Starting phenix.real_space_refine
on Sat Jul 26 09:31:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jk3_61542/07_2025/9jk3_61542.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jk3_61542/07_2025/9jk3_61542.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.45
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jk3_61542/07_2025/9jk3_61542.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jk3_61542/07_2025/9jk3_61542.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jk3_61542/07_2025/9jk3_61542.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jk3_61542/07_2025/9jk3_61542.cif"
  }
  resolution = 2.45
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.065
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      64      5.16       5
     C    5408      2.51       5
     N    1429      2.21       5
     O    1499      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 8401
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 8293
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1054, 8293
          Classifications: {'peptide': 1054}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 54, 'TRANS': 999}
          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: 5.78, per 1000 atoms: 0.69
  Number of scatterers: 8401
  At special positions: 0
  Unit cell: (86.2522, 86.2522, 159.106, 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      64     16.00
     P       1     15.00
     O    1499      8.00
     N    1429      7.00
     C    5408      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: 2.21
  Conformation dependent library (CDL) restraints added in 938.7 milliseconds
  

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2000

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 6 sheets defined
      58.7% alpha, 12.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 18 through 44
    Processing helix  chain 'A' and resid 46 through 53
    Processing helix  chain 'A' and resid 66 through 83
    Processing helix  chain 'A' and resid 93 through 122
      removed outlier: 3.556A  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: 4.534A  pdb=" N   ASN A 253 " --> pdb=" O   PRO A 249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 267 through 302
      Proline residue:  A 286  - end of helix
    Processing helix  chain 'A' and resid 309 through 323
    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: 3.596A  pdb=" N   MET A 349 " --> pdb=" O   VAL A 345 " (cutoff:3.500A)
      removed outlier: 4.156A  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 576 through 581
      removed outlier: 4.311A  pdb=" N   THR A 580 " --> pdb=" O   LEU A 577 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 582 through 594
      removed outlier: 3.568A  pdb=" N   VAL A 589 " --> pdb=" O   LEU A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 616
      removed outlier: 3.703A  pdb=" N   ARG A 604 " --> pdb=" O   GLU A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 638
      removed outlier: 3.687A  pdb=" N   ALA A 634 " --> pdb=" O   LEU A 630 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   GLY A 638 " --> pdb=" O   ALA A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 645
      removed outlier: 3.546A  pdb=" N   GLU A 645 " --> pdb=" O   GLY A 642 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 712
      removed outlier: 3.706A  pdb=" N   VAL A 709 " --> pdb=" O   THR A 705 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   LEU A 710 " --> pdb=" O   ALA A 706 " (cutoff:3.500A)
      removed outlier: 4.720A  pdb=" N   GLU A 711 " --> pdb=" O   ASP A 707 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 726 through 744
      removed outlier: 3.626A  pdb=" N   PHE A 736 " --> pdb=" O   LYS A 732 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   SER A 743 " --> pdb=" O   ARG A 739 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 759 through 763
      removed outlier: 3.556A  pdb=" N   LEU A 762 " --> pdb=" O   SER A 759 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 819
    Processing helix  chain 'A' and resid 834 through 847
    Processing helix  chain 'A' and resid 858 through 869
      removed outlier: 3.702A  pdb=" N   LYS A 868 " --> pdb=" O   VAL A 864 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET A 869 " --> pdb=" O   PHE A 865 " (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 1070 through 1072
      No H-bonds generated for 'chain 'A' and resid 1070 through 1072'
    Processing helix  chain 'A' and resid 1073 through 1113
      removed outlier: 4.536A  pdb=" N   ARG A1077 " --> pdb=" O   ILE A1073 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1120 through 1130
    Processing helix  chain 'A' and resid 1130 through 1139
    Processing helix  chain 'A' and resid 1145 through 1151
      removed outlier: 3.886A  pdb=" N   MET A1149 " --> pdb=" O   SER A1146 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   MET A1151 " --> pdb=" O   ILE A1148 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1161 through 1201
      removed outlier: 5.306A  pdb=" N   LEU A1178 " --> pdb=" O   LEU A1174 " (cutoff:3.500A)
      removed outlier: 5.386A  pdb=" N   THR A1179 " --> pdb=" O   LYS A1175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1225 through 1251
      removed outlier: 3.902A  pdb=" N   THR A1250 " --> pdb=" O   PHE A1246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1265
      removed outlier: 3.745A  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: 3.786A  pdb=" N   VAL A1305 " --> pdb=" O   LEU A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1306 through 1353
      removed outlier: 3.759A  pdb=" N   TRP A1310 " --> pdb=" O   PRO A1306 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   ASN A1353 " --> pdb=" O   LYS A1349 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 173 through 178
      removed outlier: 4.011A  pdb=" N   TRP A 167 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
      removed outlier: 5.008A  pdb=" N   ILE A 187 " --> pdb=" O   TYR A 169 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG A 241 " --> pdb=" O   LEU A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 878 through 880
      removed outlier: 6.627A  pdb=" N   ILE A 879 " --> pdb=" O   THR A 976 " (cutoff:3.500A)
      removed outlier: 8.105A  pdb=" N   PHE A 975 " --> pdb=" O   PHE A 851 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   TYR A 853 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 6.237A  pdb=" N   LEU A 413 " --> pdb=" O   VAL A 852 " (cutoff:3.500A)
      removed outlier: 7.491A  pdb=" N   PHE A 854 " --> pdb=" O   LEU A 413 " (cutoff:3.500A)
      removed outlier: 6.702A  pdb=" N   CYS A 415 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
      removed outlier: 6.649A  pdb=" N   VAL A 412 " --> pdb=" O   CYS A 998 " (cutoff:3.500A)
      removed outlier: 7.848A  pdb=" N   LEU A1000 " --> pdb=" O   VAL A 412 " (cutoff:3.500A)
      removed outlier: 6.411A  pdb=" N   CYS A 414 " --> pdb=" O   LEU A1000 " (cutoff:3.500A)
      removed outlier: 8.512A  pdb=" N   SER A1002 " --> pdb=" O   CYS A 414 " (cutoff:3.500A)
      removed outlier: 6.346A  pdb=" N   THR A 997 " --> pdb=" O   ILE A1017 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   ILE A1019 " --> pdb=" O   THR A 997 " (cutoff:3.500A)
      removed outlier: 6.142A  pdb=" N   CYS A 999 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
      removed outlier: 7.019A  pdb=" N   LEU A1021 " --> pdb=" O   CYS A 999 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   GLY A1001 " --> pdb=" O   LEU A1021 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   SER A1018 " --> pdb=" O   LEU A1065 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   PHE A1067 " --> pdb=" O   SER A1018 " (cutoff:3.500A)
      removed outlier: 6.737A  pdb=" N   ALA A1020 " --> pdb=" O   PHE A1067 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 552 through 557
      removed outlier: 3.858A  pdb=" N   GLU A 554 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   PHE A 434 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU A 556 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   GLN A 830 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 431 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   PHE A 435 " --> pdb=" O   MET A 824 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   MET A 824 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 7.554A  pdb=" N   PHE A 823 " --> pdb=" O   THR A 714 " (cutoff:3.500A)
      removed outlier: 4.666A  pdb=" N   PHE A 716 " --> pdb=" O   PHE A 823 " (cutoff:3.500A)
      removed outlier: 9.174A  pdb=" N   GLY A 825 " --> pdb=" O   PHE A 716 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 552 through 557
      removed outlier: 3.858A  pdb=" N   GLU A 554 " --> pdb=" O   PHE A 434 " (cutoff:3.500A)
      removed outlier: 4.740A  pdb=" N   PHE A 434 " --> pdb=" O   GLU A 554 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   LEU A 556 " --> pdb=" O   VAL A 432 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   GLN A 830 " --> pdb=" O   PRO A 429 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   THR A 431 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   PHE A 435 " --> pdb=" O   MET A 824 " (cutoff:3.500A)
      removed outlier: 8.178A  pdb=" N   MET A 824 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
      removed outlier: 7.722A  pdb=" N   GLN A 821 " --> pdb=" O   PRO A 753 " (cutoff:3.500A)
      removed outlier: 5.309A  pdb=" N   PHE A 823 " --> pdb=" O   TYR A 751 " (cutoff:3.500A)
      removed outlier: 7.393A  pdb=" N   TYR A 751 " --> pdb=" O   PHE A 823 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   GLY A 825 " --> pdb=" O   PHE A 749 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE A 749 " --> pdb=" O   GLY A 825 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLY A 704 " --> pdb=" O   ALA A 748 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   HIS A 703 " --> pdb=" O   ILE A 686 " (cutoff:3.500A)
      removed outlier: 4.329A  pdb=" N   SER A 683 " --> pdb=" O   ARG A 657 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   LYS A 691 " --> pdb=" O   GLN A 649 " (cutoff:3.500A)
      removed outlier: 5.593A  pdb=" N   GLN A 649 " --> pdb=" O   LYS A 691 " (cutoff:3.500A)
      removed outlier: 8.973A  pdb=" N   ILE A 767 " --> pdb=" O   HIS A 652 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ALA A 654 " --> pdb=" O   ILE A 767 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   LEU A 769 " --> pdb=" O   ALA A 654 " (cutoff:3.500A)
      removed outlier: 6.556A  pdb=" N   TYR A 656 " --> pdb=" O   LEU A 769 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 559 through 560
    Processing sheet with id=AA6, first strand: chain 'A' and resid 756 through 757

    481 hydrogen bonds defined for protein.
    1386 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.56

  Time building geometry restraints manager: 2.62 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1354
        1.32 -     1.44: 2230
        1.44 -     1.57: 4914
        1.57 -     1.69: 2
        1.69 -     1.82: 87
  Bond restraints: 8587
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.502 -0.096 2.00e-02 2.50e+03 2.29e+01
  bond pdb=" C1  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.28e+00
  bond pdb=" CG1 ILE A 987 "
       pdb=" CD1 ILE A 987 "
    ideal  model  delta    sigma   weight residual
    1.513  1.454  0.059 3.90e-02 6.57e+02 2.30e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 2.00e+00
  bond pdb=" C5  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.440 -0.027 2.00e-02 2.50e+03 1.89e+00
  ... (remaining 8582 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.72: 11558
        2.72 -     5.43: 92
        5.43 -     8.15: 5
        8.15 -    10.87: 1
       10.87 -    13.59: 1
  Bond angle restraints: 11657
  Sorted by residual:
  angle pdb=" CB  MET A 555 "
        pdb=" CG  MET A 555 "
        pdb=" SD  MET A 555 "
      ideal   model   delta    sigma   weight residual
     112.70  126.29  -13.59 3.00e+00 1.11e-01 2.05e+01
  angle pdb=" C   TRP A 875 "
        pdb=" N   ASN A 876 "
        pdb=" CA  ASN A 876 "
      ideal   model   delta    sigma   weight residual
     122.61  127.42   -4.81 1.56e+00 4.11e-01 9.52e+00
  angle pdb=" CA  LEU A 177 "
        pdb=" CB  LEU A 177 "
        pdb=" CG  LEU A 177 "
      ideal   model   delta    sigma   weight residual
     116.30  126.60  -10.30 3.50e+00 8.16e-02 8.66e+00
  angle pdb=" N   ILE A 955 "
        pdb=" CA  ILE A 955 "
        pdb=" C   ILE A 955 "
      ideal   model   delta    sigma   weight residual
     112.50  109.19    3.31 1.39e+00 5.18e-01 5.65e+00
  angle pdb=" N   TRP A  67 "
        pdb=" CA  TRP A  67 "
        pdb=" C   TRP A  67 "
      ideal   model   delta    sigma   weight residual
     109.81  114.83   -5.02 2.21e+00 2.05e-01 5.15e+00
  ... (remaining 11652 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.66: 4665
       22.66 -    45.31: 423
       45.31 -    67.97: 104
       67.97 -    90.63: 14
       90.63 -   113.28: 11
  Dihedral angle restraints: 5217
    sinusoidal: 2154
      harmonic: 3063
  Sorted by residual:
  dihedral pdb=" C2  NAG B   1 "
           pdb=" C1  NAG B   1 "
           pdb=" O5  NAG B   1 "
           pdb=" C5  NAG B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -62.96   50.32 -113.28     1      3.00e+01 1.11e-03 1.49e+01
  dihedral pdb=" C1  NAG B   2 "
           pdb=" C2  NAG B   2 "
           pdb=" C3  NAG B   2 "
           pdb=" O3  NAG B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -175.09  -67.19 -107.90     1      3.00e+01 1.11e-03 1.39e+01
  dihedral pdb=" C1  NAG B   2 "
           pdb=" C2  NAG B   2 "
           pdb=" C3  NAG B   2 "
           pdb=" C4  NAG B   2 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -52.39   54.49 -106.88     1      3.00e+01 1.11e-03 1.38e+01
  ... (remaining 5214 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 1195
       0.063 -    0.125: 163
       0.125 -    0.188: 14
       0.188 -    0.250: 1
       0.250 -    0.313: 1
  Chirality restraints: 1374
  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   -2.09   -0.31 2.00e-01 2.50e+01 2.45e+00
  chirality pdb=" CB  VAL A1320 "
            pdb=" CA  VAL A1320 "
            pdb=" CG1 VAL A1320 "
            pdb=" CG2 VAL A1320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.42   -0.21 2.00e-01 2.50e+01 1.08e+00
  chirality pdb=" CA  LEU A1319 "
            pdb=" N   LEU A1319 "
            pdb=" C   LEU A1319 "
            pdb=" CB  LEU A1319 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.57e-01
  ... (remaining 1371 not shown)

  Planarity restraints: 1449
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 313 "   -0.016 2.00e-02 2.50e+03   3.27e-02 1.07e+01
        pdb=" C   THR A 313 "    0.057 2.00e-02 2.50e+03
        pdb=" O   THR A 313 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 314 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 281 "   -0.013 2.00e-02 2.50e+03   2.64e-02 6.97e+00
        pdb=" C   LEU A 281 "    0.046 2.00e-02 2.50e+03
        pdb=" O   LEU A 281 "   -0.017 2.00e-02 2.50e+03
        pdb=" N   HIS A 282 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 312 "    0.010 2.00e-02 2.50e+03   2.05e-02 4.18e+00
        pdb=" C   TYR A 312 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   TYR A 312 "    0.013 2.00e-02 2.50e+03
        pdb=" N   THR A 313 "    0.012 2.00e-02 2.50e+03
  ... (remaining 1446 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 2101
        2.80 -     3.33: 7642
        3.33 -     3.85: 14182
        3.85 -     4.38: 16344
        4.38 -     4.90: 28048
  Nonbonded interactions: 68317
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 314 "
            pdb=" NE2 GLN A 318 "
     model   vdw
     2.279 3.120
  nonbonded pdb=" NH2 ARG A 170 "
            pdb=" OD2 ASP A 186 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OE1 GLU A 125 "
            pdb=" NH1 ARG A 129 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" O   ASP A 595 "
            pdb=" OG1 THR A 599 "
     model   vdw
     2.285 3.040
  nonbonded pdb=" OE1 GLU A 632 "
            pdb=" NH2 ARG A 635 "
     model   vdw
     2.287 3.120
  ... (remaining 68312 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:             56.400
  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:             0.020
  Extract box with map and model:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.110
  Process input model:                     24.620
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:11.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   93.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8760
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      :  0.006   0.096   8591  Z= 0.246
  Angle     :  0.632  13.585  11669  Z= 0.314
  Chirality :  0.045   0.313   1374
  Planarity :  0.005   0.048   1447
  Dihedral  : 18.935 113.284   3217
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  3.61 %
    Allowed  : 19.21 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.18 (0.26), residues: 1036
  helix:  2.28 (0.22), residues: 552
  sheet:  0.49 (0.51), residues: 112
  loop :  0.60 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A1221 
 HIS   0.004   0.001   HIS A1251 
 PHE   0.023   0.002   PHE A1093 
 TYR   0.017   0.002   TYR A 993 
 ARG   0.004   0.001   ARG A1083 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00593 (    2)
  link_NAG-ASN         : angle       2.70665 (    6)
  link_BETA1-4         : bond        0.00978 (    2)
  link_BETA1-4         : angle       2.10125 (    6)
  hydrogen bonds       : bond        0.18035 (  475)
  hydrogen bonds       : angle       5.90809 ( 1386)
  covalent geometry    : bond        0.00585 ( 8587)
  covalent geometry    : angle       0.62783 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 77
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  555 MET cc_start: 0.4507 (tpp) cc_final: 0.1781 (mmp)
REVERT: A 1162 LYS cc_start: 0.8082 (mmtt) cc_final: 0.7786 (mptt)
  outliers start: 34
  outliers final: 27
  residues processed: 107
  average time/residue: 1.6728
  time to fit residues: 189.6040
Evaluate side-chains
  102 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 75
  time to evaluate  : 1.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  149 SER
Chi-restraints excluded: chain A residue  188 ILE
Chi-restraints excluded: chain A residue  196 SER
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  857 GLU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue 1006 LEU
Chi-restraints excluded: chain A residue 1009 SER
Chi-restraints excluded: chain A residue 1064 SER
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1347 GLU
Chi-restraints excluded: chain A residue 1349 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 88 optimal weight:    0.9990
   chunk 79 optimal weight:    0.8980
   chunk 44 optimal weight:    2.9990
   chunk 27 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 82 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 50 optimal weight:    6.9990
   chunk 61 optimal weight:    0.8980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A1053 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.173861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.097059 restraints weight = 8571.980|
|-----------------------------------------------------------------------------|
r_work (start): 0.3063 rms_B_bonded: 1.96
r_work: 0.2937 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2812 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.0772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8591  Z= 0.144
  Angle     :  0.560  10.551  11669  Z= 0.278
  Chirality :  0.040   0.191   1374
  Planarity :  0.004   0.047   1447
  Dihedral  : 12.564  81.969   1298
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 4.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 17.73 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.48 (0.27), residues: 1036
  helix:  2.63 (0.22), residues: 555
  sheet:  0.37 (0.51), residues: 109
  loop :  0.59 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1310 
 HIS   0.003   0.001   HIS A1251 
 PHE   0.017   0.001   PHE A1093 
 TYR   0.013   0.001   TYR A 312 
 ARG   0.002   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00092 (    2)
  link_NAG-ASN         : angle       2.32507 (    6)
  link_BETA1-4         : bond        0.00739 (    2)
  link_BETA1-4         : angle       1.73122 (    6)
  hydrogen bonds       : bond        0.06133 (  475)
  hydrogen bonds       : angle       4.48152 ( 1386)
  covalent geometry    : bond        0.00320 ( 8587)
  covalent geometry    : angle       0.55608 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 77
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8934 (OUTLIER) cc_final: 0.8509 (mp)
REVERT: A  555 MET cc_start: 0.4673 (tpp) cc_final: 0.3097 (tmt)
REVERT: A 1162 LYS cc_start: 0.7786 (mmtt) cc_final: 0.7477 (mptt)
  outliers start: 45
  outliers final: 24
  residues processed: 115
  average time/residue: 1.9498
  time to fit residues: 236.8687
Evaluate side-chains
  104 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 79
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  551 TYR
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1009 SER
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 68 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 93 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 9 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0370
   chunk 67 optimal weight:    4.9990
   chunk 82 optimal weight:    0.6980
   overall best weight:    0.6858

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A1339 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.172999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.095854 restraints weight = 8708.991|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 1.97
r_work: 0.2914 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.2786 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.2786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8632
moved from start:          0.0995

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8591  Z= 0.126
  Angle     :  0.534  10.681  11669  Z= 0.262
  Chirality :  0.038   0.161   1374
  Planarity :  0.004   0.049   1447
  Dihedral  : 10.156  61.491   1278
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 18.47 %
    Favored  : 77.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.57 (0.27), residues: 1036
  helix:  2.83 (0.22), residues: 550
  sheet:  0.25 (0.51), residues: 110
  loop :  0.52 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1310 
 HIS   0.002   0.001   HIS A1251 
 PHE   0.016   0.001   PHE A1093 
 TYR   0.013   0.001   TYR A 312 
 ARG   0.002   0.000   ARG A 140 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00327 (    2)
  link_NAG-ASN         : angle       3.88333 (    6)
  link_BETA1-4         : bond        0.00608 (    2)
  link_BETA1-4         : angle       1.95786 (    6)
  hydrogen bonds       : bond        0.05533 (  475)
  hydrogen bonds       : angle       4.26692 ( 1386)
  covalent geometry    : bond        0.00273 ( 8587)
  covalent geometry    : angle       0.52531 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 82
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8502 (mp)
REVERT: A  379 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8381 (tt)
REVERT: A  555 MET cc_start: 0.4971 (tpp) cc_final: 0.3795 (tmm)
REVERT: A  685 MET cc_start: 0.2208 (mmt) cc_final: 0.1844 (mmm)
REVERT: A 1162 LYS cc_start: 0.7681 (mmtt) cc_final: 0.7347 (mptt)
REVERT: A 1288 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8526 (mp)
REVERT: A 1294 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8452 (mmt180)
  outliers start: 37
  outliers final: 21
  residues processed: 114
  average time/residue: 1.4809
  time to fit residues: 178.8056
Evaluate side-chains
  102 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 77
  time to evaluate  : 0.967 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  376 GLN
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1307 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 15 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 72 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
A 832 GLN
A1053 GLN
A1339 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.171371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.093608 restraints weight = 8590.930|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 1.94
r_work: 0.2878 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2748 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8691
moved from start:          0.0944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8591  Z= 0.179
  Angle     :  0.577   9.159  11669  Z= 0.282
  Chirality :  0.040   0.149   1374
  Planarity :  0.005   0.051   1447
  Dihedral  :  9.479  69.212   1274
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 17.62 %
    Favored  : 77.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.53 (0.27), residues: 1036
  helix:  2.75 (0.22), residues: 551
  sheet:  0.23 (0.51), residues: 110
  loop :  0.57 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1310 
 HIS   0.003   0.001   HIS A1251 
 PHE   0.022   0.002   PHE A1093 
 TYR   0.015   0.001   TYR A 312 
 ARG   0.003   0.000   ARG A1254 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00568 (    2)
  link_NAG-ASN         : angle       3.82276 (    6)
  link_BETA1-4         : bond        0.00537 (    2)
  link_BETA1-4         : angle       2.85844 (    6)
  hydrogen bonds       : bond        0.06329 (  475)
  hydrogen bonds       : angle       4.27014 ( 1386)
  covalent geometry    : bond        0.00429 ( 8587)
  covalent geometry    : angle       0.56725 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 80
  time to evaluate  : 0.841 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8523 (mp)
REVERT: A  122 ARG cc_start: 0.8557 (ptm160) cc_final: 0.8235 (ptp-110)
REVERT: A  379 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8398 (tt)
REVERT: A  555 MET cc_start: 0.5034 (tpp) cc_final: 0.4016 (tmm)
REVERT: A  685 MET cc_start: 0.2009 (mmt) cc_final: 0.1769 (mmm)
REVERT: A  746 CYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6523 (t)
REVERT: A 1288 LEU cc_start: 0.9053 (OUTLIER) cc_final: 0.8507 (mp)
REVERT: A 1294 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8442 (mmt180)
  outliers start: 49
  outliers final: 24
  residues processed: 121
  average time/residue: 1.4322
  time to fit residues: 183.1519
Evaluate side-chains
  112 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 83
  time to evaluate  : 0.991 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 LEU
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  746 CYS
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  815 MET
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  875 TRP
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1294 ARG
Chi-restraints excluded: chain A residue 1307 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 5 optimal weight:    0.6980
   chunk 66 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   chunk 101 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 15 optimal weight:    0.2980
   chunk 56 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 35 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 134 GLN
A 136 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 GLN
A1057 GLN
A1339 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.172761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.095856 restraints weight = 8573.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.96
r_work: 0.2916 rms_B_bonded: 2.26 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8591  Z= 0.129
  Angle     :  0.526   8.694  11669  Z= 0.258
  Chirality :  0.038   0.160   1374
  Planarity :  0.004   0.050   1447
  Dihedral  :  8.962  63.736   1274
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 4.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  4.46 %
    Allowed  : 19.21 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.67 (0.27), residues: 1036
  helix:  2.91 (0.22), residues: 547
  sheet:  0.22 (0.51), residues: 110
  loop :  0.62 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A1310 
 HIS   0.002   0.001   HIS A1251 
 PHE   0.016   0.001   PHE A1093 
 TYR   0.012   0.001   TYR A 312 
 ARG   0.003   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00323 (    2)
  link_NAG-ASN         : angle       3.28460 (    6)
  link_BETA1-4         : bond        0.00446 (    2)
  link_BETA1-4         : angle       3.27875 (    6)
  hydrogen bonds       : bond        0.05444 (  475)
  hydrogen bonds       : angle       4.15549 ( 1386)
  covalent geometry    : bond        0.00289 ( 8587)
  covalent geometry    : angle       0.51580 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 83
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8505 (mp)
REVERT: A  122 ARG cc_start: 0.8511 (ptm160) cc_final: 0.8212 (ptp-110)
REVERT: A  379 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8316 (tt)
REVERT: A  826 MET cc_start: 0.5070 (mmm) cc_final: 0.4368 (mmt)
REVERT: A 1288 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8737 (mp)
  outliers start: 42
  outliers final: 23
  residues processed: 116
  average time/residue: 1.3644
  time to fit residues: 167.6259
Evaluate side-chains
  105 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 79
  time to evaluate  : 0.900 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  578 HIS
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  835 LEU
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1288 LEU
Chi-restraints excluded: chain A residue 1307 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 103 optimal weight:    0.9980
   chunk 47 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 41 optimal weight:    9.9990
   chunk 16 optimal weight:    0.3980
   chunk 100 optimal weight:    0.0170
   chunk 69 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 GLN
A1339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.173491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.096580 restraints weight = 8573.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3054 rms_B_bonded: 1.93
r_work: 0.2930 rms_B_bonded: 2.28 restraints_weight: 0.5000
r_work: 0.2805 rms_B_bonded: 3.44 restraints_weight: 0.2500
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8591  Z= 0.117
  Angle     :  0.524   8.429  11669  Z= 0.255
  Chirality :  0.037   0.165   1374
  Planarity :  0.004   0.050   1447
  Dihedral  :  8.565  61.268   1270
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 19.11 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.75 (0.27), residues: 1036
  helix:  2.99 (0.22), residues: 547
  sheet:  0.20 (0.50), residues: 110
  loop :  0.66 (0.33), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1310 
 HIS   0.002   0.000   HIS A 703 
 PHE   0.015   0.001   PHE A1093 
 TYR   0.012   0.001   TYR A 312 
 ARG   0.004   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00256 (    2)
  link_NAG-ASN         : angle       3.08806 (    6)
  link_BETA1-4         : bond        0.00428 (    2)
  link_BETA1-4         : angle       3.33002 (    6)
  hydrogen bonds       : bond        0.05160 (  475)
  hydrogen bonds       : angle       4.09715 ( 1386)
  covalent geometry    : bond        0.00253 ( 8587)
  covalent geometry    : angle       0.51419 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 81
  time to evaluate  : 0.884 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8503 (mp)
REVERT: A  122 ARG cc_start: 0.8494 (ptm160) cc_final: 0.8200 (ptp-110)
REVERT: A  379 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8312 (tt)
REVERT: A  555 MET cc_start: 0.4775 (tpt) cc_final: 0.3310 (tmm)
  outliers start: 44
  outliers final: 22
  residues processed: 114
  average time/residue: 1.3464
  time to fit residues: 162.6525
Evaluate side-chains
  103 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 79
  time to evaluate  : 0.883 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  379 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  578 HIS
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  830 GLN
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1055 SER
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1307 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 18 optimal weight:    4.9990
   chunk 49 optimal weight:    0.0270
   chunk 27 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 79 optimal weight:    2.9990
   chunk 86 optimal weight:    0.1980
   chunk 51 optimal weight:    7.9990
   chunk 78 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   overall best weight:    0.5842

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 552 HIS
A1053 GLN
A1339 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.173861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.097155 restraints weight = 8676.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.97
r_work: 0.2939 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.48 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8627
moved from start:          0.1386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8591  Z= 0.115
  Angle     :  0.513   8.336  11669  Z= 0.251
  Chirality :  0.037   0.174   1374
  Planarity :  0.004   0.051   1447
  Dihedral  :  7.997  58.465   1266
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  4.03 %
    Allowed  : 19.53 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.78 (0.27), residues: 1036
  helix:  3.08 (0.22), residues: 542
  sheet:  0.19 (0.51), residues: 110
  loop :  0.60 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1310 
 HIS   0.006   0.000   HIS A 703 
 PHE   0.015   0.001   PHE A1093 
 TYR   0.012   0.001   TYR A1087 
 ARG   0.003   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00166 (    2)
  link_NAG-ASN         : angle       2.89047 (    6)
  link_BETA1-4         : bond        0.00390 (    2)
  link_BETA1-4         : angle       3.34377 (    6)
  hydrogen bonds       : bond        0.04955 (  475)
  hydrogen bonds       : angle       4.02076 ( 1386)
  covalent geometry    : bond        0.00250 ( 8587)
  covalent geometry    : angle       0.50344 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 80
  time to evaluate  : 1.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8508 (mp)
REVERT: A  122 ARG cc_start: 0.8498 (ptm160) cc_final: 0.8198 (ptp-110)
REVERT: A  555 MET cc_start: 0.4811 (tpt) cc_final: 0.3457 (tmm)
  outliers start: 38
  outliers final: 22
  residues processed: 107
  average time/residue: 1.7748
  time to fit residues: 203.2255
Evaluate side-chains
  103 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 80
  time to evaluate  : 1.532 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  568 ILE
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  830 GLN
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1307 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 52 optimal weight:    6.9990
   chunk 24 optimal weight:    2.9990
   chunk 96 optimal weight:    0.5980
   chunk 103 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9990
   chunk 84 optimal weight:    0.8980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 GLN
A1339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.172831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.095690 restraints weight = 8703.709|
|-----------------------------------------------------------------------------|
r_work (start): 0.3039 rms_B_bonded: 1.96
r_work: 0.2913 rms_B_bonded: 2.30 restraints_weight: 0.5000
r_work: 0.2787 rms_B_bonded: 3.50 restraints_weight: 0.2500
r_work (final): 0.2787
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8650
moved from start:          0.1372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8591  Z= 0.132
  Angle     :  0.531   8.524  11669  Z= 0.260
  Chirality :  0.038   0.179   1374
  Planarity :  0.004   0.051   1447
  Dihedral  :  7.843  60.194   1262
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 19.64 %
    Favored  : 76.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.72 (0.27), residues: 1036
  helix:  2.94 (0.22), residues: 550
  sheet:  0.21 (0.50), residues: 110
  loop :  0.65 (0.33), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1310 
 HIS   0.004   0.001   HIS A 703 
 PHE   0.018   0.001   PHE A1093 
 TYR   0.014   0.001   TYR A 312 
 ARG   0.006   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00209 (    2)
  link_NAG-ASN         : angle       2.81781 (    6)
  link_BETA1-4         : bond        0.00398 (    2)
  link_BETA1-4         : angle       3.29897 (    6)
  hydrogen bonds       : bond        0.05385 (  475)
  hydrogen bonds       : angle       4.06734 ( 1386)
  covalent geometry    : bond        0.00301 ( 8587)
  covalent geometry    : angle       0.52212 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 83
  time to evaluate  : 1.221 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8897 (OUTLIER) cc_final: 0.8489 (mp)
REVERT: A  122 ARG cc_start: 0.8516 (ptm160) cc_final: 0.8218 (ptp-110)
REVERT: A  419 GLN cc_start: 0.8607 (OUTLIER) cc_final: 0.8387 (mp10)
REVERT: A  555 MET cc_start: 0.4658 (tpt) cc_final: 0.3502 (tmm)
  outliers start: 35
  outliers final: 24
  residues processed: 108
  average time/residue: 2.0031
  time to fit residues: 230.7260
Evaluate side-chains
  106 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 1.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  419 GLN
Chi-restraints excluded: chain A residue  568 ILE
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  835 LEU
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1073 ILE
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1307 LEU
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 8 optimal weight:    0.7980
   chunk 5 optimal weight:    0.5980
   chunk 81 optimal weight:    0.6980
   chunk 48 optimal weight:    0.4980
   chunk 73 optimal weight:    0.1980
   chunk 67 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 34 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 GLN
A1339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.173877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.097055 restraints weight = 8737.635|
|-----------------------------------------------------------------------------|
r_work (start): 0.3061 rms_B_bonded: 1.99
r_work: 0.2938 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 3.49 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8628
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8591  Z= 0.112
  Angle     :  0.516   8.150  11669  Z= 0.252
  Chirality :  0.037   0.173   1374
  Planarity :  0.004   0.051   1447
  Dihedral  :  7.654  59.552   1262
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.32 %
    Favored  : 97.68 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.17 %
    Favored  : 76.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.81 (0.27), residues: 1036
  helix:  3.08 (0.22), residues: 542
  sheet:  0.26 (0.50), residues: 110
  loop :  0.62 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1310 
 HIS   0.006   0.000   HIS A 703 
 PHE   0.014   0.001   PHE A1093 
 TYR   0.013   0.001   TYR A1087 
 ARG   0.005   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00134 (    2)
  link_NAG-ASN         : angle       2.81194 (    6)
  link_BETA1-4         : bond        0.00299 (    2)
  link_BETA1-4         : angle       3.21286 (    6)
  hydrogen bonds       : bond        0.04933 (  475)
  hydrogen bonds       : angle       4.02961 ( 1386)
  covalent geometry    : bond        0.00241 ( 8587)
  covalent geometry    : angle       0.50717 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 82
  time to evaluate  : 3.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8497 (mp)
REVERT: A  122 ARG cc_start: 0.8498 (ptm160) cc_final: 0.8195 (ptp-110)
REVERT: A  379 LEU cc_start: 0.8345 (tt) cc_final: 0.8040 (mp)
REVERT: A  555 MET cc_start: 0.4613 (tpt) cc_final: 0.3492 (tmm)
REVERT: A 1070 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7895 (pm20)
  outliers start: 33
  outliers final: 24
  residues processed: 109
  average time/residue: 2.3710
  time to fit residues: 276.4850
Evaluate side-chains
  106 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 80
  time to evaluate  : 1.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  136 GLN
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   chunk 34 optimal weight:    1.9990
   chunk 67 optimal weight:    0.6980
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   chunk 37 optimal weight:    3.9990
   chunk 35 optimal weight:    4.9990
   chunk 96 optimal weight:    0.5980
   chunk 21 optimal weight:    0.8980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 GLN
A1339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.173189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3076 r_free = 0.3076 target = 0.096381 restraints weight = 8666.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.3051 rms_B_bonded: 1.97
r_work: 0.2926 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8673
moved from start:          0.1452

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8591  Z= 0.128
  Angle     :  0.530   8.386  11669  Z= 0.259
  Chirality :  0.038   0.175   1374
  Planarity :  0.004   0.051   1447
  Dihedral  :  7.667  59.180   1262
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.22 %
    Favored  : 97.78 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 20.49 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.73 (0.27), residues: 1036
  helix:  2.98 (0.22), residues: 545
  sheet:  0.29 (0.51), residues: 110
  loop :  0.60 (0.33), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A1310 
 HIS   0.006   0.001   HIS A 703 
 PHE   0.017   0.001   PHE A1093 
 TYR   0.013   0.001   TYR A1087 
 ARG   0.006   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00146 (    2)
  link_NAG-ASN         : angle       2.76883 (    6)
  link_BETA1-4         : bond        0.00355 (    2)
  link_BETA1-4         : angle       3.20258 (    6)
  hydrogen bonds       : bond        0.05188 (  475)
  hydrogen bonds       : angle       4.04815 ( 1386)
  covalent geometry    : bond        0.00293 ( 8587)
  covalent geometry    : angle       0.52146 (11657)

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

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

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2072 Ramachandran restraints generated.
    1036 Oldfield, 0 Emsley, 1036 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 82
  time to evaluate  : 0.960 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  104 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8539 (mp)
REVERT: A  122 ARG cc_start: 0.8538 (ptm160) cc_final: 0.8245 (ptp-110)
REVERT: A  555 MET cc_start: 0.4635 (tpt) cc_final: 0.3509 (tmm)
REVERT: A 1070 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7888 (pm20)
REVERT: A 1352 MET cc_start: 0.5416 (tpt) cc_final: 0.5122 (tpt)
  outliers start: 29
  outliers final: 23
  residues processed: 105
  average time/residue: 1.7752
  time to fit residues: 197.9597
Evaluate side-chains
  105 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 80
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   75 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  104 LEU
Chi-restraints excluded: chain A residue  177 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  403 LEU
Chi-restraints excluded: chain A residue  413 LEU
Chi-restraints excluded: chain A residue  568 ILE
Chi-restraints excluded: chain A residue  580 THR
Chi-restraints excluded: chain A residue  602 LEU
Chi-restraints excluded: chain A residue  703 HIS
Chi-restraints excluded: chain A residue  781 MET
Chi-restraints excluded: chain A residue  852 VAL
Chi-restraints excluded: chain A residue  860 LEU
Chi-restraints excluded: chain A residue  863 LYS
Chi-restraints excluded: chain A residue  876 ASN
Chi-restraints excluded: chain A residue  877 CYS
Chi-restraints excluded: chain A residue  950 LYS
Chi-restraints excluded: chain A residue 1021 LEU
Chi-restraints excluded: chain A residue 1053 GLN
Chi-restraints excluded: chain A residue 1070 GLU
Chi-restraints excluded: chain A residue 1092 CYS
Chi-restraints excluded: chain A residue 1110 SER
Chi-restraints excluded: chain A residue 1122 THR
Chi-restraints excluded: chain A residue 1312 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 105
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 78 optimal weight:    2.9990
   chunk 33 optimal weight:    0.1980
   chunk 48 optimal weight:    8.9990
   chunk 64 optimal weight:    0.5980
   chunk 58 optimal weight:   10.0000
   chunk 15 optimal weight:    0.9980
   chunk 98 optimal weight:    0.6980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 136 GLN
** A 318 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1053 GLN
A1339 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.173163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.096232 restraints weight = 8751.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 2.01
r_work: 0.2923 rms_B_bonded: 2.34 restraints_weight: 0.5000
r_work: 0.2794 rms_B_bonded: 3.58 restraints_weight: 0.2500
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8621
moved from start:          0.1484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8591  Z= 0.118
  Angle     :  0.520   8.244  11669  Z= 0.254
  Chirality :  0.038   0.174   1374
  Planarity :  0.004   0.051   1447
  Dihedral  :  7.583  58.128   1262
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 3.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.38 %
    Favored  : 76.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.79 (0.27), residues: 1036
  helix:  3.05 (0.22), residues: 542
  sheet:  0.30 (0.51), residues: 110
  loop :  0.62 (0.33), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A1310 
 HIS   0.006   0.001   HIS A 703 
 PHE   0.016   0.001   PHE A1093 
 TYR   0.012   0.001   TYR A1087 
 ARG   0.005   0.000   ARG A 191 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00150 (    2)
  link_NAG-ASN         : angle       2.76924 (    6)
  link_BETA1-4         : bond        0.00421 (    2)
  link_BETA1-4         : angle       3.19690 (    6)
  hydrogen bonds       : bond        0.05035 (  475)
  hydrogen bonds       : angle       4.03838 ( 1386)
  covalent geometry    : bond        0.00262 ( 8587)
  covalent geometry    : angle       0.51179 (11657)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 10355.00 seconds
wall clock time: 188 minutes 20.81 seconds (11300.81 seconds total)