Starting phenix.real_space_refine
on Mon May 12 16:34:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ens_19843/05_2025/9ens_19843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ens_19843/05_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_19843/05_2025/9ens_19843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ens_19843/05_2025/9ens_19843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ens_19843/05_2025/9ens_19843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ens_19843/05_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 5.92, per 1000 atoms: 0.65
  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: 2.87
  Conformation dependent library (CDL) restraints added in 1.2 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: 1.16
  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: 3.08

  Time building geometry restraints manager: 3.29 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:             2.200
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     25.360
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:10.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.730
-------------------------------------------------------------------------------
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  : 1.045 
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: 1.1486
  time to fit residues: 298.7842
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  : 1.018 
-------------------------------------------------------------------------------
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 = 0.126178 restraints weight = 11461.870|
|-----------------------------------------------------------------------------|
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: 0.3254 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
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  : 0.952 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8435 (mt) cc_final: 0.8084 (mp)
REVERT: A  116 ILE cc_start: 0.8297 (mm) cc_final: 0.7980 (OUTLIER)
REVERT: A  180 VAL cc_start: 0.8380 (t) cc_final: 0.8166 (p)
REVERT: A  197 GLU cc_start: 0.7554 (pm20) cc_final: 0.7296 (pm20)
REVERT: A  207 ASP cc_start: 0.7726 (m-30) cc_final: 0.7508 (m-30)
REVERT: A  211 MET cc_start: 0.8363 (mpp) cc_final: 0.7925 (mpp)
REVERT: A  708 MET cc_start: 0.8482 (mpt) cc_final: 0.8260 (mpp)
REVERT: A  762 ASN cc_start: 0.7255 (OUTLIER) cc_final: 0.6674 (t0)
REVERT: A  781 GLU cc_start: 0.7729 (tp30) cc_final: 0.7445 (tp30)
REVERT: A  891 LYS cc_start: 0.8232 (ptmm) cc_final: 0.7789 (ptmm)
REVERT: A  952 VAL cc_start: 0.8301 (t) cc_final: 0.8003 (p)
REVERT: A 1092 MET cc_start: 0.6746 (mpp) cc_final: 0.6298 (mpp)
REVERT: A 1238 ASP cc_start: 0.7486 (m-30) cc_final: 0.7190 (m-30)
  outliers start: 16
  outliers final: 6
  residues processed: 241
  average time/residue: 1.2251
  time to fit residues: 315.5768
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  : 1.100 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   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  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 = 0.3961 r_free = 0.3961 target = 0.156625 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.125827 restraints weight = 11690.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.47
r_work: 0.3431 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.66 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1116

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= 0.172
  Angle     :  0.594   7.729  12589  Z= 0.309
  Chirality :  0.046   0.146   1450
  Planarity :  0.005   0.056   1609
  Dihedral  :  8.113  98.923   1337
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 14.21 %
    Favored  : 83.11 %
  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: -0.21 (0.26), residues: 1151
  helix:  1.44 (0.29), residues: 364
  sheet: -0.42 (0.29), residues: 354
  loop : -1.19 (0.28), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A  71 
 HIS   0.003   0.001   HIS A 926 
 PHE   0.015   0.002   PHE A 549 
 TYR   0.015   0.002   TYR A 797 
 ARG   0.004   0.000   ARG A  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00281 (    1)
  link_NAG-ASN         : angle       2.28506 (    3)
  link_ALPHA1-6        : bond        0.01704 (    1)
  link_ALPHA1-6        : angle       2.38537 (    3)
  link_BETA1-4         : bond        0.00246 (    2)
  link_BETA1-4         : angle       2.38736 (    6)
  link_ALPHA1-3        : bond        0.01370 (    1)
  link_ALPHA1-3        : angle       1.46514 (    3)
  hydrogen bonds       : bond        0.04871 (  335)
  hydrogen bonds       : angle       5.03498 (  966)
  SS BOND              : bond        0.00334 (    1)
  SS BOND              : angle       1.84754 (    2)
  covalent geometry    : bond        0.00410 ( 9266)
  covalent geometry    : angle       0.58859 (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
  260 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 234
  time to evaluate  : 1.068 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8419 (mt) cc_final: 0.8076 (mp)
REVERT: A  116 ILE cc_start: 0.8300 (mm) cc_final: 0.8016 (OUTLIER)
REVERT: A  180 VAL cc_start: 0.8359 (t) cc_final: 0.8142 (p)
REVERT: A  207 ASP cc_start: 0.7674 (m-30) cc_final: 0.7457 (m-30)
REVERT: A  211 MET cc_start: 0.8381 (mpp) cc_final: 0.7947 (mpp)
REVERT: A  708 MET cc_start: 0.8442 (mpt) cc_final: 0.8123 (mpp)
REVERT: A  891 LYS cc_start: 0.8231 (ptmm) cc_final: 0.8002 (ptmm)
REVERT: A  952 VAL cc_start: 0.8361 (t) cc_final: 0.8000 (p)
REVERT: A 1092 MET cc_start: 0.6721 (mpp) cc_final: 0.6281 (mpp)
REVERT: A 1238 ASP cc_start: 0.7466 (m-30) cc_final: 0.7178 (m-30)
  outliers start: 26
  outliers final: 16
  residues processed: 240
  average time/residue: 1.1087
  time to fit residues: 284.7829
Evaluate side-chains
  244 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 229
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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  400 SER
Chi-restraints excluded: chain A residue  406 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  635 MET
Chi-restraints excluded: chain A residue  688 LYS
Chi-restraints excluded: chain A residue  766 THR
Chi-restraints excluded: chain A residue  826 LYS
Chi-restraints excluded: chain A residue  912 LYS
Chi-restraints excluded: chain A residue  964 VAL
Chi-restraints excluded: chain A residue 1018 MET
Chi-restraints excluded: chain A residue 1195 VAL
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:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0370
   chunk 106 optimal weight:    4.9990
   chunk 93 optimal weight:    1.9990
   chunk 110 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 99 optimal weight:    2.9990
   chunk 111 optimal weight:    2.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    1.8066

-------------------------------------------------------------------------------
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 472 ASN
A 582 ASN
A 718 GLN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1049 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.152760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.122317 restraints weight = 11615.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3510 rms_B_bonded: 2.39
r_work: 0.3375 rms_B_bonded: 2.73 restraints_weight: 0.5000
r_work: 0.3203 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7691
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.060   9272  Z= 0.360
  Angle     :  0.720  10.157  12589  Z= 0.380
  Chirality :  0.052   0.196   1450
  Planarity :  0.006   0.064   1609
  Dihedral  :  7.879  92.777   1337
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.56 %
    Favored  : 94.44 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 15.55 %
    Favored  : 80.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.56 (0.25), residues: 1151
  helix:  1.02 (0.28), residues: 363
  sheet: -0.55 (0.29), residues: 350
  loop : -1.31 (0.28), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A  71 
 HIS   0.007   0.002   HIS A  47 
 PHE   0.036   0.003   PHE A 549 
 TYR   0.027   0.003   TYR A 797 
 ARG   0.005   0.001   ARG A  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00550 (    1)
  link_NAG-ASN         : angle       2.53115 (    3)
  link_ALPHA1-6        : bond        0.01355 (    1)
  link_ALPHA1-6        : angle       2.45838 (    3)
  link_BETA1-4         : bond        0.00688 (    2)
  link_BETA1-4         : angle       2.88739 (    6)
  link_ALPHA1-3        : bond        0.01407 (    1)
  link_ALPHA1-3        : angle       1.50359 (    3)
  hydrogen bonds       : bond        0.06637 (  335)
  hydrogen bonds       : angle       5.21617 (  966)
  SS BOND              : bond        0.01103 (    1)
  SS BOND              : angle       2.66782 (    2)
  covalent geometry    : bond        0.00887 ( 9266)
  covalent geometry    : angle       0.71433 (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
  278 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 238
  time to evaluate  : 0.978 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8484 (mt) cc_final: 0.8127 (mp)
REVERT: A  105 LYS cc_start: 0.8322 (OUTLIER) cc_final: 0.8099 (mttt)
REVERT: A  116 ILE cc_start: 0.8387 (mm) cc_final: 0.8067 (mp)
REVERT: A  211 MET cc_start: 0.8338 (mpp) cc_final: 0.7945 (mpp)
REVERT: A  314 ASN cc_start: 0.8140 (m-40) cc_final: 0.7860 (m-40)
REVERT: A  576 ILE cc_start: 0.8495 (OUTLIER) cc_final: 0.8271 (tt)
REVERT: A  765 LEU cc_start: 0.7757 (mp) cc_final: 0.7543 (mt)
REVERT: A  793 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7905 (ttp)
REVERT: A  838 MET cc_start: 0.6640 (mmp) cc_final: 0.6368 (mmp)
REVERT: A  891 LYS cc_start: 0.8262 (ptmm) cc_final: 0.7962 (ptmm)
REVERT: A  968 LEU cc_start: 0.8668 (mp) cc_final: 0.8455 (mt)
REVERT: A 1092 MET cc_start: 0.6938 (mpp) cc_final: 0.6495 (mpp)
REVERT: A 1238 ASP cc_start: 0.7538 (m-30) cc_final: 0.7227 (m-30)
  outliers start: 40
  outliers final: 22
  residues processed: 246
  average time/residue: 1.1497
  time to fit residues: 302.4280
Evaluate side-chains
  254 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 229
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   21 ASN
Chi-restraints excluded: chain A residue  105 LYS
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  254 THR
Chi-restraints excluded: chain A residue  400 SER
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  576 ILE
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  793 MET
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  811 LEU
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 1070 LEU
Chi-restraints excluded: chain A residue 1138 SER
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    0.3980
   chunk 18 optimal weight:    0.0070
   chunk 61 optimal weight:    0.9980
   chunk 108 optimal weight:   50.0000
   chunk 21 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 23 optimal weight:    1.9990
   chunk 63 optimal weight:    0.8980
   chunk 43 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 56 optimal weight:    0.6980
   overall best weight:    0.4798

-------------------------------------------------------------------------------
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 472 ASN
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: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.156833 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.126227 restraints weight = 11480.045|
|-----------------------------------------------------------------------------|
r_work (start): 0.3565 rms_B_bonded: 2.42
r_work: 0.3430 rms_B_bonded: 2.78 restraints_weight: 0.5000
r_work: 0.3254 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9272  Z= 0.133
  Angle     :  0.583   7.821  12589  Z= 0.301
  Chirality :  0.046   0.276   1450
  Planarity :  0.005   0.066   1609
  Dihedral  :  7.135  83.608   1337
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.54 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.26), residues: 1151
  helix:  1.49 (0.29), residues: 357
  sheet: -0.56 (0.29), residues: 357
  loop : -1.20 (0.28), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A  71 
 HIS   0.004   0.001   HIS A 926 
 PHE   0.014   0.002   PHE A 936 
 TYR   0.012   0.001   TYR A 633 
 ARG   0.004   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00346 (    1)
  link_NAG-ASN         : angle       2.21561 (    3)
  link_ALPHA1-6        : bond        0.01717 (    1)
  link_ALPHA1-6        : angle       2.52742 (    3)
  link_BETA1-4         : bond        0.00376 (    2)
  link_BETA1-4         : angle       2.06519 (    6)
  link_ALPHA1-3        : bond        0.01339 (    1)
  link_ALPHA1-3        : angle       1.73277 (    3)
  hydrogen bonds       : bond        0.04121 (  335)
  hydrogen bonds       : angle       4.83400 (  966)
  SS BOND              : bond        0.01206 (    1)
  SS BOND              : angle       1.85314 (    2)
  covalent geometry    : bond        0.00308 ( 9266)
  covalent geometry    : angle       0.57817 (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: 25
    poor density    : 236
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8397 (mt) cc_final: 0.8035 (mp)
REVERT: A  116 ILE cc_start: 0.8312 (mm) cc_final: 0.7996 (OUTLIER)
REVERT: A  180 VAL cc_start: 0.8397 (t) cc_final: 0.8150 (p)
REVERT: A  197 GLU cc_start: 0.7627 (pm20) cc_final: 0.7336 (pt0)
REVERT: A  207 ASP cc_start: 0.7678 (m-30) cc_final: 0.7455 (m-30)
REVERT: A  211 MET cc_start: 0.8322 (mpp) cc_final: 0.8116 (mtp)
REVERT: A  282 ARG cc_start: 0.8255 (mtm110) cc_final: 0.8029 (mtm180)
REVERT: A  314 ASN cc_start: 0.8186 (m-40) cc_final: 0.7918 (m-40)
REVERT: A  515 GLU cc_start: 0.8223 (tp30) cc_final: 0.7912 (tp30)
REVERT: A  519 ARG cc_start: 0.8123 (mtt180) cc_final: 0.7770 (mtt180)
REVERT: A  838 MET cc_start: 0.6696 (mmp) cc_final: 0.6422 (mmp)
REVERT: A  891 LYS cc_start: 0.8203 (ptmm) cc_final: 0.7973 (ptmm)
REVERT: A  968 LEU cc_start: 0.8647 (mp) cc_final: 0.8396 (mt)
REVERT: A 1092 MET cc_start: 0.6747 (mpp) cc_final: 0.6312 (mpp)
REVERT: A 1238 ASP cc_start: 0.7544 (m-30) cc_final: 0.7229 (m-30)
  outliers start: 25
  outliers final: 13
  residues processed: 240
  average time/residue: 1.1077
  time to fit residues: 284.5380
Evaluate side-chains
  238 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 226
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
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  400 SER
Chi-restraints excluded: chain A residue  489 ILE
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  912 LYS
Chi-restraints excluded: chain A residue  964 VAL
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:    0.9990
   chunk 103 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 28 optimal weight:    3.9990
   chunk 112 optimal weight:    3.9990
   chunk 22 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9980
   chunk 3 optimal weight:    0.6980
   chunk 82 optimal weight:    0.8980
   chunk 21 optimal weight:    0.9980
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.3944 r_free = 0.3944 target = 0.155307 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.124865 restraints weight = 11534.511|
|-----------------------------------------------------------------------------|
r_work (start): 0.3543 rms_B_bonded: 2.44
r_work: 0.3407 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.1510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   9272  Z= 0.195
  Angle     :  0.624   8.417  12589  Z= 0.321
  Chirality :  0.047   0.208   1450
  Planarity :  0.005   0.057   1609
  Dihedral  :  6.765  75.087   1337
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.60 %
    Allowed  : 18.64 %
    Favored  : 77.75 %
  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: -0.31 (0.26), residues: 1151
  helix:  1.41 (0.29), residues: 357
  sheet: -0.49 (0.29), residues: 354
  loop : -1.23 (0.28), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A  71 
 HIS   0.004   0.001   HIS A1045 
 PHE   0.017   0.002   PHE A 913 
 TYR   0.017   0.002   TYR A 797 
 ARG   0.003   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00493 (    1)
  link_NAG-ASN         : angle       2.59010 (    3)
  link_ALPHA1-6        : bond        0.01899 (    1)
  link_ALPHA1-6        : angle       2.63332 (    3)
  link_BETA1-4         : bond        0.00336 (    2)
  link_BETA1-4         : angle       2.24198 (    6)
  link_ALPHA1-3        : bond        0.01325 (    1)
  link_ALPHA1-3        : angle       1.77307 (    3)
  hydrogen bonds       : bond        0.04889 (  335)
  hydrogen bonds       : angle       4.87362 (  966)
  SS BOND              : bond        0.00744 (    1)
  SS BOND              : angle       1.89990 (    2)
  covalent geometry    : bond        0.00474 ( 9266)
  covalent geometry    : angle       0.61913 (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
  264 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 229
  time to evaluate  : 1.067 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8439 (mt) cc_final: 0.8082 (mp)
REVERT: A  116 ILE cc_start: 0.8350 (mm) cc_final: 0.8032 (OUTLIER)
REVERT: A  197 GLU cc_start: 0.7661 (pm20) cc_final: 0.7367 (pt0)
REVERT: A  211 MET cc_start: 0.8357 (mpp) cc_final: 0.8146 (mtp)
REVERT: A  314 ASN cc_start: 0.8184 (m-40) cc_final: 0.7917 (m-40)
REVERT: A  515 GLU cc_start: 0.8212 (tp30) cc_final: 0.7882 (tp30)
REVERT: A  519 ARG cc_start: 0.8130 (mtt180) cc_final: 0.7810 (mtt180)
REVERT: A  838 MET cc_start: 0.6677 (mmp) cc_final: 0.6409 (mmp)
REVERT: A  891 LYS cc_start: 0.8232 (ptmm) cc_final: 0.7980 (ptmm)
REVERT: A  968 LEU cc_start: 0.8647 (mp) cc_final: 0.8397 (mt)
REVERT: A 1092 MET cc_start: 0.6818 (mpp) cc_final: 0.6404 (mpp)
REVERT: A 1238 ASP cc_start: 0.7564 (m-30) cc_final: 0.7234 (m-30)
  outliers start: 35
  outliers final: 22
  residues processed: 240
  average time/residue: 1.0897
  time to fit residues: 280.7382
Evaluate side-chains
  245 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 224
  time to evaluate  : 1.097 
-------------------------------------------------------------------------------
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  201 MET
Chi-restraints excluded: chain A residue  232 MET
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  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  766 THR
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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 8 optimal weight:    0.0970
   chunk 13 optimal weight:   20.0000
   chunk 32 optimal weight:    1.9990
   chunk 87 optimal weight:    0.8980
   chunk 52 optimal weight:    4.9990
   chunk 72 optimal weight:    2.9990
   chunk 104 optimal weight:    0.0040
   chunk 95 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.3961 r_free = 0.3961 target = 0.156732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.126255 restraints weight = 11730.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3561 rms_B_bonded: 2.44
r_work: 0.3426 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1583

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9272  Z= 0.135
  Angle     :  0.582   8.862  12589  Z= 0.298
  Chirality :  0.045   0.200   1450
  Planarity :  0.005   0.054   1609
  Dihedral  :  6.229  63.562   1337
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 20.29 %
    Favored  : 76.93 %
  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:  1.57 (0.29), residues: 357
  sheet: -0.46 (0.29), residues: 356
  loop : -1.18 (0.29), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A1228 
 HIS   0.005   0.001   HIS A 988 
 PHE   0.015   0.002   PHE A 913 
 TYR   0.012   0.002   TYR A 687 
 ARG   0.003   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00267 (    1)
  link_NAG-ASN         : angle       2.25444 (    3)
  link_ALPHA1-6        : bond        0.02360 (    1)
  link_ALPHA1-6        : angle       2.68091 (    3)
  link_BETA1-4         : bond        0.00178 (    2)
  link_BETA1-4         : angle       1.89958 (    6)
  link_ALPHA1-3        : bond        0.01378 (    1)
  link_ALPHA1-3        : angle       1.89529 (    3)
  hydrogen bonds       : bond        0.03969 (  335)
  hydrogen bonds       : angle       4.71017 (  966)
  SS BOND              : bond        0.01154 (    1)
  SS BOND              : angle       1.81365 (    2)
  covalent geometry    : bond        0.00317 ( 9266)
  covalent geometry    : angle       0.57743 (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
  255 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 228
  time to evaluate  : 0.988 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8380 (mt) cc_final: 0.8030 (mp)
REVERT: A  116 ILE cc_start: 0.8339 (mm) cc_final: 0.8019 (OUTLIER)
REVERT: A  179 GLU cc_start: 0.7552 (mt-10) cc_final: 0.7089 (mt-10)
REVERT: A  193 HIS cc_start: 0.7986 (t-90) cc_final: 0.7771 (t-90)
REVERT: A  197 GLU cc_start: 0.7649 (pm20) cc_final: 0.7245 (pt0)
REVERT: A  207 ASP cc_start: 0.7776 (m-30) cc_final: 0.7551 (m-30)
REVERT: A  211 MET cc_start: 0.8341 (mpp) cc_final: 0.8135 (mtp)
REVERT: A  314 ASN cc_start: 0.8212 (m-40) cc_final: 0.7939 (m-40)
REVERT: A  515 GLU cc_start: 0.8235 (tp30) cc_final: 0.7912 (tp30)
REVERT: A  519 ARG cc_start: 0.8091 (mtt180) cc_final: 0.7777 (mtt180)
REVERT: A  529 ASN cc_start: 0.8239 (OUTLIER) cc_final: 0.7972 (t0)
REVERT: A  838 MET cc_start: 0.6672 (mmp) cc_final: 0.6404 (mmp)
REVERT: A  891 LYS cc_start: 0.8236 (ptmm) cc_final: 0.7994 (ptmm)
REVERT: A 1084 GLU cc_start: 0.7896 (tp30) cc_final: 0.7508 (tm-30)
REVERT: A 1092 MET cc_start: 0.6765 (mpp) cc_final: 0.6363 (mpp)
REVERT: A 1238 ASP cc_start: 0.7564 (m-30) cc_final: 0.7213 (m-30)
  outliers start: 27
  outliers final: 18
  residues processed: 238
  average time/residue: 1.0961
  time to fit residues: 279.4913
Evaluate side-chains
  240 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 222
  time to evaluate  : 0.978 
-------------------------------------------------------------------------------
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  220 ASP
Chi-restraints excluded: chain A residue  232 MET
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  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 1195 VAL
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:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 58 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 67 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9980
   chunk 111 optimal weight:   20.0000
   chunk 97 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A  26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** 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**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.155713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.125107 restraints weight = 11790.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3550 rms_B_bonded: 2.45
r_work: 0.3413 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.3238 rms_B_bonded: 4.72 restraints_weight: 0.2500
r_work (final): 0.3238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7649
moved from start:          0.1617

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= 0.181
  Angle     :  0.622   8.935  12589  Z= 0.320
  Chirality :  0.046   0.198   1450
  Planarity :  0.005   0.056   1609
  Dihedral  :  6.037  57.240   1337
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 5.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.08 %
    Favored  : 76.52 %
  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: -0.20 (0.26), residues: 1151
  helix:  1.52 (0.29), residues: 357
  sheet: -0.43 (0.29), residues: 354
  loop : -1.21 (0.29), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A  71 
 HIS   0.007   0.001   HIS A 988 
 PHE   0.018   0.002   PHE A 913 
 TYR   0.017   0.002   TYR A 797 
 ARG   0.003   0.000   ARG A  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00423 (    1)
  link_NAG-ASN         : angle       2.62600 (    3)
  link_ALPHA1-6        : bond        0.02626 (    1)
  link_ALPHA1-6        : angle       2.80044 (    3)
  link_BETA1-4         : bond        0.00270 (    2)
  link_BETA1-4         : angle       2.05520 (    6)
  link_ALPHA1-3        : bond        0.01293 (    1)
  link_ALPHA1-3        : angle       1.87142 (    3)
  hydrogen bonds       : bond        0.04648 (  335)
  hydrogen bonds       : angle       4.77497 (  966)
  SS BOND              : bond        0.00588 (    1)
  SS BOND              : angle       2.02711 (    2)
  covalent geometry    : bond        0.00435 ( 9266)
  covalent geometry    : angle       0.61653 (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
  261 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 228
  time to evaluate  : 1.032 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8398 (mt) cc_final: 0.8047 (mp)
REVERT: A  116 ILE cc_start: 0.8354 (mm) cc_final: 0.8031 (OUTLIER)
REVERT: A  179 GLU cc_start: 0.7547 (mt-10) cc_final: 0.7131 (mt-10)
REVERT: A  193 HIS cc_start: 0.7992 (t-90) cc_final: 0.7777 (t-90)
REVERT: A  197 GLU cc_start: 0.7651 (pm20) cc_final: 0.7259 (pt0)
REVERT: A  207 ASP cc_start: 0.7768 (m-30) cc_final: 0.7535 (m-30)
REVERT: A  211 MET cc_start: 0.8338 (mpp) cc_final: 0.8126 (mtp)
REVERT: A  282 ARG cc_start: 0.8273 (mtp180) cc_final: 0.8070 (mtm180)
REVERT: A  314 ASN cc_start: 0.8202 (m-40) cc_final: 0.7935 (m-40)
REVERT: A  515 GLU cc_start: 0.8250 (tp30) cc_final: 0.7930 (tp30)
REVERT: A  519 ARG cc_start: 0.8111 (mtt180) cc_final: 0.7825 (mtt180)
REVERT: A  529 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7980 (t0)
REVERT: A  698 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6803 (mt-10)
REVERT: A  765 LEU cc_start: 0.7622 (mt) cc_final: 0.7388 (mp)
REVERT: A  838 MET cc_start: 0.6652 (mmp) cc_final: 0.6390 (mmp)
REVERT: A  912 LYS cc_start: 0.7732 (OUTLIER) cc_final: 0.7509 (ttpp)
REVERT: A  923 GLU cc_start: 0.7381 (mm-30) cc_final: 0.7082 (mm-30)
REVERT: A  968 LEU cc_start: 0.8628 (mp) cc_final: 0.8389 (mt)
REVERT: A 1084 GLU cc_start: 0.7899 (tp30) cc_final: 0.7531 (tm-30)
REVERT: A 1092 MET cc_start: 0.6712 (mpp) cc_final: 0.6354 (mpp)
REVERT: A 1238 ASP cc_start: 0.7573 (m-30) cc_final: 0.7230 (m-30)
  outliers start: 33
  outliers final: 25
  residues processed: 240
  average time/residue: 1.1221
  time to fit residues: 288.5789
Evaluate side-chains
  253 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 226
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
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  232 MET
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  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  794 ILE
Chi-restraints excluded: chain A residue  811 LEU
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  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 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:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 80 optimal weight:    5.9990
   chunk 88 optimal weight:    0.5980
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 8 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   overall best weight:    0.8582

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.155444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.124932 restraints weight = 11686.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 2.44
r_work: 0.3411 rms_B_bonded: 2.80 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7646
moved from start:          0.1668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   9272  Z= 0.191
  Angle     :  0.637   9.026  12589  Z= 0.329
  Chirality :  0.047   0.197   1450
  Planarity :  0.005   0.057   1609
  Dihedral  :  5.886  52.803   1337
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 20.60 %
    Favored  : 76.31 %
  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: -0.26 (0.26), residues: 1151
  helix:  1.47 (0.29), residues: 357
  sheet: -0.46 (0.29), residues: 357
  loop : -1.24 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A  71 
 HIS   0.007   0.001   HIS A 988 
 PHE   0.014   0.002   PHE A 936 
 TYR   0.017   0.002   TYR A 797 
 ARG   0.003   0.000   ARG A 335 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00410 (    1)
  link_NAG-ASN         : angle       2.60478 (    3)
  link_ALPHA1-6        : bond        0.02810 (    1)
  link_ALPHA1-6        : angle       2.87823 (    3)
  link_BETA1-4         : bond        0.00276 (    2)
  link_BETA1-4         : angle       2.06768 (    6)
  link_ALPHA1-3        : bond        0.01299 (    1)
  link_ALPHA1-3        : angle       1.94252 (    3)
  hydrogen bonds       : bond        0.04742 (  335)
  hydrogen bonds       : angle       4.78808 (  966)
  SS BOND              : bond        0.00841 (    1)
  SS BOND              : angle       2.07919 (    2)
  covalent geometry    : bond        0.00459 ( 9266)
  covalent geometry    : angle       0.63167 (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
  263 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 233
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8434 (mt) cc_final: 0.8089 (mp)
REVERT: A  116 ILE cc_start: 0.8358 (mm) cc_final: 0.8039 (OUTLIER)
REVERT: A  166 SER cc_start: 0.8249 (t) cc_final: 0.8045 (t)
REVERT: A  179 GLU cc_start: 0.7532 (mt-10) cc_final: 0.7093 (mt-10)
REVERT: A  197 GLU cc_start: 0.7664 (pm20) cc_final: 0.7296 (pt0)
REVERT: A  207 ASP cc_start: 0.7761 (m-30) cc_final: 0.7535 (m-30)
REVERT: A  211 MET cc_start: 0.8348 (mpp) cc_final: 0.8142 (mtp)
REVERT: A  282 ARG cc_start: 0.8299 (mtp180) cc_final: 0.8037 (mtm180)
REVERT: A  314 ASN cc_start: 0.8199 (m-40) cc_final: 0.7935 (m-40)
REVERT: A  515 GLU cc_start: 0.8219 (tp30) cc_final: 0.8011 (tp30)
REVERT: A  529 ASN cc_start: 0.8242 (OUTLIER) cc_final: 0.7967 (t0)
REVERT: A  698 GLU cc_start: 0.7108 (OUTLIER) cc_final: 0.6797 (mt-10)
REVERT: A  765 LEU cc_start: 0.7544 (mt) cc_final: 0.7312 (mp)
REVERT: A  838 MET cc_start: 0.6713 (mmp) cc_final: 0.6447 (mmp)
REVERT: A  912 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7482 (ttpp)
REVERT: A  923 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7025 (mm-30)
REVERT: A  968 LEU cc_start: 0.8628 (mp) cc_final: 0.8401 (mt)
REVERT: A 1084 GLU cc_start: 0.7891 (tp30) cc_final: 0.7566 (tm-30)
REVERT: A 1092 MET cc_start: 0.6739 (mpp) cc_final: 0.6372 (mpp)
REVERT: A 1238 ASP cc_start: 0.7598 (m-30) cc_final: 0.7256 (m-30)
  outliers start: 30
  outliers final: 27
  residues processed: 244
  average time/residue: 1.1412
  time to fit residues: 298.5099
Evaluate side-chains
  260 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 231
  time to evaluate  : 1.053 
-------------------------------------------------------------------------------
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  232 MET
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  760 SER
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  811 LEU
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  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 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:    0.7980
   chunk 81 optimal weight:    0.9990
   chunk 49 optimal weight:    0.1980
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 89 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 21 optimal weight:    1.9990
   chunk 96 optimal weight:    0.2980
   chunk 83 optimal weight:    0.0370
   overall best weight:    0.4658

-------------------------------------------------------------------------------
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 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.156727 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3575 r_free = 0.3575 target = 0.126037 restraints weight = 11707.196|
|-----------------------------------------------------------------------------|
r_work (start): 0.3567 rms_B_bonded: 2.45
r_work: 0.3432 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7621
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9272  Z= 0.136
  Angle     :  0.610   9.102  12589  Z= 0.312
  Chirality :  0.045   0.192   1450
  Planarity :  0.004   0.055   1609
  Dihedral  :  5.672  51.124   1337
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 21.32 %
    Favored  : 76.21 %
  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:  1.62 (0.29), residues: 357
  sheet: -0.40 (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 A1228 
 HIS   0.009   0.001   HIS A 926 
 PHE   0.014   0.002   PHE A 936 
 TYR   0.012   0.001   TYR A 797 
 ARG   0.002   0.000   ARG A 664 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00222 (    1)
  link_NAG-ASN         : angle       2.17239 (    3)
  link_ALPHA1-6        : bond        0.02892 (    1)
  link_ALPHA1-6        : angle       2.90580 (    3)
  link_BETA1-4         : bond        0.00138 (    2)
  link_BETA1-4         : angle       1.73742 (    6)
  link_ALPHA1-3        : bond        0.01266 (    1)
  link_ALPHA1-3        : angle       1.94124 (    3)
  hydrogen bonds       : bond        0.03969 (  335)
  hydrogen bonds       : angle       4.71180 (  966)
  SS BOND              : bond        0.00794 (    1)
  SS BOND              : angle       1.95599 (    2)
  covalent geometry    : bond        0.00317 ( 9266)
  covalent geometry    : angle       0.60503 (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
  256 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 232
  time to evaluate  : 0.955 
Fit side-chains
REVERT: A   95 LEU cc_start: 0.8357 (mt) cc_final: 0.8008 (mp)
REVERT: A  116 ILE cc_start: 0.8348 (mm) cc_final: 0.8033 (mp)
REVERT: A  166 SER cc_start: 0.8234 (t) cc_final: 0.8025 (t)
REVERT: A  179 GLU cc_start: 0.7478 (mt-10) cc_final: 0.7046 (mt-10)
REVERT: A  197 GLU cc_start: 0.7648 (pm20) cc_final: 0.7297 (pt0)
REVERT: A  207 ASP cc_start: 0.7779 (m-30) cc_final: 0.7566 (m-30)
REVERT: A  211 MET cc_start: 0.8350 (mpp) cc_final: 0.8145 (mtp)
REVERT: A  314 ASN cc_start: 0.8237 (m-40) cc_final: 0.7974 (m-40)
REVERT: A  515 GLU cc_start: 0.8253 (tp30) cc_final: 0.7883 (tp30)
REVERT: A  519 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7818 (mtt180)
REVERT: A  529 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7987 (t0)
REVERT: A  687 TYR cc_start: 0.7920 (t80) cc_final: 0.7030 (t80)
REVERT: A  698 GLU cc_start: 0.7107 (OUTLIER) cc_final: 0.6802 (mt-10)
REVERT: A  765 LEU cc_start: 0.7415 (mt) cc_final: 0.7188 (mp)
REVERT: A  828 LEU cc_start: 0.8569 (tt) cc_final: 0.8368 (tm)
REVERT: A  838 MET cc_start: 0.6756 (mmp) cc_final: 0.6480 (mmp)
REVERT: A  912 LYS cc_start: 0.7716 (OUTLIER) cc_final: 0.7494 (ttpp)
REVERT: A  968 LEU cc_start: 0.8599 (mp) cc_final: 0.8358 (mt)
REVERT: A 1084 GLU cc_start: 0.7897 (tp30) cc_final: 0.7590 (tm-30)
REVERT: A 1092 MET cc_start: 0.6738 (mpp) cc_final: 0.6373 (mpp)
REVERT: A 1238 ASP cc_start: 0.7571 (m-30) cc_final: 0.7217 (m-30)
  outliers start: 24
  outliers final: 19
  residues processed: 242
  average time/residue: 1.0757
  time to fit residues: 279.1266
Evaluate side-chains
  250 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 228
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
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  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  640 ILE
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:    0.6980
   chunk 107 optimal weight:    9.9990
   chunk 27 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   chunk 61 optimal weight:    0.2980
   chunk 51 optimal weight:    2.9990
   chunk 60 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    0.2980
   chunk 8 optimal weight:    0.9990
   chunk 93 optimal weight:    1.9990
   overall best weight:    0.5982

-------------------------------------------------------------------------------
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 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
A 967 ASN
** A1019 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.156442 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.125825 restraints weight = 11685.118|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.44
r_work: 0.3423 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.1820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   9272  Z= 0.151
  Angle     :  0.618   9.212  12589  Z= 0.316
  Chirality :  0.046   0.190   1450
  Planarity :  0.005   0.054   1609
  Dihedral  :  5.576  50.261   1337
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 21.73 %
    Favored  : 75.39 %
  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:  1.64 (0.29), residues: 357
  sheet: -0.39 (0.29), residues: 357
  loop : -1.21 (0.29), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A  71 
 HIS   0.009   0.001   HIS A 926 
 PHE   0.018   0.002   PHE A 889 
 TYR   0.014   0.002   TYR A 797 
 ARG   0.002   0.000   ARG A  35 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00305 (    1)
  link_NAG-ASN         : angle       2.40643 (    3)
  link_ALPHA1-6        : bond        0.02951 (    1)
  link_ALPHA1-6        : angle       2.96265 (    3)
  link_BETA1-4         : bond        0.00171 (    2)
  link_BETA1-4         : angle       1.78001 (    6)
  link_ALPHA1-3        : bond        0.01226 (    1)
  link_ALPHA1-3        : angle       1.94441 (    3)
  hydrogen bonds       : bond        0.04210 (  335)
  hydrogen bonds       : angle       4.67606 (  966)
  SS BOND              : bond        0.00673 (    1)
  SS BOND              : angle       1.97372 (    2)
  covalent geometry    : bond        0.00357 ( 9266)
  covalent geometry    : angle       0.61303 (12572)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7796.24 seconds
wall clock time: 134 minutes 35.86 seconds (8075.86 seconds total)