.6541 (m110)
REVERT: A  281 MET cc_start: 0.2613 (OUTLIER) cc_final: 0.2002 (ppp)
REVERT: A  316 LEU cc_start: 0.5621 (OUTLIER) cc_final: 0.4822 (tt)
REVERT: A  392 HIS cc_start: -0.1913 (OUTLIER) cc_final: -0.2840 (t-170)
REVERT: A  469 ARG cc_start: 0.5443 (OUTLIER) cc_final: 0.5033 (ptt90)
REVERT: A  581 MET cc_start: 0.8015 (mmp) cc_final: 0.7773 (mmt)
REVERT: A  620 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8065 (mp)
REVERT: A  757 SER cc_start: 0.7077 (OUTLIER) cc_final: 0.6533 (p)
REVERT: A  783 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7116 (pm20)
REVERT: A  816 LYS cc_start: 0.4064 (OUTLIER) cc_final: 0.2643 (ptmm)
REVERT: A  933 TYR cc_start: 0.6767 (OUTLIER) cc_final: 0.5730 (p90)
REVERT: A  954 HIS cc_start: 0.4789 (OUTLIER) cc_final: 0.4558 (t-90)
REVERT: A 1031 GLN cc_start: 0.6764 (mp10) cc_final: 0.6517 (mp10)
REVERT: A 1183 TYR cc_start: 0.5418 (OUTLIER) cc_final: 0.3901 (t80)
REVERT: A 1209 GLN cc_start: 0.6389 (OUTLIER) cc_final: 0.6070 (mt0)
REVERT: A 1230 MET cc_start: 0.5669 (tmm) cc_final: 0.2784 (ptt)
REVERT: A 1338 LEU cc_start: 0.5554 (tt) cc_final: 0.5251 (mp)
  outliers start: 75
  outliers final: 39
  residues processed: 174
  average time/residue: 0.2186
  time to fit residues: 58.1270
Evaluate side-chains
  156 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 103
  time to evaluate  : 1.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  469 ARG
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  783 GLU
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  804 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  954 HIS
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  960 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1104 PHE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1114 THR
Chi-restraints excluded: chain A residue 1183 TYR
Chi-restraints excluded: chain A residue 1209 GLN
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1282 SER
Chi-restraints excluded: chain A residue 1300 LEU
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 37 optimal weight:   20.0000
   chunk 95 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 106 optimal weight:    9.9990
   chunk 104 optimal weight:    3.9990
   chunk 116 optimal weight:    0.8980
   chunk 150 optimal weight:    0.0870
   chunk 138 optimal weight:    4.9990
   chunk 91 optimal weight:    4.9990
   overall best weight:    1.5964

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

Flipped N/Q/H residues before XYZ refinement:
A 905 ASN
A1133 HIS
A1205 GLN
A1209 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4606 r_free = 0.4606 target = 0.219252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.178719 restraints weight = 17899.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 3.64
r_work: 0.3976 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3976
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6917
moved from start:          0.6297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12614  Z= 0.177
  Angle     :  0.647  11.661  17122  Z= 0.331
  Chirality :  0.045   0.154   1837
  Planarity :  0.005   0.060   2226
  Dihedral  :  5.610  58.639   1700
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.84 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  6.96 %
    Allowed  : 27.82 %
    Favored  : 65.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.22), residues: 1530
  helix:  1.71 (0.23), residues: 515
  sheet: -0.25 (0.49), residues: 127
  loop : -1.40 (0.20), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A1453 
 HIS   0.004   0.001   HIS A 231 
 PHE   0.044   0.002   PHE A  23 
 TYR   0.020   0.002   TYR A 512 
 ARG   0.005   0.000   ARG A1116 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05497 (  414)
  hydrogen bonds       : angle       4.27244 ( 1200)
  covalent geometry    : bond        0.00413 (12614)
  covalent geometry    : angle       0.64719 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 93
    poor density    : 121
  time to evaluate  : 1.327 
Fit side-chains
REVERT: A   27 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7373 (mt0)
REVERT: A  237 ASN cc_start: 0.6964 (OUTLIER) cc_final: 0.6624 (m110)
REVERT: A  281 MET cc_start: 0.2520 (OUTLIER) cc_final: 0.2042 (ppp)
REVERT: A  316 LEU cc_start: 0.5547 (OUTLIER) cc_final: 0.4719 (tt)
REVERT: A  392 HIS cc_start: -0.2331 (OUTLIER) cc_final: -0.3161 (t-170)
REVERT: A  581 MET cc_start: 0.7996 (mmp) cc_final: 0.7754 (mmm)
REVERT: A  620 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8208 (mp)
REVERT: A  711 GLU cc_start: 0.7852 (tt0) cc_final: 0.7459 (pt0)
REVERT: A  723 ASP cc_start: 0.8057 (p0) cc_final: 0.7575 (t70)
REVERT: A  757 SER cc_start: 0.7268 (OUTLIER) cc_final: 0.6646 (p)
REVERT: A  910 ARG cc_start: 0.5446 (mmt90) cc_final: 0.4979 (mpt-90)
REVERT: A  933 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.6047 (p90)
REVERT: A  954 HIS cc_start: 0.5147 (OUTLIER) cc_final: 0.4792 (t-90)
REVERT: A  974 LEU cc_start: 0.4533 (OUTLIER) cc_final: 0.4286 (mp)
REVERT: A 1002 LEU cc_start: 0.4538 (OUTLIER) cc_final: 0.4336 (pp)
REVERT: A 1183 TYR cc_start: 0.5616 (OUTLIER) cc_final: 0.3991 (t80)
REVERT: A 1200 LEU cc_start: 0.5368 (OUTLIER) cc_final: 0.5091 (pt)
REVERT: A 1230 MET cc_start: 0.5884 (tmm) cc_final: 0.3215 (ptt)
REVERT: A 1285 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7373 (pm20)
REVERT: A 1338 LEU cc_start: 0.5741 (tt) cc_final: 0.5519 (mp)
REVERT: A 1420 ASP cc_start: 0.7483 (p0) cc_final: 0.6556 (m-30)
  outliers start: 93
  outliers final: 62
  residues processed: 198
  average time/residue: 0.2113
  time to fit residues: 64.3303
Evaluate side-chains
  181 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 76
    poor density    : 105
  time to evaluate  : 1.207 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   27 GLN
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  149 VAL
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  455 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  534 HIS
Chi-restraints excluded: chain A residue  550 LEU
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  608 CYS
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  804 VAL
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  907 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  954 HIS
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  960 LEU
Chi-restraints excluded: chain A residue  970 VAL
Chi-restraints excluded: chain A residue  974 LEU
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1002 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1114 THR
Chi-restraints excluded: chain A residue 1136 ILE
Chi-restraints excluded: chain A residue 1183 TYR
Chi-restraints excluded: chain A residue 1200 LEU
Chi-restraints excluded: chain A residue 1211 HIS
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1256 CYS
Chi-restraints excluded: chain A residue 1282 SER
Chi-restraints excluded: chain A residue 1285 GLU
Chi-restraints excluded: chain A residue 1300 LEU
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1382 THR
Chi-restraints excluded: chain A residue 1473 THR
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 43 optimal weight:    0.7980
   chunk 114 optimal weight:    2.9990
   chunk 33 optimal weight:    8.9990
   chunk 12 optimal weight:    0.0770
   chunk 128 optimal weight:    0.4980
   chunk 48 optimal weight:    3.9990
   chunk 145 optimal weight:    0.4980
   chunk 134 optimal weight:    8.9990
   chunk 63 optimal weight:    6.9990
   overall best weight:    0.5338

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

Flipped N/Q/H residues before XYZ refinement:
A1133 HIS
A1309 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4655 r_free = 0.4655 target = 0.224988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.184587 restraints weight = 18447.054|
|-----------------------------------------------------------------------------|
r_work (start): 0.4267 rms_B_bonded: 3.37
r_work: 0.4067 rms_B_bonded: 3.95 restraints_weight: 0.5000
r_work (final): 0.4067
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6776
moved from start:          0.6243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.064  12614  Z= 0.108
  Angle     :  0.543   9.401  17122  Z= 0.274
  Chirality :  0.041   0.144   1837
  Planarity :  0.004   0.039   2226
  Dihedral  :  5.144  58.454   1700
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  6.67 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 30.67 %
    Favored  : 64.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.03 (0.22), residues: 1530
  helix:  2.07 (0.23), residues: 516
  sheet: -0.22 (0.49), residues: 127
  loop : -1.28 (0.21), residues: 887

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 928 
 HIS   0.004   0.001   HIS A1316 
 PHE   0.019   0.001   PHE A  23 
 TYR   0.014   0.001   TYR A1428 
 ARG   0.002   0.000   ARG A 898 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03564 (  414)
  hydrogen bonds       : angle       3.91674 ( 1200)
  covalent geometry    : bond        0.00244 (12614)
  covalent geometry    : angle       0.54332 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 107
  time to evaluate  : 1.266 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7078 (tp40)
REVERT: A  220 HIS cc_start: 0.4493 (OUTLIER) cc_final: 0.3237 (p-80)
REVERT: A  237 ASN cc_start: 0.6828 (OUTLIER) cc_final: 0.6555 (m110)
REVERT: A  281 MET cc_start: 0.2481 (OUTLIER) cc_final: 0.1999 (ppp)
REVERT: A  392 HIS cc_start: -0.2039 (OUTLIER) cc_final: -0.3086 (t-170)
REVERT: A  620 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8040 (mp)
REVERT: A  711 GLU cc_start: 0.7727 (tt0) cc_final: 0.7316 (pt0)
REVERT: A  723 ASP cc_start: 0.7872 (p0) cc_final: 0.7368 (t0)
REVERT: A  757 SER cc_start: 0.7140 (OUTLIER) cc_final: 0.6587 (p)
REVERT: A  801 ASP cc_start: 0.7986 (p0) cc_final: 0.7680 (p0)
REVERT: A  933 TYR cc_start: 0.6793 (OUTLIER) cc_final: 0.6049 (p90)
REVERT: A  954 HIS cc_start: 0.4918 (OUTLIER) cc_final: 0.4676 (t-90)
REVERT: A 1230 MET cc_start: 0.5484 (tmm) cc_final: 0.2726 (ptt)
REVERT: A 1285 GLU cc_start: 0.8078 (OUTLIER) cc_final: 0.7171 (pm20)
REVERT: A 1338 LEU cc_start: 0.5625 (tt) cc_final: 0.5322 (mp)
REVERT: A 1420 ASP cc_start: 0.7454 (p0) cc_final: 0.6391 (m-30)
REVERT: A 1422 MET cc_start: 0.4343 (pmm) cc_final: 0.2468 (mpp)
  outliers start: 61
  outliers final: 39
  residues processed: 160
  average time/residue: 0.2157
  time to fit residues: 53.5407
Evaluate side-chains
  152 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 103
  time to evaluate  : 1.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  534 HIS
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  954 HIS
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1211 HIS
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1256 CYS
Chi-restraints excluded: chain A residue 1282 SER
Chi-restraints excluded: chain A residue 1285 GLU
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 61 optimal weight:    0.6980
   chunk 108 optimal weight:    4.9990
   chunk 135 optimal weight:   10.0000
   chunk 137 optimal weight:    0.0170
   chunk 74 optimal weight:    3.9990
   chunk 85 optimal weight:    3.9990
   chunk 129 optimal weight:    5.9990
   chunk 128 optimal weight:    0.5980
   chunk 30 optimal weight:   20.0000
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.2622

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

Flipped N/Q/H residues before XYZ refinement:
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1505 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4616 r_free = 0.4616 target = 0.220621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4258 r_free = 0.4258 target = 0.179573 restraints weight = 18363.573|
|-----------------------------------------------------------------------------|
r_work (start): 0.4217 rms_B_bonded: 3.28
r_work: 0.4010 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.4010
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6882
moved from start:          0.6649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  12614  Z= 0.148
  Angle     :  0.593  10.729  17122  Z= 0.302
  Chirality :  0.043   0.144   1837
  Planarity :  0.004   0.043   2226
  Dihedral  :  5.337  60.275   1698
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.71 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  5.61 %
    Allowed  : 28.72 %
    Favored  : 65.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.12 (0.22), residues: 1530
  helix:  1.99 (0.23), residues: 515
  sheet: -0.32 (0.49), residues: 127
  loop : -1.39 (0.20), residues: 888

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1023 
 HIS   0.004   0.001   HIS A1211 
 PHE   0.016   0.001   PHE A  23 
 TYR   0.023   0.001   TYR A1530 
 ARG   0.008   0.000   ARG A 910 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04685 (  414)
  hydrogen bonds       : angle       4.06185 ( 1200)
  covalent geometry    : bond        0.00349 (12614)
  covalent geometry    : angle       0.59286 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 111
  time to evaluate  : 1.832 
Fit side-chains
REVERT: A  130 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.7172 (tp40)
REVERT: A  220 HIS cc_start: 0.4573 (OUTLIER) cc_final: 0.3220 (p-80)
REVERT: A  237 ASN cc_start: 0.7026 (OUTLIER) cc_final: 0.6746 (m110)
REVERT: A  281 MET cc_start: 0.2612 (OUTLIER) cc_final: 0.2181 (ppp)
REVERT: A  316 LEU cc_start: 0.5665 (OUTLIER) cc_final: 0.4840 (tt)
REVERT: A  392 HIS cc_start: -0.2150 (OUTLIER) cc_final: -0.3279 (t-170)
REVERT: A  620 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8138 (mp)
REVERT: A  711 GLU cc_start: 0.7703 (tt0) cc_final: 0.7327 (pt0)
REVERT: A  723 ASP cc_start: 0.7989 (p0) cc_final: 0.7523 (t0)
REVERT: A  801 ASP cc_start: 0.8090 (p0) cc_final: 0.7780 (p0)
REVERT: A  933 TYR cc_start: 0.6759 (OUTLIER) cc_final: 0.5990 (p90)
REVERT: A  954 HIS cc_start: 0.4957 (OUTLIER) cc_final: 0.4676 (t-90)
REVERT: A 1183 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4014 (t80)
REVERT: A 1230 MET cc_start: 0.5661 (tmm) cc_final: 0.2882 (ptt)
REVERT: A 1285 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7240 (pm20)
REVERT: A 1338 LEU cc_start: 0.5727 (tt) cc_final: 0.5439 (mp)
REVERT: A 1420 ASP cc_start: 0.7524 (p0) cc_final: 0.6553 (m-30)
REVERT: A 1422 MET cc_start: 0.4590 (pmm) cc_final: 0.2631 (mpp)
REVERT: A 1502 GLU cc_start: 0.6091 (mt-10) cc_final: 0.5610 (mt-10)
  outliers start: 75
  outliers final: 53
  residues processed: 174
  average time/residue: 0.2055
  time to fit residues: 55.6710
Evaluate side-chains
  169 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 64
    poor density    : 105
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  236 TYR
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  238 LEU
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  392 HIS
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  534 HIS
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  689 THR
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  817 ILE
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  954 HIS
Chi-restraints excluded: chain A residue  956 PHE
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1136 ILE
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1183 TYR
Chi-restraints excluded: chain A residue 1211 HIS
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1256 CYS
Chi-restraints excluded: chain A residue 1282 SER
Chi-restraints excluded: chain A residue 1285 GLU
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1365 SER
Chi-restraints excluded: chain A residue 1382 THR
Chi-restraints excluded: chain A residue 1455 ILE
Chi-restraints excluded: chain A residue 1473 THR
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 100 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9990
   chunk 111 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9980
   chunk 87 optimal weight:    7.9990
   chunk 97 optimal weight:    4.9990
   chunk 67 optimal weight:    1.9990
   chunk 49 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 12 optimal weight:    0.7980
   chunk 131 optimal weight:    2.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 869 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4620 r_free = 0.4620 target = 0.220959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.179789 restraints weight = 18300.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.4221 rms_B_bonded: 3.71
r_work: 0.3999 rms_B_bonded: 4.27 restraints_weight: 0.5000
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6888
moved from start:          0.6911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12614  Z= 0.133
  Angle     :  0.570   9.787  17122  Z= 0.289
  Chirality :  0.043   0.142   1837
  Planarity :  0.004   0.039   2226
  Dihedral  :  5.319  64.340   1698
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.58 %
    Favored  : 92.29 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 29.92 %
    Favored  : 65.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.22), residues: 1530
  helix:  1.93 (0.23), residues: 522
  sheet: -0.34 (0.49), residues: 129
  loop : -1.44 (0.20), residues: 879

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 680 
 HIS   0.007   0.001   HIS A 231 
 PHE   0.014   0.001   PHE A  23 
 TYR   0.015   0.001   TYR A 512 
 ARG   0.008   0.000   ARG A 910 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04131 (  414)
  hydrogen bonds       : angle       4.03025 ( 1200)
  covalent geometry    : bond        0.00311 (12614)
  covalent geometry    : angle       0.57004 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 63
    poor density    : 110
  time to evaluate  : 1.237 
Fit side-chains
REVERT: A  112 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7572 (mt)
REVERT: A  130 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.7160 (tp40)
REVERT: A  220 HIS cc_start: 0.4518 (OUTLIER) cc_final: 0.3200 (p-80)
REVERT: A  237 ASN cc_start: 0.7069 (OUTLIER) cc_final: 0.6785 (m110)
REVERT: A  281 MET cc_start: 0.2564 (OUTLIER) cc_final: 0.2166 (ppp)
REVERT: A  316 LEU cc_start: 0.5691 (OUTLIER) cc_final: 0.4867 (tt)
REVERT: A  539 MET cc_start: 0.6977 (mmt) cc_final: 0.6762 (mmt)
REVERT: A  620 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.8078 (mp)
REVERT: A  711 GLU cc_start: 0.7760 (tt0) cc_final: 0.7355 (pt0)
REVERT: A  723 ASP cc_start: 0.7928 (p0) cc_final: 0.7512 (t0)
REVERT: A  801 ASP cc_start: 0.8090 (p0) cc_final: 0.7815 (p0)
REVERT: A  933 TYR cc_start: 0.6815 (OUTLIER) cc_final: 0.6159 (p90)
REVERT: A  954 HIS cc_start: 0.4914 (OUTLIER) cc_final: 0.4611 (t-90)
REVERT: A 1230 MET cc_start: 0.5642 (tmm) cc_final: 0.2835 (ptt)
REVERT: A 1285 GLU cc_start: 0.8072 (OUTLIER) cc_final: 0.7238 (pm20)
REVERT: A 1420 ASP cc_start: 0.7568 (p0) cc_final: 0.6730 (m-30)
REVERT: A 1422 MET cc_start: 0.4978 (pmm) cc_final: 0.3114 (tpp)
  outliers start: 63
  outliers final: 48
  residues processed: 163
  average time/residue: 0.1931
  time to fit residues: 49.7209
Evaluate side-chains
  161 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 103
  time to evaluate  : 1.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  112 ILE
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  130 GLN
Chi-restraints excluded: chain A residue  145 SER
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  512 TYR
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  516 THR
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  534 HIS
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  757 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  954 HIS
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1211 HIS
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1282 SER
Chi-restraints excluded: chain A residue 1285 GLU
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1382 THR
Chi-restraints excluded: chain A residue 1455 ILE
Chi-restraints excluded: chain A residue 1473 THR
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 3 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 88 optimal weight:    7.9990
   chunk 12 optimal weight:    0.5980
   chunk 83 optimal weight:    6.9990
   chunk 29 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0070
   chunk 82 optimal weight:    0.9990
   chunk 121 optimal weight:    0.7980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.6200

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

Flipped N/Q/H residues before XYZ refinement:
A1509 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4637 r_free = 0.4637 target = 0.222891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.181901 restraints weight = 18269.028|
|-----------------------------------------------------------------------------|
r_work (start): 0.4247 rms_B_bonded: 3.55
r_work: 0.4034 rms_B_bonded: 4.18 restraints_weight: 0.5000
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6834
moved from start:          0.6921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  12614  Z= 0.110
  Angle     :  0.554   9.194  17122  Z= 0.277
  Chirality :  0.042   0.139   1837
  Planarity :  0.004   0.047   2226
  Dihedral  :  5.112  62.019   1694
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.52 %
    Favored  : 92.42 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 30.89 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.10 (0.22), residues: 1530
  helix:  2.04 (0.23), residues: 518
  sheet: -0.31 (0.49), residues: 129
  loop : -1.41 (0.20), residues: 883

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 487 
 HIS   0.006   0.001   HIS A 231 
 PHE   0.010   0.001   PHE A1335 
 TYR   0.026   0.001   TYR A1530 
 ARG   0.005   0.000   ARG A 910 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03590 (  414)
  hydrogen bonds       : angle       3.93911 ( 1200)
  covalent geometry    : bond        0.00249 (12614)
  covalent geometry    : angle       0.55438 (17122)

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

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

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3060 Ramachandran restraints generated.
    1530 Oldfield, 0 Emsley, 1530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 108
  time to evaluate  : 1.242 
Fit side-chains
REVERT: A  220 HIS cc_start: 0.4559 (OUTLIER) cc_final: 0.3277 (p-80)
REVERT: A  237 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6859 (m110)
REVERT: A  281 MET cc_start: 0.2466 (OUTLIER) cc_final: 0.2024 (ppp)
REVERT: A  316 LEU cc_start: 0.5635 (OUTLIER) cc_final: 0.4796 (tt)
REVERT: A  539 MET cc_start: 0.6897 (mmt) cc_final: 0.6670 (mmt)
REVERT: A  620 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8059 (mp)
REVERT: A  711 GLU cc_start: 0.7770 (tt0) cc_final: 0.7317 (pt0)
REVERT: A  723 ASP cc_start: 0.7811 (p0) cc_final: 0.7492 (t0)
REVERT: A  801 ASP cc_start: 0.8054 (p0) cc_final: 0.7811 (p0)
REVERT: A  933 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.6111 (p90)
REVERT: A 1183 TYR cc_start: 0.5577 (OUTLIER) cc_final: 0.4016 (t80)
REVERT: A 1230 MET cc_start: 0.5605 (tmm) cc_final: 0.2884 (ptt)
REVERT: A 1285 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7154 (pm20)
REVERT: A 1420 ASP cc_start: 0.7574 (p0) cc_final: 0.6775 (m-30)
REVERT: A 1422 MET cc_start: 0.5006 (pmm) cc_final: 0.3217 (tpp)
  outliers start: 56
  outliers final: 43
  residues processed: 156
  average time/residue: 0.2033
  time to fit residues: 49.2030
Evaluate side-chains
  154 residues out of total 1342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 103
  time to evaluate  : 1.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   26 GLU
Chi-restraints excluded: chain A residue   65 LEU
Chi-restraints excluded: chain A residue   81 CYS
Chi-restraints excluded: chain A residue   85 LEU
Chi-restraints excluded: chain A residue  128 THR
Chi-restraints excluded: chain A residue  181 LEU
Chi-restraints excluded: chain A residue  220 HIS
Chi-restraints excluded: chain A residue  237 ASN
Chi-restraints excluded: chain A residue  258 SER
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  281 MET
Chi-restraints excluded: chain A residue  316 LEU
Chi-restraints excluded: chain A residue  403 ASN
Chi-restraints excluded: chain A residue  431 THR
Chi-restraints excluded: chain A residue  448 LEU
Chi-restraints excluded: chain A residue  505 LEU
Chi-restraints excluded: chain A residue  523 VAL
Chi-restraints excluded: chain A residue  524 ARG
Chi-restraints excluded: chain A residue  534 HIS
Chi-restraints excluded: chain A residue  546 LEU
Chi-restraints excluded: chain A residue  567 PHE
Chi-restraints excluded: chain A residue  620 LEU
Chi-restraints excluded: chain A residue  645 THR
Chi-restraints excluded: chain A residue  708 LEU
Chi-restraints excluded: chain A residue  747 SER
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  796 ILE
Chi-restraints excluded: chain A residue  816 LYS
Chi-restraints excluded: chain A residue  850 VAL
Chi-restraints excluded: chain A residue  868 THR
Chi-restraints excluded: chain A residue  887 ILE
Chi-restraints excluded: chain A residue  890 ILE
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  988 LEU
Chi-restraints excluded: chain A residue  995 LEU
Chi-restraints excluded: chain A residue 1012 ILE
Chi-restraints excluded: chain A residue 1044 SER
Chi-restraints excluded: chain A residue 1045 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1183 TYR
Chi-restraints excluded: chain A residue 1211 HIS
Chi-restraints excluded: chain A residue 1215 ILE
Chi-restraints excluded: chain A residue 1226 ILE
Chi-restraints excluded: chain A residue 1282 SER
Chi-restraints excluded: chain A residue 1285 GLU
Chi-restraints excluded: chain A residue 1313 VAL
Chi-restraints excluded: chain A residue 1382 THR
Chi-restraints excluded: chain A residue 1473 THR
Chi-restraints excluded: chain A residue 1497 TRP
Chi-restraints excluded: chain A residue 1518 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 153
   random chunks:
   chunk 142 optimal weight:    8.9990
   chunk 124 optimal weight:    3.9990
   chunk 120 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 119 optimal weight:    0.8980
   chunk 60 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 74 optimal weight:    1.9990
   chunk 89 optimal weight:    8.9990
   chunk 121 optimal weight:    2.9990
   chunk 45 optimal weight:    5.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
** A1518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4553 r_free = 0.4553 target = 0.213463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.172800 restraints weight = 17879.933|
|-----------------------------------------------------------------------------|
r_work (start): 0.4142 rms_B_bonded: 3.11
r_work: 0.3937 rms_B_bonded: 3.92 restraints_weight: 0.5000
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7016
moved from start:          0.7678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  12614  Z= 0.220
  Angle     :  0.698  11.193  17122  Z= 0.359
  Chirality :  0.047   0.177   1837
  Planarity :  0.005   0.058   2226
  Dihedral  :  5.826  78.141   1694
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  9.22 %
    Favored  : 90.72 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 30.29 %
    Favored  : 64.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.21), residues: 1530
  helix:  1.60 (0.23), residues: 516
  sheet: -0.45 (0.47), residues: 146
  loop : -1.69 (0.20), residues: 868

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 487 
 HIS   0.009   0.001   HIS A 231 
 PHE   0.028   0.002   PHE A  23 
 TYR   0.025   0.002   TYR A 923 
 ARG   0.014   0.001   ARG A 910 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06132 (  414)
  hydrogen bonds       : angle       4.45483 ( 1200)
  covalent geometry    : bond        0.00518 (12614)
  covalent geometry    : angle       0.69808 (17122)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7090.48 seconds
wall clock time: 124 minutes 12.61 seconds (7452.61 seconds total)