Starting phenix.real_space_refine
on Wed Feb 12 15:52:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7svr_25452/02_2025/7svr_25452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7svr_25452/02_2025/7svr_25452.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/7svr_25452/02_2025/7svr_25452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7svr_25452/02_2025/7svr_25452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7svr_25452/02_2025/7svr_25452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7svr_25452/02_2025/7svr_25452.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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     S      28      5.16       5
     C    5046      2.51       5
     N    1375      2.21       5
     O    1390      1.98       5
     F       2      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 7841
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7713
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1134, 7713
          Classifications: {'peptide': 1134}
          Incomplete info: {'truncation_to_alanine': 403}
          Link IDs: {'PTRANS': 28, 'TRANS': 1105}
          Chain breaks: 6
          Unresolved chain link angles: 11
          Unresolved non-hydrogen bonds: 1433
          Unresolved non-hydrogen angles: 1826
          Unresolved non-hydrogen dihedrals: 1188
          Unresolved non-hydrogen chiralities: 143
          Planarities with less than four sites: {'GLN:plan1': 22, 'HIS:plan': 7, 'TYR:plan': 13, 'ASN:plan1': 14, 'TRP:plan': 6, 'ASP:plan': 22, 'PHE:plan': 21, 'GLU:plan': 35, 'ARG:plan': 21}
          Unresolved non-hydrogen planarities: 747
    Chain: "B"
      Number of atoms: 95
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 95
          Classifications: {'peptide': 19}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'TRANS': 18}
          Unresolved non-hydrogen bonds: 38
          Unresolved non-hydrogen angles: 57
          Unresolved non-hydrogen dihedrals: 19
          Planarities with less than four sites: {'UNK:plan-1': 19}
          Unresolved non-hydrogen planarities: 19
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'VX8': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.50, per 1000 atoms: 0.70
  Number of scatterers: 7841
  At special positions: 0
  Unit cell: (103, 118.45, 112.27, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      28     16.00
     F       2      9.00
     O    1390      8.00
     N    1375      7.00
     C    5046      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.38
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2168

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 6 sheets defined
      70.5% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 16
    Processing helix  chain 'A' and resid 20 through 28
      removed outlier: 3.529A  pdb=" N   LEU A  24 " --> pdb=" O   THR A  20 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 33 through 37
    Processing helix  chain 'A' and resid 41 through 45
    Processing helix  chain 'A' and resid 46 through 64
      removed outlier: 4.187A  pdb=" N   GLU A  51 " --> pdb=" O   ASP A  47 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   LYS A  52 " --> pdb=" O   ASN A  48 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   LYS A  64 " --> pdb=" O   GLU A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 69 through 74
    Processing helix  chain 'A' and resid 77 through 103
      removed outlier: 4.310A  pdb=" N   PHE A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   LYS A  95 " --> pdb=" O   GLY A  91 " (cutoff:3.500A)
      Proline residue:  A  99  - end of helix
    Processing helix  chain 'A' and resid 104 through 108
      removed outlier: 3.503A  pdb=" N   ALA A 107 " --> pdb=" O   ARG A 104 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   SER A 108 " --> pdb=" O   ILE A 105 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 104 through 108'
    Processing helix  chain 'A' and resid 120 through 138
    Processing helix  chain 'A' and resid 138 through 165
      removed outlier: 3.593A  pdb=" N   LEU A 165 " --> pdb=" O   TYR A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 176 through 187
      removed outlier: 4.057A  pdb=" N   LEU A 180 " --> pdb=" O   SER A 176 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   VAL A 181 " --> pdb=" O   ILE A 177 " (cutoff:3.500A)
      removed outlier: 4.276A  pdb=" N   ASN A 187 " --> pdb=" O   LEU A 183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 194
      removed outlier: 3.620A  pdb=" N   GLU A 193 " --> pdb=" O   ASN A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 202 through 220
      removed outlier: 3.969A  pdb=" N   LEU A 206 " --> pdb=" O   TRP A 202 " (cutoff:3.500A)
      removed outlier: 4.240A  pdb=" N   GLY A 213 " --> pdb=" O   ALA A 209 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   TRP A 216 " --> pdb=" O   MET A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 223 through 267
      removed outlier: 3.842A  pdb=" N   LEU A 227 " --> pdb=" O   ALA A 223 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   PHE A 229 " --> pdb=" O   CYS A 225 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY A 241 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ARG A 242 " --> pdb=" O   ALA A 238 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   MET A 243 " --> pdb=" O   GLY A 239 " (cutoff:3.500A)
      removed outlier: 4.278A  pdb=" N   TYR A 247 " --> pdb=" O   MET A 243 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   GLY A 253 " --> pdb=" O   ASP A 249 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   LYS A 254 " --> pdb=" O   GLN A 250 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ILE A 261 " --> pdb=" O   GLU A 257 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   THR A 262 " --> pdb=" O   ARG A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 276
    Processing helix  chain 'A' and resid 277 through 329
      removed outlier: 4.837A  pdb=" N   THR A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   GLU A 292 " --> pdb=" O   LEU A 288 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   PHE A 310 " --> pdb=" O   ASN A 306 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   PHE A 311 " --> pdb=" O   SER A 307 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   GLY A 314 " --> pdb=" O   PHE A 310 " (cutoff:3.500A)
      removed outlier: 5.348A  pdb=" N   PHE A 315 " --> pdb=" O   PHE A 311 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   PHE A 316 " --> pdb=" O   PHE A 312 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   VAL A 318 " --> pdb=" O   GLY A 314 " (cutoff:3.500A)
      removed outlier: 4.063A  pdb=" N   SER A 321 " --> pdb=" O   VAL A 317 " (cutoff:3.500A)
      Proline residue:  A 324  - end of helix
    Processing helix  chain 'A' and resid 333 through 349
      removed outlier: 3.547A  pdb=" N   PHE A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   THR A 339 " --> pdb=" O   LYS A 335 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   SER A 341 " --> pdb=" O   PHE A 337 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 376
      removed outlier: 3.749A  pdb=" N   GLN A 376 " --> pdb=" O   GLN A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 472
    Processing helix  chain 'A' and resid 501 through 506
    Processing helix  chain 'A' and resid 513 through 524
    Processing helix  chain 'A' and resid 526 through 532
    Processing helix  chain 'A' and resid 549 through 563
    Processing helix  chain 'A' and resid 573 through 577
      removed outlier: 4.283A  pdb=" N   TYR A 577 " --> pdb=" O   PRO A 574 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 579 through 590
    Processing helix  chain 'A' and resid 609 through 613
      removed outlier: 3.850A  pdb=" N   ALA A 613 " --> pdb=" O   LEU A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 630 through 634
    Processing helix  chain 'A' and resid 637 through 645
      removed outlier: 3.937A  pdb=" N   MET A 645 " --> pdb=" O   SER A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 854
    Processing helix  chain 'A' and resid 856 through 886
      removed outlier: 4.001A  pdb=" N   ILE A 860 " --> pdb=" O   HIS A 856 " (cutoff:3.500A)
      removed outlier: 4.244A  pdb=" N   PHE A 861 " --> pdb=" O   LYS A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 911 through 916
    Processing helix  chain 'A' and resid 916 through 921
      removed outlier: 4.126A  pdb=" N   VAL A 920 " --> pdb=" O   PHE A 916 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 928
      removed outlier: 3.940A  pdb=" N   LEU A 926 " --> pdb=" O   VAL A 922 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   LEU A 927 " --> pdb=" O   ALA A 923 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 934 through 957
      removed outlier: 3.698A  pdb=" N   VAL A 938 " --> pdb=" O   GLY A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 965
    Processing helix  chain 'A' and resid 969 through 974
      removed outlier: 4.081A  pdb=" N   LEU A 973 " --> pdb=" O   ALA A 969 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   ASN A 974 " --> pdb=" O   GLY A 970 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 969 through 974'
    Processing helix  chain 'A' and resid 978 through 1012
      removed outlier: 5.055A  pdb=" N   LEU A 987 " --> pdb=" O   LEU A 983 " (cutoff:3.500A)
      Proline residue:  A 988  - end of helix
      removed outlier: 3.608A  pdb=" N   LEU A1011 " --> pdb=" O   VAL A1007 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLN A1012 " --> pdb=" O   VAL A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1061
      removed outlier: 3.560A  pdb=" N   ALA A1018 " --> pdb=" O   TYR A1014 " (cutoff:3.500A)
      Proline residue:  A1021  - end of helix
      removed outlier: 4.027A  pdb=" N   ALA A1025 " --> pdb=" O   PRO A1021 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   GLN A1035 " --> pdb=" O   ALA A1031 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   THR A1036 " --> pdb=" O   TYR A1032 " (cutoff:3.500A)
      removed outlier: 4.164A  pdb=" N   SER A1049 " --> pdb=" O   SER A1045 " (cutoff:3.500A)
      Proline residue:  A1050  - end of helix
    Processing helix  chain 'A' and resid 1061 through 1069
    Processing helix  chain 'A' and resid 1070 through 1120
      removed outlier: 3.801A  pdb=" N   PHE A1074 " --> pdb=" O   ARG A1070 " (cutoff:3.500A)
      removed outlier: 3.993A  pdb=" N   ASN A1088 " --> pdb=" O   LEU A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1139
      removed outlier: 4.138A  pdb=" N   ASN A1138 " --> pdb=" O   THR A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1139 through 1168
      removed outlier: 4.385A  pdb=" N   ARG A1158 " --> pdb=" O   ASP A1154 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   SER A1159 " --> pdb=" O   SER A1155 " (cutoff:3.500A)
      removed outlier: 4.233A  pdb=" N   VAL A1160 " --> pdb=" O   LEU A1156 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1250 through 1257
    Processing helix  chain 'A' and resid 1278 through 1283
    Processing helix  chain 'A' and resid 1299 through 1305
      removed outlier: 3.529A  pdb=" N   ASP A1305 " --> pdb=" O   ARG A1301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1321
    Processing helix  chain 'A' and resid 1324 through 1330
      removed outlier: 3.933A  pdb=" N   GLN A1330 " --> pdb=" O   SER A1326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1344
      removed outlier: 3.995A  pdb=" N   CYS A1344 " --> pdb=" O   VAL A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1347 through 1362
      removed outlier: 4.275A  pdb=" N   SER A1362 " --> pdb=" O   ARG A1358 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1371 through 1376
      removed outlier: 3.954A  pdb=" N   HIS A1375 " --> pdb=" O   GLU A1371 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU A1376 " --> pdb=" O   PRO A1372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1371 through 1376'
    Processing helix  chain 'A' and resid 1377 through 1391
      removed outlier: 3.588A  pdb=" N   GLN A1390 " --> pdb=" O   ARG A1386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1403 through 1408
      removed outlier: 4.152A  pdb=" N   MET A1407 " --> pdb=" O   ARG A1403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1429 through 1434
    Processing helix  chain 'B' and resid 9 through 18
      removed outlier: 4.140A  pdb=" N   UNK B  13 " --> pdb=" O   UNK B   9 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   UNK B  15 " --> pdb=" O   UNK B  11 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   UNK B  16 " --> pdb=" O   UNK B  12 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 444 through 448
      removed outlier: 7.091A  pdb=" N   PHE A 446 " --> pdb=" O   GLU A 395 " (cutoff:3.500A)
      removed outlier: 5.007A  pdb=" N   GLU A 395 " --> pdb=" O   PHE A 446 " (cutoff:3.500A)
      removed outlier: 7.391A  pdb=" N   ILE A 448 " --> pdb=" O   VAL A 393 " (cutoff:3.500A)
      removed outlier: 5.617A  pdb=" N   VAL A 393 " --> pdb=" O   ILE A 448 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 600 through 603
      removed outlier: 3.625A  pdb=" N   LEU A 602 " --> pdb=" O   LEU A 454 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   LEU A 453 " --> pdb=" O   LYS A 615 " (cutoff:3.500A)
      removed outlier: 8.607A  pdb=" N   LEU A 617 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   ALA A 455 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 7.995A  pdb=" N   LEU A 619 " --> pdb=" O   ALA A 455 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   ALA A 457 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
      removed outlier: 7.235A  pdb=" N   ILE A 616 " --> pdb=" O   TYR A 627 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   TYR A 627 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   ILE A 618 " --> pdb=" O   TYR A 625 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 488 through 491
      removed outlier: 6.686A  pdb=" N   SER A 489 " --> pdb=" O   LEU A 570 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1230 through 1234
      removed outlier: 5.565A  pdb=" N   ILE A1230 " --> pdb=" O   ASP A1214 " (cutoff:3.500A)
      removed outlier: 4.911A  pdb=" N   LEU A1215 " --> pdb=" O   GLU A1264 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   GLU A1264 " --> pdb=" O   LEU A1215 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   ALA A1217 " --> pdb=" O   ASN A1262 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   ASN A1262 " --> pdb=" O   ALA A1217 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1240 through 1241
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1286 through 1289
      removed outlier: 3.636A  pdb=" N   ILE A1289 " --> pdb=" O   LEU A1368 " (cutoff:3.500A)

    515 hydrogen bonds defined for protein.
    1509 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: 2.90

  Time building geometry restraints manager: 2.69 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1283
        1.31 -     1.44: 2064
        1.44 -     1.56: 4571
        1.56 -     1.68: 0
        1.68 -     1.81: 50
  Bond restraints: 7968
  Sorted by residual:
  bond pdb=" C12 VX8 A1501 "
       pdb=" N2  VX8 A1501 "
    ideal  model  delta    sigma   weight residual
    1.359  1.468 -0.109 2.00e-02 2.50e+03 2.96e+01
  bond pdb=" C11 VX8 A1501 "
       pdb=" N2  VX8 A1501 "
    ideal  model  delta    sigma   weight residual
    1.397  1.467 -0.070 2.00e-02 2.50e+03 1.23e+01
  bond pdb=" C3  VX8 A1501 "
       pdb=" C4  VX8 A1501 "
    ideal  model  delta    sigma   weight residual
    1.482  1.548 -0.066 2.00e-02 2.50e+03 1.10e+01
  bond pdb=" C13 VX8 A1501 "
       pdb=" C14 VX8 A1501 "
    ideal  model  delta    sigma   weight residual
    1.494  1.544 -0.050 2.00e-02 2.50e+03 6.19e+00
  bond pdb=" C16 VX8 A1501 "
       pdb=" O5  VX8 A1501 "
    ideal  model  delta    sigma   weight residual
    1.368  1.416 -0.048 2.00e-02 2.50e+03 5.88e+00
  ... (remaining 7963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.42: 10848
        4.42 -     8.85: 26
        8.85 -    13.27: 2
       13.27 -    17.69: 0
       17.69 -    22.11: 1
  Bond angle restraints: 10877
  Sorted by residual:
  angle pdb=" C14 VX8 A1501 "
        pdb=" C13 VX8 A1501 "
        pdb=" C22 VX8 A1501 "
      ideal   model   delta    sigma   weight residual
     117.72  139.83  -22.11 3.00e+00 1.11e-01 5.43e+01
  angle pdb=" C11 VX8 A1501 "
        pdb=" N2  VX8 A1501 "
        pdb=" C12 VX8 A1501 "
      ideal   model   delta    sigma   weight residual
     127.44  115.04   12.40 3.00e+00 1.11e-01 1.71e+01
  angle pdb=" N   ARG A 104 "
        pdb=" CA  ARG A 104 "
        pdb=" C   ARG A 104 "
      ideal   model   delta    sigma   weight residual
     114.31  109.71    4.60 1.29e+00 6.01e-01 1.27e+01
  angle pdb=" C12 VX8 A1501 "
        pdb=" C13 VX8 A1501 "
        pdb=" C14 VX8 A1501 "
      ideal   model   delta    sigma   weight residual
     117.71  107.49   10.22 3.00e+00 1.11e-01 1.16e+01
  angle pdb=" N   VAL A 956 "
        pdb=" CA  VAL A 956 "
        pdb=" C   VAL A 956 "
      ideal   model   delta    sigma   weight residual
     112.90  109.82    3.08 9.60e-01 1.09e+00 1.03e+01
  ... (remaining 10872 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.27: 4570
       30.27 -    60.54: 94
       60.54 -    90.81: 7
       90.81 -   121.08: 3
      121.08 -   151.35: 3
  Dihedral angle restraints: 4677
    sinusoidal: 1341
      harmonic: 3336
  Sorted by residual:
  dihedral pdb=" C12 VX8 A1501 "
           pdb=" C13 VX8 A1501 "
           pdb=" C21 VX8 A1501 "
           pdb=" C22 VX8 A1501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     253.58  102.23  151.35     1      3.00e+01 1.11e-03 2.00e+01
  dihedral pdb=" C16 VX8 A1501 "
           pdb=" C20 VX8 A1501 "
           pdb=" O5  VX8 A1501 "
           pdb=" F2  VX8 A1501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     236.98  101.86  135.12     1      3.00e+01 1.11e-03 1.82e+01
  dihedral pdb=" C17 VX8 A1501 "
           pdb=" C20 VX8 A1501 "
           pdb=" O4  VX8 A1501 "
           pdb=" F2  VX8 A1501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     122.94 -101.99 -135.07     1      3.00e+01 1.11e-03 1.82e+01
  ... (remaining 4674 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 1326
       0.122 -    0.244: 6
       0.244 -    0.366: 0
       0.366 -    0.488: 0
       0.488 -    0.610: 1
  Chirality restraints: 1333
  Sorted by residual:
  chirality pdb=" C13 VX8 A1501 "
            pdb=" C12 VX8 A1501 "
            pdb=" C14 VX8 A1501 "
            pdb=" C22 VX8 A1501 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       1.48    0.87    0.61 2.00e-01 2.50e+01 9.30e+00
  chirality pdb=" CA  HIS A 139 "
            pdb=" N   HIS A 139 "
            pdb=" C   HIS A 139 "
            pdb=" CB  HIS A 139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 5.03e-01
  chirality pdb=" CA  ILE A1289 "
            pdb=" N   ILE A1289 "
            pdb=" C   ILE A1289 "
            pdb=" CB  ILE A1289 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.97e-01
  ... (remaining 1330 not shown)

  Planarity restraints: 1386
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 286 "   -0.009 2.00e-02 2.50e+03   1.72e-02 2.97e+00
        pdb=" C   GLU A 286 "    0.030 2.00e-02 2.50e+03
        pdb=" O   GLU A 286 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ASN A 287 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 350 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" C   VAL A 350 "    0.028 2.00e-02 2.50e+03
        pdb=" O   VAL A 350 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   THR A 351 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 959 "   -0.022 5.00e-02 4.00e+02   3.40e-02 1.85e+00
        pdb=" N   PRO A 960 "    0.059 5.00e-02 4.00e+02
        pdb=" CA  PRO A 960 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 960 "   -0.019 5.00e-02 4.00e+02
  ... (remaining 1383 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1350
        2.76 -     3.29: 8013
        3.29 -     3.83: 12496
        3.83 -     4.36: 13030
        4.36 -     4.90: 22783
  Nonbonded interactions: 57672
  Sorted by model distance:
  nonbonded pdb=" O   ILE A1015 "
            pdb=" OG1 THR A1019 "
     model   vdw
     2.223 3.040
  nonbonded pdb=" NH2 ARG A 153 "
            pdb=" OD2 ASP A 192 "
     model   vdw
     2.243 3.120
  nonbonded pdb=" O   LEU A 850 "
            pdb=" OG1 THR A 854 "
     model   vdw
     2.312 3.040
  nonbonded pdb=" OG  SER A 313 "
            pdb=" NH1 ARG A 347 "
     model   vdw
     2.314 3.120
  nonbonded pdb=" O   PRO A  67 "
            pdb=" NE2 GLN A 372 "
     model   vdw
     2.325 3.120
  ... (remaining 57667 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             2.490
  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:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     22.510
  Find NCS groups from input model:        0.090
  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:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7310
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   0.109   7968  Z= 0.284
  Angle     :  0.799  22.113  10877  Z= 0.456
  Chirality :  0.045   0.610   1333
  Planarity :  0.003   0.034   1386
  Dihedral  : 14.298 151.349   2509
  Min Nonbonded Distance : 2.223

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.68 %
    Favored  : 99.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.10 (0.24), residues: 1120
  helix: -0.49 (0.19), residues: 680
  sheet: -4.59 (0.46), residues: 49
  loop : -2.48 (0.29), residues: 391

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A  19 
 HIS   0.003   0.001   HIS A 147 
 PHE   0.019   0.002   PHE A 224 
 TYR   0.017   0.002   TYR A1092 
 ARG   0.005   0.001   ARG A1158 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.885 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  128 CYS cc_start: 0.6869 (m) cc_final: 0.6626 (t)
REVERT: A  129 LEU cc_start: 0.8837 (mm) cc_final: 0.8456 (tt)
REVERT: A  265 MET cc_start: 0.8656 (tmm) cc_final: 0.8399 (tmm)
REVERT: A 1164 PHE cc_start: 0.7750 (m-80) cc_final: 0.7513 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 111
  average time/residue: 0.1749
  time to fit residues: 27.9574
Evaluate side-chains
  79 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:   20.0000
   chunk 86 optimal weight:    0.7980
   chunk 47 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0980
   chunk 46 optimal weight:    2.9990
   chunk 89 optimal weight:    0.9990
   chunk 34 optimal weight:    0.5980
   chunk 54 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   chunk 103 optimal weight:   10.0000
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 270 GLN
A 949 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.119659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.108571 restraints weight = 21305.217|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.110754 restraints weight = 11184.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.112038 restraints weight = 6837.031|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7432
moved from start:          0.1462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7968  Z= 0.164
  Angle     :  0.563   7.312  10877  Z= 0.294
  Chirality :  0.040   0.152   1333
  Planarity :  0.004   0.066   1386
  Dihedral  : 10.901 147.087   1235
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 5.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.18 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  :  7.77 %
    Favored  : 91.39 %
  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: -0.62 (0.25), residues: 1120
  helix:  0.72 (0.20), residues: 707
  sheet: -4.20 (0.50), residues: 49
  loop : -2.08 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  79 
 HIS   0.009   0.001   HIS A 199 
 PHE   0.019   0.001   PHE A 224 
 TYR   0.013   0.001   TYR A 161 
 ARG   0.004   0.001   ARG A  25 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.781 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7899 (m-30) cc_final: 0.7538 (t0)
REVERT: A  129 LEU cc_start: 0.8957 (mm) cc_final: 0.8420 (tt)
REVERT: A 1137 MET cc_start: 0.7946 (tpp) cc_final: 0.7679 (tpp)
  outliers start: 5
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1582
  time to fit residues: 25.1253
Evaluate side-chains
  90 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  878 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 84 optimal weight:    0.9990
   chunk 113 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 79 optimal weight:    2.9990
   chunk 42 optimal weight:    0.3980
   chunk 6 optimal weight:    5.9990
   chunk 16 optimal weight:    5.9990
   chunk 106 optimal weight:    5.9990
   chunk 52 optimal weight:   20.0000
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 HIS ** 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 = 0.3862 r_free = 0.3862 target = 0.118794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.107714 restraints weight = 21736.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.109811 restraints weight = 11735.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.111053 restraints weight = 7383.416|
|-----------------------------------------------------------------------------|
r_work (final): 0.3731
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.1900

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7968  Z= 0.179
  Angle     :  0.524   6.704  10877  Z= 0.273
  Chirality :  0.040   0.194   1333
  Planarity :  0.003   0.052   1386
  Dihedral  : 10.873 147.149   1235
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 6.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 12.16 %
    Favored  : 85.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.18 (0.26), residues: 1120
  helix:  1.05 (0.20), residues: 719
  sheet: -4.03 (0.55), residues: 44
  loop : -2.00 (0.31), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  79 
 HIS   0.007   0.001   HIS A 199 
 PHE   0.013   0.001   PHE A 131 
 TYR   0.016   0.001   TYR A  89 
 ARG   0.002   0.000   ARG A1158 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7938 (m-30) cc_final: 0.7471 (t0)
  outliers start: 15
  outliers final: 9
  residues processed: 102
  average time/residue: 0.1651
  time to fit residues: 24.7033
Evaluate side-chains
  96 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 87
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1115 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 76 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 96 optimal weight:    3.9990
   chunk 16 optimal weight:    5.9990
   chunk 37 optimal weight:   20.0000
   chunk 86 optimal weight:    0.7980
   chunk 63 optimal weight:    0.8980
   chunk 21 optimal weight:    6.9990
   chunk 41 optimal weight:   20.0000
   chunk 113 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 HIS ** 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 = 0.3867 r_free = 0.3867 target = 0.119237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.108084 restraints weight = 21597.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.110211 restraints weight = 11690.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.111434 restraints weight = 7300.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
moved from start:          0.2177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7968  Z= 0.174
  Angle     :  0.516   6.612  10877  Z= 0.267
  Chirality :  0.040   0.187   1333
  Planarity :  0.003   0.046   1386
  Dihedral  : 10.787 146.782   1235
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 15.71 %
    Favored  : 81.42 %
  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:  0.02 (0.26), residues: 1120
  helix:  1.16 (0.20), residues: 727
  sheet: -3.92 (0.57), residues: 44
  loop : -1.91 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.021   0.001   PHE A1164 
 TYR   0.028   0.001   TYR A  89 
 ARG   0.002   0.000   ARG A 851 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 89
  time to evaluate  : 0.919 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7927 (m-30) cc_final: 0.7503 (t0)
REVERT: A   92 GLU cc_start: 0.8562 (mm-30) cc_final: 0.8317 (mm-30)
REVERT: A  243 MET cc_start: 0.6368 (mmp) cc_final: 0.5656 (mmp)
REVERT: A 1046 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7196 (mt-10)
  outliers start: 17
  outliers final: 11
  residues processed: 101
  average time/residue: 0.1581
  time to fit residues: 23.8041
Evaluate side-chains
  97 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.812 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1169 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 84 optimal weight:    0.8980
   chunk 91 optimal weight:   20.0000
   chunk 61 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 60 optimal weight:    4.9990
   chunk 97 optimal weight:    6.9990
   chunk 15 optimal weight:    6.9990
   chunk 65 optimal weight:    0.0040
   chunk 110 optimal weight:   30.0000
   overall best weight:    1.1594

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS
A 290 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.119439 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.108349 restraints weight = 21221.499|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.110460 restraints weight = 11550.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.111683 restraints weight = 7217.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7457
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7968  Z= 0.163
  Angle     :  0.518   7.767  10877  Z= 0.263
  Chirality :  0.039   0.174   1333
  Planarity :  0.003   0.043   1386
  Dihedral  : 10.772 146.258   1235
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 16.39 %
    Favored  : 80.74 %
  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:  0.27 (0.26), residues: 1120
  helix:  1.31 (0.20), residues: 730
  sheet: -3.78 (0.61), residues: 44
  loop : -1.74 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 199 
 PHE   0.011   0.001   PHE A1107 
 TYR   0.036   0.002   TYR A 247 
 ARG   0.002   0.000   ARG A 851 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.795 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7862 (m-30) cc_final: 0.7472 (t0)
REVERT: A   92 GLU cc_start: 0.8519 (mm-30) cc_final: 0.8278 (mm-30)
REVERT: A 1046 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7208 (mt-10)
  outliers start: 17
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1551
  time to fit residues: 24.0308
Evaluate side-chains
  101 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  995 ILE
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1112 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 53 optimal weight:   20.0000
   chunk 50 optimal weight:   20.0000
   chunk 92 optimal weight:   30.0000
   chunk 20 optimal weight:    0.9980
   chunk 39 optimal weight:   20.0000
   chunk 8 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 101 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0040
   chunk 6 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    1.1396

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.119365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.108023 restraints weight = 21474.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.110169 restraints weight = 11473.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.111613 restraints weight = 7145.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7451
moved from start:          0.2649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7968  Z= 0.163
  Angle     :  0.529   7.933  10877  Z= 0.265
  Chirality :  0.040   0.193   1333
  Planarity :  0.003   0.041   1386
  Dihedral  : 10.700 146.650   1235
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 18.07 %
    Favored  : 79.39 %
  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:  0.43 (0.26), residues: 1120
  helix:  1.42 (0.20), residues: 731
  sheet: -3.77 (0.60), residues: 44
  loop : -1.63 (0.33), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  79 
 HIS   0.004   0.001   HIS A 199 
 PHE   0.011   0.001   PHE A1107 
 TYR   0.024   0.001   TYR A  89 
 ARG   0.002   0.000   ARG A 851 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 91
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7919 (m-30) cc_final: 0.7496 (t0)
REVERT: A   92 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8332 (mm-30)
REVERT: A 1046 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7166 (mt-10)
  outliers start: 15
  outliers final: 10
  residues processed: 104
  average time/residue: 0.1733
  time to fit residues: 26.4346
Evaluate side-chains
  99 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1115 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 106 optimal weight:    9.9990
   chunk 64 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 110 optimal weight:   40.0000
   chunk 54 optimal weight:    0.9990
   chunk 90 optimal weight:   20.0000
   chunk 19 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 75 optimal weight:    0.0470
   chunk 22 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0060
   overall best weight:    0.5896

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

Flipped N/Q/H residues before XYZ refinement:
A 146 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.120263 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.108733 restraints weight = 21538.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.110905 restraints weight = 11492.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.112350 restraints weight = 7123.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3755
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
moved from start:          0.2956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   7968  Z= 0.135
  Angle     :  0.503   8.061  10877  Z= 0.252
  Chirality :  0.039   0.151   1333
  Planarity :  0.003   0.038   1386
  Dihedral  : 10.556 145.935   1235
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 19.09 %
    Favored  : 78.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (0.27), residues: 1120
  helix:  1.59 (0.20), residues: 738
  sheet: -3.89 (0.68), residues: 36
  loop : -1.45 (0.33), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A 199 
 PHE   0.011   0.001   PHE A1107 
 TYR   0.022   0.001   TYR A  89 
 ARG   0.002   0.000   ARG A 248 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.917 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7962 (m-30) cc_final: 0.7514 (t0)
REVERT: A   92 GLU cc_start: 0.8513 (mm-30) cc_final: 0.8225 (mm-30)
REVERT: A 1046 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.7133 (mt-10)
  outliers start: 12
  outliers final: 10
  residues processed: 105
  average time/residue: 0.1657
  time to fit residues: 25.4217
Evaluate side-chains
  100 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  249 ASP
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue 1046 GLU
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1115 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 52 optimal weight:    0.9990
   chunk 66 optimal weight:    7.9990
   chunk 51 optimal weight:    7.9990
   chunk 4 optimal weight:    6.9990
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    5.9990
   chunk 57 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 77 optimal weight:    4.9990
   chunk 47 optimal weight:    9.9990
   overall best weight:    3.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 HIS ** 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 = 0.3804 r_free = 0.3804 target = 0.114978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.103456 restraints weight = 22201.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.105482 restraints weight = 12381.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.106856 restraints weight = 7912.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3669
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   7968  Z= 0.333
  Angle     :  0.659   8.624  10877  Z= 0.338
  Chirality :  0.044   0.157   1333
  Planarity :  0.004   0.045   1386
  Dihedral  : 10.867 145.593   1235
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.52 %
    Favored  : 93.48 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 19.93 %
    Favored  : 77.20 %
  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: -0.02 (0.26), residues: 1120
  helix:  1.10 (0.20), residues: 728
  sheet: -3.41 (0.56), residues: 62
  loop : -1.79 (0.33), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  79 
 HIS   0.006   0.001   HIS A 199 
 PHE   0.014   0.002   PHE A1111 
 TYR   0.017   0.002   TYR A  89 
 ARG   0.004   0.001   ARG A  74 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 88
  time to evaluate  : 0.851 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.8061 (m-30) cc_final: 0.7628 (t0)
  outliers start: 17
  outliers final: 12
  residues processed: 101
  average time/residue: 0.1475
  time to fit residues: 22.6079
Evaluate side-chains
  98 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.837 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  878 LEU
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue  995 ILE
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1169 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 35 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 19 optimal weight:    0.0770
   chunk 58 optimal weight:    8.9990
   chunk 34 optimal weight:    0.9990
   chunk 96 optimal weight:   20.0000
   chunk 33 optimal weight:    0.9980
   chunk 1 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 HIS ** 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 = 0.3864 r_free = 0.3864 target = 0.118965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.107367 restraints weight = 21789.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3708 r_free = 0.3708 target = 0.109464 restraints weight = 11678.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.110985 restraints weight = 7317.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7445
moved from start:          0.3030

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   7968  Z= 0.146
  Angle     :  0.569   9.510  10877  Z= 0.278
  Chirality :  0.039   0.199   1333
  Planarity :  0.003   0.038   1386
  Dihedral  : 10.608 146.007   1235
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 21.96 %
    Favored  : 75.84 %
  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:  0.64 (0.26), residues: 1120
  helix:  1.54 (0.20), residues: 729
  sheet: -3.87 (0.65), residues: 43
  loop : -1.42 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A 199 
 PHE   0.013   0.001   PHE A1111 
 TYR   0.020   0.001   TYR A  89 
 ARG   0.004   0.000   ARG A 248 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.7966 (m-30) cc_final: 0.7534 (t0)
REVERT: A  998 LEU cc_start: 0.8534 (tt) cc_final: 0.8288 (tt)
  outliers start: 13
  outliers final: 12
  residues processed: 98
  average time/residue: 0.1523
  time to fit residues: 22.7037
Evaluate side-chains
  98 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 86
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1145 TRP
Chi-restraints excluded: chain A residue 1169 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 106 optimal weight:    8.9990
   chunk 100 optimal weight:   20.0000
   chunk 25 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    7.9990
   chunk 29 optimal weight:    4.9990
   chunk 37 optimal weight:   20.0000
   chunk 108 optimal weight:    9.9990
   chunk 94 optimal weight:   10.0000
   chunk 2 optimal weight:    0.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 147 HIS ** 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 = 0.3818 r_free = 0.3818 target = 0.116005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.104249 restraints weight = 21826.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.106309 restraints weight = 11894.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.107505 restraints weight = 7558.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7535
moved from start:          0.3031

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7968  Z= 0.252
  Angle     :  0.622   8.584  10877  Z= 0.309
  Chirality :  0.043   0.330   1333
  Planarity :  0.003   0.043   1386
  Dihedral  : 10.721 145.361   1235
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.71 %
    Favored  : 94.29 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 21.45 %
    Favored  : 76.01 %
  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:  0.35 (0.26), residues: 1120
  helix:  1.38 (0.20), residues: 727
  sheet: -3.40 (0.59), residues: 61
  loop : -1.60 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  79 
 HIS   0.005   0.001   HIS A 199 
 PHE   0.015   0.001   PHE A 224 
 TYR   0.029   0.002   TYR A  89 
 ARG   0.003   0.001   ARG A  74 

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

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

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2240 Ramachandran restraints generated.
    1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.856 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 ASP cc_start: 0.8053 (m-30) cc_final: 0.7645 (t0)
  outliers start: 15
  outliers final: 14
  residues processed: 95
  average time/residue: 0.1460
  time to fit residues: 21.0534
Evaluate side-chains
  98 residues out of total 995 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 84
  time to evaluate  : 0.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   23 ILE
Chi-restraints excluded: chain A residue   40 ILE
Chi-restraints excluded: chain A residue  122 TYR
Chi-restraints excluded: chain A residue  128 CYS
Chi-restraints excluded: chain A residue  240 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  333 LEU
Chi-restraints excluded: chain A residue  348 MET
Chi-restraints excluded: chain A residue  351 THR
Chi-restraints excluded: chain A residue  925 THR
Chi-restraints excluded: chain A residue 1112 ILE
Chi-restraints excluded: chain A residue 1115 THR
Chi-restraints excluded: chain A residue 1145 TRP
Chi-restraints excluded: chain A residue 1169 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 106 optimal weight:    1.9990
   chunk 20 optimal weight:    3.9990
   chunk 91 optimal weight:   20.0000
   chunk 24 optimal weight:    0.6980
   chunk 96 optimal weight:    5.9990
   chunk 73 optimal weight:    0.9990
   chunk 71 optimal weight:    0.0870
   chunk 88 optimal weight:    0.8980
   chunk 15 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7160

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

Flipped N/Q/H residues before XYZ refinement:
** A  98 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 = 0.3863 r_free = 0.3863 target = 0.119053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.107321 restraints weight = 21479.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.109469 restraints weight = 11435.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.110760 restraints weight = 7150.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7450
moved from start:          0.3194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   7968  Z= 0.145
  Angle     :  0.565   9.352  10877  Z= 0.276
  Chirality :  0.040   0.390   1333
  Planarity :  0.003   0.039   1386
  Dihedral  : 10.565 145.973   1235
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 21.45 %
    Favored  : 75.84 %
  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:  0.76 (0.27), residues: 1120
  helix:  1.64 (0.20), residues: 730
  sheet: -3.91 (0.67), residues: 43
  loop : -1.37 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A  79 
 HIS   0.003   0.001   HIS A 199 
 PHE   0.012   0.001   PHE A1111 
 TYR   0.027   0.001   TYR A  89 
 ARG   0.003   0.000   ARG A 248 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2106.85 seconds
wall clock time: 38 minutes 35.97 seconds (2315.97 seconds total)