Starting phenix.real_space_refine
on Fri Sep 19 07:13:41 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ayc_43985/09_2025/9ayc_43985.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ayc_43985/09_2025/9ayc_43985.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.23
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ayc_43985/09_2025/9ayc_43985.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ayc_43985/09_2025/9ayc_43985.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ayc_43985/09_2025/9ayc_43985.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ayc_43985/09_2025/9ayc_43985.map"
  }
  resolution = 3.23
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
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: 6
    Type Number    sf(0)   Gaussians
     P       4      5.49       5
     S      54      5.16       5
     C    7599      2.51       5
     N    1983      2.21       5
     O    2136      1.98       5
     H   11947      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 23723
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 23723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1481, 23723
          Classifications: {'peptide': 1481}
          Link IDs: {'PCIS': 2, 'PTRANS': 41, 'TRANS': 1437}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 3, 'TPO:plan-1': 1}
          Unresolved non-hydrogen planarities: 25
  Time building chain proxies: 4.30, per 1000 atoms: 0.18
  Number of scatterers: 23723
  At special positions: 0
  Unit cell: (88.776, 133.986, 152.892, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      54     16.00
     P       4     15.00
     O    2136      8.00
     N    1983      7.00
     C    7599      6.00
     H   11947      1.00
    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: 2.24
  Conformation dependent library (CDL) restraints added in 677.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2800

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 7 sheets defined
      72.2% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.72
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2 through 13
      removed outlier: 3.706A  pdb=" N   CYS A  10 " --> pdb=" O   VAL A   6 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   LYS A  11 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   LEU A  12 " --> pdb=" O   TRP A   8 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   CYS A  13 " --> pdb=" O   ALA A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 36
    Processing helix  chain 'A' and resid 36 through 59
    Processing helix  chain 'A' and resid 69 through 92
      removed outlier: 3.727A  pdb=" N   VAL A  73 " --> pdb=" O   ASN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 99
    Processing helix  chain 'A' and resid 100 through 128
      removed outlier: 3.631A  pdb=" N   VAL A 104 " --> pdb=" O   ASN A 100 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   PHE A 115 " --> pdb=" O   MET A 111 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   VAL A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   TRP A 122 " --> pdb=" O   LEU A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 132 through 161
    Processing helix  chain 'A' and resid 165 through 189
    Processing helix  chain 'A' and resid 196 through 204
      removed outlier: 3.609A  pdb=" N   HIS A 199 " --> pdb=" O   PRO A 196 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   ILE A 200 " --> pdb=" O   HIS A 197 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   THR A 203 " --> pdb=" O   ILE A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 216 through 223
    Processing helix  chain 'A' and resid 225 through 236
      removed outlier: 4.551A  pdb=" N   LEU A 229 " --> pdb=" O   TRP A 225 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 243
    Processing helix  chain 'A' and resid 247 through 250
    Processing helix  chain 'A' and resid 251 through 270
    Processing helix  chain 'A' and resid 274 through 283
    Processing helix  chain 'A' and resid 284 through 302
    Processing helix  chain 'A' and resid 303 through 327
    Processing helix  chain 'A' and resid 342 through 391
      removed outlier: 3.585A  pdb=" N   PHE A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 353 " --> pdb=" O   ALA A 349 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   VAL A 391 " --> pdb=" O   GLN A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 400
    Processing helix  chain 'A' and resid 401 through 411
      removed outlier: 3.709A  pdb=" N   MET A 409 " --> pdb=" O   ILE A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 423
      removed outlier: 3.813A  pdb=" N   GLN A 421 " --> pdb=" O   GLN A 417 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TRP A 422 " --> pdb=" O   ASP A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 445
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 447 through 493
      removed outlier: 4.097A  pdb=" N   GLY A 451 " --> pdb=" O   SER A 447 " (cutoff:3.500A)
      Proline residue:  A 460  - end of helix
    Processing helix  chain 'A' and resid 493 through 500
    Processing helix  chain 'A' and resid 502 through 555
      removed outlier: 3.544A  pdb=" N   TYR A 506 " --> pdb=" O   TRP A 502 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   LEU A 519 " --> pdb=" O   ASN A 515 " (cutoff:3.500A)
      removed outlier: 4.610A  pdb=" N   LYS A 520 " --> pdb=" O   ASN A 516 " (cutoff:3.500A)
      Proline residue:  A 540  - end of helix
      removed outlier: 3.886A  pdb=" N   SER A 544 " --> pdb=" O   PRO A 540 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   TYR A 553 " --> pdb=" O   ALA A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 563
    Processing helix  chain 'A' and resid 564 through 603
      removed outlier: 4.086A  pdb=" N   PHE A 576 " --> pdb=" O   ASN A 572 " (cutoff:3.500A)
      Proline residue:  A 577  - end of helix
      removed outlier: 3.984A  pdb=" N   ILE A 581 " --> pdb=" O   PRO A 577 " (cutoff:3.500A)
      Proline residue:  A 582  - end of helix
    Processing helix  chain 'A' and resid 608 through 612
      removed outlier: 4.499A  pdb=" N   VAL A 612 " --> pdb=" O   PRO A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 668 through 677
    Processing helix  chain 'A' and resid 706 through 713
    Processing helix  chain 'A' and resid 718 through 729
    Processing helix  chain 'A' and resid 731 through 738
    Processing helix  chain 'A' and resid 740 through 744
    Processing helix  chain 'A' and resid 754 through 770
      removed outlier: 3.518A  pdb=" N   ALA A 766 " --> pdb=" O   SER A 762 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ARG A 770 " --> pdb=" O   ALA A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 778 through 783
      removed outlier: 3.685A  pdb=" N   ALA A 781 " --> pdb=" O   ASP A 778 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ALA A 782 " --> pdb=" O   PRO A 779 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 784 through 795
    Processing helix  chain 'A' and resid 800 through 805
      removed outlier: 3.554A  pdb=" N   HIS A 803 " --> pdb=" O   GLY A 800 " (cutoff:3.500A)
      removed outlier: 4.669A  pdb=" N   THR A 804 " --> pdb=" O   LEU A 801 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 813 through 820
      removed outlier: 3.739A  pdb=" N   ILE A 819 " --> pdb=" O   SER A 815 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 843
    Processing helix  chain 'A' and resid 846 through 856
      removed outlier: 3.728A  pdb=" N   LYS A 850 " --> pdb=" O   SER A 846 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   LEU A 852 " --> pdb=" O   LEU A 848 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   TYR A 855 " --> pdb=" O   LEU A 851 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLY A 856 " --> pdb=" O   LEU A 852 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 883 through 889
    Processing helix  chain 'A' and resid 919 through 926
    Processing helix  chain 'A' and resid 935 through 946
      removed outlier: 3.872A  pdb=" N   TYR A 939 " --> pdb=" O   LYS A 935 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 947 through 983
    Processing helix  chain 'A' and resid 987 through 1016
    Processing helix  chain 'A' and resid 1017 through 1036
    Processing helix  chain 'A' and resid 1037 through 1044
      removed outlier: 3.779A  pdb=" N   PHE A1041 " --> pdb=" O   PRO A1037 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1063
      removed outlier: 3.565A  pdb=" N   ASP A1056 " --> pdb=" O   ARG A1052 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   ILE A1057 " --> pdb=" O   PHE A1053 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1063 through 1089
    Processing helix  chain 'A' and resid 1092 through 1138
      Proline residue:  A1098  - end of helix
      removed outlier: 3.925A  pdb=" N   SER A1126 " --> pdb=" O   SER A1122 " (cutoff:3.500A)
      Proline residue:  A1127  - end of helix
      removed outlier: 3.604A  pdb=" N   GLY A1138 " --> pdb=" O   GLU A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1138 through 1146
    Processing helix  chain 'A' and resid 1147 through 1201
      Proline residue:  A1168  - end of helix
      removed outlier: 3.944A  pdb=" N   ASN A1173 " --> pdb=" O   SER A1169 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ARG A1174 " --> pdb=" O   ILE A1170 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   ARG A1179 " --> pdb=" O   TRP A1175 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN A1201 " --> pdb=" O   PHE A1197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1205 through 1218
      removed outlier: 3.533A  pdb=" N   VAL A1209 " --> pdb=" O   THR A1205 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   GLN A1218 " --> pdb=" O   SER A1214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1218 through 1248
      removed outlier: 3.895A  pdb=" N   THR A1222 " --> pdb=" O   GLN A1218 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   VAL A1238 " --> pdb=" O   GLU A1234 " (cutoff:3.500A)
      removed outlier: 4.784A  pdb=" N   SER A1239 " --> pdb=" O   THR A1235 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   VAL A1240 " --> pdb=" O   ASN A1236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1313 through 1320
      removed outlier: 3.955A  pdb=" N   LEU A1317 " --> pdb=" O   SER A1313 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE A1320 " --> pdb=" O   THR A1316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1341 through 1348
      removed outlier: 3.760A  pdb=" N   LYS A1348 " --> pdb=" O   ASP A1344 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1374 through 1385
    Processing helix  chain 'A' and resid 1387 through 1395
      removed outlier: 3.711A  pdb=" N   SER A1395 " --> pdb=" O   VAL A1391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1397 through 1400
      removed outlier: 4.184A  pdb=" N   ASP A1400 " --> pdb=" O   ASP A1397 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1397 through 1400'
    Processing helix  chain 'A' and resid 1404 through 1408
      removed outlier: 3.644A  pdb=" N   GLY A1408 " --> pdb=" O   GLU A1405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1411 through 1426
      removed outlier: 3.610A  pdb=" N   VAL A1426 " --> pdb=" O   ARG A1422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1442 through 1456
      removed outlier: 3.567A  pdb=" N   PHE A1456 " --> pdb=" O   ILE A1452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1467 through 1471
      removed outlier: 3.637A  pdb=" N   THR A1470 " --> pdb=" O   ARG A1467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1490 through 1497
    Processing helix  chain 'A' and resid 1500 through 1509
    Processing helix  chain 'A' and resid 1510 through 1515
      removed outlier: 3.587A  pdb=" N   GLU A1514 " --> pdb=" O   GLY A1510 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 613 through 615
      removed outlier: 6.609A  pdb=" N   THR A 633 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   GLY A 685 " --> pdb=" O   ASP A 631 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   ASP A 631 " --> pdb=" O   GLY A 685 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   ALA A 687 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   GLY A 629 " --> pdb=" O   ALA A 687 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   VAL A 689 " --> pdb=" O   ASN A 627 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   ASN A 627 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
      removed outlier: 5.427A  pdb=" N   ALA A 632 " --> pdb=" O   ASN A 648 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 613 through 615
      removed outlier: 6.609A  pdb=" N   THR A 633 " --> pdb=" O   VAL A 683 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   GLY A 685 " --> pdb=" O   ASP A 631 " (cutoff:3.500A)
      removed outlier: 7.897A  pdb=" N   ASP A 631 " --> pdb=" O   GLY A 685 " (cutoff:3.500A)
      removed outlier: 5.962A  pdb=" N   ALA A 687 " --> pdb=" O   GLY A 629 " (cutoff:3.500A)
      removed outlier: 7.809A  pdb=" N   GLY A 629 " --> pdb=" O   ALA A 687 " (cutoff:3.500A)
      removed outlier: 5.652A  pdb=" N   VAL A 689 " --> pdb=" O   ASN A 627 " (cutoff:3.500A)
      removed outlier: 7.598A  pdb=" N   ASN A 627 " --> pdb=" O   VAL A 689 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 693 through 696
      removed outlier: 6.118A  pdb=" N   TYR A 774 " --> pdb=" O   VAL A 808 " (cutoff:3.500A)
      removed outlier: 6.409A  pdb=" N   THR A 659 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 6.317A  pdb=" N   LEU A 658 " --> pdb=" O   SER A 822 " (cutoff:3.500A)
      removed outlier: 7.747A  pdb=" N   ALA A 824 " --> pdb=" O   LEU A 658 " (cutoff:3.500A)
      removed outlier: 6.351A  pdb=" N   CYS A 660 " --> pdb=" O   ALA A 824 " (cutoff:3.500A)
      removed outlier: 7.186A  pdb=" N   LEU A 826 " --> pdb=" O   CYS A 660 " (cutoff:3.500A)
      removed outlier: 5.873A  pdb=" N   VAL A 662 " --> pdb=" O   LEU A 826 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   ILE A 823 " --> pdb=" O   GLN A 834 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   GLN A 834 " --> pdb=" O   ILE A 823 " (cutoff:3.500A)
      removed outlier: 7.041A  pdb=" N   LEU A 825 " --> pdb=" O   THR A 832 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1287 through 1292
      removed outlier: 6.518A  pdb=" N   THR A1279 " --> pdb=" O   VAL A1288 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LYS A1290 " --> pdb=" O   TYR A1277 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   TYR A1277 " --> pdb=" O   LYS A1290 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE A1292 " --> pdb=" O   ASN A1275 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ASN A1275 " --> pdb=" O   ILE A1292 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   ILE A1272 " --> pdb=" O   ILE A1296 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1287 through 1292
      removed outlier: 6.518A  pdb=" N   THR A1279 " --> pdb=" O   VAL A1288 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   LYS A1290 " --> pdb=" O   TYR A1277 " (cutoff:3.500A)
      removed outlier: 6.312A  pdb=" N   TYR A1277 " --> pdb=" O   LYS A1290 " (cutoff:3.500A)
      removed outlier: 6.377A  pdb=" N   ILE A1292 " --> pdb=" O   ASN A1275 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ASN A1275 " --> pdb=" O   ILE A1292 " (cutoff:3.500A)
      removed outlier: 5.387A  pdb=" N   PHE A1274 " --> pdb=" O   VAL A1331 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   VAL A1331 " --> pdb=" O   PHE A1274 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   ASN A1276 " --> pdb=" O   ASN A1329 " (cutoff:3.500A)
      removed outlier: 5.198A  pdb=" N   ASN A1329 " --> pdb=" O   ASN A1276 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1350 through 1352
      removed outlier: 6.527A  pdb=" N   VAL A1302 " --> pdb=" O   THR A1463 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ALA A1465 " --> pdb=" O   VAL A1302 " (cutoff:3.500A)
      removed outlier: 6.470A  pdb=" N   ILE A1304 " --> pdb=" O   ALA A1465 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   LYS A1301 " --> pdb=" O   ARG A1476 " (cutoff:3.500A)
      removed outlier: 7.278A  pdb=" N   ILE A1478 " --> pdb=" O   LYS A1301 " (cutoff:3.500A)
      removed outlier: 6.269A  pdb=" N   GLY A1303 " --> pdb=" O   ILE A1478 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   LEU A1480 " --> pdb=" O   GLY A1303 " (cutoff:3.500A)
      removed outlier: 6.366A  pdb=" N   VAL A1305 " --> pdb=" O   LEU A1480 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ASP A1489 " --> pdb=" O   ILE A1477 " (cutoff:3.500A)
      removed outlier: 6.761A  pdb=" N   ASP A1481 " --> pdb=" O   VAL A1485 " (cutoff:3.500A)
      removed outlier: 5.377A  pdb=" N   VAL A1485 " --> pdb=" O   ASP A1481 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1361 through 1362

    771 hydrogen bonds defined for protein.
    2244 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: 5.89

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 11925
        1.03 -     1.23: 22
        1.23 -     1.42: 4986
        1.42 -     1.62: 6946
        1.62 -     1.81: 89
  Bond restraints: 23968
  Sorted by residual:
  bond pdb=" CG2 TPO A 911 "
       pdb="HG21 TPO A 911 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.61e+01
  bond pdb=" CG2 TPO A 911 "
       pdb="HG23 TPO A 911 "
    ideal  model  delta    sigma   weight residual
    0.970  1.090 -0.120 2.00e-02 2.50e+03 3.58e+01
  bond pdb=" CG2 TPO A 911 "
       pdb="HG22 TPO A 911 "
    ideal  model  delta    sigma   weight residual
    0.970  1.089 -0.119 2.00e-02 2.50e+03 3.56e+01
  bond pdb=" CB  TPO A 911 "
       pdb=" HB  TPO A 911 "
    ideal  model  delta    sigma   weight residual
    0.970  1.089 -0.119 2.00e-02 2.50e+03 3.53e+01
  bond pdb=" OG1 TPO A 911 "
       pdb=" P   TPO A 911 "
    ideal  model  delta    sigma   weight residual
    1.717  1.612  0.105 2.00e-02 2.50e+03 2.74e+01
  ... (remaining 23963 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 43087
        2.47 -     4.94: 253
        4.94 -     7.41: 22
        7.41 -     9.88: 0
        9.88 -    12.35: 1
  Bond angle restraints: 43363
  Sorted by residual:
  angle pdb=" OG1 TPO A 911 "
        pdb=" P   TPO A 911 "
        pdb=" O1P TPO A 911 "
      ideal   model   delta    sigma   weight residual
     100.43  112.78  -12.35 3.00e+00 1.11e-01 1.70e+01
  angle pdb=" N   ILE A1367 "
        pdb=" CA  ILE A1367 "
        pdb=" C   ILE A1367 "
      ideal   model   delta    sigma   weight residual
     111.62  109.39    2.23 7.90e-01 1.60e+00 7.94e+00
  angle pdb=" N   GLY A1398 "
        pdb=" CA  GLY A1398 "
        pdb=" C   GLY A1398 "
      ideal   model   delta    sigma   weight residual
     111.67  114.21   -2.54 9.20e-01 1.18e+00 7.64e+00
  angle pdb=" C   ASP A1333 "
        pdb=" N   ASN A1334 "
        pdb=" CA  ASN A1334 "
      ideal   model   delta    sigma   weight residual
     122.08  125.47   -3.39 1.47e+00 4.63e-01 5.32e+00
  angle pdb=" O1P TPO A 911 "
        pdb=" P   TPO A 911 "
        pdb=" O2P TPO A 911 "
      ideal   model   delta    sigma   weight residual
     114.94  108.24    6.70 3.00e+00 1.11e-01 4.98e+00
  ... (remaining 43358 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.63: 10198
       17.63 -    35.25: 701
       35.25 -    52.87: 182
       52.87 -    70.50: 113
       70.50 -    88.12: 16
  Dihedral angle restraints: 11210
    sinusoidal: 6056
      harmonic: 5154
  Sorted by residual:
  dihedral pdb=" CA  GLU A 930 "
           pdb=" C   GLU A 930 "
           pdb=" N   GLN A 931 "
           pdb=" CA  GLN A 931 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.78   24.22     0      5.00e+00 4.00e-02 2.35e+01
  dihedral pdb=" CA  GLN A 931 "
           pdb=" C   GLN A 931 "
           pdb=" N   GLY A 932 "
           pdb=" CA  GLY A 932 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.24   18.76     0      5.00e+00 4.00e-02 1.41e+01
  dihedral pdb=" CA  LEU A 189 "
           pdb=" C   LEU A 189 "
           pdb=" N   PRO A 190 "
           pdb=" CA  PRO A 190 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.79  -18.21     0      5.00e+00 4.00e-02 1.33e+01
  ... (remaining 11207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1289
       0.034 -    0.068: 438
       0.068 -    0.101: 104
       0.101 -    0.135: 45
       0.135 -    0.169: 7
  Chirality restraints: 1883
  Sorted by residual:
  chirality pdb=" CA  ILE A 628 "
            pdb=" N   ILE A 628 "
            pdb=" C   ILE A 628 "
            pdb=" CB  ILE A 628 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.15e-01
  chirality pdb=" CA  ILE A 661 "
            pdb=" N   ILE A 661 "
            pdb=" C   ILE A 661 "
            pdb=" CB  ILE A 661 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.83e-01
  chirality pdb=" CA  ILE A 626 "
            pdb=" N   ILE A 626 "
            pdb=" C   ILE A 626 "
            pdb=" CB  ILE A 626 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.19e-01
  ... (remaining 1880 not shown)

  Planarity restraints: 3469
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1126 "   -0.030 5.00e-02 4.00e+02   4.46e-02 3.19e+00
        pdb=" N   PRO A1127 "    0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO A1127 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A1127 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 565 "   -0.027 5.00e-02 4.00e+02   4.01e-02 2.57e+00
        pdb=" N   PRO A 566 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 566 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 566 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 429 "   -0.026 5.00e-02 4.00e+02   3.91e-02 2.45e+00
        pdb=" N   PRO A 430 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 430 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 430 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 3466 not shown)

  Histogram of nonbonded interaction distances:
        1.75 -     2.32: 4906
        2.32 -     2.89: 54539
        2.89 -     3.46: 61060
        3.46 -     4.03: 81233
        4.03 -     4.60: 126402
  Nonbonded interactions: 328140
  Sorted by model distance:
  nonbonded pdb="HH11 ARG A 716 "
            pdb=" O3P SEP A 908 "
     model   vdw
     1.747 2.450
  nonbonded pdb=" HZ3 LYS A 617 "
            pdb=" O1P SEP A 903 "
     model   vdw
     1.752 2.450
  nonbonded pdb=" O   GLN A1070 "
            pdb="HD21 ASN A1074 "
     model   vdw
     1.757 2.450
  nonbonded pdb=" O   ARG A  67 "
            pdb=" HH  TYR A 125 "
     model   vdw
     1.761 2.450
  nonbonded pdb=" H   VAL A 239 "
            pdb=" OD2 ASP A 242 "
     model   vdw
     1.767 2.450
  ... (remaining 328135 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.480
  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:             0.120
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.070
  Set scattering table:                    0.060
  Process input model:                     23.350
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.030
  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:1.390
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.820
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
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   0.105  12021  Z= 0.174
  Angle     :  0.610  12.354  16297  Z= 0.318
  Chirality :  0.039   0.169   1883
  Planarity :  0.004   0.045   2035
  Dihedral  : 11.285  88.124   4375
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 0.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.78 %
    Favored  : 99.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.11 (0.21), residues: 1461
  helix:  0.94 (0.16), residues: 968
  sheet:  0.31 (0.58), residues: 66
  loop :  0.65 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 485 
 TYR   0.014   0.001   TYR A 506 
 PHE   0.013   0.001   PHE A 431 
 TRP   0.015   0.001   TRP A 636 
 HIS   0.006   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (12021)
  covalent geometry    : angle       0.61031 (16297)
  hydrogen bonds       : bond        0.18909 (  764)
  hydrogen bonds       : angle       6.66127 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  217 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.646 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLU cc_start: 0.8737 (tt0) cc_final: 0.8405 (tm-30)
REVERT: A  528 TYR cc_start: 0.7768 (m-80) cc_final: 0.7513 (m-80)
REVERT: A  684 LYS cc_start: 0.9036 (tppt) cc_final: 0.8807 (ttpt)
REVERT: A 1038 MET cc_start: 0.8327 (mmm) cc_final: 0.8110 (mmm)
REVERT: A 1241 GLU cc_start: 0.8844 (tp30) cc_final: 0.8602 (tp30)
REVERT: A 1350 SER cc_start: 0.8954 (t) cc_final: 0.8747 (p)
REVERT: A 1372 GLN cc_start: 0.8965 (tp40) cc_final: 0.8374 (tm-30)
REVERT: A 1376 GLU cc_start: 0.8631 (mp0) cc_final: 0.8323 (mp0)
REVERT: A 1481 ASP cc_start: 0.8470 (t0) cc_final: 0.8197 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.3302
  time to fit residues: 96.0601
Evaluate side-chains
  124 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.661 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    2.9990
   chunk 122 optimal weight:    0.8980
   chunk 91 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  92 ASN
A 106 GLN
A1334 ASN
A1416 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.103349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.073525 restraints weight = 71138.325|
|-----------------------------------------------------------------------------|
r_work (start): 0.3137 rms_B_bonded: 2.71
r_work: 0.3028 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.2257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058  12021  Z= 0.211
  Angle     :  0.548   5.270  16297  Z= 0.308
  Chirality :  0.038   0.145   1883
  Planarity :  0.004   0.043   2035
  Dihedral  :  4.902  73.874   1607
  Min Nonbonded Distance : 2.348

Molprobity Statistics.
  All-atom Clashscore : 2.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  4.98 %
    Favored  : 94.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.21 (0.22), residues: 1461
  helix:  1.90 (0.16), residues: 976
  sheet:  0.33 (0.56), residues: 75
  loop :  0.80 (0.32), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1115 
 TYR   0.018   0.001   TYR A1105 
 PHE   0.013   0.001   PHE A1502 
 TRP   0.008   0.001   TRP A 849 
 HIS   0.008   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00449 (12021)
  covalent geometry    : angle       0.54753 (16297)
  hydrogen bonds       : bond        0.05792 (  764)
  hydrogen bonds       : angle       4.87841 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  132 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 126
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLU cc_start: 0.8903 (tt0) cc_final: 0.8659 (tm-30)
REVERT: A  528 TYR cc_start: 0.7867 (m-80) cc_final: 0.7585 (m-80)
REVERT: A  642 TYR cc_start: 0.6999 (OUTLIER) cc_final: 0.6398 (t80)
REVERT: A  684 LYS cc_start: 0.9052 (tppt) cc_final: 0.8770 (ttpt)
REVERT: A  817 LEU cc_start: 0.9491 (mt) cc_final: 0.9278 (mt)
REVERT: A 1038 MET cc_start: 0.8460 (mmm) cc_final: 0.8060 (mmm)
REVERT: A 1241 GLU cc_start: 0.9121 (tp30) cc_final: 0.8918 (tp30)
REVERT: A 1372 GLN cc_start: 0.9081 (tp40) cc_final: 0.8449 (tm-30)
REVERT: A 1376 GLU cc_start: 0.8888 (mp0) cc_final: 0.8667 (mp0)
  outliers start: 6
  outliers final: 4
  residues processed: 129
  average time/residue: 0.2921
  time to fit residues: 51.4117
Evaluate side-chains
  114 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.465 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue 1096 ILE
Chi-restraints excluded: chain A residue 1187 ILE
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1384 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 123 optimal weight:    0.2980
   chunk 37 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 45 optimal weight:    0.7980
   chunk 132 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 140 optimal weight:   10.0000
   chunk 4 optimal weight:    1.9990
   chunk 89 optimal weight:    9.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
A 854 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.103208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.072710 restraints weight = 71786.493|
|-----------------------------------------------------------------------------|
r_work (start): 0.3121 rms_B_bonded: 2.83
r_work: 0.3007 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2883 rms_B_bonded: 4.98 restraints_weight: 0.2500
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8521
moved from start:          0.2721

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  12021  Z= 0.163
  Angle     :  0.497   6.295  16297  Z= 0.272
  Chirality :  0.037   0.138   1883
  Planarity :  0.003   0.041   2035
  Dihedral  :  4.791  75.965   1607
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 2.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.30 %
    Favored  : 98.70 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  5.84 %
    Favored  : 93.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.39 (0.22), residues: 1461
  helix:  2.07 (0.16), residues: 984
  sheet:  0.16 (0.55), residues: 75
  loop :  0.80 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1115 
 TYR   0.017   0.001   TYR A1105 
 PHE   0.016   0.001   PHE A 576 
 TRP   0.013   0.001   TRP A 849 
 HIS   0.007   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 (12021)
  covalent geometry    : angle       0.49672 (16297)
  hydrogen bonds       : bond        0.05052 (  764)
  hydrogen bonds       : angle       4.51294 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  124 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLU cc_start: 0.8898 (tt0) cc_final: 0.8684 (tm-30)
REVERT: A  642 TYR cc_start: 0.7024 (OUTLIER) cc_final: 0.6502 (t80)
REVERT: A  684 LYS cc_start: 0.9067 (tppt) cc_final: 0.8779 (ttpt)
REVERT: A  817 LEU cc_start: 0.9463 (mt) cc_final: 0.9239 (mt)
REVERT: A 1241 GLU cc_start: 0.9144 (tp30) cc_final: 0.8933 (tp30)
REVERT: A 1372 GLN cc_start: 0.9075 (tp40) cc_final: 0.8729 (tp40)
REVERT: A 1376 GLU cc_start: 0.8942 (mp0) cc_final: 0.8668 (mp0)
  outliers start: 11
  outliers final: 5
  residues processed: 119
  average time/residue: 0.3057
  time to fit residues: 50.4271
Evaluate side-chains
  115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.669 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1384 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 95 optimal weight:    2.9990
   chunk 40 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 123 optimal weight:    4.9990
   chunk 113 optimal weight:    0.9980
   chunk 136 optimal weight:    9.9990
   chunk 83 optimal weight:    0.3980
   chunk 103 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.102494 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.071752 restraints weight = 71745.350|
|-----------------------------------------------------------------------------|
r_work (start): 0.3112 rms_B_bonded: 2.84
r_work: 0.2999 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.96 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.2989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  12021  Z= 0.148
  Angle     :  0.473   6.437  16297  Z= 0.257
  Chirality :  0.036   0.154   1883
  Planarity :  0.003   0.037   2035
  Dihedral  :  4.708  75.827   1607
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.51 %
    Favored  : 98.49 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  :  5.84 %
    Favored  : 92.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.55 (0.22), residues: 1461
  helix:  2.22 (0.16), residues: 986
  sheet:  0.11 (0.56), residues: 75
  loop :  0.78 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1380 
 TYR   0.016   0.001   TYR A1105 
 PHE   0.016   0.001   PHE A 576 
 TRP   0.013   0.001   TRP A 849 
 HIS   0.007   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (12021)
  covalent geometry    : angle       0.47262 (16297)
  hydrogen bonds       : bond        0.04552 (  764)
  hydrogen bonds       : angle       4.31758 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  129 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.670 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLU cc_start: 0.8877 (tt0) cc_final: 0.8676 (tm-30)
REVERT: A  642 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6600 (t80)
REVERT: A  684 LYS cc_start: 0.9067 (tppt) cc_final: 0.8754 (ttpt)
REVERT: A 1241 GLU cc_start: 0.9110 (tp30) cc_final: 0.8894 (tp30)
REVERT: A 1372 GLN cc_start: 0.9084 (tp40) cc_final: 0.8761 (tp40)
REVERT: A 1507 MET cc_start: 0.8292 (tpt) cc_final: 0.7895 (mtp)
  outliers start: 16
  outliers final: 10
  residues processed: 122
  average time/residue: 0.3003
  time to fit residues: 51.9416
Evaluate side-chains
  116 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 105
  time to evaluate  : 0.790 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  931 GLN
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1316 THR
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1480 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 146 optimal weight:    9.9990
   chunk 60 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 131 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 105 optimal weight:    0.5980
   chunk 123 optimal weight:    0.9980
   chunk 83 optimal weight:    0.4980
   chunk 94 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A1354 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.102990 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.072113 restraints weight = 71573.447|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.85
r_work: 0.3013 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.95 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8471
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  12021  Z= 0.123
  Angle     :  0.452   6.122  16297  Z= 0.244
  Chirality :  0.036   0.188   1883
  Planarity :  0.003   0.034   2035
  Dihedral  :  4.638  76.613   1607
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 2.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.64 %
    Favored  : 98.36 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  6.39 %
    Favored  : 92.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.75 (0.22), residues: 1461
  helix:  2.37 (0.16), residues: 989
  sheet:  0.20 (0.58), residues: 75
  loop :  0.88 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1380 
 TYR   0.015   0.001   TYR A1105 
 PHE   0.016   0.001   PHE A 576 
 TRP   0.010   0.001   TRP A1014 
 HIS   0.006   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (12021)
  covalent geometry    : angle       0.45172 (16297)
  hydrogen bonds       : bond        0.04307 (  764)
  hydrogen bonds       : angle       4.19639 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.674 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLU cc_start: 0.8860 (tt0) cc_final: 0.8659 (tm-30)
REVERT: A  642 TYR cc_start: 0.7264 (OUTLIER) cc_final: 0.6735 (t80)
REVERT: A  684 LYS cc_start: 0.9074 (tppt) cc_final: 0.8751 (ttpt)
REVERT: A 1241 GLU cc_start: 0.9127 (tp30) cc_final: 0.8908 (tp30)
REVERT: A 1372 GLN cc_start: 0.9080 (tp40) cc_final: 0.8488 (tm-30)
  outliers start: 11
  outliers final: 8
  residues processed: 116
  average time/residue: 0.2832
  time to fit residues: 46.1951
Evaluate side-chains
  115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  143 THR
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  848 LEU
Chi-restraints excluded: chain A residue  931 GLN
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1480 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 16 optimal weight:    3.9990
   chunk 92 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 114 optimal weight:    1.9990
   chunk 14 optimal weight:    1.9990
   chunk 142 optimal weight:    3.9990
   chunk 129 optimal weight:    4.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 521 ASN
A 854 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.100565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.070359 restraints weight = 72104.899|
|-----------------------------------------------------------------------------|
r_work (start): 0.3073 rms_B_bonded: 2.75
r_work: 0.2964 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2843 rms_B_bonded: 4.88 restraints_weight: 0.2500
r_work (final): 0.2843
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031  12021  Z= 0.224
  Angle     :  0.500   6.478  16297  Z= 0.277
  Chirality :  0.037   0.159   1883
  Planarity :  0.003   0.029   2035
  Dihedral  :  4.680  75.910   1607
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.62 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.66 (0.22), residues: 1461
  helix:  2.31 (0.16), residues: 991
  sheet:  0.09 (0.59), residues: 75
  loop :  0.83 (0.34), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1380 
 TYR   0.020   0.001   TYR A1105 
 PHE   0.018   0.001   PHE A 576 
 TRP   0.011   0.001   TRP A1014 
 HIS   0.008   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 (12021)
  covalent geometry    : angle       0.50038 (16297)
  hydrogen bonds       : bond        0.04619 (  764)
  hydrogen bonds       : angle       4.31681 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  121 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 108
  time to evaluate  : 0.669 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  260 GLU cc_start: 0.8900 (tt0) cc_final: 0.8688 (tm-30)
REVERT: A  642 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.6894 (t80)
REVERT: A  676 MET cc_start: 0.8978 (tpp) cc_final: 0.8691 (mmt)
REVERT: A  684 LYS cc_start: 0.9087 (tppt) cc_final: 0.8778 (ttpt)
REVERT: A  825 LEU cc_start: 0.6941 (mt) cc_final: 0.6558 (tp)
REVERT: A 1241 GLU cc_start: 0.9176 (tp30) cc_final: 0.8968 (tp30)
REVERT: A 1372 GLN cc_start: 0.9078 (tp40) cc_final: 0.8784 (tp40)
REVERT: A 1507 MET cc_start: 0.8272 (tpt) cc_final: 0.7854 (mtp)
  outliers start: 13
  outliers final: 10
  residues processed: 116
  average time/residue: 0.3191
  time to fit residues: 51.8411
Evaluate side-chains
  117 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  854 ASN
Chi-restraints excluded: chain A residue  931 GLN
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1480 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 114 optimal weight:    0.9980
   chunk 74 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9980
   chunk 99 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 79 optimal weight:    0.7980
   chunk 106 optimal weight:    0.9990
   chunk 94 optimal weight:    1.9990
   chunk 55 optimal weight:    0.7980
   chunk 13 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.102040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.071394 restraints weight = 71750.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.79
r_work: 0.2992 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2870 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8533
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12021  Z= 0.135
  Angle     :  0.468   8.092  16297  Z= 0.254
  Chirality :  0.036   0.143   1883
  Planarity :  0.003   0.029   2035
  Dihedral  :  4.652  76.593   1607
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  1.01 %
    Allowed  :  6.62 %
    Favored  : 92.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.79 (0.22), residues: 1461
  helix:  2.41 (0.16), residues: 993
  sheet:  0.13 (0.59), residues: 75
  loop :  0.86 (0.34), residues: 393

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1380 
 TYR   0.016   0.001   TYR A1105 
 PHE   0.016   0.001   PHE A 576 
 TRP   0.010   0.001   TRP A1014 
 HIS   0.006   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00286 (12021)
  covalent geometry    : angle       0.46826 (16297)
  hydrogen bonds       : bond        0.04372 (  764)
  hydrogen bonds       : angle       4.16408 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.694 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 TYR cc_start: 0.7469 (OUTLIER) cc_final: 0.6853 (t80)
REVERT: A  676 MET cc_start: 0.8969 (tpp) cc_final: 0.8690 (mmt)
REVERT: A  684 LYS cc_start: 0.9076 (tppt) cc_final: 0.8750 (ttpt)
REVERT: A 1241 GLU cc_start: 0.9166 (tp30) cc_final: 0.8945 (tp30)
REVERT: A 1372 GLN cc_start: 0.9053 (tp40) cc_final: 0.8764 (tp40)
REVERT: A 1507 MET cc_start: 0.8310 (tpt) cc_final: 0.7874 (mtp)
  outliers start: 13
  outliers final: 10
  residues processed: 111
  average time/residue: 0.2959
  time to fit residues: 46.0319
Evaluate side-chains
  110 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 99
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  931 GLN
Chi-restraints excluded: chain A residue 1006 THR
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1480 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 132 optimal weight:    4.9990
   chunk 117 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 45 optimal weight:    0.3980
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 42 optimal weight:    0.0980
   chunk 55 optimal weight:    1.9990
   chunk 128 optimal weight:    0.6980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.103190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.072770 restraints weight = 71679.245|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.80
r_work: 0.3002 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2880 rms_B_bonded: 4.94 restraints_weight: 0.2500
r_work (final): 0.2880
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  12021  Z= 0.105
  Angle     :  0.444   8.141  16297  Z= 0.237
  Chirality :  0.035   0.141   1883
  Planarity :  0.003   0.030   2035
  Dihedral  :  4.593  77.559   1607
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.17 %
    Favored  : 92.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.05 (0.22), residues: 1461
  helix:  2.59 (0.16), residues: 992
  sheet:  0.32 (0.60), residues: 75
  loop :  0.98 (0.33), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1380 
 TYR   0.013   0.001   TYR A1105 
 PHE   0.009   0.001   PHE A 954 
 TRP   0.009   0.001   TRP A1014 
 HIS   0.005   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 (12021)
  covalent geometry    : angle       0.44390 (16297)
  hydrogen bonds       : bond        0.04066 (  764)
  hydrogen bonds       : angle       4.00929 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  117 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 107
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 TYR cc_start: 0.7499 (OUTLIER) cc_final: 0.6940 (t80)
REVERT: A  676 MET cc_start: 0.8946 (tpp) cc_final: 0.8657 (mmt)
REVERT: A  684 LYS cc_start: 0.9074 (tppt) cc_final: 0.8746 (ttpt)
REVERT: A 1241 GLU cc_start: 0.9148 (tp30) cc_final: 0.8934 (tp30)
REVERT: A 1372 GLN cc_start: 0.9067 (tp40) cc_final: 0.8778 (tp40)
REVERT: A 1472 MET cc_start: 0.8653 (mmm) cc_final: 0.8426 (mmm)
REVERT: A 1507 MET cc_start: 0.8238 (tpt) cc_final: 0.7832 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 113
  average time/residue: 0.2944
  time to fit residues: 46.4625
Evaluate side-chains
  112 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.571 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  931 GLN
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1480 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 72 optimal weight:    5.9990
   chunk 64 optimal weight:    3.9990
   chunk 128 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 1 optimal weight:    0.0970
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.102904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.072577 restraints weight = 71759.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3119 rms_B_bonded: 2.80
r_work: 0.3007 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.91 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8482
moved from start:          0.3701

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12021  Z= 0.118
  Angle     :  0.447   8.671  16297  Z= 0.238
  Chirality :  0.035   0.140   1883
  Planarity :  0.003   0.029   2035
  Dihedral  :  4.574  77.781   1607
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Rotamer:
    Outliers :  0.86 %
    Allowed  :  7.24 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.14 (0.22), residues: 1461
  helix:  2.65 (0.16), residues: 989
  sheet:  0.43 (0.61), residues: 75
  loop :  1.03 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1380 
 TYR   0.014   0.001   TYR A1105 
 PHE   0.020   0.001   PHE A 576 
 TRP   0.009   0.001   TRP A1014 
 HIS   0.006   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 (12021)
  covalent geometry    : angle       0.44673 (16297)
  hydrogen bonds       : bond        0.04018 (  764)
  hydrogen bonds       : angle       3.98096 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  115 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 104
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 TYR cc_start: 0.7466 (OUTLIER) cc_final: 0.6921 (t80)
REVERT: A  676 MET cc_start: 0.8957 (tpp) cc_final: 0.8647 (mmt)
REVERT: A  684 LYS cc_start: 0.9051 (tppt) cc_final: 0.8698 (ttpt)
REVERT: A 1241 GLU cc_start: 0.9131 (tp30) cc_final: 0.8908 (tp30)
REVERT: A 1372 GLN cc_start: 0.9062 (tp40) cc_final: 0.8775 (tp40)
REVERT: A 1472 MET cc_start: 0.8601 (mmm) cc_final: 0.8394 (mmm)
REVERT: A 1507 MET cc_start: 0.8234 (tpt) cc_final: 0.7811 (mtp)
  outliers start: 11
  outliers final: 9
  residues processed: 111
  average time/residue: 0.2901
  time to fit residues: 45.0485
Evaluate side-chains
  114 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 104
  time to evaluate  : 0.709 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  931 GLN
Chi-restraints excluded: chain A residue 1011 ILE
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1480 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 68 optimal weight:    0.0970
   chunk 25 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 137 optimal weight:    3.9990
   chunk 39 optimal weight:    6.9990
   chunk 110 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   chunk 76 optimal weight:    3.9990
   chunk 122 optimal weight:    0.4980
   chunk 102 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 476 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.102300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.071633 restraints weight = 71918.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 2.84
r_work: 0.2998 rms_B_bonded: 3.03 restraints_weight: 0.5000
r_work: 0.2877 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.2877
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.3783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022  12021  Z= 0.139
  Angle     :  0.454   9.060  16297  Z= 0.243
  Chirality :  0.036   0.139   1883
  Planarity :  0.003   0.028   2035
  Dihedral  :  4.589  77.822   1607
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.78 %
    Allowed  :  7.32 %
    Favored  : 91.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.12 (0.22), residues: 1461
  helix:  2.64 (0.16), residues: 989
  sheet:  0.34 (0.62), residues: 74
  loop :  1.04 (0.33), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1380 
 TYR   0.015   0.001   TYR A1105 
 PHE   0.010   0.001   PHE A 954 
 TRP   0.010   0.001   TRP A1014 
 HIS   0.006   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (12021)
  covalent geometry    : angle       0.45413 (16297)
  hydrogen bonds       : bond        0.04071 (  764)
  hydrogen bonds       : angle       3.99906 ( 2244)

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

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

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2922 Ramachandran restraints generated.
    1461 Oldfield, 0 Emsley, 1461 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Residue THR  203 is missing expected H atoms. Skipping.
Residue LEU  204 is missing expected H atoms. Skipping.
Residue THR  205 is missing expected H atoms. Skipping.
Residue LEU  885 is missing expected H atoms. Skipping.
Residue LEU  888 is missing expected H atoms. Skipping.
Residue LYS  890 is missing expected H atoms. Skipping.
Residue LEU  891 is missing expected H atoms. Skipping.
Evaluate side-chains
  113 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.662 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  642 TYR cc_start: 0.7490 (OUTLIER) cc_final: 0.6922 (t80)
REVERT: A  676 MET cc_start: 0.9033 (tpp) cc_final: 0.8718 (mmt)
REVERT: A  684 LYS cc_start: 0.9077 (tppt) cc_final: 0.8744 (ttpt)
REVERT: A 1241 GLU cc_start: 0.9161 (tp30) cc_final: 0.8942 (tp30)
REVERT: A 1372 GLN cc_start: 0.9059 (tp40) cc_final: 0.8460 (tm-30)
REVERT: A 1507 MET cc_start: 0.8213 (tpt) cc_final: 0.7810 (mtp)
  outliers start: 10
  outliers final: 8
  residues processed: 109
  average time/residue: 0.3095
  time to fit residues: 47.3748
Evaluate side-chains
  109 residues out of total 1297 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 100
  time to evaluate  : 0.716 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   19 PHE
Chi-restraints excluded: chain A residue  409 MET
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  642 TYR
Chi-restraints excluded: chain A residue  821 ASP
Chi-restraints excluded: chain A residue  931 GLN
Chi-restraints excluded: chain A residue 1350 SER
Chi-restraints excluded: chain A residue 1384 LEU
Chi-restraints excluded: chain A residue 1480 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 148
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 106 optimal weight:    0.8980
   chunk 2 optimal weight:    0.5980
   chunk 131 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 137 optimal weight:    3.9990
   chunk 108 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 85 optimal weight:    4.9990
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.102686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.072671 restraints weight = 71161.364|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.74
r_work: 0.3013 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.84 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.3810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022  12021  Z= 0.118
  Angle     :  0.445   9.666  16297  Z= 0.238
  Chirality :  0.035   0.141   1883
  Planarity :  0.003   0.029   2035
  Dihedral  :  4.534  78.310   1607
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  7.71 %
    Favored  : 91.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  3.19 (0.22), residues: 1461
  helix:  2.69 (0.16), residues: 990
  sheet:  0.36 (0.62), residues: 74
  loop :  1.06 (0.33), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1380 
 TYR   0.014   0.001   TYR A1105 
 PHE   0.024   0.001   PHE A 576 
 TRP   0.009   0.001   TRP A1014 
 HIS   0.006   0.001   HIS A 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (12021)
  covalent geometry    : angle       0.44547 (16297)
  hydrogen bonds       : bond        0.03990 (  764)
  hydrogen bonds       : angle       3.93565 ( 2244)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6338.12 seconds
wall clock time: 108 minutes 3.95 seconds (6483.95 seconds total)