Starting phenix.real_space_refine
on Mon Dec 30 07:46:17 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vvc_43550/12_2024/8vvc_43550.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vvc_43550/12_2024/8vvc_43550.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.32
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vvc_43550/12_2024/8vvc_43550.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vvc_43550/12_2024/8vvc_43550.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vvc_43550/12_2024/8vvc_43550.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vvc_43550/12_2024/8vvc_43550.cif"
  }
  resolution = 4.32
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 1758 atoms to isotropic.
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      60      5.16       5
     C    7130      2.51       5
     N    1822      2.21       5
     O    1977      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 10989
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10989
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1390, 10989
          Classifications: {'peptide': 1390}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 51, 'TRANS': 1336}
          Chain breaks: 2
  Time building chain proxies: 7.96, per 1000 atoms: 0.72
  Number of scatterers: 10989
  At special positions: 0
  Unit cell: (133.927, 129.889, 131.235, 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      60     16.00
     O    1977      8.00
     N    1822      7.00
     C    7130      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  32 " 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
  Time building additional restraints: 2.91
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2624

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 8 sheets defined
      68.0% alpha, 5.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.45
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 8
      removed outlier: 4.107A  pdb=" N   SER A   8 " --> pdb=" O   ARG A   4 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 17 through 22
    Processing helix  chain 'A' and resid 30 through 58
      removed outlier: 4.247A  pdb=" N   LEU A  38 " --> pdb=" O   GLN A  34 " (cutoff:3.500A)
      removed outlier: 5.041A  pdb=" N   VAL A  39 " --> pdb=" O   ASN A  35 " (cutoff:3.500A)
      Proline residue:  A  42  - end of helix
      removed outlier: 3.571A  pdb=" N   TYR A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      Proline residue:  A  51  - end of helix
    Processing helix  chain 'A' and resid 68 through 98
      removed outlier: 3.656A  pdb=" N   LYS A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 107
    Processing helix  chain 'A' and resid 108 through 131
      removed outlier: 3.921A  pdb=" N   LEU A 112 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   LEU A 113 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   GLY A 114 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   ILE A 115 " --> pdb=" O   THR A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 161
      removed outlier: 3.699A  pdb=" N   LEU A 161 " --> pdb=" O   ILE A 157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 170 through 189
    Processing helix  chain 'A' and resid 208 through 212
    Processing helix  chain 'A' and resid 214 through 221
    Processing helix  chain 'A' and resid 222 through 234
      removed outlier: 3.711A  pdb=" N   GLY A 226 " --> pdb=" O   TRP A 222 " (cutoff:3.500A)
      removed outlier: 4.409A  pdb=" N   ARG A 233 " --> pdb=" O   VAL A 229 " (cutoff:3.500A)
      removed outlier: 4.353A  pdb=" N   GLN A 234 " --> pdb=" O   ARG A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 241
      removed outlier: 3.717A  pdb=" N   ASP A 240 " --> pdb=" O   GLU A 237 " (cutoff:3.500A)
      removed outlier: 4.024A  pdb=" N   LEU A 241 " --> pdb=" O   GLY A 238 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 237 through 241'
    Processing helix  chain 'A' and resid 249 through 268
      removed outlier: 3.567A  pdb=" N   VAL A 253 " --> pdb=" O   THR A 249 " (cutoff:3.500A)
      Proline residue:  A 255  - end of helix
    Processing helix  chain 'A' and resid 312 through 318
      removed outlier: 3.512A  pdb=" N   VAL A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 321 through 324
    Processing helix  chain 'A' and resid 325 through 355
      removed outlier: 4.130A  pdb=" N   LYS A 332 " --> pdb=" O   SER A 328 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   ALA A 333 " --> pdb=" O   PHE A 329 " (cutoff:3.500A)
      removed outlier: 3.965A  pdb=" N   ILE A 334 " --> pdb=" O   PHE A 330 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   MET A 339 " --> pdb=" O   HIS A 335 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   PHE A 340 " --> pdb=" O   ASP A 336 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 359 through 410
      removed outlier: 4.269A  pdb=" N   GLY A 363 " --> pdb=" O   PRO A 359 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   TYR A 364 " --> pdb=" O   ASP A 360 " (cutoff:3.500A)
      removed outlier: 3.802A  pdb=" N   LEU A 369 " --> pdb=" O   PHE A 365 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 370 " --> pdb=" O   TYR A 366 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   PHE A 371 " --> pdb=" O   THR A 367 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   VAL A 372 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
      removed outlier: 4.931A  pdb=" N   GLN A 383 " --> pdb=" O   LEU A 379 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   TYR A 384 " --> pdb=" O   VAL A 380 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   HIS A 386 " --> pdb=" O   HIS A 382 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ILE A 387 " --> pdb=" O   GLN A 383 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   TYR A 404 " --> pdb=" O   ILE A 400 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ARG A 405 " --> pdb=" O   GLY A 401 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   VAL A 409 " --> pdb=" O   ARG A 405 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE A 410 " --> pdb=" O   LYS A 406 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 433
    Processing helix  chain 'A' and resid 435 through 441
    Processing helix  chain 'A' and resid 442 through 462
      removed outlier: 3.771A  pdb=" N   SER A 446 " --> pdb=" O   ASN A 442 " (cutoff:3.500A)
      Proline residue:  A 448  - end of helix
      removed outlier: 3.874A  pdb=" N   VAL A 451 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 464 through 512
      Proline residue:  A 478  - end of helix
      removed outlier: 3.510A  pdb=" N   ALA A 481 " --> pdb=" O   VAL A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 519 through 571
      removed outlier: 4.412A  pdb=" N   ALA A 523 " --> pdb=" O   ALA A 519 " (cutoff:3.500A)
      Proline residue:  A 557  - end of helix
    Processing helix  chain 'A' and resid 578 through 599
      removed outlier: 4.524A  pdb=" N   PHE A 594 " --> pdb=" O   ASN A 590 " (cutoff:3.500A)
      Proline residue:  A 595  - end of helix
    Processing helix  chain 'A' and resid 601 through 621
      removed outlier: 3.576A  pdb=" N   LYS A 614 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ARG A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   LEU A 616 " --> pdb=" O   SER A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 692
    Processing helix  chain 'A' and resid 722 through 728
    Processing helix  chain 'A' and resid 735 through 745
    Processing helix  chain 'A' and resid 745 through 753
      removed outlier: 4.581A  pdb=" N   ASP A 749 " --> pdb=" O   ALA A 745 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 784
    Processing helix  chain 'A' and resid 794 through 798
      removed outlier: 4.252A  pdb=" N   ALA A 797 " --> pdb=" O   PRO A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 799 through 810
    Processing helix  chain 'A' and resid 852 through 859
      removed outlier: 3.824A  pdb=" N   ASP A 859 " --> pdb=" O   LEU A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 860 through 868
    Processing helix  chain 'A' and resid 974 through 1001
      removed outlier: 3.663A  pdb=" N   ASP A1001 " --> pdb=" O   SER A 997 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1012 through 1058
    Processing helix  chain 'A' and resid 1061 through 1066
      removed outlier: 4.446A  pdb=" N   ARG A1066 " --> pdb=" O   SER A1062 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1069 through 1085
      removed outlier: 3.687A  pdb=" N   VAL A1073 " --> pdb=" O   SER A1069 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LYS A1078 " --> pdb=" O   ASN A1074 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   SER A1085 " --> pdb=" O   ASP A1081 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1086 through 1110
      removed outlier: 3.749A  pdb=" N   MET A1093 " --> pdb=" O   GLU A1089 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1117
      removed outlier: 3.785A  pdb=" N   ALA A1116 " --> pdb=" O   PRO A1113 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ILE A1117 " --> pdb=" O   ILE A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1161
      removed outlier: 3.830A  pdb=" N   LEU A1122 " --> pdb=" O   ILE A1118 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   ARG A1138 " --> pdb=" O   VAL A1134 " (cutoff:3.500A)
      removed outlier: 5.082A  pdb=" N   GLN A1139 " --> pdb=" O   ALA A1135 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   LEU A1140 " --> pdb=" O   SER A1136 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A1143 " --> pdb=" O   GLN A1139 " (cutoff:3.500A)
      removed outlier: 3.990A  pdb=" N   GLU A1144 " --> pdb=" O   LEU A1140 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   SER A1145 " --> pdb=" O   LYS A1141 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER A1149 " --> pdb=" O   SER A1145 " (cutoff:3.500A)
      Proline residue:  A1150  - end of helix
    Processing helix  chain 'A' and resid 1161 through 1168
    Processing helix  chain 'A' and resid 1171 through 1220
      removed outlier: 3.890A  pdb=" N   ALA A1188 " --> pdb=" O   GLU A1184 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   TYR A1189 " --> pdb=" O   ASN A1185 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   TYR A1190 " --> pdb=" O   GLN A1186 " (cutoff:3.500A)
      Proline residue:  A1191  - end of helix
      removed outlier: 3.814A  pdb=" N   VAL A1194 " --> pdb=" O   TYR A1190 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   ALA A1195 " --> pdb=" O   PRO A1191 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ALA A1200 " --> pdb=" O   ASN A1196 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   CYS A1205 " --> pdb=" O   VAL A1201 " (cutoff:3.500A)
      removed outlier: 4.564A  pdb=" N   VAL A1206 " --> pdb=" O   ARG A1202 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   GLY A1207 " --> pdb=" O   LEU A1203 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ALA A1218 " --> pdb=" O   ALA A1214 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A1220 " --> pdb=" O   LEU A1216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1221 through 1225
      removed outlier: 3.505A  pdb=" N   SER A1224 " --> pdb=" O   SER A1221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1226 through 1254
      removed outlier: 3.564A  pdb=" N   VAL A1230 " --> pdb=" O   SER A1226 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   SER A1237 " --> pdb=" O   SER A1233 " (cutoff:3.500A)
      removed outlier: 4.424A  pdb=" N   LEU A1238 " --> pdb=" O   VAL A1234 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   GLN A1239 " --> pdb=" O   SER A1235 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1254 through 1268
    Processing helix  chain 'A' and resid 1332 through 1342
      removed outlier: 3.578A  pdb=" N   ARG A1342 " --> pdb=" O   LEU A1338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1362 through 1368
    Processing helix  chain 'A' and resid 1384 through 1388
    Processing helix  chain 'A' and resid 1395 through 1406
      removed outlier: 3.662A  pdb=" N   VAL A1399 " --> pdb=" O   SER A1395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1409 through 1415
    Processing helix  chain 'A' and resid 1417 through 1420
    Processing helix  chain 'A' and resid 1424 through 1428
      removed outlier: 3.513A  pdb=" N   GLU A1428 " --> pdb=" O   GLU A1425 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1431 through 1447
      removed outlier: 3.706A  pdb=" N   ARG A1435 " --> pdb=" O   SER A1431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1461 through 1477
    Processing helix  chain 'A' and resid 1510 through 1517
    Processing helix  chain 'A' and resid 1519 through 1528
      removed outlier: 3.617A  pdb=" N   ALA A1528 " --> pdb=" O   MET A1524 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 661 through 669
      removed outlier: 6.565A  pdb=" N   ASN A 662 " --> pdb=" O   THR A 650 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   THR A 650 " --> pdb=" O   ASN A 662 " (cutoff:3.500A)
      removed outlier: 5.094A  pdb=" N   ILE A 664 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   ALA A 649 " --> pdb=" O   GLU A 699 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   GLU A 699 " --> pdb=" O   ALA A 649 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   PHE A 651 " --> pdb=" O   LYS A 697 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   LYS A 697 " --> pdb=" O   PHE A 651 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 708 through 711
      removed outlier: 6.370A  pdb=" N   ALA A 709 " --> pdb=" O   LEU A 790 " (cutoff:3.500A)
      removed outlier: 8.069A  pdb=" N   ASP A 792 " --> pdb=" O   ALA A 709 " (cutoff:3.500A)
      removed outlier: 7.390A  pdb=" N   VAL A 711 " --> pdb=" O   ASP A 792 " (cutoff:3.500A)
      removed outlier: 6.238A  pdb=" N   TYR A 789 " --> pdb=" O   ILE A 823 " (cutoff:3.500A)
      removed outlier: 8.174A  pdb=" N   VAL A 825 " --> pdb=" O   TYR A 789 " (cutoff:3.500A)
      removed outlier: 6.716A  pdb=" N   PHE A 791 " --> pdb=" O   VAL A 825 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LEU A 824 " --> pdb=" O   VAL A 674 " (cutoff:3.500A)
      removed outlier: 6.493A  pdb=" N   LEU A 673 " --> pdb=" O   VAL A 837 " (cutoff:3.500A)
      removed outlier: 7.740A  pdb=" N   ILE A 839 " --> pdb=" O   LEU A 673 " (cutoff:3.500A)
      removed outlier: 6.307A  pdb=" N   ALA A 675 " --> pdb=" O   ILE A 839 " (cutoff:3.500A)
      removed outlier: 7.715A  pdb=" N   MET A 841 " --> pdb=" O   ALA A 675 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   VAL A 677 " --> pdb=" O   MET A 841 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   ILE A 838 " --> pdb=" O   MET A 849 " (cutoff:3.500A)
      removed outlier: 5.211A  pdb=" N   MET A 849 " --> pdb=" O   ILE A 838 " (cutoff:3.500A)
      removed outlier: 7.222A  pdb=" N   VAL A 840 " --> pdb=" O   SER A 847 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 720 through 721
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1295 through 1298
      removed outlier: 5.363A  pdb=" N   ILE A1313 " --> pdb=" O   ASN A1297 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1324 through 1326
      removed outlier: 5.337A  pdb=" N   GLY A1324 " --> pdb=" O   ILE A1498 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   LEU A1500 " --> pdb=" O   GLY A1324 " (cutoff:3.500A)
      removed outlier: 7.482A  pdb=" N   VAL A1326 " --> pdb=" O   LEU A1500 " (cutoff:3.500A)
      removed outlier: 6.231A  pdb=" N   VAL A1497 " --> pdb=" O   TYR A1508 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   TYR A1508 " --> pdb=" O   VAL A1497 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   VAL A1499 " --> pdb=" O   GLN A1506 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1352 through 1353
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1371 through 1372
      removed outlier: 3.655A  pdb=" N   THR A1371 " --> pdb=" O   ILE A1450 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1382 through 1383

    642 hydrogen bonds defined for protein.
    1878 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: 4.01

  Time building geometry restraints manager: 3.32 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1854
        1.32 -     1.45: 2939
        1.45 -     1.57: 6349
        1.57 -     1.70: 0
        1.70 -     1.82: 95
  Bond restraints: 11237
  Sorted by residual:
  bond pdb=" N   VAL A 477 "
       pdb=" CA  VAL A 477 "
    ideal  model  delta    sigma   weight residual
    1.461  1.503 -0.042 1.23e-02 6.61e+03 1.14e+01
  bond pdb=" C   VAL A 466 "
       pdb=" O   VAL A 466 "
    ideal  model  delta    sigma   weight residual
    1.238  1.198  0.039 1.32e-02 5.74e+03 8.78e+00
  bond pdb=" N   ILE A 100 "
       pdb=" CA  ILE A 100 "
    ideal  model  delta    sigma   weight residual
    1.460  1.492 -0.033 1.10e-02 8.26e+03 8.74e+00
  bond pdb=" N   VAL A 472 "
       pdb=" CA  VAL A 472 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.10e+00
  bond pdb=" N   VAL A 105 "
       pdb=" CA  VAL A 105 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 1.19e-02 7.06e+03 6.80e+00
  ... (remaining 11232 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 14819
        1.90 -     3.81: 345
        3.81 -     5.71: 76
        5.71 -     7.61: 19
        7.61 -     9.52: 5
  Bond angle restraints: 15264
  Sorted by residual:
  angle pdb=" N   LEU A 467 "
        pdb=" CA  LEU A 467 "
        pdb=" C   LEU A 467 "
      ideal   model   delta    sigma   weight residual
     112.23  104.72    7.51 1.26e+00 6.30e-01 3.55e+01
  angle pdb=" C   LYS A1418 "
        pdb=" CA  LYS A1418 "
        pdb=" CB  LYS A1418 "
      ideal   model   delta    sigma   weight residual
     117.23  110.11    7.12 1.36e+00 5.41e-01 2.74e+01
  angle pdb=" N   VAL A 466 "
        pdb=" CA  VAL A 466 "
        pdb=" C   VAL A 466 "
      ideal   model   delta    sigma   weight residual
     113.07  106.55    6.52 1.36e+00 5.41e-01 2.30e+01
  angle pdb=" N   VAL A 470 "
        pdb=" CA  VAL A 470 "
        pdb=" C   VAL A 470 "
      ideal   model   delta    sigma   weight residual
     110.72  105.93    4.79 1.01e+00 9.80e-01 2.25e+01
  angle pdb=" N   ALA A 468 "
        pdb=" CA  ALA A 468 "
        pdb=" C   ALA A 468 "
      ideal   model   delta    sigma   weight residual
     111.82  106.34    5.48 1.16e+00 7.43e-01 2.23e+01
  ... (remaining 15259 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6072
       17.99 -    35.98: 487
       35.98 -    53.97: 102
       53.97 -    71.96: 14
       71.96 -    89.96: 11
  Dihedral angle restraints: 6686
    sinusoidal: 2630
      harmonic: 4056
  Sorted by residual:
  dihedral pdb=" CA  MET A1254 "
           pdb=" C   MET A1254 "
           pdb=" N   GLU A1255 "
           pdb=" CA  GLU A1255 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.83   28.17     0      5.00e+00 4.00e-02 3.17e+01
  dihedral pdb=" CA  ILE A  65 "
           pdb=" C   ILE A  65 "
           pdb=" N   GLN A  66 "
           pdb=" CA  GLN A  66 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.94  -21.06     0      5.00e+00 4.00e-02 1.77e+01
  dihedral pdb=" CA  LYS A 246 "
           pdb=" C   LYS A 246 "
           pdb=" N   GLU A 247 "
           pdb=" CA  GLU A 247 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.01   19.99     0      5.00e+00 4.00e-02 1.60e+01
  ... (remaining 6683 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1396
       0.051 -    0.103: 316
       0.103 -    0.154: 49
       0.154 -    0.205: 10
       0.205 -    0.257: 3
  Chirality restraints: 1774
  Sorted by residual:
  chirality pdb=" CA  VAL A 470 "
            pdb=" N   VAL A 470 "
            pdb=" C   VAL A 470 "
            pdb=" CB  VAL A 470 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.70   -0.26 2.00e-01 2.50e+01 1.65e+00
  chirality pdb=" CB  ILE A1373 "
            pdb=" CA  ILE A1373 "
            pdb=" CG1 ILE A1373 "
            pdb=" CG2 ILE A1373 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  VAL A 477 "
            pdb=" CA  VAL A 477 "
            pdb=" CG1 VAL A 477 "
            pdb=" CG2 VAL A 477 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1771 not shown)

  Planarity restraints: 1906
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A1248 "    0.010 2.00e-02 2.50e+03   2.04e-02 4.18e+00
        pdb=" C   VAL A1248 "   -0.035 2.00e-02 2.50e+03
        pdb=" O   VAL A1248 "    0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A1249 "    0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 500 "   -0.010 2.00e-02 2.50e+03   2.02e-02 4.09e+00
        pdb=" C   ASN A 500 "    0.035 2.00e-02 2.50e+03
        pdb=" O   ASN A 500 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG A 501 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 489 "    0.009 2.00e-02 2.50e+03   1.90e-02 3.60e+00
        pdb=" C   THR A 489 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   THR A 489 "    0.012 2.00e-02 2.50e+03
        pdb=" N   TYR A 490 "    0.011 2.00e-02 2.50e+03
  ... (remaining 1903 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 868
        2.74 -     3.28: 12305
        3.28 -     3.82: 18742
        3.82 -     4.36: 20286
        4.36 -     4.90: 33538
  Nonbonded interactions: 85739
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A  68 "
            pdb=" OD1 ASN A  71 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" O   VAL A1248 "
            pdb=" OG  SER A1252 "
     model   vdw
     2.216 3.040
  nonbonded pdb=" OG  SER A 418 "
            pdb=" O   VAL A 420 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   VAL A 548 "
            pdb=" OG1 THR A 552 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   LEU A 317 "
            pdb=" N   GLY A 322 "
     model   vdw
     2.245 3.120
  ... (remaining 85734 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             3.150
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     29.130
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  11237  Z= 0.203
  Angle     :  0.749   9.518  15264  Z= 0.416
  Chirality :  0.045   0.257   1774
  Planarity :  0.005   0.044   1906
  Dihedral  : 14.066  89.956   4059
  Min Nonbonded Distance : 2.196

Molprobity Statistics.
  All-atom Clashscore : 13.22
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.73 %
    Favored  : 92.20 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  0.33 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.65 (0.23), residues: 1384
  helix:  0.35 (0.18), residues: 843
  sheet: -0.55 (0.65), residues: 58
  loop : -1.73 (0.29), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 520 
 HIS   0.007   0.001   HIS A 801 
 PHE   0.015   0.001   PHE A 583 
 TYR   0.016   0.001   TYR A1033 
 ARG   0.010   0.000   ARG A1473 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 141
  time to evaluate  : 1.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  983 MET cc_start: 0.9641 (mmp) cc_final: 0.9338 (mmp)
REVERT: A 1276 TRP cc_start: 0.8738 (m100) cc_final: 0.8506 (m100)
  outliers start: 3
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2141
  time to fit residues: 46.2351
Evaluate side-chains
  116 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 117 optimal weight:    8.9990
   chunk 105 optimal weight:    2.9990
   chunk 58 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 71 optimal weight:   10.0000
   chunk 56 optimal weight:    4.9990
   chunk 108 optimal weight:    9.9990
   chunk 42 optimal weight:    0.9980
   chunk 66 optimal weight:   10.0000
   chunk 81 optimal weight:   20.0000
   chunk 126 optimal weight:   30.0000
   overall best weight:    3.1786

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

Flipped N/Q/H residues before XYZ refinement:
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 805 HIS
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1364 HIS
A1387 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.1218

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  11237  Z= 0.229
  Angle     :  0.666   7.579  15264  Z= 0.348
  Chirality :  0.043   0.167   1774
  Planarity :  0.005   0.054   1906
  Dihedral  :  4.789  26.441   1499
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.43 %
    Favored  : 93.50 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  5.68 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.33 (0.23), residues: 1384
  helix:  0.69 (0.18), residues: 852
  sheet: -0.96 (0.60), residues: 68
  loop : -1.77 (0.28), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 553 
 HIS   0.007   0.001   HIS A1421 
 PHE   0.038   0.001   PHE A 524 
 TYR   0.055   0.002   TYR A 490 
 ARG   0.004   0.001   ARG A 775 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 141
  time to evaluate  : 1.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8664 (tpp) cc_final: 0.8360 (tpp)
REVERT: A  251 GLU cc_start: 0.9149 (mt-10) cc_final: 0.8920 (tm-30)
REVERT: A  510 ASN cc_start: 0.8163 (m110) cc_final: 0.7925 (m110)
REVERT: A  983 MET cc_start: 0.9668 (mmp) cc_final: 0.9328 (mmp)
REVERT: A 1090 VAL cc_start: 0.9390 (t) cc_final: 0.8912 (t)
  outliers start: 1
  outliers final: 0
  residues processed: 142
  average time/residue: 0.2190
  time to fit residues: 47.4090
Evaluate side-chains
  106 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 70 optimal weight:    8.9990
   chunk 39 optimal weight:    4.9990
   chunk 105 optimal weight:    1.9990
   chunk 85 optimal weight:    8.9990
   chunk 34 optimal weight:    7.9990
   chunk 126 optimal weight:   40.0000
   chunk 136 optimal weight:    0.2980
   chunk 112 optimal weight:    8.9990
   chunk 125 optimal weight:    7.9990
   chunk 43 optimal weight:    0.9990
   chunk 101 optimal weight:    9.9990
   overall best weight:    3.2588

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

Flipped N/Q/H residues before XYZ refinement:
A  34 GLN
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11237  Z= 0.226
  Angle     :  0.652   8.757  15264  Z= 0.338
  Chirality :  0.043   0.198   1774
  Planarity :  0.004   0.041   1906
  Dihedral  :  4.779  23.163   1499
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 12.41
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.01 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.93 %
    Favored  : 94.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.27 (0.23), residues: 1384
  helix:  0.75 (0.18), residues: 859
  sheet: -0.92 (0.62), residues: 68
  loop : -1.82 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 553 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.034   0.001   PHE A 524 
 TYR   0.027   0.002   TYR A1243 
 ARG   0.025   0.001   ARG A 501 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 1.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 GLU cc_start: 0.9141 (mt-10) cc_final: 0.8938 (tm-30)
REVERT: A  510 ASN cc_start: 0.8013 (m110) cc_final: 0.7807 (m110)
REVERT: A  983 MET cc_start: 0.9670 (mmp) cc_final: 0.9328 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 136
  average time/residue: 0.2120
  time to fit residues: 43.5733
Evaluate side-chains
  102 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 124 optimal weight:    8.9990
   chunk 95 optimal weight:    2.9990
   chunk 65 optimal weight:   10.0000
   chunk 13 optimal weight:    8.9990
   chunk 60 optimal weight:    5.9990
   chunk 84 optimal weight:    5.9990
   chunk 126 optimal weight:    9.9990
   chunk 134 optimal weight:    4.9990
   chunk 66 optimal weight:    6.9990
   chunk 120 optimal weight:   20.0000
   chunk 36 optimal weight:    8.9990
   overall best weight:    5.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 718 GLN
A1185 ASN
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8165
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  11237  Z= 0.317
  Angle     :  0.739   7.890  15264  Z= 0.388
  Chirality :  0.045   0.167   1774
  Planarity :  0.005   0.057   1906
  Dihedral  :  5.018  24.258   1499
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 14.75
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.95 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.51 (0.22), residues: 1384
  helix:  0.49 (0.17), residues: 872
  sheet: -1.24 (0.64), residues: 60
  loop : -1.75 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 716 
 HIS   0.007   0.002   HIS A1421 
 PHE   0.031   0.002   PHE A 524 
 TYR   0.024   0.002   TYR A1243 
 ARG   0.012   0.001   ARG A1473 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.8898 (m-30) cc_final: 0.8610 (m-30)
REVERT: A  182 LEU cc_start: 0.9318 (tt) cc_final: 0.8932 (tt)
REVERT: A  185 GLN cc_start: 0.9583 (tp40) cc_final: 0.8999 (tm-30)
REVERT: A  510 ASN cc_start: 0.7911 (m110) cc_final: 0.7704 (m110)
REVERT: A  983 MET cc_start: 0.9695 (mmp) cc_final: 0.9347 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2157
  time to fit residues: 42.3691
Evaluate side-chains
  101 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 111 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 100 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 114 optimal weight:    8.9990
   chunk 92 optimal weight:    7.9990
   chunk 0 optimal weight:    5.9990
   chunk 68 optimal weight:    8.9990
   chunk 120 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
A 252 GLN
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1054 HIS
** A1239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8116
moved from start:          0.2639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  11237  Z= 0.203
  Angle     :  0.663   8.325  15264  Z= 0.343
  Chirality :  0.043   0.184   1774
  Planarity :  0.004   0.040   1906
  Dihedral  :  4.906  23.534   1499
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 12.32
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.15 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.88 %
    Favored  : 97.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.25 (0.22), residues: 1384
  helix:  0.73 (0.17), residues: 871
  sheet: -1.18 (0.65), residues: 60
  loop : -1.74 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP A 716 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.027   0.001   PHE A 551 
 TYR   0.023   0.001   TYR A1033 
 ARG   0.008   0.000   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 137
  time to evaluate  : 1.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.8878 (m-30) cc_final: 0.8625 (m-30)
REVERT: A  182 LEU cc_start: 0.9280 (tt) cc_final: 0.8918 (tt)
REVERT: A  185 GLN cc_start: 0.9565 (tp40) cc_final: 0.9044 (tm-30)
REVERT: A  193 ASP cc_start: 0.8462 (t0) cc_final: 0.8255 (t0)
REVERT: A  427 MET cc_start: 0.8870 (tpp) cc_final: 0.8654 (tpp)
REVERT: A  510 ASN cc_start: 0.7927 (m110) cc_final: 0.7719 (m110)
REVERT: A  983 MET cc_start: 0.9677 (mmp) cc_final: 0.9357 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 138
  average time/residue: 0.2284
  time to fit residues: 46.6220
Evaluate side-chains
  102 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 45 optimal weight:    5.9990
   chunk 120 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 78 optimal weight:   20.0000
   chunk 33 optimal weight:    7.9990
   chunk 134 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 62 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   chunk 44 optimal weight:    8.9990
   chunk 70 optimal weight:    9.9990
   overall best weight:    3.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1185 ASN
A1314 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  11237  Z= 0.248
  Angle     :  0.691   9.868  15264  Z= 0.359
  Chirality :  0.044   0.184   1774
  Planarity :  0.004   0.045   1906
  Dihedral  :  4.967  24.692   1499
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 12.95
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.23 %
    Favored  : 92.63 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.22), residues: 1384
  helix:  0.73 (0.17), residues: 873
  sheet: -1.23 (0.65), residues: 60
  loop : -1.76 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 716 
 HIS   0.008   0.001   HIS A 386 
 PHE   0.023   0.002   PHE A 524 
 TYR   0.023   0.002   TYR A1033 
 ARG   0.011   0.001   ARG A 633 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.204 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.9325 (tt) cc_final: 0.8922 (tt)
REVERT: A  185 GLN cc_start: 0.9588 (tp40) cc_final: 0.8946 (tm-30)
REVERT: A  251 GLU cc_start: 0.8821 (tm-30) cc_final: 0.8566 (tm-30)
REVERT: A  427 MET cc_start: 0.8849 (tpp) cc_final: 0.8522 (tpp)
REVERT: A  510 ASN cc_start: 0.7917 (m110) cc_final: 0.7703 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.2211
  time to fit residues: 42.0627
Evaluate side-chains
  99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 129 optimal weight:    7.9990
   chunk 15 optimal weight:    9.9990
   chunk 76 optimal weight:    7.9990
   chunk 98 optimal weight:    0.8980
   chunk 113 optimal weight:   10.0000
   chunk 75 optimal weight:   10.0000
   chunk 133 optimal weight:   10.0000
   chunk 83 optimal weight:    0.9990
   chunk 81 optimal weight:    8.9990
   chunk 61 optimal weight:   10.0000
   chunk 82 optimal weight:    1.9990
   overall best weight:    3.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1185 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  11237  Z= 0.247
  Angle     :  0.690   9.274  15264  Z= 0.359
  Chirality :  0.044   0.199   1774
  Planarity :  0.004   0.044   1906
  Dihedral  :  4.994  24.493   1499
  Min Nonbonded Distance : 2.350

Molprobity Statistics.
  All-atom Clashscore : 13.35
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.01 %
    Favored  : 92.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.06 %
    Favored  : 97.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.25 (0.22), residues: 1384
  helix:  0.76 (0.17), residues: 866
  sheet: -1.30 (0.64), residues: 61
  loop : -1.77 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 242 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.023   0.002   PHE A 524 
 TYR   0.023   0.002   TYR A1033 
 ARG   0.008   0.001   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 ASP cc_start: 0.9011 (m-30) cc_final: 0.8798 (m-30)
REVERT: A  182 LEU cc_start: 0.9294 (tt) cc_final: 0.8861 (tt)
REVERT: A  185 GLN cc_start: 0.9596 (tp40) cc_final: 0.8931 (tm-30)
REVERT: A  427 MET cc_start: 0.8936 (tpp) cc_final: 0.8593 (tpp)
REVERT: A  510 ASN cc_start: 0.7917 (m110) cc_final: 0.7698 (m110)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.2212
  time to fit residues: 40.4180
Evaluate side-chains
  98 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 1.369 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 53 optimal weight:    8.9990
   chunk 80 optimal weight:    9.9990
   chunk 40 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 25 optimal weight:    4.9990
   chunk 85 optimal weight:    6.9990
   chunk 91 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 12 optimal weight:    0.7980
   chunk 105 optimal weight:    2.9990
   chunk 121 optimal weight:    0.8980
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
moved from start:          0.3335

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  11237  Z= 0.183
  Angle     :  0.673   9.630  15264  Z= 0.341
  Chirality :  0.043   0.187   1774
  Planarity :  0.004   0.042   1906
  Dihedral  :  4.886  23.954   1499
  Min Nonbonded Distance : 2.359

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.72 %
    Favored  : 93.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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 (0.23), residues: 1384
  helix:  0.88 (0.18), residues: 865
  sheet: -1.05 (0.61), residues: 68
  loop : -1.70 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 242 
 HIS   0.004   0.001   HIS A 986 
 PHE   0.022   0.001   PHE A 524 
 TYR   0.023   0.001   TYR A1033 
 ARG   0.004   0.000   ARG A 633 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 1.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  182 LEU cc_start: 0.9290 (tt) cc_final: 0.8873 (tt)
REVERT: A  185 GLN cc_start: 0.9568 (tp40) cc_final: 0.8940 (tm-30)
REVERT: A  510 ASN cc_start: 0.7904 (m110) cc_final: 0.7684 (m110)
REVERT: A  524 PHE cc_start: 0.8614 (p90) cc_final: 0.8362 (p90)
REVERT: A  983 MET cc_start: 0.9657 (mmp) cc_final: 0.9348 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.2141
  time to fit residues: 42.4877
Evaluate side-chains
  99 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 1.627 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 128 optimal weight:   30.0000
   chunk 117 optimal weight:    7.9990
   chunk 124 optimal weight:   10.0000
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    3.9990
   chunk 98 optimal weight:    3.9990
   chunk 38 optimal weight:    7.9990
   chunk 112 optimal weight:    7.9990
   chunk 118 optimal weight:    1.9990
   chunk 81 optimal weight:    7.9990
   chunk 132 optimal weight:    8.9990
   overall best weight:    4.9990

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1185 ASN
** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  11237  Z= 0.294
  Angle     :  0.727   8.790  15264  Z= 0.377
  Chirality :  0.045   0.234   1774
  Planarity :  0.005   0.044   1906
  Dihedral  :  5.035  25.844   1499
  Min Nonbonded Distance : 2.344

Molprobity Statistics.
  All-atom Clashscore : 14.44
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.51 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.48 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.28 (0.22), residues: 1384
  helix:  0.74 (0.17), residues: 869
  sheet: -1.42 (0.67), residues: 55
  loop : -1.79 (0.28), residues: 460

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 242 
 HIS   0.006   0.001   HIS A1421 
 PHE   0.025   0.002   PHE A 524 
 TYR   0.022   0.002   TYR A1033 
 ARG   0.007   0.001   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 1.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8885 (tpp) cc_final: 0.8591 (tpp)
REVERT: A  513 LYS cc_start: 0.9075 (tmtt) cc_final: 0.8749 (mttp)
REVERT: A  524 PHE cc_start: 0.8613 (p90) cc_final: 0.8363 (p90)
REVERT: A  983 MET cc_start: 0.9692 (mmp) cc_final: 0.9349 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.2238
  time to fit residues: 42.4688
Evaluate side-chains
  92 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 80 optimal weight:   20.0000
   chunk 62 optimal weight:    9.9990
   chunk 91 optimal weight:    9.9990
   chunk 138 optimal weight:    6.9990
   chunk 127 optimal weight:   50.0000
   chunk 110 optimal weight:    5.9990
   chunk 11 optimal weight:    5.9990
   chunk 85 optimal weight:   10.0000
   chunk 67 optimal weight:    5.9990
   chunk 87 optimal weight:   10.0000
   chunk 117 optimal weight:    7.9990
   overall best weight:    6.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1011 HIS
A1185 ASN
** A1364 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1387 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8192
moved from start:          0.4035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  11237  Z= 0.377
  Angle     :  0.812   8.691  15264  Z= 0.427
  Chirality :  0.047   0.235   1774
  Planarity :  0.005   0.049   1906
  Dihedral  :  5.383  28.661   1499
  Min Nonbonded Distance : 2.300

Molprobity Statistics.
  All-atom Clashscore : 17.05
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  7.95 %
    Favored  : 91.98 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.66 (0.22), residues: 1384
  helix:  0.45 (0.17), residues: 860
  sheet: -1.78 (0.66), residues: 56
  loop : -1.88 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 553 
 HIS   0.006   0.001   HIS A 986 
 PHE   0.033   0.002   PHE A 325 
 TYR   0.023   0.002   TYR A  91 
 ARG   0.007   0.001   ARG A1066 

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

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

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2768 Ramachandran restraints generated.
    1384 Oldfield, 0 Emsley, 1384 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 120
  time to evaluate  : 1.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 MET cc_start: 0.8952 (tpp) cc_final: 0.8656 (tpp)
REVERT: A  490 TYR cc_start: 0.7671 (m-10) cc_final: 0.7228 (m-80)
REVERT: A  510 ASN cc_start: 0.7938 (m110) cc_final: 0.7715 (m110)
REVERT: A  979 ILE cc_start: 0.9063 (mm) cc_final: 0.8724 (mm)
REVERT: A  983 MET cc_start: 0.9717 (mmp) cc_final: 0.9338 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 120
  average time/residue: 0.2059
  time to fit residues: 37.4157
Evaluate side-chains
  92 residues out of total 1214 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 1.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 139
   random chunks:
   chunk 33 optimal weight:    7.9990
   chunk 101 optimal weight:   10.0000
   chunk 16 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 110 optimal weight:    0.9980
   chunk 46 optimal weight:   10.0000
   chunk 113 optimal weight:    6.9990
   chunk 13 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   chunk 96 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   overall best weight:    2.1184

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 480 ASN
A 491 GLN
A1364 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.086046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.062308 restraints weight = 66776.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.063419 restraints weight = 40326.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.064290 restraints weight = 28902.249|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11237  Z= 0.202
  Angle     :  0.715  10.105  15264  Z= 0.365
  Chirality :  0.045   0.221   1774
  Planarity :  0.004   0.043   1906
  Dihedral  :  5.154  26.854   1499
  Min Nonbonded Distance : 2.322

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  6.94 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.16 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.77 %
    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: -0.34 (0.22), residues: 1384
  helix:  0.70 (0.17), residues: 862
  sheet: -1.66 (0.68), residues: 56
  loop : -1.74 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 242 
 HIS   0.005   0.001   HIS A1421 
 PHE   0.022   0.001   PHE A 179 
 TYR   0.020   0.002   TYR A  91 
 ARG   0.004   0.000   ARG A1066 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2656.06 seconds
wall clock time: 49 minutes 50.84 seconds (2990.84 seconds total)