Starting phenix.real_space_refine
on Wed Apr 30 03:30:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ens_19843/04_2025/9ens_19843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ens_19843/04_2025/9ens_19843.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ens_19843/04_2025/9ens_19843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ens_19843/04_2025/9ens_19843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ens_19843/04_2025/9ens_19843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ens_19843/04_2025/9ens_19843.cif"
  }
  resolution = 3.0
  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=   0.001 sd=   0.021
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      48      5.16       5
     C    5764      2.51       5
     N    1552      2.21       5
     O    1712      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9076
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1161, 9015
          Classifications: {'peptide': 1161}
          Incomplete info: {'truncation_to_alanine': 94}
          Link IDs: {'PTRANS': 61, 'TRANS': 1099}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 319
          Unresolved non-hydrogen angles: 397
          Unresolved non-hydrogen dihedrals: 263
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 5, 'TYR:plan': 2, 'ASN:plan1': 8, 'TRP:plan': 2, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 10, 'ARG:plan': 8}
          Unresolved non-hydrogen planarities: 186
    Chain: "B"
      Number of atoms: 61
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 61
          Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 5.68, per 1000 atoms: 0.63
  Number of scatterers: 9076
  At special positions: 0
  Unit cell: (81.2544, 90.5648, 134.578, 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      48     16.00
     O    1712      8.00
     N    1552      7.00
     C    5764      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 178 " - pdb=" SG  CYS A 222 " distance=2.04

  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
  Links applied
    ALPHA1-3
      " BMA B   3 " - " MAN B   4 "
    ALPHA1-6
      " BMA B   3 " - " MAN B   5 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 296 "
  Time building additional restraints: 2.93
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      35.2% alpha, 19.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 91 through 95
    Processing helix  chain 'A' and resid 126 through 138
    Processing helix  chain 'A' and resid 139 through 141
      No H-bonds generated for 'chain 'A' and resid 139 through 141'
    Processing helix  chain 'A' and resid 152 through 157
      removed outlier: 3.714A  pdb=" N   GLN A 156 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 195
    Processing helix  chain 'A' and resid 196 through 199
    Processing helix  chain 'A' and resid 201 through 206
      removed outlier: 4.090A  pdb=" N   LEU A 204 " --> pdb=" O   MET A 201 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   LYS A 205 " --> pdb=" O   PRO A 202 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   GLY A 206 " --> pdb=" O   THR A 203 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 201 through 206'
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 412 through 417
      removed outlier: 3.972A  pdb=" N   GLY A 417 " --> pdb=" O   GLY A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 420 through 436
    Processing helix  chain 'A' and resid 438 through 440
      No H-bonds generated for 'chain 'A' and resid 438 through 440'
    Processing helix  chain 'A' and resid 441 through 446
    Processing helix  chain 'A' and resid 446 through 458
    Processing helix  chain 'A' and resid 459 through 461
      No H-bonds generated for 'chain 'A' and resid 459 through 461'
    Processing helix  chain 'A' and resid 462 through 473
    Processing helix  chain 'A' and resid 488 through 505
      removed outlier: 4.222A  pdb=" N   GLY A 505 " --> pdb=" O   ILE A 501 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 520
    Processing helix  chain 'A' and resid 524 through 534
      removed outlier: 3.617A  pdb=" N   LYS A 533 " --> pdb=" O   ASN A 529 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   LEU A 534 " --> pdb=" O   ILE A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 537
      No H-bonds generated for 'chain 'A' and resid 535 through 537'
    Processing helix  chain 'A' and resid 542 through 554
    Processing helix  chain 'A' and resid 555 through 561
      removed outlier: 3.606A  pdb=" N   GLU A 561 " --> pdb=" O   LYS A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 581
      removed outlier: 3.623A  pdb=" N   THR A 566 " --> pdb=" O   GLN A 562 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   ALA A 567 " --> pdb=" O   PHE A 563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 589
    Processing helix  chain 'A' and resid 591 through 596
    Processing helix  chain 'A' and resid 604 through 625
      removed outlier: 5.410A  pdb=" N   ILE A 611 " --> pdb=" O   TYR A 607 " (cutoff:3.500A)
      Proline residue:  A 612  - end of helix
    Processing helix  chain 'A' and resid 626 through 641
      removed outlier: 3.755A  pdb=" N   ILE A 640 " --> pdb=" O   ALA A 636 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLY A 641 " --> pdb=" O   LEU A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 655
      removed outlier: 4.134A  pdb=" N   SER A 647 " --> pdb=" O   PRO A 643 " (cutoff:3.500A)
      Proline residue:  A 651  - end of helix
      removed outlier: 3.750A  pdb=" N   GLY A 655 " --> pdb=" O   PRO A 651 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 670
    Processing helix  chain 'A' and resid 671 through 678
      removed outlier: 3.505A  pdb=" N   THR A 675 " --> pdb=" O   LEU A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 692
      removed outlier: 3.676A  pdb=" N   ASN A 692 " --> pdb=" O   LYS A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 708
      removed outlier: 4.117A  pdb=" N   THR A 702 " --> pdb=" O   GLU A 698 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   MET A 708 " --> pdb=" O   VAL A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 723
    Processing helix  chain 'A' and resid 729 through 743
    Processing helix  chain 'A' and resid 751 through 762
    Processing helix  chain 'A' and resid 763 through 765
      No H-bonds generated for 'chain 'A' and resid 763 through 765'
    Processing helix  chain 'A' and resid 833 through 845
      removed outlier: 3.532A  pdb=" N   VAL A 845 " --> pdb=" O   SER A 841 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 908
      Proline residue:  A 898  - end of helix
    Processing helix  chain 'A' and resid 1052 through 1056
    Processing helix  chain 'A' and resid 1145 through 1150
    Processing helix  chain 'A' and resid 1169 through 1183
      removed outlier: 3.770A  pdb=" N   ARG A1174 " --> pdb=" O   SER A1170 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   GLN A1175 " --> pdb=" O   LYS A1171 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   MET A1178 " --> pdb=" O   ARG A1174 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   ARG A1179 " --> pdb=" O   GLN A1175 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 26 through 39
      removed outlier: 4.323A  pdb=" N   ASN A  26 " --> pdb=" O   ALA A  60 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU A  55 " --> pdb=" O   ASN A  72 " (cutoff:3.500A)
      removed outlier: 4.889A  pdb=" N   ASN A  72 " --> pdb=" O   LEU A  55 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   THR A  57 " --> pdb=" O   VAL A  70 " (cutoff:3.500A)
      removed outlier: 5.704A  pdb=" N   VAL A  70 " --> pdb=" O   THR A  57 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   GLN A  59 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
      removed outlier: 5.512A  pdb=" N   ALA A  68 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 98 through 99
    current: chain 'A' and resid 115 through 120
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 115 through 120
    current: chain 'A' and resid 177 through 186
      removed outlier: 10.094A  pdb=" N   LYS A 177 " --> pdb=" O   ASP A 220 " (cutoff:3.500A)
      removed outlier: 8.923A  pdb=" N   ASP A 220 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLU A 179 " --> pdb=" O   ASN A 218 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   SER A 253 " --> pdb=" O   LYS A 217 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   PHE A 219 " --> pdb=" O   ARG A 251 " (cutoff:3.500A)
      removed outlier: 8.455A  pdb=" N   ARG A 251 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   SER A 252 " --> pdb=" O   SER A 275 " (cutoff:3.500A)
      removed outlier: 4.057A  pdb=" N   SER A 275 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
      removed outlier: 6.726A  pdb=" N   THR A 254 " --> pdb=" O   THR A 273 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   THR A 273 " --> pdb=" O   THR A 254 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   ARG A 256 " --> pdb=" O   SER A 271 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   SER A 271 " --> pdb=" O   ARG A 256 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   VAL A 258 " --> pdb=" O   GLN A 269 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   GLN A 269 " --> pdb=" O   LEU A 299 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 228 through 230
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 228 through 230
    current: chain 'A' and resid 935 through 954
      removed outlier: 3.614A  pdb=" N   SER A 973 " --> pdb=" O   LEU A 945 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LYS A 947 " --> pdb=" O   THR A 971 " (cutoff:3.500A)
      removed outlier: 3.819A  pdb=" N   GLN A 953 " --> pdb=" O   ASN A 965 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   ARG A 989 " --> pdb=" O   THR A 984 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 989 through 1002
    current: chain 'A' and resid 1060 through 1061
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 1060 through 1061
    current: chain 'A' and resid 1079 through 1083
    Processing sheet with id=AA3, first strand: chain 'A' and resid 776 through 784
      removed outlier: 3.597A  pdb=" N   TYR A 797 " --> pdb=" O   ARG A 776 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ILE A 789 " --> pdb=" O   LEU A 784 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   ILE A 808 " --> pdb=" O   VAL A 798 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 808 through 813
    current: chain 'A' and resid 820 through 821
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 820 through 821
    current: chain 'A' and resid 873 through 879
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137
      removed outlier: 3.908A  pdb=" N   SER A1136 " --> pdb=" O   ARG A1196 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   VAL A1195 " --> pdb=" O   LEU A1209 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1227 through 1230
      removed outlier: 3.642A  pdb=" N   VAL A1241 " --> pdb=" O   TRP A1228 " (cutoff:3.500A)

    335 hydrogen bonds defined for protein.
    966 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: 2.88

  Time building geometry restraints manager: 3.02 seconds

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

  Histogram of bond lengths:
        1.22 -     1.35: 2962
        1.35 -     1.47: 2097
        1.47 -     1.59: 4117
        1.59 -     1.71: 0
        1.71 -     1.84: 90
  Bond restraints: 9266
  Sorted by residual:
  bond pdb=" C5  MAN B   5 "
       pdb=" O5  MAN B   5 "
    ideal  model  delta    sigma   weight residual
    1.418  1.458 -0.040 2.00e-02 2.50e+03 4.03e+00
  bond pdb=" C1  MAN B   5 "
       pdb=" C2  MAN B   5 "
    ideal  model  delta    sigma   weight residual
    1.526  1.562 -0.036 2.00e-02 2.50e+03 3.17e+00
  bond pdb=" C1  MAN B   4 "
       pdb=" C2  MAN B   4 "
    ideal  model  delta    sigma   weight residual
    1.526  1.553 -0.027 2.00e-02 2.50e+03 1.80e+00
  bond pdb=" C1  MAN B   5 "
       pdb=" O5  MAN B   5 "
    ideal  model  delta    sigma   weight residual
    1.399  1.425 -0.026 2.00e-02 2.50e+03 1.65e+00
  bond pdb=" C5  MAN B   4 "
       pdb=" O5  MAN B   4 "
    ideal  model  delta    sigma   weight residual
    1.418  1.442 -0.024 2.00e-02 2.50e+03 1.44e+00
  ... (remaining 9261 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.54: 12203
        1.54 -     3.08: 294
        3.08 -     4.62: 58
        4.62 -     6.16: 15
        6.16 -     7.70: 2
  Bond angle restraints: 12572
  Sorted by residual:
  angle pdb=" C   SER A 260 "
        pdb=" N   GLU A 261 "
        pdb=" CA  GLU A 261 "
      ideal   model   delta    sigma   weight residual
     121.31  125.35   -4.04 1.49e+00 4.50e-01 7.37e+00
  angle pdb=" C   LEU A 457 "
        pdb=" N   MET A 458 "
        pdb=" CA  MET A 458 "
      ideal   model   delta    sigma   weight residual
     121.94  116.65    5.29 2.00e+00 2.50e-01 6.99e+00
  angle pdb=" CA  HIS A 763 "
        pdb=" C   HIS A 763 "
        pdb=" O   HIS A 763 "
      ideal   model   delta    sigma   weight residual
     120.51  116.99    3.52 1.43e+00 4.89e-01 6.07e+00
  angle pdb=" CA  HIS A 763 "
        pdb=" C   HIS A 763 "
        pdb=" N   LEU A 764 "
      ideal   model   delta    sigma   weight residual
     116.84  121.01   -4.17 1.71e+00 3.42e-01 5.95e+00
  angle pdb=" N   GLU A 261 "
        pdb=" CA  GLU A 261 "
        pdb=" C   GLU A 261 "
      ideal   model   delta    sigma   weight residual
     110.35  113.55   -3.20 1.40e+00 5.10e-01 5.23e+00
  ... (remaining 12567 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.35: 5362
       24.35 -    48.70: 311
       48.70 -    73.06: 30
       73.06 -    97.41: 12
       97.41 -   121.76: 5
  Dihedral angle restraints: 5720
    sinusoidal: 2310
      harmonic: 3410
  Sorted by residual:
  dihedral pdb=" C2  MAN B   5 "
           pdb=" C1  MAN B   5 "
           pdb=" O5  MAN B   5 "
           pdb=" C5  MAN B   5 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -57.62   64.14 -121.76     1      3.00e+01 1.11e-03 1.63e+01
  dihedral pdb=" CA  TRP A1023 "
           pdb=" C   TRP A1023 "
           pdb=" N   PRO A1024 "
           pdb=" CA  PRO A1024 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.47   19.53     0      5.00e+00 4.00e-02 1.53e+01
  dihedral pdb=" O4  BMA B   3 "
           pdb=" C4  BMA B   3 "
           pdb=" C5  BMA B   3 "
           pdb=" O5  BMA B   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -71.29 -178.71  107.42     1      3.00e+01 1.11e-03 1.39e+01
  ... (remaining 5717 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1208
       0.060 -    0.120: 216
       0.120 -    0.179: 25
       0.179 -    0.239: 0
       0.239 -    0.299: 1
  Chirality restraints: 1450
  Sorted by residual:
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.57    0.30 2.00e-01 2.50e+01 2.23e+00
  chirality pdb=" CA  TRP A  71 "
            pdb=" N   TRP A  71 "
            pdb=" C   TRP A  71 "
            pdb=" CB  TRP A  71 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.55e-01
  chirality pdb=" CA  ILE A1063 "
            pdb=" N   ILE A1063 "
            pdb=" C   ILE A1063 "
            pdb=" CB  ILE A1063 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.99e-01
  ... (remaining 1447 not shown)

  Planarity restraints: 1610
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  71 "   -0.021 2.00e-02 2.50e+03   1.46e-02 5.36e+00
        pdb=" CG  TRP A  71 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  71 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  71 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  71 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  71 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  71 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  71 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  71 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  71 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 642 "    0.035 5.00e-02 4.00e+02   5.26e-02 4.43e+00
        pdb=" N   PRO A 643 "   -0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO A 643 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO A 643 "    0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 296 "   -0.018 2.00e-02 2.50e+03   1.71e-02 3.64e+00
        pdb=" CG  ASN A 296 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 296 "   -0.003 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 296 "    0.016 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1607 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 687
        2.74 -     3.28: 8583
        3.28 -     3.82: 14086
        3.82 -     4.36: 16122
        4.36 -     4.90: 29013
  Nonbonded interactions: 68491
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 282 "
            pdb=" O   ASN A1113 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" NH1 ARG A 664 "
            pdb=" OE1 GLU A 695 "
     model   vdw
     2.199 3.120
  nonbonded pdb=" OG1 THR A1085 "
            pdb=" OE1 GLU A1090 "
     model   vdw
     2.208 3.040
  nonbonded pdb=" OD2 ASP A 484 "
            pdb=" OG  SER A 486 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OE1 GLU A 435 "
            pdb=" OG1 THR A 447 "
     model   vdw
     2.257 3.040
  ... (remaining 68486 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             33.030
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     24.840
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.440
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   72.060
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7191
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9272  Z= 0.177
  Angle     :  0.613   7.697  12589  Z= 0.309
  Chirality :  0.046   0.299   1450
  Planarity :  0.004   0.053   1609
  Dihedral  : 15.315 121.759   3497
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 6.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.10 %
    Favored  : 99.90 %
  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 (0.26), residues: 1151
  helix:  1.49 (0.30), residues: 348
  sheet: -0.46 (0.29), residues: 359
  loop : -1.04 (0.29), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A1045 
 PHE   0.015   0.002   PHE A 549 
 TYR   0.016   0.002   TYR A 797 
 ARG   0.007   0.000   ARG A 619 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00256 (    1)
  link_NAG-ASN         : angle       2.95503 (    3)
  link_ALPHA1-6        : bond        0.00893 (    1)
  link_ALPHA1-6        : angle       1.77159 (    3)
  link_BETA1-4         : bond        0.00170 (    2)
  link_BETA1-4         : angle       2.45445 (    6)
  link_ALPHA1-3        : bond        0.00522 (    1)
  link_ALPHA1-3        : angle       1.88284 (    3)
  hydrogen bonds       : bond        0.20432 (  335)
  hydrogen bonds       : angle       6.73279 (  966)
  SS BOND              : bond        0.00487 (    1)
  SS BOND              : angle       2.62731 (    2)
  covalent geometry    : bond        0.00419 ( 9266)
  covalent geometry    : angle       0.60761 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 1.016 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8677 (mt) cc_final: 0.8423 (mp)
REVERT: A  116 ILE cc_start: 0.8321 (mm) cc_final: 0.8011 (OUTLIER)
REVERT: A  171 GLU cc_start: 0.7181 (mm-30) cc_final: 0.6963 (mm-30)
REVERT: A  180 VAL cc_start: 0.8320 (t) cc_final: 0.8059 (p)
REVERT: A  207 ASP cc_start: 0.7039 (m-30) cc_final: 0.6823 (m-30)
REVERT: A  411 LYS cc_start: 0.7959 (mmtp) cc_final: 0.7749 (mmtt)
REVERT: A  472 ASN cc_start: 0.7545 (t0) cc_final: 0.7002 (t0)
REVERT: A  688 LYS cc_start: 0.8334 (tptm) cc_final: 0.8094 (mmmm)
REVERT: A  891 LYS cc_start: 0.7842 (ptmm) cc_final: 0.7569 (ptmm)
REVERT: A 1092 MET cc_start: 0.6326 (mpp) cc_final: 0.5929 (mpp)
REVERT: A 1238 ASP cc_start: 0.7101 (m-30) cc_final: 0.6879 (m-30)
  outliers start: 0
  outliers final: 3
  residues processed: 243
  average time/residue: 1.2619
  time to fit residues: 328.1457
Evaluate side-chains
  233 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 231
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 ASP
Chi-restraints excluded: chain A residue  576 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.0870
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    0.5980
   chunk 30 optimal weight:    4.9990
   chunk 59 optimal weight:    0.5980
   chunk 46 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 67 optimal weight:    1.9990
   chunk 105 optimal weight:   40.0000
   overall best weight:    0.7360

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

Flipped N/Q/H residues before XYZ refinement:
A  26 ASN
A 131 ASN
A 141 GLN
A 718 GLN
A 762 ASN
** A 953 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1044 ASN
A1049 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.156915 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126181 restraints weight = 11461.869|
|-----------------------------------------------------------------------------|
r_work (start): 0.3570 rms_B_bonded: 2.49
r_work: 0.3433 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.0924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9272  Z= 0.170
  Angle     :  0.601   7.322  12589  Z= 0.315
  Chirality :  0.046   0.144   1450
  Planarity :  0.005   0.055   1609
  Dihedral  :  8.921 106.850   1341
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.65 %
    Allowed  : 12.26 %
    Favored  : 86.10 %
  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 (0.26), residues: 1151
  helix:  1.45 (0.29), residues: 360
  sheet: -0.39 (0.29), residues: 354
  loop : -1.14 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A1045 
 PHE   0.015   0.002   PHE A 563 
 TYR   0.015   0.002   TYR A 182 
 ARG   0.004   0.000   ARG A  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00261 (    1)
  link_NAG-ASN         : angle       2.49608 (    3)
  link_ALPHA1-6        : bond        0.01565 (    1)
  link_ALPHA1-6        : angle       2.00047 (    3)
  link_BETA1-4         : bond        0.00209 (    2)
  link_BETA1-4         : angle       2.42023 (    6)
  link_ALPHA1-3        : bond        0.01162 (    1)
  link_ALPHA1-3        : angle       1.47954 (    3)
  hydrogen bonds       : bond        0.05243 (  335)
  hydrogen bonds       : angle       5.27490 (  966)
  SS BOND              : bond        0.00280 (    1)
  SS BOND              : angle       2.46315 (    2)
  covalent geometry    : bond        0.00404 ( 9266)
  covalent geometry    : angle       0.59569 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 237
  time to evaluate  : 1.645 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8428 (mt) cc_final: 0.8075 (mp)
REVERT: A  116 ILE cc_start: 0.8290 (mm) cc_final: 0.7974 (OUTLIER)
REVERT: A  180 VAL cc_start: 0.8379 (t) cc_final: 0.8166 (p)
REVERT: A  197 GLU cc_start: 0.7548 (pm20) cc_final: 0.7287 (pm20)
REVERT: A  207 ASP cc_start: 0.7717 (m-30) cc_final: 0.7501 (m-30)
REVERT: A  211 MET cc_start: 0.8360 (mpp) cc_final: 0.7921 (mpp)
REVERT: A  708 MET cc_start: 0.8479 (mpt) cc_final: 0.8259 (mpp)
REVERT: A  762 ASN cc_start: 0.7252 (OUTLIER) cc_final: 0.6669 (t0)
REVERT: A  781 GLU cc_start: 0.7731 (tp30) cc_final: 0.7447 (tp30)
REVERT: A  891 LYS cc_start: 0.8229 (ptmm) cc_final: 0.7786 (ptmm)
REVERT: A  952 VAL cc_start: 0.8302 (t) cc_final: 0.8004 (p)
REVERT: A 1092 MET cc_start: 0.6746 (mpp) cc_final: 0.6299 (mpp)
REVERT: A 1238 ASP cc_start: 0.7490 (m-30) cc_final: 0.7195 (m-30)
  outliers start: 16
  outliers final: 6
  residues processed: 241
  average time/residue: 1.2966
  time to fit residues: 334.0223
Evaluate side-chains
  230 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 224
  time to evaluate  : 1.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  762 ASN
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue 1195 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 75 optimal weight:    2.9990
   chunk 56 optimal weight:    0.5980
   chunk 13 optimal weight:   20.0000
   chunk 23 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 66 optimal weight:    0.6980
   chunk 101 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 28 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A  64 ASN
A 141 GLN
A 472 ASN
A 658 GLN
A 718 GLN
A 762 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.153687 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.123098 restraints weight = 11765.735|
|-----------------------------------------------------------------------------|
r_work (start): 0.3522 rms_B_bonded: 2.40
r_work: 0.3387 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3215 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.3215
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.1205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052   9272  Z= 0.295
  Angle     :  0.676   9.262  12589  Z= 0.357
  Chirality :  0.050   0.175   1450
  Planarity :  0.005   0.062   1609
  Dihedral  :  8.304  99.046   1337
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 13.80 %
    Favored  : 82.49 %
  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: -0.46 (0.25), residues: 1151
  helix:  1.16 (0.29), residues: 357
  sheet: -0.53 (0.29), residues: 354
  loop : -1.26 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A  71 
 HIS   0.006   0.001   HIS A  47 
 PHE   0.027   0.003   PHE A 549 
 TYR   0.023   0.002   TYR A 797 
 ARG   0.005   0.001   ARG A  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00433 (    1)
  link_NAG-ASN         : angle       2.39850 (    3)
  link_ALPHA1-6        : bond        0.01341 (    1)
  link_ALPHA1-6        : angle       2.24820 (    3)
  link_BETA1-4         : bond        0.00455 (    2)
  link_BETA1-4         : angle       2.81437 (    6)
  link_ALPHA1-3        : bond        0.01273 (    1)
  link_ALPHA1-3        : angle       1.33778 (    3)
  hydrogen bonds       : bond        0.06222 (  335)
  hydrogen bonds       : angle       5.22042 (  966)
  SS BOND              : bond        0.01507 (    1)
  SS BOND              : angle       2.45372 (    2)
  covalent geometry    : bond        0.00724 ( 9266)
  covalent geometry    : angle       0.67112 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  270 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 234
  time to evaluate  : 0.962 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8457 (mt) cc_final: 0.8113 (mp)
REVERT: A  116 ILE cc_start: 0.8322 (mm) cc_final: 0.8048 (OUTLIER)
REVERT: A  211 MET cc_start: 0.8336 (mpp) cc_final: 0.7905 (mpp)
REVERT: A  438 ASP cc_start: 0.7254 (t0) cc_final: 0.7036 (t0)
REVERT: A  576 ILE cc_start: 0.8471 (tp) cc_final: 0.8236 (tt)
REVERT: A  891 LYS cc_start: 0.8245 (ptmm) cc_final: 0.7969 (ptmm)
REVERT: A  968 LEU cc_start: 0.8658 (mp) cc_final: 0.8421 (mt)
REVERT: A 1092 MET cc_start: 0.6788 (mpp) cc_final: 0.6328 (mpp)
REVERT: A 1238 ASP cc_start: 0.7534 (m-30) cc_final: 0.7231 (m-30)
  outliers start: 36
  outliers final: 20
  residues processed: 238
  average time/residue: 1.3880
  time to fit residues: 353.1978
Evaluate side-chains
  248 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 229
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  217 LYS
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  608 ASP
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  688 LYS
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  716 MET
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  953 GLN
Chi-restraints excluded: chain A residue 1070 LEU
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1229 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 103 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9990
   chunk 14 optimal weight:    0.2980
   chunk 106 optimal weight:    6.9990
   chunk 93 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 99 optimal weight:    4.9990
   chunk 111 optimal weight:    0.1980
   chunk 72 optimal weight:    1.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
A 141 GLN
A 472 ASN
A 582 ASN
A 718 GLN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.156616 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.125913 restraints weight = 11448.811|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.44
r_work: 0.3424 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3251 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9272  Z= 0.151
  Angle     :  0.585   7.210  12589  Z= 0.302
  Chirality :  0.045   0.177   1450
  Planarity :  0.005   0.062   1609
  Dihedral  :  7.509  89.999   1337
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.58 %
    Favored  : 80.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.26), residues: 1151
  helix:  1.46 (0.29), residues: 358
  sheet: -0.55 (0.29), residues: 357
  loop : -1.16 (0.28), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A  71 
 HIS   0.004   0.001   HIS A 926 
 PHE   0.013   0.002   PHE A 936 
 TYR   0.013   0.002   TYR A 797 
 ARG   0.003   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00353 (    1)
  link_NAG-ASN         : angle       2.35668 (    3)
  link_ALPHA1-6        : bond        0.01538 (    1)
  link_ALPHA1-6        : angle       2.41068 (    3)
  link_BETA1-4         : bond        0.00195 (    2)
  link_BETA1-4         : angle       2.24039 (    6)
  link_ALPHA1-3        : bond        0.01416 (    1)
  link_ALPHA1-3        : angle       1.65838 (    3)
  hydrogen bonds       : bond        0.04389 (  335)
  hydrogen bonds       : angle       4.89149 (  966)
  SS BOND              : bond        0.00632 (    1)
  SS BOND              : angle       2.03162 (    2)
  covalent geometry    : bond        0.00359 ( 9266)
  covalent geometry    : angle       0.57987 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 235
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8413 (mt) cc_final: 0.8055 (mp)
REVERT: A  116 ILE cc_start: 0.8328 (mm) cc_final: 0.8016 (OUTLIER)
REVERT: A  180 VAL cc_start: 0.8385 (t) cc_final: 0.8140 (p)
REVERT: A  207 ASP cc_start: 0.7672 (m-30) cc_final: 0.7444 (m-30)
REVERT: A  211 MET cc_start: 0.8310 (mpp) cc_final: 0.7906 (mpp)
REVERT: A  314 ASN cc_start: 0.8172 (m-40) cc_final: 0.7906 (m-40)
REVERT: A  793 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7944 (ttp)
REVERT: A  838 MET cc_start: 0.6666 (mmp) cc_final: 0.6396 (mmp)
REVERT: A  891 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7907 (ptmm)
REVERT: A 1092 MET cc_start: 0.6736 (mpp) cc_final: 0.6302 (mpp)
REVERT: A 1238 ASP cc_start: 0.7490 (m-30) cc_final: 0.7189 (m-30)
  outliers start: 29
  outliers final: 16
  residues processed: 243
  average time/residue: 1.2226
  time to fit residues: 318.0663
Evaluate side-chains
  243 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 227
  time to evaluate  : 1.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  688 LYS
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  793 MET
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1229 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0870
   chunk 61 optimal weight:    0.7980
   chunk 108 optimal weight:   50.0000
   chunk 21 optimal weight:    1.9990
   chunk 89 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 43 optimal weight:    0.9980
   chunk 33 optimal weight:    0.0980
   chunk 56 optimal weight:    0.9980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 ASN
A 141 GLN
A 582 ASN
A 718 GLN
A 967 ASN
A 990 HIS
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.156467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.126196 restraints weight = 11574.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.42
r_work: 0.3432 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7617
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9272  Z= 0.139
  Angle     :  0.577   8.006  12589  Z= 0.297
  Chirality :  0.045   0.209   1450
  Planarity :  0.005   0.057   1609
  Dihedral  :  6.942  81.315   1337
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.85 %
    Favored  : 78.48 %
  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: -0.17 (0.26), residues: 1151
  helix:  1.58 (0.29), residues: 357
  sheet: -0.48 (0.29), residues: 357
  loop : -1.14 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  71 
 HIS   0.003   0.001   HIS A 577 
 PHE   0.013   0.002   PHE A 936 
 TYR   0.013   0.001   TYR A 797 
 ARG   0.003   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00332 (    1)
  link_NAG-ASN         : angle       2.34537 (    3)
  link_ALPHA1-6        : bond        0.01829 (    1)
  link_ALPHA1-6        : angle       2.59575 (    3)
  link_BETA1-4         : bond        0.00185 (    2)
  link_BETA1-4         : angle       2.02021 (    6)
  link_ALPHA1-3        : bond        0.01346 (    1)
  link_ALPHA1-3        : angle       1.74764 (    3)
  hydrogen bonds       : bond        0.04111 (  335)
  hydrogen bonds       : angle       4.76232 (  966)
  SS BOND              : bond        0.01317 (    1)
  SS BOND              : angle       1.84995 (    2)
  covalent geometry    : bond        0.00327 ( 9266)
  covalent geometry    : angle       0.57226 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 235
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8413 (mt) cc_final: 0.8055 (mp)
REVERT: A  116 ILE cc_start: 0.8338 (mm) cc_final: 0.8020 (OUTLIER)
REVERT: A  207 ASP cc_start: 0.7737 (m-30) cc_final: 0.7504 (m-30)
REVERT: A  314 ASN cc_start: 0.8195 (m-40) cc_final: 0.7929 (m-40)
REVERT: A  515 GLU cc_start: 0.8206 (tp30) cc_final: 0.7811 (tp30)
REVERT: A  519 ARG cc_start: 0.8067 (mtt180) cc_final: 0.7745 (mtt180)
REVERT: A  838 MET cc_start: 0.6681 (mmp) cc_final: 0.6404 (mmp)
REVERT: A  891 LYS cc_start: 0.8218 (ptmm) cc_final: 0.7973 (ptmm)
REVERT: A  968 LEU cc_start: 0.8601 (mp) cc_final: 0.8386 (mt)
REVERT: A 1092 MET cc_start: 0.6681 (mpp) cc_final: 0.6250 (mpp)
REVERT: A 1238 ASP cc_start: 0.7506 (m-30) cc_final: 0.7188 (m-30)
  outliers start: 26
  outliers final: 19
  residues processed: 243
  average time/residue: 1.1477
  time to fit residues: 299.0766
Evaluate side-chains
  243 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 225
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  688 LYS
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue 1123 MET
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1229 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 24 optimal weight:    0.9980
   chunk 103 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 112 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 113 optimal weight:    0.3980
   chunk 3 optimal weight:    0.9980
   chunk 82 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
A 718 GLN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3950 r_free = 0.3950 target = 0.155566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.125273 restraints weight = 11580.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 2.41
r_work: 0.3423 rms_B_bonded: 2.76 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.1531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9272  Z= 0.172
  Angle     :  0.610   8.723  12589  Z= 0.312
  Chirality :  0.046   0.192   1450
  Planarity :  0.005   0.055   1609
  Dihedral  :  6.538  69.745   1337
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 19.16 %
    Favored  : 77.55 %
  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: -0.19 (0.26), residues: 1151
  helix:  1.54 (0.29), residues: 357
  sheet: -0.44 (0.29), residues: 356
  loop : -1.19 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A 988 
 PHE   0.015   0.002   PHE A 913 
 TYR   0.016   0.002   TYR A 797 
 ARG   0.003   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00673 (    1)
  link_NAG-ASN         : angle       2.94667 (    3)
  link_ALPHA1-6        : bond        0.02268 (    1)
  link_ALPHA1-6        : angle       2.72764 (    3)
  link_BETA1-4         : bond        0.00184 (    2)
  link_BETA1-4         : angle       2.47492 (    6)
  link_ALPHA1-3        : bond        0.01296 (    1)
  link_ALPHA1-3        : angle       1.69715 (    3)
  hydrogen bonds       : bond        0.04555 (  335)
  hydrogen bonds       : angle       4.80652 (  966)
  SS BOND              : bond        0.00808 (    1)
  SS BOND              : angle       1.74936 (    2)
  covalent geometry    : bond        0.00415 ( 9266)
  covalent geometry    : angle       0.60371 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  259 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 227
  time to evaluate  : 1.042 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8404 (mt) cc_final: 0.8061 (mp)
REVERT: A  116 ILE cc_start: 0.8348 (mm) cc_final: 0.8042 (OUTLIER)
REVERT: A  179 GLU cc_start: 0.7529 (mt-10) cc_final: 0.7100 (mt-10)
REVERT: A  193 HIS cc_start: 0.7980 (t-90) cc_final: 0.7765 (t-90)
REVERT: A  314 ASN cc_start: 0.8172 (m-40) cc_final: 0.7912 (m-40)
REVERT: A  515 GLU cc_start: 0.8200 (tp30) cc_final: 0.7775 (tp30)
REVERT: A  519 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7780 (mtt180)
REVERT: A  780 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7597 (m-30)
REVERT: A  793 MET cc_start: 0.8132 (OUTLIER) cc_final: 0.7924 (ttp)
REVERT: A  838 MET cc_start: 0.6693 (mmp) cc_final: 0.6422 (mmp)
REVERT: A  891 LYS cc_start: 0.8215 (ptmm) cc_final: 0.7926 (ptmm)
REVERT: A  968 LEU cc_start: 0.8646 (mp) cc_final: 0.8402 (mt)
REVERT: A 1092 MET cc_start: 0.6735 (mpp) cc_final: 0.6350 (mpp)
REVERT: A 1238 ASP cc_start: 0.7514 (m-30) cc_final: 0.7194 (m-30)
  outliers start: 32
  outliers final: 20
  residues processed: 241
  average time/residue: 1.2101
  time to fit residues: 314.7202
Evaluate side-chains
  244 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 223
  time to evaluate  : 1.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  688 LYS
Chi-restraints excluded: chain A residue  780 ASP
Chi-restraints excluded: chain A residue  793 MET
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue 1138 SER
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1227 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    0.2980
   chunk 13 optimal weight:    6.9990
   chunk 32 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9980
   chunk 52 optimal weight:    3.9990
   chunk 72 optimal weight:    0.3980
   chunk 104 optimal weight:    0.0670
   chunk 95 optimal weight:    0.9990
   chunk 47 optimal weight:    0.8980
   chunk 38 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 ASN
A 141 GLN
A 718 GLN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.156572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.125981 restraints weight = 11740.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3564 rms_B_bonded: 2.44
r_work: 0.3426 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1605

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9272  Z= 0.134
  Angle     :  0.586   8.878  12589  Z= 0.298
  Chirality :  0.045   0.204   1450
  Planarity :  0.004   0.054   1609
  Dihedral  :  6.074  60.590   1337
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 19.77 %
    Favored  : 77.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.26), residues: 1151
  helix:  1.66 (0.29), residues: 357
  sheet: -0.39 (0.29), residues: 356
  loop : -1.15 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  71 
 HIS   0.006   0.001   HIS A 988 
 PHE   0.016   0.002   PHE A 913 
 TYR   0.012   0.001   TYR A 797 
 ARG   0.003   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00268 (    1)
  link_NAG-ASN         : angle       2.26920 (    3)
  link_ALPHA1-6        : bond        0.02539 (    1)
  link_ALPHA1-6        : angle       2.74763 (    3)
  link_BETA1-4         : bond        0.00155 (    2)
  link_BETA1-4         : angle       2.02360 (    6)
  link_ALPHA1-3        : bond        0.01322 (    1)
  link_ALPHA1-3        : angle       1.92950 (    3)
  hydrogen bonds       : bond        0.03911 (  335)
  hydrogen bonds       : angle       4.66494 (  966)
  SS BOND              : bond        0.00506 (    1)
  SS BOND              : angle       1.74472 (    2)
  covalent geometry    : bond        0.00314 ( 9266)
  covalent geometry    : angle       0.58142 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 229
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8366 (mt) cc_final: 0.8010 (mp)
REVERT: A  116 ILE cc_start: 0.8325 (mm) cc_final: 0.8016 (OUTLIER)
REVERT: A  179 GLU cc_start: 0.7524 (mt-10) cc_final: 0.7081 (mt-10)
REVERT: A  193 HIS cc_start: 0.7976 (t-90) cc_final: 0.7775 (t-90)
REVERT: A  207 ASP cc_start: 0.7801 (m-30) cc_final: 0.7591 (m-30)
REVERT: A  282 ARG cc_start: 0.8222 (mtm110) cc_final: 0.7981 (mtm180)
REVERT: A  314 ASN cc_start: 0.8190 (m-40) cc_final: 0.7935 (m-40)
REVERT: A  515 GLU cc_start: 0.8211 (tp30) cc_final: 0.7802 (tp30)
REVERT: A  519 ARG cc_start: 0.8092 (mtt180) cc_final: 0.7788 (mtt180)
REVERT: A  762 ASN cc_start: 0.7258 (t160) cc_final: 0.6671 (t160)
REVERT: A  780 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7562 (m-30)
REVERT: A  793 MET cc_start: 0.8136 (OUTLIER) cc_final: 0.7932 (ttp)
REVERT: A  828 LEU cc_start: 0.8552 (tt) cc_final: 0.8331 (tm)
REVERT: A  838 MET cc_start: 0.6711 (mmp) cc_final: 0.6435 (mmp)
REVERT: A 1092 MET cc_start: 0.6727 (mpp) cc_final: 0.6341 (mpp)
REVERT: A 1238 ASP cc_start: 0.7534 (m-30) cc_final: 0.7203 (m-30)
  outliers start: 29
  outliers final: 24
  residues processed: 241
  average time/residue: 1.1193
  time to fit residues: 289.0354
Evaluate side-chains
  247 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 222
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  253 SER
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  780 ASP
Chi-restraints excluded: chain A residue  793 MET
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  988 HIS
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1227 PHE
Chi-restraints excluded: chain A residue 1229 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 30 optimal weight:    3.9990
   chunk 58 optimal weight:    0.2980
   chunk 44 optimal weight:    1.9990
   chunk 15 optimal weight:    0.6980
   chunk 67 optimal weight:    0.7980
   chunk 103 optimal weight:    0.8980
   chunk 111 optimal weight:   20.0000
   chunk 97 optimal weight:    0.1980
   chunk 3 optimal weight:    0.6980
   chunk 65 optimal weight:    0.2980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
** A  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
A 718 GLN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.157114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.126527 restraints weight = 11781.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3573 rms_B_bonded: 2.44
r_work: 0.3437 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3264 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.1682

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9272  Z= 0.126
  Angle     :  0.586   8.931  12589  Z= 0.296
  Chirality :  0.045   0.199   1450
  Planarity :  0.004   0.052   1609
  Dihedral  :  5.767  54.245   1337
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.08 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.01 (0.26), residues: 1151
  helix:  1.75 (0.29), residues: 357
  sheet: -0.34 (0.29), residues: 356
  loop : -1.14 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1228 
 HIS   0.006   0.001   HIS A 988 
 PHE   0.019   0.002   PHE A 889 
 TYR   0.011   0.001   TYR A 797 
 ARG   0.002   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00255 (    1)
  link_NAG-ASN         : angle       2.30432 (    3)
  link_ALPHA1-6        : bond        0.02791 (    1)
  link_ALPHA1-6        : angle       2.83553 (    3)
  link_BETA1-4         : bond        0.00161 (    2)
  link_BETA1-4         : angle       1.80878 (    6)
  link_ALPHA1-3        : bond        0.01278 (    1)
  link_ALPHA1-3        : angle       1.91987 (    3)
  hydrogen bonds       : bond        0.03753 (  335)
  hydrogen bonds       : angle       4.58122 (  966)
  SS BOND              : bond        0.00649 (    1)
  SS BOND              : angle       1.80978 (    2)
  covalent geometry    : bond        0.00294 ( 9266)
  covalent geometry    : angle       0.58128 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 232
  time to evaluate  : 1.018 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8371 (mt) cc_final: 0.8012 (mp)
REVERT: A  116 ILE cc_start: 0.8328 (mm) cc_final: 0.8014 (OUTLIER)
REVERT: A  179 GLU cc_start: 0.7492 (mt-10) cc_final: 0.7065 (mt-10)
REVERT: A  183 ASP cc_start: 0.7565 (t0) cc_final: 0.7350 (t0)
REVERT: A  193 HIS cc_start: 0.7977 (t-90) cc_final: 0.7753 (t-90)
REVERT: A  207 ASP cc_start: 0.7759 (m-30) cc_final: 0.7537 (m-30)
REVERT: A  314 ASN cc_start: 0.8212 (m-40) cc_final: 0.7951 (m-40)
REVERT: A  515 GLU cc_start: 0.8259 (tp30) cc_final: 0.7879 (tp30)
REVERT: A  519 ARG cc_start: 0.8088 (mtt180) cc_final: 0.7788 (mtt180)
REVERT: A  780 ASP cc_start: 0.7834 (OUTLIER) cc_final: 0.7555 (m-30)
REVERT: A  838 MET cc_start: 0.6733 (mmp) cc_final: 0.6459 (mmp)
REVERT: A  912 LYS cc_start: 0.7733 (OUTLIER) cc_final: 0.7509 (ttpp)
REVERT: A  923 GLU cc_start: 0.7287 (mm-30) cc_final: 0.6905 (mm-30)
REVERT: A  968 LEU cc_start: 0.8535 (mp) cc_final: 0.8330 (mt)
REVERT: A 1019 GLN cc_start: 0.6800 (tm-30) cc_final: 0.6445 (tm-30)
REVERT: A 1084 GLU cc_start: 0.7892 (tp30) cc_final: 0.7514 (tm-30)
REVERT: A 1092 MET cc_start: 0.6606 (mpp) cc_final: 0.6226 (mpp)
REVERT: A 1238 ASP cc_start: 0.7508 (m-30) cc_final: 0.7177 (m-30)
  outliers start: 30
  outliers final: 26
  residues processed: 244
  average time/residue: 1.1928
  time to fit residues: 311.9707
Evaluate side-chains
  250 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 223
  time to evaluate  : 0.953 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  716 MET
Chi-restraints excluded: chain A residue  780 ASP
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue  988 HIS
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1047 ILE
Chi-restraints excluded: chain A residue 1123 MET
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1227 PHE
Chi-restraints excluded: chain A residue 1229 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 23 optimal weight:    2.9990
   chunk 53 optimal weight:    0.9980
   chunk 80 optimal weight:    5.9990
   chunk 88 optimal weight:    0.9980
   chunk 0 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9990
   chunk 112 optimal weight:    4.9990
   chunk 65 optimal weight:    0.5980
   chunk 8 optimal weight:    0.8980
   chunk 77 optimal weight:    2.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 141 GLN
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.156131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.125482 restraints weight = 11667.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3556 rms_B_bonded: 2.46
r_work: 0.3421 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3248 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.1685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9272  Z= 0.197
  Angle     :  0.638   9.001  12589  Z= 0.328
  Chirality :  0.047   0.193   1450
  Planarity :  0.005   0.056   1609
  Dihedral  :  5.781  52.134   1337
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 20.08 %
    Favored  : 76.62 %
  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: -0.13 (0.26), residues: 1151
  helix:  1.61 (0.29), residues: 357
  sheet: -0.37 (0.29), residues: 356
  loop : -1.20 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  71 
 HIS   0.009   0.001   HIS A 926 
 PHE   0.018   0.002   PHE A 889 
 TYR   0.019   0.002   TYR A 797 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00437 (    1)
  link_NAG-ASN         : angle       2.81331 (    3)
  link_ALPHA1-6        : bond        0.02843 (    1)
  link_ALPHA1-6        : angle       2.89387 (    3)
  link_BETA1-4         : bond        0.00275 (    2)
  link_BETA1-4         : angle       2.08141 (    6)
  link_ALPHA1-3        : bond        0.01233 (    1)
  link_ALPHA1-3        : angle       1.95380 (    3)
  hydrogen bonds       : bond        0.04736 (  335)
  hydrogen bonds       : angle       4.72751 (  966)
  SS BOND              : bond        0.00683 (    1)
  SS BOND              : angle       2.10941 (    2)
  covalent geometry    : bond        0.00477 ( 9266)
  covalent geometry    : angle       0.63262 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 229
  time to evaluate  : 1.024 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8379 (mt) cc_final: 0.8022 (mp)
REVERT: A  116 ILE cc_start: 0.8337 (mm) cc_final: 0.8025 (OUTLIER)
REVERT: A  179 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7102 (mt-10)
REVERT: A  183 ASP cc_start: 0.7645 (t0) cc_final: 0.7431 (t0)
REVERT: A  193 HIS cc_start: 0.7995 (t-90) cc_final: 0.7777 (t-90)
REVERT: A  282 ARG cc_start: 0.8218 (mtm110) cc_final: 0.7978 (mtm180)
REVERT: A  314 ASN cc_start: 0.8160 (m-40) cc_final: 0.7906 (m-40)
REVERT: A  515 GLU cc_start: 0.8298 (tp30) cc_final: 0.7933 (tp30)
REVERT: A  519 ARG cc_start: 0.8120 (mtt180) cc_final: 0.7833 (mtt180)
REVERT: A  698 GLU cc_start: 0.7165 (OUTLIER) cc_final: 0.6855 (mt-10)
REVERT: A  828 LEU cc_start: 0.8518 (tm) cc_final: 0.8189 (tp)
REVERT: A  838 MET cc_start: 0.6714 (mmp) cc_final: 0.6449 (mmp)
REVERT: A  912 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7454 (ttpp)
REVERT: A  923 GLU cc_start: 0.7279 (mm-30) cc_final: 0.6951 (mm-30)
REVERT: A  968 LEU cc_start: 0.8619 (mp) cc_final: 0.8375 (mt)
REVERT: A 1084 GLU cc_start: 0.7906 (tp30) cc_final: 0.7576 (tm-30)
REVERT: A 1092 MET cc_start: 0.6761 (mpp) cc_final: 0.6391 (mpp)
REVERT: A 1238 ASP cc_start: 0.7565 (m-30) cc_final: 0.7234 (m-30)
  outliers start: 32
  outliers final: 26
  residues processed: 240
  average time/residue: 1.3305
  time to fit residues: 341.3940
Evaluate side-chains
  252 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 225
  time to evaluate  : 1.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  232 MET
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  688 LYS
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  951 THR
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue  988 HIS
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1047 ILE
Chi-restraints excluded: chain A residue 1070 LEU
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1227 PHE
Chi-restraints excluded: chain A residue 1229 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 81 optimal weight:    1.9990
   chunk 49 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 89 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 96 optimal weight:    0.6980
   chunk 83 optimal weight:    0.0270
   overall best weight:    0.7040

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

Flipped N/Q/H residues before XYZ refinement:
** A  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 ASN
A 718 GLN
** A 762 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.155909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.125478 restraints weight = 11731.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 2.38
r_work: 0.3431 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9272  Z= 0.166
  Angle     :  0.631   9.124  12589  Z= 0.325
  Chirality :  0.046   0.191   1450
  Planarity :  0.005   0.055   1609
  Dihedral  :  5.680  51.235   1337
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.11 %
    Favored  : 76.00 %
  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 (0.26), residues: 1151
  helix:  1.63 (0.29), residues: 357
  sheet: -0.38 (0.29), residues: 357
  loop : -1.20 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A  71 
 HIS   0.008   0.001   HIS A 763 
 PHE   0.018   0.002   PHE A 889 
 TYR   0.016   0.002   TYR A 797 
 ARG   0.002   0.000   ARG A  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00352 (    1)
  link_NAG-ASN         : angle       2.61152 (    3)
  link_ALPHA1-6        : bond        0.02968 (    1)
  link_ALPHA1-6        : angle       2.96512 (    3)
  link_BETA1-4         : bond        0.00180 (    2)
  link_BETA1-4         : angle       1.90603 (    6)
  link_ALPHA1-3        : bond        0.01337 (    1)
  link_ALPHA1-3        : angle       2.03550 (    3)
  hydrogen bonds       : bond        0.04382 (  335)
  hydrogen bonds       : angle       4.71948 (  966)
  SS BOND              : bond        0.00813 (    1)
  SS BOND              : angle       2.07733 (    2)
  covalent geometry    : bond        0.00398 ( 9266)
  covalent geometry    : angle       0.62582 (12572)

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

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

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2302 Ramachandran restraints generated.
    1151 Oldfield, 0 Emsley, 1151 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 225
  time to evaluate  : 1.030 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8408 (mt) cc_final: 0.8076 (mp)
REVERT: A  116 ILE cc_start: 0.8339 (mm) cc_final: 0.8026 (OUTLIER)
REVERT: A  179 GLU cc_start: 0.7466 (mt-10) cc_final: 0.7020 (mt-10)
REVERT: A  183 ASP cc_start: 0.7608 (t0) cc_final: 0.7397 (t0)
REVERT: A  193 HIS cc_start: 0.7966 (t-90) cc_final: 0.7733 (t-90)
REVERT: A  207 ASP cc_start: 0.7753 (m-30) cc_final: 0.7540 (m-30)
REVERT: A  314 ASN cc_start: 0.8174 (m-40) cc_final: 0.7927 (m-40)
REVERT: A  515 GLU cc_start: 0.8206 (tp30) cc_final: 0.7832 (tp30)
REVERT: A  519 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7765 (mtt180)
REVERT: A  529 ASN cc_start: 0.8228 (OUTLIER) cc_final: 0.7969 (t0)
REVERT: A  698 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6775 (mt-10)
REVERT: A  828 LEU cc_start: 0.8528 (tm) cc_final: 0.8319 (tt)
REVERT: A  838 MET cc_start: 0.6725 (mmp) cc_final: 0.6456 (mmp)
REVERT: A  912 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7472 (ttpp)
REVERT: A  923 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6976 (mm-30)
REVERT: A  968 LEU cc_start: 0.8605 (mp) cc_final: 0.8369 (mt)
REVERT: A 1019 GLN cc_start: 0.6777 (tm-30) cc_final: 0.6394 (tm-30)
REVERT: A 1084 GLU cc_start: 0.7857 (tp30) cc_final: 0.7540 (tm-30)
REVERT: A 1092 MET cc_start: 0.6685 (mpp) cc_final: 0.6314 (mpp)
REVERT: A 1238 ASP cc_start: 0.7557 (m-30) cc_final: 0.7209 (m-30)
  outliers start: 28
  outliers final: 24
  residues processed: 237
  average time/residue: 1.2574
  time to fit residues: 317.9684
Evaluate side-chains
  252 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 226
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  121 VAL
Chi-restraints excluded: chain A residue  172 ASP
Chi-restraints excluded: chain A residue  174 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  418 LYS
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  529 ASN
Chi-restraints excluded: chain A residue  594 THR
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  640 ILE
Chi-restraints excluded: chain A residue  688 LYS
Chi-restraints excluded: chain A residue  693 THR
Chi-restraints excluded: chain A residue  698 GLU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  948 THR
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue  988 HIS
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1047 ILE
Chi-restraints excluded: chain A residue 1195 VAL
Chi-restraints excluded: chain A residue 1227 PHE
Chi-restraints excluded: chain A residue 1229 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 91 optimal weight:    0.8980
   chunk 107 optimal weight:    5.9990
   chunk 27 optimal weight:    1.9990
   chunk 85 optimal weight:    0.5980
   chunk 61 optimal weight:    0.0010
   chunk 51 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 8 optimal weight:    0.6980
   chunk 93 optimal weight:    2.9990
   overall best weight:    0.5786

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

Flipped N/Q/H residues before XYZ refinement:
** A  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  64 ASN
A 210 HIS
** A 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 ASN
A 718 GLN
A 762 ASN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.156588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.125920 restraints weight = 11678.687|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 2.43
r_work: 0.3430 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7622
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9272  Z= 0.145
  Angle     :  0.604   9.206  12589  Z= 0.310
  Chirality :  0.045   0.187   1450
  Planarity :  0.005   0.055   1609
  Dihedral  :  5.512  50.062   1337
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 21.63 %
    Favored  : 75.80 %
  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: -0.07 (0.26), residues: 1151
  helix:  1.68 (0.29), residues: 357
  sheet: -0.34 (0.29), residues: 357
  loop : -1.19 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  71 
 HIS   0.008   0.001   HIS A 763 
 PHE   0.018   0.002   PHE A 889 
 TYR   0.014   0.002   TYR A 797 
 ARG   0.002   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00299 (    1)
  link_NAG-ASN         : angle       2.44668 (    3)
  link_ALPHA1-6        : bond        0.02950 (    1)
  link_ALPHA1-6        : angle       2.96768 (    3)
  link_BETA1-4         : bond        0.00166 (    2)
  link_BETA1-4         : angle       1.78996 (    6)
  link_ALPHA1-3        : bond        0.01193 (    1)
  link_ALPHA1-3        : angle       1.93971 (    3)
  hydrogen bonds       : bond        0.04058 (  335)
  hydrogen bonds       : angle       4.65318 (  966)
  SS BOND              : bond        0.00619 (    1)
  SS BOND              : angle       1.99551 (    2)
  covalent geometry    : bond        0.00342 ( 9266)
  covalent geometry    : angle       0.59941 (12572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 8679.93 seconds
wall clock time: 152 minutes 12.00 seconds (9132.00 seconds total)