Starting phenix.real_space_refine
on Mon Jun  9 23:52:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vqc_43438/06_2025/8vqc_43438.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vqc_43438/06_2025/8vqc_43438.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vqc_43438/06_2025/8vqc_43438.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vqc_43438/06_2025/8vqc_43438.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vqc_43438/06_2025/8vqc_43438.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vqc_43438/06_2025/8vqc_43438.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.020
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      69      5.16       5
     C    7242      2.51       5
     N    1733      2.21       5
     O    1910      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 10954
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 10225
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1288, 10225
          Classifications: {'peptide': 1288}
          Incomplete info: {'truncation_to_alanine': 91}
          Link IDs: {'PTRANS': 45, 'TRANS': 1242}
          Chain breaks: 3
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 328
          Unresolved non-hydrogen angles: 417
          Unresolved non-hydrogen dihedrals: 269
          Unresolved non-hydrogen chiralities: 30
          Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 5, 'GLU:plan': 6, 'ARG:plan': 9}
          Unresolved non-hydrogen planarities: 187
    Chain: "H"
      Number of atoms: 506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 64, 506
          Classifications: {'peptide': 64}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 60}
    Chain: "B"
      Number of atoms: 83
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 83
          Unusual residues: {'BMA': 5, 'NAG': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 7
    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: "D"
      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: "E"
      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: "G"
      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: 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
  Time building chain proxies: 8.77, per 1000 atoms: 0.80
  Number of scatterers: 10954
  At special positions: 0
  Unit cell: (127.38, 133.98, 125.4, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      69     16.00
     O    1910      8.00
     N    1733      7.00
     C    7242      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 288 " - pdb=" SG  CYS A 337 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 328 " - pdb=" SG  CYS A 343 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 709 " - pdb=" SG  CYS A 717 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1011 " - pdb=" SG  CYS A1030 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1368 " - pdb=" SG  CYS A1381 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  12 " - pdb=" SG  CYS H  63 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  16 " - pdb=" SG  CYS H  36 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  46 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  26 " - pdb=" SG  CYS H  48 " distance=2.03

  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
    BETA1-3
      " BMA B   3 " - " BMA B   4 "
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG G   1 " - " NAG G   2 "
    BETA1-6
      " BMA B   3 " - " BMA B   6 "
      " BMA B   4 " - " BMA B   5 "
      " BMA B   6 " - " BMA B   7 "
    NAG-ASN
      " NAG A1601 " - " ASN A 308 "
      " NAG A1602 " - " ASN A1028 "
      " NAG B   1 " - " ASN A 330 "
      " NAG C   1 " - " ASN A1034 "
      " NAG D   1 " - " ASN A1015 "
      " NAG E   1 " - " ASN A 312 "
      " NAG G   1 " - " ASN A 300 "
  Time building additional restraints: 2.82
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2568

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 3 sheets defined
      70.3% alpha, 0.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.01
  Creating SS restraints...
    Processing helix  chain 'A' and resid 95 through 111
    Processing helix  chain 'A' and resid 128 through 139
      removed outlier: 3.622A  pdb=" N   VAL A 132 " --> pdb=" O   PRO A 128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 157
      removed outlier: 3.679A  pdb=" N   SER A 143 " --> pdb=" O   GLN A 139 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 188
    Processing helix  chain 'A' and resid 191 through 197
      removed outlier: 3.994A  pdb=" N   ALA A 195 " --> pdb=" O   LEU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 216
      removed outlier: 3.564A  pdb=" N   LEU A 204 " --> pdb=" O   PRO A 200 " (cutoff:3.500A)
      removed outlier: 3.840A  pdb=" N   ASP A 205 " --> pdb=" O   TRP A 201 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   LEU A 216 " --> pdb=" O   GLY A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 240
      removed outlier: 3.911A  pdb=" N   VAL A 231 " --> pdb=" O   ALA A 228 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   ARG A 233 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ILE A 240 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 280
      removed outlier: 4.282A  pdb=" N   ILE A 247 " --> pdb=" O   GLY A 243 " (cutoff:3.500A)
      removed outlier: 4.925A  pdb=" N   ASP A 260 " --> pdb=" O   THR A 256 " (cutoff:3.500A)
      removed outlier: 4.639A  pdb=" N   LEU A 261 " --> pdb=" O   SER A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 303 through 311
      removed outlier: 4.058A  pdb=" N   PHE A 307 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 360 through 373
    Processing helix  chain 'A' and resid 376 through 389
      removed outlier: 4.397A  pdb=" N   LEU A 380 " --> pdb=" O   TYR A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 392 through 402
      removed outlier: 3.752A  pdb=" N   PHE A 396 " --> pdb=" O   HIS A 392 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 431
      removed outlier: 4.625A  pdb=" N   ASN A 409 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 503 through 518
    Processing helix  chain 'A' and resid 518 through 537
      removed outlier: 3.712A  pdb=" N   GLU A 522 " --> pdb=" O   SER A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 573
    Processing helix  chain 'A' and resid 574 through 579
    Processing helix  chain 'A' and resid 581 through 601
      removed outlier: 3.879A  pdb=" N   VAL A 585 " --> pdb=" O   ASP A 581 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU A 601 " --> pdb=" O   GLU A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 613
      removed outlier: 4.202A  pdb=" N   PHE A 612 " --> pdb=" O   VAL A 608 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   ARG A 613 " --> pdb=" O   PHE A 609 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 608 through 613'
    Processing helix  chain 'A' and resid 614 through 619
      removed outlier: 4.144A  pdb=" N   PHE A 618 " --> pdb=" O   LEU A 614 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   ARG A 619 " --> pdb=" O   LEU A 615 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 614 through 619'
    Processing helix  chain 'A' and resid 620 through 623
    Processing helix  chain 'A' and resid 626 through 636
      removed outlier: 4.188A  pdb=" N   LYS A 636 " --> pdb=" O   SER A 632 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 637 through 670
      removed outlier: 3.776A  pdb=" N   VAL A 642 " --> pdb=" O   TYR A 638 " (cutoff:3.500A)
      removed outlier: 4.927A  pdb=" N   ASN A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
      removed outlier: 5.495A  pdb=" N   MET A 665 " --> pdb=" O   GLN A 661 " (cutoff:3.500A)
      removed outlier: 5.498A  pdb=" N   ASN A 666 " --> pdb=" O   LEU A 662 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ASN A 670 " --> pdb=" O   ASN A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 700
    Processing helix  chain 'A' and resid 702 through 712
      removed outlier: 3.533A  pdb=" N   VAL A 712 " --> pdb=" O   ASP A 708 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 714 through 716
      No H-bonds generated for 'chain 'A' and resid 714 through 716'
    Processing helix  chain 'A' and resid 717 through 727
      removed outlier: 3.797A  pdb=" N   PHE A 721 " --> pdb=" O   CYS A 717 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   VAL A 722 " --> pdb=" O   ILE A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 744
    Processing helix  chain 'A' and resid 834 through 855
    Processing helix  chain 'A' and resid 855 through 875
      removed outlier: 3.812A  pdb=" N   GLN A 859 " --> pdb=" O   ASN A 855 " (cutoff:3.500A)
      removed outlier: 3.948A  pdb=" N   LEU A 875 " --> pdb=" O   VAL A 871 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 883 through 912
      removed outlier: 4.081A  pdb=" N   VAL A 887 " --> pdb=" O   ARG A 883 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   ASN A 888 " --> pdb=" O   PRO A 884 " (cutoff:3.500A)
      removed outlier: 4.754A  pdb=" N   ILE A 889 " --> pdb=" O   VAL A 885 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   VAL A 896 " --> pdb=" O   TYR A 892 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 913 through 920
    Processing helix  chain 'A' and resid 920 through 942
      removed outlier: 3.743A  pdb=" N   TRP A 924 " --> pdb=" O   SER A 920 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   LEU A 925 " --> pdb=" O   LYS A 921 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   ASP A 926 " --> pdb=" O   TRP A 922 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 942 " --> pdb=" O   VAL A 938 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 953 through 958
      removed outlier: 3.793A  pdb=" N   ARG A 957 " --> pdb=" O   LEU A 953 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   LEU A 958 " --> pdb=" O   ARG A 954 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 953 through 958'
    Processing helix  chain 'A' and resid 958 through 963
    Processing helix  chain 'A' and resid 964 through 966
      No H-bonds generated for 'chain 'A' and resid 964 through 966'
    Processing helix  chain 'A' and resid 967 through 1005
      removed outlier: 4.009A  pdb=" N   VAL A 971 " --> pdb=" O   GLY A 967 " (cutoff:3.500A)
      Proline residue:  A 980  - end of helix
      removed outlier: 4.410A  pdb=" N   MET A 999 " --> pdb=" O   VAL A 995 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLN A1002 " --> pdb=" O   ILE A 998 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1026 through 1033
      removed outlier: 3.715A  pdb=" N   CYS A1030 " --> pdb=" O   ASP A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1046 through 1059
    Processing helix  chain 'A' and resid 1062 through 1071
      removed outlier: 4.190A  pdb=" N   ILE A1066 " --> pdb=" O   GLY A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1088 through 1097
      removed outlier: 3.719A  pdb=" N   PHE A1092 " --> pdb=" O   MET A1088 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1105 through 1124
      removed outlier: 4.092A  pdb=" N   CYS A1109 " --> pdb=" O   LYS A1105 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   ASP A1113 " --> pdb=" O   CYS A1109 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   ILE A1114 " --> pdb=" O   ILE A1110 " (cutoff:3.500A)
      removed outlier: 4.190A  pdb=" N   GLY A1124 " --> pdb=" O   ARG A1120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1131 through 1146
    Processing helix  chain 'A' and resid 1157 through 1168
    Processing helix  chain 'A' and resid 1169 through 1189
      removed outlier: 3.699A  pdb=" N   GLU A1173 " --> pdb=" O   ASN A1169 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   ILE A1189 " --> pdb=" O   ALA A1185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1195 through 1224
      removed outlier: 3.724A  pdb=" N   GLU A1200 " --> pdb=" O   MET A1196 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A1201 " --> pdb=" O   GLU A1197 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   SER A1222 " --> pdb=" O   VAL A1218 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLY A1223 " --> pdb=" O   ILE A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1234 through 1257
      removed outlier: 3.811A  pdb=" N   PHE A1238 " --> pdb=" O   ASN A1234 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   LEU A1243 " --> pdb=" O   LEU A1239 " (cutoff:3.500A)
      removed outlier: 8.249A  pdb=" N   ASP A1252 " --> pdb=" O   LEU A1248 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   VAL A1253 " --> pdb=" O   MET A1249 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1268
      removed outlier: 4.658A  pdb=" N   LEU A1263 " --> pdb=" O   ILE A1259 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   LEU A1264 " --> pdb=" O   SER A1260 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   ARG A1265 " --> pdb=" O   PRO A1261 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ARG A1268 " --> pdb=" O   LEU A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1269 through 1273
      removed outlier: 3.632A  pdb=" N   GLY A1273 " --> pdb=" O   LEU A1270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1282 through 1295
      removed outlier: 4.047A  pdb=" N   ARG A1286 " --> pdb=" O   ALA A1282 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA A1295 " --> pdb=" O   ALA A1291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1295 through 1321
    Processing helix  chain 'A' and resid 1338 through 1351
      removed outlier: 4.260A  pdb=" N   THR A1351 " --> pdb=" O   PHE A1347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1363
      removed outlier: 3.709A  pdb=" N   VAL A1358 " --> pdb=" O   GLY A1354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1384 through 1398
      removed outlier: 3.973A  pdb=" N   SER A1393 " --> pdb=" O   ALA A1389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1401 through 1424
      removed outlier: 3.688A  pdb=" N   ILE A1410 " --> pdb=" O   TYR A1406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1426 through 1439
      removed outlier: 3.728A  pdb=" N   GLN A1439 " --> pdb=" O   GLU A1435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1451 through 1459
      removed outlier: 3.889A  pdb=" N   GLU A1455 " --> pdb=" O   ASP A1451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1470 through 1477
    Processing helix  chain 'A' and resid 1488 through 1505
      removed outlier: 3.523A  pdb=" N   VAL A1492 " --> pdb=" O   PHE A1488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1508 through 1521
      Proline residue:  A1516  - end of helix
      removed outlier: 3.507A  pdb=" N   ALA A1521 " --> pdb=" O   ASN A1517 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 18 through 29
      removed outlier: 3.610A  pdb=" N   CYS H  26 " --> pdb=" O   CYS H  22 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ASN H  29 " --> pdb=" O   LEU H  25 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290
    Processing sheet with id=AA2, first strand: chain 'A' and resid 1009 through 1012
    Processing sheet with id=AA3, first strand: chain 'H' and resid 34 through 35

    631 hydrogen bonds defined for protein.
    1857 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 4.00

  Time building geometry restraints manager: 3.35 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3306
        1.34 -     1.46: 3016
        1.46 -     1.58: 4817
        1.58 -     1.70: 0
        1.70 -     1.82: 111
  Bond restraints: 11250
  Sorted by residual:
  bond pdb=" C1  NAG B   1 "
       pdb=" O5  NAG B   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.472 -0.066 2.00e-02 2.50e+03 1.08e+01
  bond pdb=" C   LEU A1276 "
       pdb=" N   ARG A1277 "
    ideal  model  delta    sigma   weight residual
    1.335  1.308  0.027 1.30e-02 5.92e+03 4.25e+00
  bond pdb=" C5  BMA B   3 "
       pdb=" O5  BMA B   3 "
    ideal  model  delta    sigma   weight residual
    1.417  1.452 -0.035 2.00e-02 2.50e+03 3.01e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.439 -0.033 2.00e-02 2.50e+03 2.80e+00
  bond pdb=" CA  LEU A1276 "
       pdb=" C   LEU A1276 "
    ideal  model  delta    sigma   weight residual
    1.522  1.500  0.022 1.39e-02 5.18e+03 2.59e+00
  ... (remaining 11245 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.36: 15025
        2.36 -     4.72: 228
        4.72 -     7.08: 47
        7.08 -     9.44: 10
        9.44 -    11.79: 5
  Bond angle restraints: 15315
  Sorted by residual:
  angle pdb=" CA  GLU A1443 "
        pdb=" CB  GLU A1443 "
        pdb=" CG  GLU A1443 "
      ideal   model   delta    sigma   weight residual
     114.10  123.56   -9.46 2.00e+00 2.50e-01 2.24e+01
  angle pdb=" CB  ARG H   2 "
        pdb=" CG  ARG H   2 "
        pdb=" CD  ARG H   2 "
      ideal   model   delta    sigma   weight residual
     111.30  120.75   -9.45 2.30e+00 1.89e-01 1.69e+01
  angle pdb=" CB  MET A1196 "
        pdb=" CG  MET A1196 "
        pdb=" SD  MET A1196 "
      ideal   model   delta    sigma   weight residual
     112.70  124.49  -11.79 3.00e+00 1.11e-01 1.55e+01
  angle pdb=" CB  GLU A1443 "
        pdb=" CG  GLU A1443 "
        pdb=" CD  GLU A1443 "
      ideal   model   delta    sigma   weight residual
     112.60  119.20   -6.60 1.70e+00 3.46e-01 1.51e+01
  angle pdb=" C   ILE A 146 "
        pdb=" N   MET A 147 "
        pdb=" CA  MET A 147 "
      ideal   model   delta    sigma   weight residual
     121.14  115.02    6.12 1.75e+00 3.27e-01 1.22e+01
  ... (remaining 15310 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.84: 5957
       21.84 -    43.68: 642
       43.68 -    65.52: 78
       65.52 -    87.37: 43
       87.37 -   109.21: 29
  Dihedral angle restraints: 6749
    sinusoidal: 2766
      harmonic: 3983
  Sorted by residual:
  dihedral pdb=" CB  CYS A1368 "
           pdb=" SG  CYS A1368 "
           pdb=" SG  CYS A1381 "
           pdb=" CB  CYS A1381 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00   -3.84  -82.16     1      1.00e+01 1.00e-02 8.29e+01
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  46 "
           pdb=" CB  CYS H  46 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -163.21   77.21     1      1.00e+01 1.00e-02 7.47e+01
  dihedral pdb=" CB  CYS A1011 "
           pdb=" SG  CYS A1011 "
           pdb=" SG  CYS A1030 "
           pdb=" CB  CYS A1030 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -148.92   62.92     1      1.00e+01 1.00e-02 5.23e+01
  ... (remaining 6746 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1639
       0.078 -    0.156: 134
       0.156 -    0.234: 6
       0.234 -    0.312: 5
       0.312 -    0.389: 2
  Chirality restraints: 1786
  Sorted by residual:
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 330 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.79    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" C4  NAG B   1 "
            pdb=" C3  NAG B   1 "
            pdb=" C5  NAG B   1 "
            pdb=" O4  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.53   -2.20   -0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" C5  BMA B   6 "
            pdb=" C4  BMA B   6 "
            pdb=" C6  BMA B   6 "
            pdb=" O5  BMA B   6 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.55    0.28 2.00e-01 2.50e+01 1.90e+00
  ... (remaining 1783 not shown)

  Planarity restraints: 1883
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 244 "    0.016 2.00e-02 2.50e+03   1.69e-02 7.13e+00
        pdb=" CG  TRP A 244 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 244 "    0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 244 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 244 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 244 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 244 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 244 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 244 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 244 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A1443 "    0.010 2.00e-02 2.50e+03   2.03e-02 4.12e+00
        pdb=" C   GLU A1443 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   GLU A1443 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ALA A1444 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 192 "   -0.033 5.00e-02 4.00e+02   4.97e-02 3.95e+00
        pdb=" N   PRO A 193 "    0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 193 "   -0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 193 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 1880 not shown)

  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 40
        2.41 -     3.03: 7161
        3.03 -     3.66: 16889
        3.66 -     4.28: 22951
        4.28 -     4.90: 36867
  Nonbonded interactions: 83908
  Sorted by model distance:
  nonbonded pdb=" O   THR A1059 "
            pdb=" NZ  LYS A1061 "
     model   vdw
     1.791 3.120
  nonbonded pdb=" O   SER A 632 "
            pdb=" OG1 THR A 635 "
     model   vdw
     2.173 3.040
  nonbonded pdb=" OD1 ASP A1129 "
            pdb=" N   SER A1130 "
     model   vdw
     2.185 3.120
  nonbonded pdb=" ND2 ASN H  23 "
            pdb=" O   GLY H  34 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   LYS A 915 "
            pdb=" OG1 THR A 919 "
     model   vdw
     2.243 3.040
  ... (remaining 83903 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 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'G'
}

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 group one per residue
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:             7.300
  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:             0.030
  Extract box with map and model:          0.540
  Check model and map are aligned:         0.070
  Set scattering table:                    0.090
  Process input model:                     29.520
  Find NCS groups from input model:        0.170
  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:2.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   40.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  11276  Z= 0.178
  Angle     :  0.778  13.428  15384  Z= 0.373
  Chirality :  0.047   0.389   1786
  Planarity :  0.004   0.058   1876
  Dihedral  : 19.496 109.206   4154
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.45 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 28.18 %
    Favored  : 71.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.24), residues: 1342
  helix:  0.88 (0.18), residues: 854
  sheet: -2.32 (1.42), residues: 12
  loop : -2.01 (0.29), residues: 476

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A1486 
 PHE   0.027   0.001   PHE A 861 
 TYR   0.022   0.001   TYR H  21 
 ARG   0.014   0.000   ARG H   2 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00314 (    7)
  link_NAG-ASN         : angle       3.87442 (   21)
  link_BETA1-4         : bond        0.00625 (    6)
  link_BETA1-4         : angle       3.53688 (   18)
  hydrogen bonds       : bond        0.11852 (  631)
  hydrogen bonds       : angle       5.10106 ( 1857)
  link_BETA1-6         : bond        0.00636 (    3)
  link_BETA1-6         : angle       1.22112 (    9)
  SS BOND              : bond        0.00329 (    9)
  SS BOND              : angle       0.76378 (   18)
  link_BETA1-3         : bond        0.00389 (    1)
  link_BETA1-3         : angle       0.85576 (    3)
  covalent geometry    : bond        0.00375 (11250)
  covalent geometry    : angle       0.75594 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 230
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  947 LEU cc_start: 0.7731 (OUTLIER) cc_final: 0.7529 (tt)
REVERT: A 1275 LEU cc_start: 0.8036 (mp) cc_final: 0.7704 (tt)
  outliers start: 8
  outliers final: 4
  residues processed: 234
  average time/residue: 0.2137
  time to fit residues: 72.6207
Evaluate side-chains
  228 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 223
  time to evaluate  : 1.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  367 SER
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  650 LEU
Chi-restraints excluded: chain A residue  947 LEU
Chi-restraints excluded: chain A residue 1226 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 113 optimal weight:    0.0270
   chunk 101 optimal weight:   10.0000
   chunk 56 optimal weight:    0.1980
   chunk 34 optimal weight:    0.9980
   chunk 68 optimal weight:    6.9990
   chunk 54 optimal weight:    0.5980
   chunk 105 optimal weight:    0.5980
   chunk 40 optimal weight:    6.9990
   chunk 63 optimal weight:    1.9990
   chunk 78 optimal weight:    6.9990
   chunk 121 optimal weight:    6.9990
   overall best weight:    0.4838

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

Flipped N/Q/H residues before XYZ refinement:
A1079 GLN
A1169 ASN
A1227 HIS
H  23 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.160666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.120168 restraints weight = 21729.967|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.120988 restraints weight = 13252.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.121179 restraints weight = 9414.028|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7693
moved from start:          0.0836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11276  Z= 0.128
  Angle     :  0.656  10.117  15384  Z= 0.320
  Chirality :  0.044   0.307   1786
  Planarity :  0.004   0.053   1876
  Dihedral  : 12.730  88.702   1829
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.00 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 24.57 %
    Favored  : 71.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.24), residues: 1342
  helix:  0.96 (0.18), residues: 891
  sheet: -2.73 (1.23), residues: 12
  loop : -2.18 (0.30), residues: 439

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A 291 
 PHE   0.016   0.001   PHE A 861 
 TYR   0.022   0.001   TYR A1240 
 ARG   0.010   0.001   ARG H   2 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00355 (    7)
  link_NAG-ASN         : angle       3.06368 (   21)
  link_BETA1-4         : bond        0.00573 (    6)
  link_BETA1-4         : angle       3.05676 (   18)
  hydrogen bonds       : bond        0.04001 (  631)
  hydrogen bonds       : angle       3.93232 ( 1857)
  link_BETA1-6         : bond        0.00738 (    3)
  link_BETA1-6         : angle       2.20458 (    9)
  SS BOND              : bond        0.00277 (    9)
  SS BOND              : angle       0.80309 (   18)
  link_BETA1-3         : bond        0.01551 (    1)
  link_BETA1-3         : angle       2.20578 (    3)
  covalent geometry    : bond        0.00266 (11250)
  covalent geometry    : angle       0.63555 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 242
  time to evaluate  : 1.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8542 (OUTLIER) cc_final: 0.8178 (p)
REVERT: A  715 TRP cc_start: 0.6696 (p90) cc_final: 0.6218 (p90)
REVERT: A 1102 PHE cc_start: 0.8765 (t80) cc_final: 0.8532 (t80)
REVERT: A 1227 HIS cc_start: 0.7342 (OUTLIER) cc_final: 0.7090 (t70)
REVERT: H    2 ARG cc_start: 0.7878 (mmm160) cc_final: 0.7508 (mmm160)
  outliers start: 43
  outliers final: 21
  residues processed: 268
  average time/residue: 0.1991
  time to fit residues: 78.2762
Evaluate side-chains
  250 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 227
  time to evaluate  : 1.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  741 LEU
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1227 HIS
Chi-restraints excluded: chain A residue 1248 LEU
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1362 ILE
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 23 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 103 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   chunk 54 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 98 optimal weight:    0.9980
   chunk 127 optimal weight:    4.9990
   chunk 97 optimal weight:    0.7980
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 ASN
A1056 GLN
** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1227 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1234 ASN
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.159238 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.118917 restraints weight = 21969.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.119724 restraints weight = 13445.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.120005 restraints weight = 9941.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.1123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11276  Z= 0.145
  Angle     :  0.661  10.575  15384  Z= 0.322
  Chirality :  0.044   0.292   1786
  Planarity :  0.004   0.054   1876
  Dihedral  : 10.323  79.410   1822
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.15 %
    Allowed  :  7.00 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 25.65 %
    Favored  : 69.65 %
  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: -0.11 (0.24), residues: 1342
  helix:  0.92 (0.18), residues: 893
  sheet: -2.89 (1.18), residues: 12
  loop : -2.11 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A1227 
 PHE   0.015   0.001   PHE A1321 
 TYR   0.017   0.001   TYR A 895 
 ARG   0.007   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00288 (    7)
  link_NAG-ASN         : angle       3.05161 (   21)
  link_BETA1-4         : bond        0.00520 (    6)
  link_BETA1-4         : angle       3.24556 (   18)
  hydrogen bonds       : bond        0.03898 (  631)
  hydrogen bonds       : angle       3.84915 ( 1857)
  link_BETA1-6         : bond        0.00630 (    3)
  link_BETA1-6         : angle       1.83689 (    9)
  SS BOND              : bond        0.00307 (    9)
  SS BOND              : angle       0.86840 (   18)
  link_BETA1-3         : bond        0.01051 (    1)
  link_BETA1-3         : angle       1.95059 (    3)
  covalent geometry    : bond        0.00328 (11250)
  covalent geometry    : angle       0.64070 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 233
  time to evaluate  : 1.104 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  547 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8336 (t80)
REVERT: A  715 TRP cc_start: 0.6796 (p90) cc_final: 0.6330 (p90)
REVERT: A  984 ASN cc_start: 0.8253 (t0) cc_final: 0.8009 (t0)
REVERT: A 1102 PHE cc_start: 0.8804 (t80) cc_final: 0.8597 (t80)
REVERT: A 1276 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8348 (tt)
REVERT: A 1432 MET cc_start: 0.7674 (ptt) cc_final: 0.7210 (ptt)
  outliers start: 52
  outliers final: 28
  residues processed: 263
  average time/residue: 0.2029
  time to fit residues: 78.4108
Evaluate side-chains
  252 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 222
  time to evaluate  : 1.169 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  423 VAL
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain A residue  547 PHE
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1248 LEU
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1324 ILE
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1418 TYR
Chi-restraints excluded: chain A residue 1492 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 75 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 79 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 120 optimal weight:    0.0370
   chunk 77 optimal weight:    0.9990
   chunk 87 optimal weight:    0.9990
   chunk 81 optimal weight:    0.0670
   chunk 40 optimal weight:    7.9990
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.5398

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

Flipped N/Q/H residues before XYZ refinement:
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1227 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.159974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.115886 restraints weight = 21830.444|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.117311 restraints weight = 11801.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.117822 restraints weight = 7880.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3568
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7801
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11276  Z= 0.126
  Angle     :  0.661  14.000  15384  Z= 0.318
  Chirality :  0.044   0.281   1786
  Planarity :  0.004   0.054   1876
  Dihedral  :  8.545  67.490   1822
  Min Nonbonded Distance : 2.384

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.15 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 26.29 %
    Favored  : 69.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.24), residues: 1342
  helix:  0.94 (0.18), residues: 893
  sheet: -2.57 (1.24), residues: 12
  loop : -2.10 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A1226 
 PHE   0.020   0.001   PHE A 900 
 TYR   0.017   0.001   TYR A 895 
 ARG   0.007   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00331 (    7)
  link_NAG-ASN         : angle       2.95028 (   21)
  link_BETA1-4         : bond        0.00594 (    6)
  link_BETA1-4         : angle       3.20143 (   18)
  hydrogen bonds       : bond        0.03707 (  631)
  hydrogen bonds       : angle       3.77109 ( 1857)
  link_BETA1-6         : bond        0.00676 (    3)
  link_BETA1-6         : angle       1.73884 (    9)
  SS BOND              : bond        0.00311 (    9)
  SS BOND              : angle       0.77009 (   18)
  link_BETA1-3         : bond        0.00849 (    1)
  link_BETA1-3         : angle       2.35625 (    3)
  covalent geometry    : bond        0.00274 (11250)
  covalent geometry    : angle       0.64109 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 229
  time to evaluate  : 1.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8208 (p)
REVERT: A  378 GLU cc_start: 0.7981 (OUTLIER) cc_final: 0.7599 (mt-10)
REVERT: A  715 TRP cc_start: 0.6704 (p90) cc_final: 0.6246 (p90)
REVERT: A  984 ASN cc_start: 0.8272 (t0) cc_final: 0.8049 (t0)
REVERT: A 1102 PHE cc_start: 0.8813 (t80) cc_final: 0.8597 (t80)
REVERT: A 1197 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6697 (tt0)
REVERT: A 1224 LEU cc_start: 0.7171 (tp) cc_final: 0.6822 (tt)
REVERT: A 1276 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8307 (tt)
REVERT: A 1341 GLN cc_start: 0.8292 (OUTLIER) cc_final: 0.7802 (mp10)
REVERT: A 1499 ASP cc_start: 0.8525 (m-30) cc_final: 0.8226 (t0)
  outliers start: 51
  outliers final: 29
  residues processed: 260
  average time/residue: 0.2047
  time to fit residues: 78.3262
Evaluate side-chains
  258 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 224
  time to evaluate  : 1.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  427 ASP
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1243 LEU
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1341 GLN
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 48 optimal weight:    0.8980
   chunk 27 optimal weight:    0.0770
   chunk 96 optimal weight:    0.8980
   chunk 119 optimal weight:    0.3980
   chunk 110 optimal weight:    2.9990
   chunk 42 optimal weight:    6.9990
   chunk 92 optimal weight:    0.8980
   chunk 106 optimal weight:    0.5980
   chunk 34 optimal weight:    0.9990
   chunk 111 optimal weight:    1.9990
   chunk 129 optimal weight:   10.0000
   overall best weight:    0.5738

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

Flipped N/Q/H residues before XYZ refinement:
** A1194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.160070 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.119554 restraints weight = 21921.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.120246 restraints weight = 13708.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.120523 restraints weight = 9786.664|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.1476

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11276  Z= 0.125
  Angle     :  0.664  13.527  15384  Z= 0.317
  Chirality :  0.044   0.275   1786
  Planarity :  0.004   0.053   1876
  Dihedral  :  7.304  57.663   1820
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 9.94
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.38 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  5.33 %
    Allowed  : 25.75 %
    Favored  : 68.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1342
  helix:  0.99 (0.18), residues: 892
  sheet: -2.70 (1.26), residues: 12
  loop : -2.07 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A1226 
 PHE   0.023   0.001   PHE A 900 
 TYR   0.015   0.001   TYR A 895 
 ARG   0.009   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00328 (    7)
  link_NAG-ASN         : angle       2.92757 (   21)
  link_BETA1-4         : bond        0.00662 (    6)
  link_BETA1-4         : angle       3.18595 (   18)
  hydrogen bonds       : bond        0.03623 (  631)
  hydrogen bonds       : angle       3.72021 ( 1857)
  link_BETA1-6         : bond        0.00696 (    3)
  link_BETA1-6         : angle       1.81905 (    9)
  SS BOND              : bond        0.00301 (    9)
  SS BOND              : angle       0.76172 (   18)
  link_BETA1-3         : bond        0.00734 (    1)
  link_BETA1-3         : angle       3.07817 (    3)
  covalent geometry    : bond        0.00269 (11250)
  covalent geometry    : angle       0.64418 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 59
    poor density    : 231
  time to evaluate  : 2.124 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8106 (p)
REVERT: A  378 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7642 (mt-10)
REVERT: A  379 ASP cc_start: 0.7688 (OUTLIER) cc_final: 0.7262 (t0)
REVERT: A  420 THR cc_start: 0.9225 (t) cc_final: 0.8973 (t)
REVERT: A  636 LYS cc_start: 0.8101 (pttm) cc_final: 0.7760 (tppt)
REVERT: A  715 TRP cc_start: 0.6722 (p90) cc_final: 0.6290 (p90)
REVERT: A  947 LEU cc_start: 0.8193 (tp) cc_final: 0.7932 (tt)
REVERT: A  984 ASN cc_start: 0.8263 (t0) cc_final: 0.8025 (t0)
REVERT: A 1019 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8484 (mm)
REVERT: A 1102 PHE cc_start: 0.8779 (t80) cc_final: 0.8537 (t80)
REVERT: A 1197 GLU cc_start: 0.6969 (OUTLIER) cc_final: 0.6691 (tt0)
REVERT: A 1258 PHE cc_start: 0.7463 (OUTLIER) cc_final: 0.7122 (t80)
REVERT: A 1276 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8413 (tt)
REVERT: A 1341 GLN cc_start: 0.8299 (OUTLIER) cc_final: 0.7776 (mp10)
REVERT: A 1499 ASP cc_start: 0.8272 (m-30) cc_final: 0.8063 (t0)
  outliers start: 59
  outliers final: 35
  residues processed: 271
  average time/residue: 0.2118
  time to fit residues: 85.7017
Evaluate side-chains
  267 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 224
  time to evaluate  : 1.103 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  614 LEU
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1104 LEU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1221 VAL
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1341 GLN
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1362 ILE
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Chi-restraints excluded: chain H residue    1 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 132 optimal weight:    6.9990
   chunk 79 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9990
   chunk 126 optimal weight:    0.9980
   chunk 95 optimal weight:    4.9990
   chunk 62 optimal weight:    5.9990
   chunk 113 optimal weight:    6.9990
   chunk 52 optimal weight:    0.7980
   chunk 111 optimal weight:    0.7980
   chunk 48 optimal weight:    0.9980
   chunk 120 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1194 GLN
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.159171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.118740 restraints weight = 22081.905|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.119684 restraints weight = 13741.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.119957 restraints weight = 9857.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11276  Z= 0.142
  Angle     :  0.681  12.107  15384  Z= 0.325
  Chirality :  0.044   0.271   1786
  Planarity :  0.004   0.053   1876
  Dihedral  :  6.734  57.770   1820
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.23 %
    Favored  : 92.70 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 26.38 %
    Favored  : 68.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.24), residues: 1342
  helix:  1.02 (0.18), residues: 887
  sheet: -2.57 (1.29), residues: 12
  loop : -1.98 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A 421 
 PHE   0.025   0.001   PHE A 900 
 TYR   0.016   0.001   TYR A 895 
 ARG   0.011   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00287 (    7)
  link_NAG-ASN         : angle       2.92799 (   21)
  link_BETA1-4         : bond        0.00606 (    6)
  link_BETA1-4         : angle       3.18813 (   18)
  hydrogen bonds       : bond        0.03646 (  631)
  hydrogen bonds       : angle       3.70435 ( 1857)
  link_BETA1-6         : bond        0.00537 (    3)
  link_BETA1-6         : angle       1.90441 (    9)
  SS BOND              : bond        0.00329 (    9)
  SS BOND              : angle       0.98378 (   18)
  link_BETA1-3         : bond        0.00566 (    1)
  link_BETA1-3         : angle       3.54469 (    3)
  covalent geometry    : bond        0.00321 (11250)
  covalent geometry    : angle       0.66097 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 229
  time to evaluate  : 1.068 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8506 (OUTLIER) cc_final: 0.8161 (p)
REVERT: A  378 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7607 (mt-10)
REVERT: A  379 ASP cc_start: 0.7671 (OUTLIER) cc_final: 0.7241 (t0)
REVERT: A  715 TRP cc_start: 0.6680 (p90) cc_final: 0.6273 (p90)
REVERT: A  876 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6692 (tm-30)
REVERT: A  984 ASN cc_start: 0.8268 (t0) cc_final: 0.8028 (t0)
REVERT: A 1019 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8543 (mm)
REVERT: A 1042 MET cc_start: 0.7137 (tpp) cc_final: 0.6879 (mmp)
REVERT: A 1102 PHE cc_start: 0.8811 (t80) cc_final: 0.8401 (t80)
REVERT: A 1197 GLU cc_start: 0.6989 (OUTLIER) cc_final: 0.6723 (tt0)
REVERT: A 1258 PHE cc_start: 0.7479 (OUTLIER) cc_final: 0.7172 (t80)
REVERT: A 1499 ASP cc_start: 0.8262 (m-30) cc_final: 0.8046 (t0)
REVERT: H    2 ARG cc_start: 0.8458 (mmm160) cc_final: 0.7790 (mmm160)
  outliers start: 61
  outliers final: 39
  residues processed: 272
  average time/residue: 0.1967
  time to fit residues: 79.8709
Evaluate side-chains
  268 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 222
  time to evaluate  : 1.068 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1024 THR
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1346 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Chi-restraints excluded: chain A residue 1453 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 28 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 42 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 60 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 32 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.159518 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3642 r_free = 0.3642 target = 0.119468 restraints weight = 22128.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.120728 restraints weight = 13627.263|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.121002 restraints weight = 9738.362|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7701
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11276  Z= 0.132
  Angle     :  0.692  11.358  15384  Z= 0.330
  Chirality :  0.043   0.261   1786
  Planarity :  0.004   0.052   1876
  Dihedral  :  6.376  58.706   1820
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.45 %
    Favored  : 92.47 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 27.19 %
    Favored  : 68.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.00 (0.24), residues: 1342
  helix:  1.02 (0.18), residues: 887
  sheet: -2.67 (1.32), residues: 12
  loop : -2.05 (0.31), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A1226 
 PHE   0.030   0.001   PHE A 900 
 TYR   0.015   0.001   TYR A 895 
 ARG   0.011   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00309 (    7)
  link_NAG-ASN         : angle       2.90349 (   21)
  link_BETA1-4         : bond        0.00622 (    6)
  link_BETA1-4         : angle       3.06360 (   18)
  hydrogen bonds       : bond        0.03580 (  631)
  hydrogen bonds       : angle       3.71412 ( 1857)
  link_BETA1-6         : bond        0.00550 (    3)
  link_BETA1-6         : angle       1.94252 (    9)
  SS BOND              : bond        0.00428 (    9)
  SS BOND              : angle       0.92718 (   18)
  link_BETA1-3         : bond        0.00619 (    1)
  link_BETA1-3         : angle       3.61887 (    3)
  covalent geometry    : bond        0.00293 (11250)
  covalent geometry    : angle       0.67253 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 234
  time to evaluate  : 1.044 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8097 (p)
REVERT: A  378 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7607 (mt-10)
REVERT: A  379 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7208 (t0)
REVERT: A  715 TRP cc_start: 0.6656 (p90) cc_final: 0.6236 (p90)
REVERT: A  876 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6580 (tm-30)
REVERT: A  984 ASN cc_start: 0.8250 (t0) cc_final: 0.8013 (t0)
REVERT: A 1019 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8569 (mm)
REVERT: A 1042 MET cc_start: 0.7166 (tpp) cc_final: 0.6843 (mmp)
REVERT: A 1102 PHE cc_start: 0.8803 (t80) cc_final: 0.8397 (t80)
REVERT: A 1196 MET cc_start: 0.8634 (mmm) cc_final: 0.8382 (mmm)
REVERT: A 1197 GLU cc_start: 0.6965 (OUTLIER) cc_final: 0.6679 (tt0)
REVERT: A 1258 PHE cc_start: 0.7467 (OUTLIER) cc_final: 0.7154 (t80)
  outliers start: 53
  outliers final: 39
  residues processed: 271
  average time/residue: 0.2214
  time to fit residues: 90.3905
Evaluate side-chains
  268 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 222
  time to evaluate  : 1.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  359 ASP
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1081 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1346 LEU
Chi-restraints excluded: chain A residue 1362 ILE
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1406 TYR
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 21 optimal weight:    0.3980
   chunk 12 optimal weight:    0.9980
   chunk 61 optimal weight:   10.0000
   chunk 92 optimal weight:    0.9980
   chunk 114 optimal weight:    0.6980
   chunk 73 optimal weight:    2.9990
   chunk 25 optimal weight:    0.2980
   chunk 4 optimal weight:    1.9990
   chunk 118 optimal weight:    0.8980
   chunk 120 optimal weight:    0.0170
   chunk 44 optimal weight:    1.9990
   overall best weight:    0.4618

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

Flipped N/Q/H residues before XYZ refinement:
A 948 GLN
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1191 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.160713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.120306 restraints weight = 21992.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.121117 restraints weight = 13548.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.121424 restraints weight = 9868.178|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  11276  Z= 0.125
  Angle     :  0.690  10.661  15384  Z= 0.327
  Chirality :  0.043   0.253   1786
  Planarity :  0.004   0.052   1876
  Dihedral  :  6.133  59.445   1820
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.86 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  4.79 %
    Allowed  : 27.82 %
    Favored  : 67.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.00 (0.24), residues: 1342
  helix:  1.01 (0.18), residues: 887
  sheet: -2.56 (1.34), residues: 12
  loop : -2.04 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A1021 
 PHE   0.025   0.001   PHE A 900 
 TYR   0.017   0.001   TYR H  21 
 ARG   0.008   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00326 (    7)
  link_NAG-ASN         : angle       2.86402 (   21)
  link_BETA1-4         : bond        0.00580 (    6)
  link_BETA1-4         : angle       2.92836 (   18)
  hydrogen bonds       : bond        0.03502 (  631)
  hydrogen bonds       : angle       3.70360 ( 1857)
  link_BETA1-6         : bond        0.00574 (    3)
  link_BETA1-6         : angle       1.94974 (    9)
  SS BOND              : bond        0.00330 (    9)
  SS BOND              : angle       0.86844 (   18)
  link_BETA1-3         : bond        0.00630 (    1)
  link_BETA1-3         : angle       3.55308 (    3)
  covalent geometry    : bond        0.00275 (11250)
  covalent geometry    : angle       0.67149 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 234
  time to evaluate  : 1.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.7689 (p)
REVERT: A  344 LEU cc_start: 0.8869 (mp) cc_final: 0.8483 (mp)
REVERT: A  378 GLU cc_start: 0.8094 (OUTLIER) cc_final: 0.7612 (mt-10)
REVERT: A  379 ASP cc_start: 0.7620 (OUTLIER) cc_final: 0.7172 (t0)
REVERT: A  715 TRP cc_start: 0.6657 (p90) cc_final: 0.6217 (p90)
REVERT: A  876 GLU cc_start: 0.7013 (OUTLIER) cc_final: 0.6749 (tm-30)
REVERT: A  984 ASN cc_start: 0.8226 (t0) cc_final: 0.7987 (t0)
REVERT: A 1019 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8540 (mm)
REVERT: A 1042 MET cc_start: 0.7195 (tpp) cc_final: 0.6836 (mmp)
REVERT: A 1102 PHE cc_start: 0.8792 (t80) cc_final: 0.8382 (t80)
REVERT: A 1197 GLU cc_start: 0.6934 (OUTLIER) cc_final: 0.6669 (tt0)
REVERT: A 1258 PHE cc_start: 0.7496 (OUTLIER) cc_final: 0.7189 (t80)
REVERT: A 1432 MET cc_start: 0.7901 (ptt) cc_final: 0.7546 (ttp)
REVERT: H    2 ARG cc_start: 0.8443 (mmm160) cc_final: 0.7727 (mmm160)
  outliers start: 53
  outliers final: 34
  residues processed: 271
  average time/residue: 0.1939
  time to fit residues: 78.5827
Evaluate side-chains
  263 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 222
  time to evaluate  : 1.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  974 THR
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1002 GLN
Chi-restraints excluded: chain A residue 1019 LEU
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1345 LEU
Chi-restraints excluded: chain A residue 1346 LEU
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Chi-restraints excluded: chain H residue    1 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 31 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   chunk 36 optimal weight:   40.0000
   chunk 47 optimal weight:    1.9990
   chunk 102 optimal weight:    2.9990
   chunk 27 optimal weight:    0.3980
   chunk 24 optimal weight:    4.9990
   chunk 20 optimal weight:    0.1980
   chunk 13 optimal weight:   20.0000
   chunk 35 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   overall best weight:    1.3184

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 742 ASN
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.157580 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.117105 restraints weight = 22218.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.117199 restraints weight = 14201.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.117730 restraints weight = 10873.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  11276  Z= 0.174
  Angle     :  0.743  11.943  15384  Z= 0.356
  Chirality :  0.044   0.263   1786
  Planarity :  0.004   0.052   1876
  Dihedral  :  6.080  58.248   1820
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.93
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.53 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 28.18 %
    Favored  : 66.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.24), residues: 1342
  helix:  0.99 (0.18), residues: 888
  sheet: -3.00 (1.33), residues: 10
  loop : -2.06 (0.30), residues: 444

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.001   TRP A 244 
 HIS   0.003   0.001   HIS A 421 
 PHE   0.039   0.001   PHE A 900 
 TYR   0.013   0.001   TYR A1334 
 ARG   0.007   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00245 (    7)
  link_NAG-ASN         : angle       2.99534 (   21)
  link_BETA1-4         : bond        0.00510 (    6)
  link_BETA1-4         : angle       3.06121 (   18)
  hydrogen bonds       : bond        0.03766 (  631)
  hydrogen bonds       : angle       3.78557 ( 1857)
  link_BETA1-6         : bond        0.00446 (    3)
  link_BETA1-6         : angle       2.11553 (    9)
  SS BOND              : bond        0.00324 (    9)
  SS BOND              : angle       1.02619 (   18)
  link_BETA1-3         : bond        0.00343 (    1)
  link_BETA1-3         : angle       3.72954 (    3)
  covalent geometry    : bond        0.00402 (11250)
  covalent geometry    : angle       0.72466 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  275 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 221
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8525 (OUTLIER) cc_final: 0.7784 (p)
REVERT: A  344 LEU cc_start: 0.8927 (mp) cc_final: 0.8523 (mp)
REVERT: A  378 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7650 (mt-10)
REVERT: A  379 ASP cc_start: 0.7702 (OUTLIER) cc_final: 0.7284 (t0)
REVERT: A  715 TRP cc_start: 0.6779 (p90) cc_final: 0.6327 (p90)
REVERT: A  876 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6665 (tm-30)
REVERT: A  984 ASN cc_start: 0.8264 (t0) cc_final: 0.8036 (t0)
REVERT: A 1042 MET cc_start: 0.7316 (tpp) cc_final: 0.6913 (mmp)
REVERT: A 1102 PHE cc_start: 0.8833 (t80) cc_final: 0.8432 (t80)
REVERT: A 1197 GLU cc_start: 0.6997 (OUTLIER) cc_final: 0.6728 (tt0)
REVERT: A 1258 PHE cc_start: 0.7572 (OUTLIER) cc_final: 0.7283 (t80)
REVERT: A 1432 MET cc_start: 0.7997 (ptt) cc_final: 0.7704 (ttm)
REVERT: A 1499 ASP cc_start: 0.8235 (m-30) cc_final: 0.8014 (t0)
REVERT: H    2 ARG cc_start: 0.8511 (mmm160) cc_final: 0.7805 (mmm160)
  outliers start: 54
  outliers final: 33
  residues processed: 260
  average time/residue: 0.2015
  time to fit residues: 78.0221
Evaluate side-chains
  260 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 221
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  262 VAL
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  397 ILE
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  722 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  933 TYR
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue  986 ILE
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1110 ILE
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1184 VAL
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1315 VAL
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    5.9990
   chunk 110 optimal weight:    0.9990
   chunk 28 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 124 optimal weight:    0.0770
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
A 742 ASN
** A1043 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.159618 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.119410 restraints weight = 21970.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.120405 restraints weight = 13739.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.120711 restraints weight = 9887.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7713
moved from start:          0.1997

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  11276  Z= 0.134
  Angle     :  0.741  13.595  15384  Z= 0.350
  Chirality :  0.044   0.256   1786
  Planarity :  0.004   0.053   1876
  Dihedral  :  5.971  59.446   1820
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.00 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 28.64 %
    Favored  : 67.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.24), residues: 1342
  helix:  0.95 (0.18), residues: 889
  sheet: -2.95 (1.35), residues: 10
  loop : -2.07 (0.30), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.001   TRP A 244 
 HIS   0.002   0.001   HIS A1021 
 PHE   0.024   0.001   PHE A 858 
 TYR   0.021   0.001   TYR H  21 
 ARG   0.007   0.000   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00317 (    7)
  link_NAG-ASN         : angle       2.86207 (   21)
  link_BETA1-4         : bond        0.00504 (    6)
  link_BETA1-4         : angle       2.83563 (   18)
  hydrogen bonds       : bond        0.03596 (  631)
  hydrogen bonds       : angle       3.76618 ( 1857)
  link_BETA1-6         : bond        0.00541 (    3)
  link_BETA1-6         : angle       2.00358 (    9)
  SS BOND              : bond        0.00322 (    9)
  SS BOND              : angle       0.81748 (   18)
  link_BETA1-3         : bond        0.00593 (    1)
  link_BETA1-3         : angle       3.43510 (    3)
  covalent geometry    : bond        0.00300 (11250)
  covalent geometry    : angle       0.72462 (15315)

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 227
  time to evaluate  : 1.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  342 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.7699 (p)
REVERT: A  344 LEU cc_start: 0.8886 (mp) cc_final: 0.8513 (mp)
REVERT: A  378 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7611 (mt-10)
REVERT: A  379 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7212 (t0)
REVERT: A  715 TRP cc_start: 0.6752 (p90) cc_final: 0.6293 (p90)
REVERT: A  876 GLU cc_start: 0.6966 (OUTLIER) cc_final: 0.6617 (tm-30)
REVERT: A  984 ASN cc_start: 0.8245 (t0) cc_final: 0.8011 (t0)
REVERT: A 1042 MET cc_start: 0.7175 (tpp) cc_final: 0.6811 (mmp)
REVERT: A 1102 PHE cc_start: 0.8815 (t80) cc_final: 0.8411 (t80)
REVERT: A 1197 GLU cc_start: 0.6952 (OUTLIER) cc_final: 0.6673 (tt0)
REVERT: A 1258 PHE cc_start: 0.7548 (OUTLIER) cc_final: 0.7257 (t80)
REVERT: H    2 ARG cc_start: 0.8407 (mmm160) cc_final: 0.7763 (mmm160)
  outliers start: 39
  outliers final: 28
  residues processed: 255
  average time/residue: 0.2033
  time to fit residues: 77.1296
Evaluate side-chains
  257 residues out of total 1200 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 223
  time to evaluate  : 1.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  147 MET
Chi-restraints excluded: chain A residue  321 ASP
Chi-restraints excluded: chain A residue  342 THR
Chi-restraints excluded: chain A residue  372 VAL
Chi-restraints excluded: chain A residue  378 GLU
Chi-restraints excluded: chain A residue  379 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  404 THR
Chi-restraints excluded: chain A residue  635 THR
Chi-restraints excluded: chain A residue  671 MET
Chi-restraints excluded: chain A residue  694 VAL
Chi-restraints excluded: chain A residue  724 VAL
Chi-restraints excluded: chain A residue  736 LEU
Chi-restraints excluded: chain A residue  871 VAL
Chi-restraints excluded: chain A residue  873 LEU
Chi-restraints excluded: chain A residue  876 GLU
Chi-restraints excluded: chain A residue  877 ASP
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  897 LEU
Chi-restraints excluded: chain A residue  924 TRP
Chi-restraints excluded: chain A residue  934 LEU
Chi-restraints excluded: chain A residue  979 VAL
Chi-restraints excluded: chain A residue 1018 VAL
Chi-restraints excluded: chain A residue 1038 GLU
Chi-restraints excluded: chain A residue 1128 THR
Chi-restraints excluded: chain A residue 1165 ASP
Chi-restraints excluded: chain A residue 1182 LEU
Chi-restraints excluded: chain A residue 1197 GLU
Chi-restraints excluded: chain A residue 1258 PHE
Chi-restraints excluded: chain A residue 1266 ILE
Chi-restraints excluded: chain A residue 1324 ILE
Chi-restraints excluded: chain A residue 1343 ILE
Chi-restraints excluded: chain A residue 1391 LEU
Chi-restraints excluded: chain A residue 1418 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 134
   random chunks:
   chunk 40 optimal weight:    8.9990
   chunk 129 optimal weight:    4.9990
   chunk 132 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 119 optimal weight:    0.9990
   chunk 37 optimal weight:    5.9990
   chunk 33 optimal weight:    0.5980
   chunk 106 optimal weight:    0.7980
   chunk 84 optimal weight:    2.9990
   chunk 71 optimal weight:    5.9990
   chunk 20 optimal weight:    0.4980
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.159022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.119209 restraints weight = 21977.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.119264 restraints weight = 13631.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.119998 restraints weight = 11152.121|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7726
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  11276  Z= 0.140
  Angle     :  0.754  17.015  15384  Z= 0.354
  Chirality :  0.044   0.255   1786
  Planarity :  0.004   0.065   1876
  Dihedral  :  5.887  59.422   1820
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 12.02
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.38 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 28.91 %
    Favored  : 67.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.24), residues: 1342
  helix:  0.94 (0.18), residues: 890
  sheet: -2.95 (1.37), residues: 10
  loop : -2.08 (0.30), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.001   TRP A 244 
 HIS   0.004   0.001   HIS A 421 
 PHE   0.025   0.001   PHE A 189 
 TYR   0.013   0.001   TYR A 895 
 ARG   0.016   0.001   ARG A 613 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00298 (    7)
  link_NAG-ASN         : angle       2.89085 (   21)
  link_BETA1-4         : bond        0.00459 (    6)
  link_BETA1-4         : angle       2.78161 (   18)
  hydrogen bonds       : bond        0.03591 (  631)
  hydrogen bonds       : angle       3.79012 ( 1857)
  link_BETA1-6         : bond        0.00507 (    3)
  link_BETA1-6         : angle       1.99465 (    9)
  SS BOND              : bond        0.00291 (    9)
  SS BOND              : angle       0.86642 (   18)
  link_BETA1-3         : bond        0.00525 (    1)
  link_BETA1-3         : angle       3.44590 (    3)
  covalent geometry    : bond        0.00317 (11250)
  covalent geometry    : angle       0.73824 (15315)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4292.58 seconds
wall clock time: 75 minutes 0.88 seconds (4500.88 seconds total)