Starting phenix.real_space_refine
on Wed Sep 17 11:42:16 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jjk_61530/09_2025/9jjk_61530.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jjk_61530/09_2025/9jjk_61530.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jjk_61530/09_2025/9jjk_61530.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jjk_61530/09_2025/9jjk_61530.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jjk_61530/09_2025/9jjk_61530.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jjk_61530/09_2025/9jjk_61530.map"
  }
  resolution = 2.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.064
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      63      5.16       5
     C    5382      2.51       5
     N    1421      2.21       5
     O    1491      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8358
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8250
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1048, 8250
          Classifications: {'peptide': 1048}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 54, 'TRANS': 993}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 15
          Unresolved non-hydrogen angles: 19
          Unresolved non-hydrogen dihedrals: 11
          Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'POV': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.73, per 1000 atoms: 0.21
  Number of scatterers: 8358
  At special positions: 0
  Unit cell: (73.87, 90.47, 166.83, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      63     16.00
     P       1     15.00
     O    1491      8.00
     N    1421      7.00
     C    5382      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG B   1 " - " ASN A1202 "
      " NAG C   1 " - " ASN A1205 "
  Time building additional restraints: 0.81
  Conformation dependent library (CDL) restraints added in 286.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1990

  Finding SS restraints...
    Secondary structure from input PDB file:
      42 helices and 6 sheets defined
      58.2% alpha, 10.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 44
      removed outlier: 3.650A  pdb=" N   CYS A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 46 through 53
    Processing helix  chain 'A' and resid 66 through 83
      removed outlier: 3.550A  pdb=" N   ALA A  70 " --> pdb=" O   HIS A  66 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 122
      removed outlier: 3.608A  pdb=" N   VAL A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   ARG A 122 " --> pdb=" O   ARG A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 122 through 140
    Processing helix  chain 'A' and resid 148 through 152
    Processing helix  chain 'A' and resid 180 through 182
      No H-bonds generated for 'chain 'A' and resid 180 through 182'
    Processing helix  chain 'A' and resid 249 through 260
      removed outlier: 4.481A  pdb=" N   ASN A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 302
      removed outlier: 4.346A  pdb=" N   VAL A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 309 through 323
      removed outlier: 5.185A  pdb=" N   GLN A 318 " --> pdb=" O   LEU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 326
      No H-bonds generated for 'chain 'A' and resid 324 through 326'
    Processing helix  chain 'A' and resid 329 through 350
      removed outlier: 3.746A  pdb=" N   SER A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 391
    Processing helix  chain 'A' and resid 402 through 408
    Processing helix  chain 'A' and resid 578 through 594
      removed outlier: 3.644A  pdb=" N   LEU A 582 " --> pdb=" O   HIS A 578 " (cutoff:3.500A)
      Proline residue:  A 584  - end of helix
    Processing helix  chain 'A' and resid 595 through 616
      removed outlier: 3.833A  pdb=" N   ARG A 601 " --> pdb=" O   SER A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 638
      removed outlier: 3.598A  pdb=" N   ALA A 634 " --> pdb=" O   LEU A 630 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 645
    Processing helix  chain 'A' and resid 705 through 712
      removed outlier: 3.552A  pdb=" N   GLU A 711 " --> pdb=" O   ASP A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 744
      removed outlier: 3.726A  pdb=" N   SER A 743 " --> pdb=" O   ARG A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 763
    Processing helix  chain 'A' and resid 814 through 819
      removed outlier: 3.682A  pdb=" N   LEU A 818 " --> pdb=" O   CYS A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 834 through 847
    Processing helix  chain 'A' and resid 858 through 869
      removed outlier: 3.665A  pdb=" N   LYS A 868 " --> pdb=" O   VAL A 864 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 956
      No H-bonds generated for 'chain 'A' and resid 954 through 956'
    Processing helix  chain 'A' and resid 957 through 965
    Processing helix  chain 'A' and resid 967 through 971
    Processing helix  chain 'A' and resid 979 through 993
    Processing helix  chain 'A' and resid 1005 through 1007
      No H-bonds generated for 'chain 'A' and resid 1005 through 1007'
    Processing helix  chain 'A' and resid 1008 through 1015
    Processing helix  chain 'A' and resid 1050 through 1060
    Processing helix  chain 'A' and resid 1071 through 1073
      No H-bonds generated for 'chain 'A' and resid 1071 through 1073'
    Processing helix  chain 'A' and resid 1074 through 1113
    Processing helix  chain 'A' and resid 1120 through 1138
      Proline residue:  A1133  - end of helix
      removed outlier: 3.618A  pdb=" N   SER A1138 " --> pdb=" O   LEU A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1139 through 1141
      No H-bonds generated for 'chain 'A' and resid 1139 through 1141'
    Processing helix  chain 'A' and resid 1147 through 1151
      removed outlier: 3.845A  pdb=" N   MET A1151 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1161 through 1201
      removed outlier: 3.529A  pdb=" N   GLN A1165 " --> pdb=" O   PRO A1161 " (cutoff:3.500A)
      removed outlier: 5.480A  pdb=" N   LEU A1178 " --> pdb=" O   LEU A1174 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   THR A1179 " --> pdb=" O   LYS A1175 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG A1199 " --> pdb=" O   CYS A1195 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   ASP A1200 " --> pdb=" O   ASP A1196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1225 through 1251
      removed outlier: 3.530A  pdb=" N   LEU A1230 " --> pdb=" O   ALA A1226 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   THR A1250 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1265
      removed outlier: 3.751A  pdb=" N   THR A1265 " --> pdb=" O   SER A1262 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1262 through 1265'
    Processing helix  chain 'A' and resid 1266 through 1291
      Proline residue:  A1274  - end of helix
    Processing helix  chain 'A' and resid 1301 through 1305
      removed outlier: 3.897A  pdb=" N   VAL A1305 " --> pdb=" O   LEU A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1348
      removed outlier: 3.838A  pdb=" N   TRP A1310 " --> pdb=" O   PRO A1306 " (cutoff:3.500A)
      removed outlier: 4.295A  pdb=" N   VAL A1321 " --> pdb=" O   LEU A1317 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   VAL A1322 " --> pdb=" O   VAL A1318 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   THR A1323 " --> pdb=" O   LEU A1319 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   ARG A1337 " --> pdb=" O   ARG A1333 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178
      removed outlier: 4.349A  pdb=" N   TRP A 167 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   ILE A 187 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ARG A 241 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 879 through 880
      removed outlier: 6.604A  pdb=" N   ILE A 879 " --> pdb=" O   THR A 976 " (cutoff:3.500A)
      removed outlier: 8.328A  pdb=" N   PHE A 975 " --> pdb=" O   PHE A 851 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   TYR A 853 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 6.395A  pdb=" N   LEU A 413 " --> pdb=" O   VAL A 852 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   PHE A 854 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   CYS A 415 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
      removed outlier: 6.551A  pdb=" N   THR A 997 " --> pdb=" O   ILE A1017 " (cutoff:3.500A)
      removed outlier: 8.196A  pdb=" N   ILE A1019 " --> pdb=" O   THR A 997 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   CYS A 999 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
      removed outlier: 7.440A  pdb=" N   LEU A1021 " --> pdb=" O   CYS A 999 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   GLY A1001 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
      removed outlier: 6.669A  pdb=" N   SER A1018 " --> pdb=" O   LEU A1065 " (cutoff:3.500A)
      removed outlier: 8.172A  pdb=" N   PHE A1067 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
      removed outlier: 6.829A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1067 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 552 through 557
      removed outlier: 6.011A  pdb=" N   GLN A 830 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   THR A 431 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 5.417A  pdb=" N   GLY A 825 " --> pdb=" O   PHE A 749 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   PHE A 749 " --> pdb=" O   GLY A 825 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   VAL A 827 " --> pdb=" O   SER A 747 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   SER A 702 " --> pdb=" O   ALA A 750 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   LYS A 752 " --> pdb=" O   MET A 700 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   SER A 683 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   LYS A 691 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 5.372A  pdb=" N   GLN A 649 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 9.004A  pdb=" N   ILE A 767 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
      removed outlier: 6.673A  pdb=" N   ALA A 654 " --> pdb=" O   ILE A 767 " (cutoff:3.500A)
      removed outlier: 7.469A  pdb=" N   LEU A 769 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   TYR A 656 " --> pdb=" O   LEU A 769 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 559 through 560
    Processing sheet with id=AA5, first strand: chain 'A' and resid 722 through 724
      removed outlier: 5.803A  pdb=" N   GLN A 821 " --> pdb=" O   CYS A 713 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 756 through 757

    467 hydrogen bonds defined for protein.
    1350 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1561
        1.33 -     1.45: 2036
        1.45 -     1.58: 4860
        1.58 -     1.70: 2
        1.70 -     1.82: 85
  Bond restraints: 8544
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.498 -0.092 2.00e-02 2.50e+03 2.12e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.436 -0.030 2.00e-02 2.50e+03 2.32e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.441 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.431 -0.025 2.00e-02 2.50e+03 1.51e+00
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.27e+00
  ... (remaining 8539 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.38: 11488
        2.38 -     4.77: 104
        4.77 -     7.15: 6
        7.15 -     9.54: 0
        9.54 -    11.92: 3
  Bond angle restraints: 11601
  Sorted by residual:
  angle pdb=" CB  MET A 826 "
        pdb=" CG  MET A 826 "
        pdb=" SD  MET A 826 "
      ideal   model   delta    sigma   weight residual
     112.70  124.62  -11.92 3.00e+00 1.11e-01 1.58e+01
  angle pdb=" CB  MET A 378 "
        pdb=" CG  MET A 378 "
        pdb=" SD  MET A 378 "
      ideal   model   delta    sigma   weight residual
     112.70  123.47  -10.77 3.00e+00 1.11e-01 1.29e+01
  angle pdb=" CA  LEU A 602 "
        pdb=" CB  LEU A 602 "
        pdb=" CG  LEU A 602 "
      ideal   model   delta    sigma   weight residual
     116.30  126.19   -9.89 3.50e+00 8.16e-02 7.98e+00
  angle pdb=" N   VAL A1113 "
        pdb=" CA  VAL A1113 "
        pdb=" C   VAL A1113 "
      ideal   model   delta    sigma   weight residual
     112.80  109.76    3.04 1.15e+00 7.56e-01 6.99e+00
  angle pdb=" C   CYS A1131 "
        pdb=" N   TYR A1132 "
        pdb=" CA  TYR A1132 "
      ideal   model   delta    sigma   weight residual
     121.80  115.39    6.41 2.44e+00 1.68e-01 6.89e+00
  ... (remaining 11596 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.40: 4592
       22.40 -    44.79: 471
       44.79 -    67.19: 103
       67.19 -    89.59: 11
       89.59 -   111.98: 12
  Dihedral angle restraints: 5189
    sinusoidal: 2142
      harmonic: 3047
  Sorted by residual:
  dihedral pdb=" C1  NAG B   1 "
           pdb=" C5  NAG B   1 "
           pdb=" O5  NAG B   1 "
           pdb=" C4  NAG B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.11   47.87 -111.98     1      3.00e+01 1.11e-03 1.47e+01
  dihedral pdb=" C1  NAG B   1 "
           pdb=" C5  NAG B   1 "
           pdb=" O5  NAG B   1 "
           pdb=" C6  NAG B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     171.16  -77.36 -111.48     1      3.00e+01 1.11e-03 1.46e+01
  dihedral pdb=" CA  ASN A1202 "
           pdb=" C   ASN A1202 "
           pdb=" N   LEU A1203 "
           pdb=" CA  LEU A1203 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.13  -18.87     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 5186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1288
       0.078 -    0.156: 79
       0.156 -    0.234: 0
       0.234 -    0.311: 0
       0.311 -    0.389: 1
  Chirality restraints: 1368
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A1202 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.01   -0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CA  TRP A  67 "
            pdb=" N   TRP A  67 "
            pdb=" C   TRP A  67 "
            pdb=" CB  TRP A  67 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.67e-01
  chirality pdb=" CA  ASN A 876 "
            pdb=" N   ASN A 876 "
            pdb=" C   ASN A 876 "
            pdb=" CB  ASN A 876 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.49e-01
  ... (remaining 1365 not shown)

  Planarity restraints: 1442
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 313 "    0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   THR A 313 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   THR A 313 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 314 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A1128 "   -0.014 2.00e-02 2.50e+03   2.88e-02 8.27e+00
        pdb=" C   SER A1128 "    0.050 2.00e-02 2.50e+03
        pdb=" O   SER A1128 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   CYS A1129 "   -0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A1202 "    0.023 2.00e-02 2.50e+03   2.13e-02 5.68e+00
        pdb=" CG  ASN A1202 "   -0.031 2.00e-02 2.50e+03
        pdb=" OD1 ASN A1202 "    0.007 2.00e-02 2.50e+03
        pdb=" ND2 ASN A1202 "   -0.019 2.00e-02 2.50e+03
        pdb=" C1  NAG B   1 "    0.020 2.00e-02 2.50e+03
  ... (remaining 1439 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1642
        2.78 -     3.31: 7336
        3.31 -     3.84: 13494
        3.84 -     4.37: 15372
        4.37 -     4.90: 27496
  Nonbonded interactions: 65340
  Sorted by model distance:
  nonbonded pdb=" N   GLU A 207 "
            pdb=" OE1 GLU A 207 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   LEU A1288 "
            pdb=" OG1 THR A1292 "
     model   vdw
     2.263 3.040
  nonbonded pdb=" O   ALA A 613 "
            pdb=" OG  SER A 617 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OG1 THR A 580 "
            pdb=" O   GLY A 719 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" NH2 ARG A  20 "
            pdb=" O   ARG A 143 "
     model   vdw
     2.347 3.120
  ... (remaining 65335 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
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
}

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:             3.790
  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:          0.190
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.320
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.260
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8399
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      :  0.003   0.092   8548  Z= 0.142
  Angle     :  0.562  11.924  11613  Z= 0.277
  Chirality :  0.039   0.389   1368
  Planarity :  0.005   0.057   1440
  Dihedral  : 18.955 111.983   3199
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 22.73 %
    Favored  : 73.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.31 (0.27), residues: 1030
  helix:  2.80 (0.23), residues: 536
  sheet:  0.69 (0.46), residues: 112
  loop : -0.06 (0.32), residues: 382

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 601 
 TYR   0.018   0.001   TYR A1087 
 PHE   0.013   0.001   PHE A1093 
 TRP   0.013   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 8544)
  covalent geometry    : angle       0.55307 (11601)
  hydrogen bonds       : bond        0.18273 (  467)
  hydrogen bonds       : angle       5.29934 ( 1350)
  link_BETA1-4         : bond        0.00798 (    2)
  link_BETA1-4         : angle       2.17420 (    6)
  link_NAG-ASN         : bond        0.01467 (    2)
  link_NAG-ASN         : angle       3.84723 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 83
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
REVERT: A 1260 ARG cc_start: 0.7722 (OUTLIER) cc_final: 0.7461 (mtt90)
  outliers start: 38
  outliers final: 33
  residues processed: 118
  average time/residue: 0.5882
  time to fit residues: 73.9481
Evaluate side-chains
  116 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 82
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  208 HIS
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1017 ILE
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1064 SER
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1127 LEU
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1182 SER
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1213 SER
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1256 LYS
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1311 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Chi-restraints excluded: chain A residue 1320 VAL
Chi-restraints excluded: chain A residue 1323 THR
Chi-restraints excluded: chain A residue 1347 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    9.9990
   chunk 97 optimal weight:    0.7980
   chunk 53 optimal weight:   20.0000
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:   40.0000
   chunk 100 optimal weight:    0.1980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    8.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.181901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.108349 restraints weight = 8229.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 3.67
r_work: 0.2996 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.2871 rms_B_bonded: 3.76 restraints_weight: 0.2500
r_work (final): 0.2871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8579
moved from start:          0.0653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8548  Z= 0.146
  Angle     :  0.604  11.154  11613  Z= 0.298
  Chirality :  0.041   0.208   1368
  Planarity :  0.005   0.053   1440
  Dihedral  : 12.758  84.292   1304
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 21.13 %
    Favored  : 74.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.27), residues: 1030
  helix:  2.59 (0.22), residues: 554
  sheet:  0.54 (0.46), residues: 117
  loop : -0.10 (0.33), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 739 
 TYR   0.012   0.001   TYR A 312 
 PHE   0.018   0.001   PHE A1093 
 TRP   0.010   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 8544)
  covalent geometry    : angle       0.59858 (11601)
  hydrogen bonds       : bond        0.07654 (  467)
  hydrogen bonds       : angle       4.20764 ( 1350)
  link_BETA1-4         : bond        0.00695 (    2)
  link_BETA1-4         : angle       2.19118 (    6)
  link_NAG-ASN         : bond        0.00955 (    2)
  link_NAG-ASN         : angle       2.99419 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 77
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8394 (mp)
REVERT: A  344 ARG cc_start: 0.8374 (OUTLIER) cc_final: 0.7769 (mtp180)
REVERT: A  555 MET cc_start: 0.4715 (ppp) cc_final: 0.4327 (ppp)
REVERT: A  826 MET cc_start: 0.5587 (mmm) cc_final: 0.5352 (mmm)
REVERT: A 1000 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8400 (mp)
REVERT: A 1225 PHE cc_start: 0.8238 (OUTLIER) cc_final: 0.7985 (m-80)
REVERT: A 1260 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7729 (mtp85)
  outliers start: 45
  outliers final: 22
  residues processed: 113
  average time/residue: 0.5598
  time to fit residues: 67.3098
Evaluate side-chains
  104 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 77
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  195 GLU
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1155 LYS
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 93 optimal weight:    0.8980
   chunk 34 optimal weight:    5.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 98 optimal weight:    0.9980
   chunk 19 optimal weight:    6.9990
   chunk 82 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 63 optimal weight:    0.9990
   chunk 68 optimal weight:    0.3980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.182680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.110644 restraints weight = 8158.731|
|-----------------------------------------------------------------------------|
r_work (start): 0.3217 rms_B_bonded: 3.91
r_work: 0.3025 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2900 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.0799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8548  Z= 0.132
  Angle     :  0.553   7.456  11613  Z= 0.277
  Chirality :  0.039   0.232   1368
  Planarity :  0.005   0.053   1440
  Dihedral  : 10.274  84.257   1276
  Min Nonbonded Distance : 2.325

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  5.02 %
    Allowed  : 20.60 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.26 (0.27), residues: 1030
  helix:  2.72 (0.22), residues: 550
  sheet:  0.47 (0.46), residues: 113
  loop : -0.05 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1201 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.018   0.001   PHE A 736 
 TRP   0.011   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00267 ( 8544)
  covalent geometry    : angle       0.54635 (11601)
  hydrogen bonds       : bond        0.06983 (  467)
  hydrogen bonds       : angle       4.05074 ( 1350)
  link_BETA1-4         : bond        0.00386 (    2)
  link_BETA1-4         : angle       2.03286 (    6)
  link_NAG-ASN         : bond        0.00391 (    2)
  link_NAG-ASN         : angle       3.16571 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 80
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7332 (OUTLIER) cc_final: 0.6474 (ttmt)
REVERT: A   78 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8360 (mp)
REVERT: A  186 ASP cc_start: 0.8967 (OUTLIER) cc_final: 0.8312 (t0)
REVERT: A  344 ARG cc_start: 0.8297 (OUTLIER) cc_final: 0.7695 (mtp180)
REVERT: A 1000 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8379 (mp)
REVERT: A 1070 GLU cc_start: 0.7251 (OUTLIER) cc_final: 0.7023 (pm20)
REVERT: A 1225 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7824 (m-80)
  outliers start: 47
  outliers final: 23
  residues processed: 118
  average time/residue: 0.5682
  time to fit residues: 71.2710
Evaluate side-chains
  108 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 78
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 52 optimal weight:    7.9990
   chunk 57 optimal weight:    8.9990
   chunk 19 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0030
   chunk 42 optimal weight:    0.0570
   chunk 12 optimal weight:    4.9990
   chunk 26 optimal weight:    1.9990
   chunk 79 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.5712

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.183660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.111516 restraints weight = 8369.125|
|-----------------------------------------------------------------------------|
r_work (start): 0.3233 rms_B_bonded: 3.69
r_work: 0.3010 rms_B_bonded: 2.79 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.0910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8548  Z= 0.124
  Angle     :  0.532   7.473  11613  Z= 0.267
  Chirality :  0.039   0.198   1368
  Planarity :  0.004   0.052   1440
  Dihedral  :  9.248  85.141   1264
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  4.80 %
    Allowed  : 20.60 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.27), residues: 1030
  helix:  2.80 (0.22), residues: 550
  sheet:  0.33 (0.46), residues: 112
  loop : -0.02 (0.33), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 380 
 TYR   0.009   0.001   TYR A 312 
 PHE   0.014   0.001   PHE A1093 
 TRP   0.011   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00245 ( 8544)
  covalent geometry    : angle       0.52774 (11601)
  hydrogen bonds       : bond        0.06485 (  467)
  hydrogen bonds       : angle       4.04063 ( 1350)
  link_BETA1-4         : bond        0.00574 (    2)
  link_BETA1-4         : angle       1.95447 (    6)
  link_NAG-ASN         : bond        0.00714 (    2)
  link_NAG-ASN         : angle       2.36082 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 78
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7319 (OUTLIER) cc_final: 0.6476 (ttmt)
REVERT: A   78 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8354 (mp)
REVERT: A  186 ASP cc_start: 0.8957 (OUTLIER) cc_final: 0.8291 (t0)
REVERT: A  403 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8333 (mp)
REVERT: A 1000 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8403 (mp)
REVERT: A 1053 GLN cc_start: 0.8193 (OUTLIER) cc_final: 0.7911 (pt0)
REVERT: A 1225 PHE cc_start: 0.8131 (OUTLIER) cc_final: 0.7593 (m-80)
REVERT: A 1260 ARG cc_start: 0.8068 (OUTLIER) cc_final: 0.7691 (mtp85)
  outliers start: 45
  outliers final: 21
  residues processed: 111
  average time/residue: 0.5813
  time to fit residues: 68.8246
Evaluate side-chains
  106 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0870
   chunk 37 optimal weight:    4.9990
   chunk 100 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 54 optimal weight:    5.9990
   chunk 51 optimal weight:   40.0000
   chunk 44 optimal weight:    7.9990
   chunk 91 optimal weight:    1.9990
   chunk 101 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   overall best weight:    1.4166

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 832 GLN
A 876 ASN
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.179945 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.109360 restraints weight = 8216.656|
|-----------------------------------------------------------------------------|
r_work (start): 0.3198 rms_B_bonded: 2.60
r_work: 0.2990 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2861 rms_B_bonded: 3.64 restraints_weight: 0.2500
r_work (final): 0.2861
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
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   0.035   8548  Z= 0.171
  Angle     :  0.607   7.867  11613  Z= 0.305
  Chirality :  0.041   0.170   1368
  Planarity :  0.005   0.051   1440
  Dihedral  :  9.310  87.296   1261
  Min Nonbonded Distance : 2.305

Molprobity Statistics.
  All-atom Clashscore : 2.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 20.06 %
    Favored  : 75.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.27), residues: 1030
  helix:  2.48 (0.22), residues: 557
  sheet:  0.21 (0.45), residues: 115
  loop : -0.23 (0.32), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 122 
 TYR   0.014   0.001   TYR A 993 
 PHE   0.022   0.002   PHE A1093 
 TRP   0.009   0.001   TRP A1310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 8544)
  covalent geometry    : angle       0.60363 (11601)
  hydrogen bonds       : bond        0.08459 (  467)
  hydrogen bonds       : angle       4.12294 ( 1350)
  link_BETA1-4         : bond        0.00373 (    2)
  link_BETA1-4         : angle       2.22514 (    6)
  link_NAG-ASN         : bond        0.00700 (    2)
  link_NAG-ASN         : angle       2.06594 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 84
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7190 (OUTLIER) cc_final: 0.6325 (ttmt)
REVERT: A   78 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8203 (mp)
REVERT: A  186 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8236 (t0)
REVERT: A  344 ARG cc_start: 0.8281 (OUTLIER) cc_final: 0.7658 (mtp180)
REVERT: A  428 SER cc_start: 0.7732 (t) cc_final: 0.7247 (p)
REVERT: A  555 MET cc_start: 0.4463 (ppp) cc_final: 0.4230 (ppp)
REVERT: A 1000 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8347 (mp)
REVERT: A 1087 TYR cc_start: 0.7022 (t80) cc_final: 0.6595 (t80)
REVERT: A 1225 PHE cc_start: 0.8259 (OUTLIER) cc_final: 0.7967 (m-80)
REVERT: A 1260 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7553 (mtp85)
REVERT: A 1294 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.7570 (mmp80)
  outliers start: 46
  outliers final: 26
  residues processed: 116
  average time/residue: 0.6356
  time to fit residues: 78.2406
Evaluate side-chains
  115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 81
  time to evaluate  : 0.327 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1127 LEU
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1267 LEU
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 42 optimal weight:   20.0000
   chunk 1 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 64 optimal weight:    0.0270
   chunk 52 optimal weight:   20.0000
   chunk 17 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   overall best weight:    0.9442

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 832 GLN
A 963 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.181554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.110813 restraints weight = 8189.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3231 rms_B_bonded: 3.42
r_work: 0.3004 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   8548  Z= 0.144
  Angle     :  0.564   8.581  11613  Z= 0.285
  Chirality :  0.040   0.186   1368
  Planarity :  0.005   0.051   1440
  Dihedral  :  9.078  87.295   1259
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 2.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.48 %
    Allowed  : 20.60 %
    Favored  : 74.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.27), residues: 1030
  helix:  2.62 (0.22), residues: 551
  sheet:  0.23 (0.45), residues: 115
  loop : -0.19 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 122 
 TYR   0.016   0.001   TYR A 551 
 PHE   0.015   0.001   PHE A1093 
 TRP   0.012   0.001   TRP A 310 
 HIS   0.003   0.000   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8544)
  covalent geometry    : angle       0.56026 (11601)
  hydrogen bonds       : bond        0.07504 (  467)
  hydrogen bonds       : angle       4.05640 ( 1350)
  link_BETA1-4         : bond        0.00418 (    2)
  link_BETA1-4         : angle       2.07575 (    6)
  link_NAG-ASN         : bond        0.00609 (    2)
  link_NAG-ASN         : angle       1.91574 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 83
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7141 (OUTLIER) cc_final: 0.6341 (ttmt)
REVERT: A   78 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8185 (mp)
REVERT: A  186 ASP cc_start: 0.8885 (OUTLIER) cc_final: 0.8257 (t0)
REVERT: A  344 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7585 (mtp180)
REVERT: A  555 MET cc_start: 0.4391 (ppp) cc_final: 0.4148 (ppp)
REVERT: A 1000 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8328 (mp)
REVERT: A 1053 GLN cc_start: 0.8150 (pt0) cc_final: 0.7868 (pt0)
REVERT: A 1070 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7083 (pm20)
REVERT: A 1087 TYR cc_start: 0.7005 (t80) cc_final: 0.6570 (t80)
REVERT: A 1225 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.7881 (m-80)
REVERT: A 1260 ARG cc_start: 0.7988 (OUTLIER) cc_final: 0.7573 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.7992 (mp)
REVERT: A 1294 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7573 (mmp80)
  outliers start: 42
  outliers final: 22
  residues processed: 114
  average time/residue: 0.5871
  time to fit residues: 70.9297
Evaluate side-chains
  113 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 81
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  988 LYS
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1127 LEU
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 72 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 96 optimal weight:    0.1980
   chunk 47 optimal weight:    9.9990
   chunk 13 optimal weight:    0.4980
   chunk 56 optimal weight:    7.9990
   chunk 19 optimal weight:    4.9990
   chunk 40 optimal weight:    0.3980
   chunk 24 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   chunk 18 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 146 GLN
A 426 ASN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.186290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.116786 restraints weight = 8261.509|
|-----------------------------------------------------------------------------|
r_work (start): 0.3314 rms_B_bonded: 2.94
r_work: 0.3126 rms_B_bonded: 2.46 restraints_weight: 0.5000
r_work: 0.3006 rms_B_bonded: 3.71 restraints_weight: 0.2500
r_work (final): 0.3006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1139

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8548  Z= 0.125
  Angle     :  0.528   8.660  11613  Z= 0.267
  Chirality :  0.038   0.194   1368
  Planarity :  0.004   0.051   1440
  Dihedral  :  8.760  88.813   1259
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.24 %
    Favored  : 74.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.27), residues: 1030
  helix:  2.88 (0.22), residues: 543
  sheet:  0.19 (0.45), residues: 112
  loop : -0.05 (0.32), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 601 
 TYR   0.011   0.001   TYR A 551 
 PHE   0.013   0.001   PHE A1093 
 TRP   0.013   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8544)
  covalent geometry    : angle       0.52495 (11601)
  hydrogen bonds       : bond        0.06354 (  467)
  hydrogen bonds       : angle       3.89363 ( 1350)
  link_BETA1-4         : bond        0.00330 (    2)
  link_BETA1-4         : angle       2.11058 (    6)
  link_NAG-ASN         : bond        0.00670 (    2)
  link_NAG-ASN         : angle       1.72584 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 80
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7288 (OUTLIER) cc_final: 0.6458 (ttmt)
REVERT: A   78 LEU cc_start: 0.8745 (OUTLIER) cc_final: 0.8329 (mp)
REVERT: A  186 ASP cc_start: 0.8933 (OUTLIER) cc_final: 0.8317 (t0)
REVERT: A  403 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8361 (mp)
REVERT: A 1000 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8315 (mp)
REVERT: A 1087 TYR cc_start: 0.6934 (t80) cc_final: 0.6353 (t80)
REVERT: A 1225 PHE cc_start: 0.8083 (OUTLIER) cc_final: 0.7684 (m-80)
REVERT: A 1260 ARG cc_start: 0.8034 (OUTLIER) cc_final: 0.7640 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8146 (mp)
REVERT: A 1294 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.7612 (mmp80)
  outliers start: 37
  outliers final: 20
  residues processed: 108
  average time/residue: 0.5640
  time to fit residues: 64.8367
Evaluate side-chains
  106 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  137 ASP
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 22 optimal weight:    0.4980
   chunk 53 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9990
   chunk 14 optimal weight:    0.1980
   chunk 78 optimal weight:    3.9990
   chunk 62 optimal weight:    3.9990
   chunk 56 optimal weight:    7.9990
   chunk 87 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.181544 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.113563 restraints weight = 8197.830|
|-----------------------------------------------------------------------------|
r_work (start): 0.3242 rms_B_bonded: 2.84
r_work: 0.3033 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2902 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.2902
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.1228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8548  Z= 0.151
  Angle     :  0.580   9.422  11613  Z= 0.292
  Chirality :  0.040   0.168   1368
  Planarity :  0.005   0.050   1440
  Dihedral  :  8.745  89.412   1257
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 3.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 21.13 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.12 (0.27), residues: 1030
  helix:  2.67 (0.22), residues: 551
  sheet:  0.18 (0.44), residues: 115
  loop : -0.16 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1254 
 TYR   0.011   0.001   TYR A 312 
 PHE   0.019   0.001   PHE A1093 
 TRP   0.009   0.001   TRP A 310 
 HIS   0.003   0.001   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 8544)
  covalent geometry    : angle       0.57732 (11601)
  hydrogen bonds       : bond        0.07506 (  467)
  hydrogen bonds       : angle       4.00743 ( 1350)
  link_BETA1-4         : bond        0.00379 (    2)
  link_BETA1-4         : angle       2.00404 (    6)
  link_NAG-ASN         : bond        0.00811 (    2)
  link_NAG-ASN         : angle       1.53326 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 80
  time to evaluate  : 0.320 
Fit side-chains
REVERT: A   43 LYS cc_start: 0.7088 (OUTLIER) cc_final: 0.6256 (ttmt)
REVERT: A   78 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8099 (mp)
REVERT: A  186 ASP cc_start: 0.8849 (OUTLIER) cc_final: 0.8176 (t0)
REVERT: A  344 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7502 (mtp180)
REVERT: A 1000 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8260 (mp)
REVERT: A 1087 TYR cc_start: 0.6930 (t80) cc_final: 0.6407 (t80)
REVERT: A 1225 PHE cc_start: 0.8093 (OUTLIER) cc_final: 0.7748 (m-80)
REVERT: A 1260 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.7504 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.7976 (mp)
REVERT: A 1294 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.7534 (mmp80)
  outliers start: 40
  outliers final: 24
  residues processed: 109
  average time/residue: 0.5667
  time to fit residues: 65.6923
Evaluate side-chains
  112 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  708 VAL
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1127 LEU
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0980
   chunk 87 optimal weight:    2.9990
   chunk 83 optimal weight:    0.0370
   chunk 1 optimal weight:    0.9980
   chunk 30 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 17 optimal weight:    7.9990
   chunk 91 optimal weight:    3.9990
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.7660

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

Flipped N/Q/H residues before XYZ refinement:
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.185107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.116076 restraints weight = 8289.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 3.30
r_work: 0.3078 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2955 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2955
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8548
moved from start:          0.1222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8548  Z= 0.134
  Angle     :  0.570  10.435  11613  Z= 0.284
  Chirality :  0.039   0.184   1368
  Planarity :  0.004   0.050   1440
  Dihedral  :  8.654  88.804   1257
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 3.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  3.95 %
    Allowed  : 21.66 %
    Favored  : 74.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.24 (0.27), residues: 1030
  helix:  2.77 (0.22), residues: 547
  sheet:  0.19 (0.44), residues: 116
  loop : -0.06 (0.32), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 380 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.015   0.001   PHE A1093 
 TRP   0.012   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8544)
  covalent geometry    : angle       0.56773 (11601)
  hydrogen bonds       : bond        0.06935 (  467)
  hydrogen bonds       : angle       3.98633 ( 1350)
  link_BETA1-4         : bond        0.00312 (    2)
  link_BETA1-4         : angle       1.95239 (    6)
  link_NAG-ASN         : bond        0.00631 (    2)
  link_NAG-ASN         : angle       1.49283 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 80
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7272 (OUTLIER) cc_final: 0.6426 (ttmt)
REVERT: A   78 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8357 (mp)
REVERT: A  186 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8323 (t0)
REVERT: A  344 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7699 (mtp180)
REVERT: A 1000 LEU cc_start: 0.8678 (OUTLIER) cc_final: 0.8344 (mp)
REVERT: A 1087 TYR cc_start: 0.7129 (t80) cc_final: 0.6429 (t80)
REVERT: A 1225 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7785 (m-80)
REVERT: A 1260 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7692 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8107 (mp)
REVERT: A 1294 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7628 (mmp80)
  outliers start: 37
  outliers final: 21
  residues processed: 106
  average time/residue: 0.6372
  time to fit residues: 71.6430
Evaluate side-chains
  109 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 79
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 74 optimal weight:    0.0270
   chunk 102 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 95 optimal weight:    0.8980
   chunk 35 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 48 optimal weight:    0.9980
   chunk 96 optimal weight:    0.6980
   chunk 77 optimal weight:    0.5980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
A 146 GLN
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.185819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.117297 restraints weight = 8234.130|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 3.25
r_work: 0.3092 rms_B_bonded: 2.67 restraints_weight: 0.5000
r_work: 0.2969 rms_B_bonded: 4.03 restraints_weight: 0.2500
r_work (final): 0.2969
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8558
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8548  Z= 0.129
  Angle     :  0.568  10.695  11613  Z= 0.282
  Chirality :  0.039   0.258   1368
  Planarity :  0.004   0.050   1440
  Dihedral  :  8.474  87.480   1255
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.94 %
    Favored  : 98.06 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.88 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.35 (0.27), residues: 1030
  helix:  2.92 (0.22), residues: 541
  sheet:  0.17 (0.45), residues: 113
  loop : -0.02 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1201 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.014   0.001   PHE A1093 
 TRP   0.012   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 8544)
  covalent geometry    : angle       0.56349 (11601)
  hydrogen bonds       : bond        0.06605 (  467)
  hydrogen bonds       : angle       3.96035 ( 1350)
  link_BETA1-4         : bond        0.00402 (    2)
  link_BETA1-4         : angle       1.99144 (    6)
  link_NAG-ASN         : bond        0.01461 (    2)
  link_NAG-ASN         : angle       2.68981 (    6)

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

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

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2060 Ramachandran restraints generated.
    1030 Oldfield, 0 Emsley, 1030 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 79
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   43 LYS cc_start: 0.7342 (OUTLIER) cc_final: 0.6481 (ttmt)
REVERT: A   78 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8376 (mp)
REVERT: A  186 ASP cc_start: 0.8932 (OUTLIER) cc_final: 0.8272 (t0)
REVERT: A  344 ARG cc_start: 0.8293 (OUTLIER) cc_final: 0.7690 (mtp180)
REVERT: A  700 MET cc_start: 0.2546 (OUTLIER) cc_final: 0.1234 (ptm)
REVERT: A 1000 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8349 (mp)
REVERT: A 1087 TYR cc_start: 0.7149 (t80) cc_final: 0.6454 (t80)
REVERT: A 1178 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8140 (mt)
REVERT: A 1225 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7781 (m-80)
REVERT: A 1260 ARG cc_start: 0.8087 (OUTLIER) cc_final: 0.7697 (mtp85)
REVERT: A 1288 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8173 (mp)
REVERT: A 1294 ARG cc_start: 0.8788 (OUTLIER) cc_final: 0.7640 (mmp80)
  outliers start: 36
  outliers final: 22
  residues processed: 106
  average time/residue: 0.6092
  time to fit residues: 68.4538
Evaluate side-chains
  112 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 79
  time to evaluate  : 0.257 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LYS
Chi-restraints excluded: chain A residue   43 LYS
Chi-restraints excluded: chain A residue   78 LEU
Chi-restraints excluded: chain A residue  126 ARG
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  186 ASP
Chi-restraints excluded: chain A residue  216 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  344 ARG
Chi-restraints excluded: chain A residue  393 THR
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  700 MET
Chi-restraints excluded: chain A residue  778 ILE
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue 1000 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1072 THR
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1178 LEU
Chi-restraints excluded: chain A residue 1195 CYS
Chi-restraints excluded: chain A residue 1225 PHE
Chi-restraints excluded: chain A residue 1229 LEU
Chi-restraints excluded: chain A residue 1235 LEU
Chi-restraints excluded: chain A residue 1250 THR
Chi-restraints excluded: chain A residue 1260 ARG
Chi-restraints excluded: chain A residue 1278 LEU
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1295 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 20 optimal weight:    2.9990
   chunk 98 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 15 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   chunk 10 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0980
   chunk 75 optimal weight:    0.8980
   chunk 0 optimal weight:    5.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 588 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 652 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 ASN
A 963 GLN
A1053 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.185587 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.116458 restraints weight = 8200.399|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.99
r_work: 0.3114 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2995 rms_B_bonded: 3.60 restraints_weight: 0.2500
r_work (final): 0.2995
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8548  Z= 0.133
  Angle     :  0.572  10.754  11613  Z= 0.284
  Chirality :  0.039   0.245   1368
  Planarity :  0.004   0.050   1440
  Dihedral  :  8.401  85.840   1255
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 21.88 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.32 (0.27), residues: 1030
  helix:  2.89 (0.22), residues: 541
  sheet:  0.15 (0.45), residues: 113
  loop : -0.03 (0.32), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 380 
 TYR   0.010   0.001   TYR A 312 
 PHE   0.016   0.001   PHE A1093 
 TRP   0.011   0.001   TRP A 310 
 HIS   0.002   0.000   HIS A1253 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 8544)
  covalent geometry    : angle       0.56765 (11601)
  hydrogen bonds       : bond        0.06734 (  467)
  hydrogen bonds       : angle       3.96365 ( 1350)
  link_BETA1-4         : bond        0.00357 (    2)
  link_BETA1-4         : angle       2.02333 (    6)
  link_NAG-ASN         : bond        0.01389 (    2)
  link_NAG-ASN         : angle       2.59008 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3925.61 seconds
wall clock time: 67 minutes 25.51 seconds (4045.51 seconds total)