Starting phenix.real_space_refine
on Sat Dec 28 09:52:19 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jlf_36395/12_2024/8jlf_36395.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jlf_36395/12_2024/8jlf_36395.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.01
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jlf_36395/12_2024/8jlf_36395.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jlf_36395/12_2024/8jlf_36395.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jlf_36395/12_2024/8jlf_36395.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jlf_36395/12_2024/8jlf_36395.cif"
  }
  resolution = 3.01
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.033
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    5283      2.51       5
     N    1360      2.21       5
     O    1487      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib"
  Total number of atoms: 8177
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4674
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 592, 4674
          Classifications: {'peptide': 592}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 576}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3437
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3437
          Classifications: {'peptide': 420}
          Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 411}
    Chain: "E"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 38
          Unusual residues: {'FUC': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.53, per 1000 atoms: 0.68
  Number of scatterers: 8177
  At special positions: 0
  Unit cell: (83, 81.34, 148.57, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1487      8.00
     N    1360      7.00
     C    5283      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
    BETA1-6
      " NAG E   1 " - " FUC E   3 "
       ~> Even though FUC is an alpha isomer, a beta linkage is required...
    NAG-ASN
      " NAG A 801 " - " ASN A 498 "
      " NAG A 802 " - " ASN A 548 "
      " NAG E   1 " - " ASN A 573 "
  Time building additional restraints: 2.28
  Conformation dependent library (CDL) restraints added in 976.5 milliseconds
  

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1866

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 10 sheets defined
      44.1% alpha, 26.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.02
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 160
      removed outlier: 3.505A  pdb=" N   GLU A 153 " --> pdb=" O   ALA A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 183
      removed outlier: 3.663A  pdb=" N   ASP A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 184 through 198
      Proline residue:  A 191  - end of helix
      removed outlier: 4.247A  pdb=" N   LYS A 195 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 230
      removed outlier: 3.634A  pdb=" N   PHE A 220 " --> pdb=" O   MET A 216 " (cutoff:3.500A)
      removed outlier: 4.132A  pdb=" N   ASP A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 250
    Processing helix  chain 'A' and resid 255 through 270
    Processing helix  chain 'A' and resid 271 through 281
    Processing helix  chain 'A' and resid 282 through 284
      No H-bonds generated for 'chain 'A' and resid 282 through 284'
    Processing helix  chain 'A' and resid 285 through 288
      removed outlier: 3.915A  pdb=" N   LYS A 288 " --> pdb=" O   ALA A 285 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 285 through 288'
    Processing helix  chain 'A' and resid 289 through 295
    Processing helix  chain 'A' and resid 297 through 315
      removed outlier: 4.130A  pdb=" N   MET A 301 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.772A  pdb=" N   VAL A 335 " --> pdb=" O   HIS A 331 " (cutoff:3.500A)
      Proline residue:  A 343  - end of helix
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.508A  pdb=" N   PHE A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 366 through 386
      removed outlier: 3.942A  pdb=" N   ALA A 370 " --> pdb=" O   LYS A 366 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 439
      removed outlier: 3.595A  pdb=" N   PHE A 439 " --> pdb=" O   PHE A 435 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 483
      Proline residue:  A 469  - end of helix
    Processing helix  chain 'A' and resid 562 through 564
      No H-bonds generated for 'chain 'A' and resid 562 through 564'
    Processing helix  chain 'A' and resid 592 through 605
      removed outlier: 3.890A  pdb=" N   MET A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 607 through 623
      removed outlier: 4.461A  pdb=" N   GLY A 611 " --> pdb=" O   ALA A 607 " (cutoff:3.500A)
      removed outlier: 5.140A  pdb=" N   ASP A 620 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   LYS A 621 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 642
      removed outlier: 3.760A  pdb=" N   MET A 634 " --> pdb=" O   GLY A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 643 through 645
      No H-bonds generated for 'chain 'A' and resid 643 through 645'
    Processing helix  chain 'A' and resid 647 through 676
      removed outlier: 3.716A  pdb=" N   ILE A 663 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 5.133A  pdb=" N   ALA A 664 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
      removed outlier: 4.519A  pdb=" N   SER A 665 " --> pdb=" O   VAL A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 706
    Processing helix  chain 'A' and resid 712 through 731
    Processing helix  chain 'B' and resid 929 through 933
      removed outlier: 3.790A  pdb=" N   VAL B 933 " --> pdb=" O   ASN B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 958
      removed outlier: 3.727A  pdb=" N   ASN B 957 " --> pdb=" O   SER B 954 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1080 through 1092
    Processing helix  chain 'B' and resid 1210 through 1214
      removed outlier: 3.926A  pdb=" N   VAL B1214 " --> pdb=" O   ILE B1211 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1265 through 1273
    Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 496
      removed outlier: 6.161A  pdb=" N   GLY A 509 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ARG A 491 " --> pdb=" O   GLY A 509 " (cutoff:3.500A)
      removed outlier: 7.013A  pdb=" N   TYR A 511 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
      removed outlier: 7.140A  pdb=" N   GLU A 493 " --> pdb=" O   TYR A 511 " (cutoff:3.500A)
      removed outlier: 7.166A  pdb=" N   ASN A 513 " --> pdb=" O   GLU A 493 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   VAL A 495 " --> pdb=" O   ASN A 513 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567
      removed outlier: 5.920A  pdb=" N   PHE A 546 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 8.590A  pdb=" N   PHE A 545 " --> pdb=" O   LYS A 522 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL A 524 " --> pdb=" O   PHE A 545 " (cutoff:3.500A)
      removed outlier: 8.117A  pdb=" N   ARG A 547 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 6.370A  pdb=" N   PHE A 526 " --> pdb=" O   ARG A 547 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   VAL A 539 " --> pdb=" O   GLY A 518 " (cutoff:3.500A)
      removed outlier: 7.159A  pdb=" N   ARG A 520 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   SER A 541 " --> pdb=" O   ARG A 520 " (cutoff:3.500A)
      removed outlier: 6.865A  pdb=" N   LYS A 522 " --> pdb=" O   SER A 541 " (cutoff:3.500A)
      removed outlier: 5.807A  pdb=" N   PHE A 536 " --> pdb=" O   TYR A 557 " (cutoff:3.500A)
      removed outlier: 5.433A  pdb=" N   THR A 559 " --> pdb=" O   PHE A 536 " (cutoff:3.500A)
      removed outlier: 7.331A  pdb=" N   ASP A 538 " --> pdb=" O   THR A 559 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.661A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   LEU B 879 " --> pdb=" O   LEU B1074 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE B1072 " --> pdb=" O   ILE B 881 " (cutoff:3.500A)
      removed outlier: 10.063A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 12.770A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   TYR B 905 " --> pdb=" O   LYS B 915 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.661A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   LEU B 879 " --> pdb=" O   LEU B1074 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   PHE B1072 " --> pdb=" O   ILE B 881 " (cutoff:3.500A)
      removed outlier: 10.063A  pdb=" N   TYR B 883 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 12.770A  pdb=" N   LYS B1070 " --> pdb=" O   TYR B 883 " (cutoff:3.500A)
      removed outlier: 5.758A  pdb=" N   ILE B1069 " --> pdb=" O   LYS B 948 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   LYS B 948 " --> pdb=" O   ILE B1069 " (cutoff:3.500A)
      removed outlier: 5.742A  pdb=" N   TYR B1071 " --> pdb=" O   TRP B 946 " (cutoff:3.500A)
      removed outlier: 4.325A  pdb=" N   TRP B 946 " --> pdb=" O   TYR B1071 " (cutoff:3.500A)
      removed outlier: 3.557A  pdb=" N   PHE B 941 " --> pdb=" O   ASN B1021 " (cutoff:3.500A)
      removed outlier: 6.814A  pdb=" N   SER B1027 " --> pdb=" O   GLN B1038 " (cutoff:3.500A)
      removed outlier: 4.661A  pdb=" N   GLN B1038 " --> pdb=" O   SER B1027 " (cutoff:3.500A)
      removed outlier: 7.264A  pdb=" N   ILE B1029 " --> pdb=" O   ILE B1036 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE B1036 " --> pdb=" O   ILE B1029 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900
      removed outlier: 3.600A  pdb=" N   VAL B 926 " --> pdb=" O   ILE B1053 " (cutoff:3.500A)
      removed outlier: 7.376A  pdb=" N   LYS B1052 " --> pdb=" O   ILE B 968 " (cutoff:3.500A)
      removed outlier: 5.081A  pdb=" N   ILE B 968 " --> pdb=" O   LYS B1052 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   ILE B 964 " --> pdb=" O   LYS B1056 " (cutoff:3.500A)
      removed outlier: 5.787A  pdb=" N   ASP B1058 " --> pdb=" O   TYR B 962 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   TYR B 962 " --> pdb=" O   ASP B1058 " (cutoff:3.500A)
      removed outlier: 5.564A  pdb=" N   THR B 963 " --> pdb=" O   LEU B 978 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   LEU B 978 " --> pdb=" O   THR B 963 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   TRP B 974 " --> pdb=" O   CYS B 967 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   GLN B 995 " --> pdb=" O   LEU B 987 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 1112 through 1115
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1122 through 1125
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1160 through 1164
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1160 through 1164
      removed outlier: 3.947A  pdb=" N   ASP B1178 " --> pdb=" O   MET B1223 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL B1220 " --> pdb=" O   GLN B1240 " (cutoff:3.500A)
      removed outlier: 5.679A  pdb=" N   LYS B1226 " --> pdb=" O   LYS B1234 " (cutoff:3.500A)
      removed outlier: 8.226A  pdb=" N   LYS B1234 " --> pdb=" O   LYS B1226 " (cutoff:3.500A)
      removed outlier: 27.135A  pdb=" N   ASN B1233 " --> pdb=" O   LEU B1254 " (cutoff:3.500A)
      removed outlier: 23.390A  pdb=" N   LEU B1254 " --> pdb=" O   ASN B1233 " (cutoff:3.500A)
      removed outlier: 15.594A  pdb=" N   CYS B1235 " --> pdb=" O   PHE B1252 " (cutoff:3.500A)
      removed outlier: 10.929A  pdb=" N   PHE B1252 " --> pdb=" O   CYS B1235 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   MET B1237 " --> pdb=" O   ILE B1250 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLY B1248 " --> pdb=" O   LEU B1239 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   SER B1264 " --> pdb=" O   PHE B1249 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1192 through 1194

    432 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.82

  Time building geometry restraints manager: 2.56 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1545
        1.32 -     1.46: 3185
        1.46 -     1.60: 3565
        1.60 -     1.74: 2
        1.74 -     1.87: 74
  Bond restraints: 8371
  Sorted by residual:
  bond pdb=" NE  ARG A 682 "
       pdb=" CZ  ARG A 682 "
    ideal  model  delta    sigma   weight residual
    1.326  1.263  0.063 1.10e-02 8.26e+03 3.24e+01
  bond pdb=" C   THR A 456 "
       pdb=" O   THR A 456 "
    ideal  model  delta    sigma   weight residual
    1.237  1.286 -0.049 1.16e-02 7.43e+03 1.80e+01
  bond pdb=" CG  MET A 310 "
       pdb=" SD  MET A 310 "
    ideal  model  delta    sigma   weight residual
    1.803  1.697  0.106 2.50e-02 1.60e+03 1.79e+01
  bond pdb=" C   VAL A 276 "
       pdb=" N   PHE A 277 "
    ideal  model  delta    sigma   weight residual
    1.334  1.280  0.055 1.33e-02 5.65e+03 1.69e+01
  bond pdb=" CE1 HIS A 161 "
       pdb=" NE2 HIS A 161 "
    ideal  model  delta    sigma   weight residual
    1.321  1.281  0.040 1.00e-02 1.00e+04 1.57e+01
  ... (remaining 8366 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 10796
        2.30 -     4.60: 481
        4.60 -     6.90: 30
        6.90 -     9.20: 8
        9.20 -    11.50: 4
  Bond angle restraints: 11319
  Sorted by residual:
  angle pdb=" NE  ARG A 231 "
        pdb=" CZ  ARG A 231 "
        pdb=" NH1 ARG A 231 "
      ideal   model   delta    sigma   weight residual
     121.50  114.32    7.18 1.00e+00 1.00e+00 5.15e+01
  angle pdb=" CB  PHE A 686 "
        pdb=" CG  PHE A 686 "
        pdb=" CD1 PHE A 686 "
      ideal   model   delta    sigma   weight residual
     120.70  132.20  -11.50 1.70e+00 3.46e-01 4.58e+01
  angle pdb=" CA  GLY A 268 "
        pdb=" C   GLY A 268 "
        pdb=" N   ILE A 269 "
      ideal   model   delta    sigma   weight residual
     117.04  122.54   -5.50 9.90e-01 1.02e+00 3.09e+01
  angle pdb=" NE  ARG A 231 "
        pdb=" CZ  ARG A 231 "
        pdb=" NH2 ARG A 231 "
      ideal   model   delta    sigma   weight residual
     119.20  124.01   -4.81 9.00e-01 1.23e+00 2.86e+01
  angle pdb=" CB  PHE A 686 "
        pdb=" CG  PHE A 686 "
        pdb=" CD2 PHE A 686 "
      ideal   model   delta    sigma   weight residual
     120.70  111.75    8.95 1.70e+00 3.46e-01 2.77e+01
  ... (remaining 11314 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.21: 4703
       22.21 -    44.41: 207
       44.41 -    66.61: 28
       66.61 -    88.82: 7
       88.82 -   111.02: 3
  Dihedral angle restraints: 4948
    sinusoidal: 2025
      harmonic: 2923
  Sorted by residual:
  dihedral pdb=" CA  THR B1145 "
           pdb=" C   THR B1145 "
           pdb=" N   THR B1146 "
           pdb=" CA  THR B1146 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.20  -21.80     0      5.00e+00 4.00e-02 1.90e+01
  dihedral pdb=" CA  LEU A 209 "
           pdb=" C   LEU A 209 "
           pdb=" N   ILE A 210 "
           pdb=" CA  ILE A 210 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.24  -20.76     0      5.00e+00 4.00e-02 1.72e+01
  dihedral pdb=" CA  VAL B 998 "
           pdb=" C   VAL B 998 "
           pdb=" N   PHE B 999 "
           pdb=" CA  PHE B 999 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.68   20.32     0      5.00e+00 4.00e-02 1.65e+01
  ... (remaining 4945 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.133: 1162
       0.133 -    0.266: 74
       0.266 -    0.399: 5
       0.399 -    0.532: 0
       0.532 -    0.665: 2
  Chirality restraints: 1243
  Sorted by residual:
  chirality pdb=" C1  FUC E   3 "
            pdb=" O6  NAG E   1 "
            pdb=" C2  FUC E   3 "
            pdb=" O5  FUC E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 3.94e+01
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.29   -0.11 2.00e-02 2.50e+03 3.30e+01
  chirality pdb=" C1  NAG A 802 "
            pdb=" ND2 ASN A 548 "
            pdb=" C2  NAG A 802 "
            pdb=" O5  NAG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.73   -0.67 2.00e-01 2.50e+01 1.11e+01
  ... (remaining 1240 not shown)

  Planarity restraints: 1429
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 666 "   -0.036 2.00e-02 2.50e+03   5.49e-02 7.53e+01
        pdb=" CG  TRP A 666 "    0.002 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 666 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 666 "   -0.018 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 666 "    0.023 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 666 "    0.057 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 666 "   -0.042 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 666 "   -0.100 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 666 "    0.107 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 666 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 277 "   -0.065 2.00e-02 2.50e+03   5.59e-02 5.47e+01
        pdb=" CG  PHE A 277 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 277 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 277 "    0.092 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 277 "    0.048 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 277 "   -0.052 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 277 "   -0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 801 "    0.067 2.00e-02 2.50e+03   5.55e-02 3.86e+01
        pdb=" C7  NAG A 801 "   -0.024 2.00e-02 2.50e+03
        pdb=" C8  NAG A 801 "    0.053 2.00e-02 2.50e+03
        pdb=" N2  NAG A 801 "   -0.086 2.00e-02 2.50e+03
        pdb=" O7  NAG A 801 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 1426 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1514
        2.78 -     3.31: 7827
        3.31 -     3.84: 13469
        3.84 -     4.37: 16260
        4.37 -     4.90: 28194
  Nonbonded interactions: 67264
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" O   PRO A 355 "
     model   vdw
     2.246 3.040
  nonbonded pdb=" O   TRP B1266 "
            pdb=" NE2 GLN B1270 "
     model   vdw
     2.254 3.120
  nonbonded pdb=" O   SER B1092 "
            pdb=" NZ  LYS B1098 "
     model   vdw
     2.267 3.120
  nonbonded pdb=" OG  SER B1050 "
            pdb=" O   LYS B1052 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" NE2 GLN A 323 "
            pdb=" O   TYR A 328 "
     model   vdw
     2.278 3.120
  ... (remaining 67259 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.910
  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:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     22.260
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
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      :  0.011   0.106   8371  Z= 0.686
  Angle     :  1.106  11.504  11319  Z= 0.710
  Chirality :  0.079   0.665   1243
  Planarity :  0.009   0.076   1426
  Dihedral  : 13.105 111.023   3082
  Min Nonbonded Distance : 2.246

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.71 %
    Favored  : 98.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.19 (0.26), residues: 1006
  helix:  0.61 (0.25), residues: 412
  sheet:  0.69 (0.42), residues: 151
  loop : -1.10 (0.29), residues: 443

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.107   0.011   TRP A 666 
 HIS   0.021   0.004   HIS A 474 
 PHE   0.092   0.012   PHE A 277 
 TYR   0.090   0.010   TYR A 279 
 ARG   0.032   0.003   ARG A 231 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.799 
Fit side-chains
REVERT: A  444 ARG cc_start: 0.5636 (ttp-110) cc_final: 0.5192 (ttt180)
REVERT: A  513 ASN cc_start: 0.8012 (t0) cc_final: 0.7667 (t0)
REVERT: A  568 ASN cc_start: 0.7872 (t0) cc_final: 0.7544 (t0)
REVERT: B  903 ARG cc_start: 0.7085 (mtp85) cc_final: 0.6683 (ttm-80)
REVERT: B  961 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7733 (tt0)
REVERT: B 1000 LYS cc_start: 0.7688 (pptt) cc_final: 0.7297 (tttm)
REVERT: B 1037 ASP cc_start: 0.5885 (t0) cc_final: 0.5471 (t0)
REVERT: B 1043 ASN cc_start: 0.7491 (m-40) cc_final: 0.7290 (t0)
REVERT: B 1191 TYR cc_start: 0.5951 (m-80) cc_final: 0.5612 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.2676
  time to fit residues: 53.2704
Evaluate side-chains
  112 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.6980
   chunk 76 optimal weight:   30.0000
   chunk 42 optimal weight:    0.9980
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 40 optimal weight:    0.5980
   chunk 79 optimal weight:    9.9990
   chunk 30 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 286 GLN
A 612 ASN
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8371  Z= 0.186
  Angle     :  0.534  10.818  11319  Z= 0.288
  Chirality :  0.044   0.362   1243
  Planarity :  0.003   0.044   1426
  Dihedral  :  6.557  77.986   1205
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  :  6.94 %
    Favored  : 92.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1006
  helix:  1.57 (0.25), residues: 407
  sheet:  0.97 (0.43), residues: 152
  loop : -1.06 (0.28), residues: 447

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 333 
 HIS   0.003   0.000   HIS A 331 
 PHE   0.034   0.002   PHE A 497 
 TYR   0.020   0.001   TYR B 938 
 ARG   0.004   0.000   ARG A 334 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 128
  time to evaluate  : 0.902 
Fit side-chains
REVERT: A  142 ARG cc_start: 0.6921 (ttm170) cc_final: 0.6712 (mtt180)
REVERT: A  253 GLN cc_start: 0.6386 (mm-40) cc_final: 0.6094 (mm110)
REVERT: A  444 ARG cc_start: 0.5336 (ttp-110) cc_final: 0.4843 (ttm-80)
REVERT: A  544 THR cc_start: 0.8566 (OUTLIER) cc_final: 0.8273 (p)
REVERT: A  568 ASN cc_start: 0.7795 (t0) cc_final: 0.7472 (t0)
REVERT: B  902 ASP cc_start: 0.7692 (m-30) cc_final: 0.7419 (t0)
REVERT: B 1000 LYS cc_start: 0.7646 (pptt) cc_final: 0.7277 (tttm)
REVERT: B 1037 ASP cc_start: 0.6146 (t0) cc_final: 0.5649 (t70)
REVERT: B 1043 ASN cc_start: 0.7467 (m-40) cc_final: 0.7239 (t0)
REVERT: B 1190 GLU cc_start: 0.7311 (mp0) cc_final: 0.6698 (mt-10)
REVERT: B 1191 TYR cc_start: 0.5911 (m-80) cc_final: 0.5617 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 132
  average time/residue: 0.2416
  time to fit residues: 42.5156
Evaluate side-chains
  123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 0.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  720 SER
Chi-restraints excluded: chain A residue  727 SER
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    0.5980
   chunk 28 optimal weight:    3.9990
   chunk 76 optimal weight:   30.0000
   chunk 62 optimal weight:    7.9990
   chunk 25 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0010
   chunk 99 optimal weight:    7.9990
   chunk 81 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9990
   overall best weight:    0.7190

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1021 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7205
moved from start:          0.1912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8371  Z= 0.176
  Angle     :  0.478   7.415  11319  Z= 0.259
  Chirality :  0.042   0.197   1243
  Planarity :  0.003   0.036   1426
  Dihedral  :  4.996  36.351   1205
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 6.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  :  8.65 %
    Favored  : 90.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.26), residues: 1006
  helix:  1.89 (0.25), residues: 409
  sheet:  0.99 (0.43), residues: 146
  loop : -0.99 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 333 
 HIS   0.002   0.000   HIS A 506 
 PHE   0.023   0.001   PHE A 497 
 TYR   0.015   0.001   TYR B1030 
 ARG   0.007   0.000   ARG B 903 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 119
  time to evaluate  : 0.872 
Fit side-chains
   revert: symmetry clash
REVERT: A  142 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6744 (mtt180)
REVERT: A  444 ARG cc_start: 0.5277 (ttp-110) cc_final: 0.4848 (ttm-80)
REVERT: A  487 PHE cc_start: 0.7138 (m-80) cc_final: 0.6892 (m-10)
REVERT: A  568 ASN cc_start: 0.7747 (t0) cc_final: 0.7407 (t0)
REVERT: A  707 PHE cc_start: 0.6602 (m-10) cc_final: 0.6323 (m-10)
REVERT: A  732 LYS cc_start: 0.6200 (mmtt) cc_final: 0.5931 (mtpt)
REVERT: B  902 ASP cc_start: 0.7760 (m-30) cc_final: 0.7354 (t0)
REVERT: B  903 ARG cc_start: 0.7086 (mmm-85) cc_final: 0.6561 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7650 (pptt) cc_final: 0.7357 (tttm)
REVERT: B 1037 ASP cc_start: 0.6335 (t0) cc_final: 0.5822 (t0)
REVERT: B 1191 TYR cc_start: 0.5854 (m-80) cc_final: 0.5569 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 127
  average time/residue: 0.2421
  time to fit residues: 40.8773
Evaluate side-chains
  120 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 114
  time to evaluate  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  720 SER
Chi-restraints excluded: chain B residue 1289 ASP
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 69 optimal weight:    3.9990
   chunk 47 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0670
   chunk 92 optimal weight:    3.9990
   chunk 97 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.8126

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7267
moved from start:          0.2107

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060   8371  Z= 0.337
  Angle     :  0.548   6.543  11319  Z= 0.298
  Chirality :  0.044   0.180   1243
  Planarity :  0.004   0.036   1426
  Dihedral  :  4.958  38.581   1205
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  8.99 %
    Favored  : 89.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.26), residues: 1006
  helix:  1.66 (0.26), residues: 407
  sheet:  0.90 (0.43), residues: 146
  loop : -1.13 (0.27), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 333 
 HIS   0.003   0.001   HIS A 331 
 PHE   0.022   0.002   PHE A 686 
 TYR   0.021   0.002   TYR B1001 
 ARG   0.007   0.001   ARG B 996 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 110
  time to evaluate  : 0.910 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 ARG cc_start: 0.5301 (ttp-110) cc_final: 0.4882 (ttm-80)
REVERT: A  568 ASN cc_start: 0.7746 (t0) cc_final: 0.7402 (t0)
REVERT: A  732 LYS cc_start: 0.6185 (mmtt) cc_final: 0.5938 (mttm)
REVERT: A  742 GLN cc_start: 0.7208 (tm-30) cc_final: 0.6949 (tp40)
REVERT: B  902 ASP cc_start: 0.7903 (m-30) cc_final: 0.7551 (t0)
REVERT: B  903 ARG cc_start: 0.7052 (mmm-85) cc_final: 0.6630 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7669 (pptt) cc_final: 0.7376 (tttm)
REVERT: B 1037 ASP cc_start: 0.6473 (t0) cc_final: 0.5967 (t0)
  outliers start: 13
  outliers final: 11
  residues processed: 119
  average time/residue: 0.2342
  time to fit residues: 37.4456
Evaluate side-chains
  121 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 110
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  720 SER
Chi-restraints excluded: chain A residue  727 SER
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue  963 THR
Chi-restraints excluded: chain B residue 1144 VAL
Chi-restraints excluded: chain B residue 1289 ASP
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9990
   chunk 72 optimal weight:    0.8980
   chunk 40 optimal weight:    0.0170
   chunk 83 optimal weight:    3.9990
   chunk 67 optimal weight:    0.3980
   chunk 0 optimal weight:   10.0000
   chunk 49 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 24 optimal weight:    0.9990
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.5218

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7208
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043   8371  Z= 0.144
  Angle     :  0.450   5.891  11319  Z= 0.248
  Chirality :  0.041   0.183   1243
  Planarity :  0.003   0.034   1426
  Dihedral  :  4.617  37.580   1205
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.39 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.02 %
    Allowed  : 10.81 %
    Favored  : 88.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.27), residues: 1006
  helix:  2.03 (0.26), residues: 408
  sheet:  0.92 (0.44), residues: 145
  loop : -0.99 (0.28), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 333 
 HIS   0.001   0.000   HIS A 506 
 PHE   0.023   0.001   PHE A 497 
 TYR   0.014   0.001   TYR B1191 
 ARG   0.004   0.000   ARG B 903 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 110
  time to evaluate  : 0.969 
Fit side-chains
   revert: symmetry clash
REVERT: A  444 ARG cc_start: 0.5337 (ttp-110) cc_final: 0.4937 (ttm-80)
REVERT: A  513 ASN cc_start: 0.7870 (t0) cc_final: 0.7266 (t0)
REVERT: A  533 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.6938 (mp0)
REVERT: A  568 ASN cc_start: 0.7757 (t0) cc_final: 0.7416 (t0)
REVERT: A  732 LYS cc_start: 0.6209 (mmtt) cc_final: 0.5952 (mttm)
REVERT: A  742 GLN cc_start: 0.7085 (tm-30) cc_final: 0.6834 (tp40)
REVERT: B  902 ASP cc_start: 0.7920 (m-30) cc_final: 0.7595 (t0)
REVERT: B  903 ARG cc_start: 0.7069 (mmm-85) cc_final: 0.6658 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7725 (pptt) cc_final: 0.7367 (tttm)
REVERT: B 1037 ASP cc_start: 0.6463 (t0) cc_final: 0.5954 (t0)
  outliers start: 9
  outliers final: 6
  residues processed: 118
  average time/residue: 0.2603
  time to fit residues: 40.5802
Evaluate side-chains
  114 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 107
  time to evaluate  : 0.773 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1144 VAL
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    4.9990
   chunk 19 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 32 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 94 optimal weight:    0.6980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7237
moved from start:          0.2372

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   8371  Z= 0.228
  Angle     :  0.475   5.982  11319  Z= 0.260
  Chirality :  0.042   0.165   1243
  Planarity :  0.003   0.034   1426
  Dihedral  :  4.567  37.416   1205
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.47 %
    Favored  : 88.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.81 (0.26), residues: 1006
  helix:  1.99 (0.26), residues: 408
  sheet:  0.97 (0.43), residues: 146
  loop : -1.03 (0.28), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 333 
 HIS   0.002   0.000   HIS A 331 
 PHE   0.024   0.001   PHE A 497 
 TYR   0.015   0.001   TYR A 306 
 ARG   0.006   0.000   ARG B 996 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 0.875 
Fit side-chains
REVERT: A  444 ARG cc_start: 0.5299 (ttp-110) cc_final: 0.4883 (ttm-80)
REVERT: A  533 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7058 (mp0)
REVERT: A  568 ASN cc_start: 0.7817 (t0) cc_final: 0.7472 (t0)
REVERT: A  732 LYS cc_start: 0.6237 (mmtt) cc_final: 0.5997 (mttm)
REVERT: A  742 GLN cc_start: 0.7145 (tm-30) cc_final: 0.6931 (tp40)
REVERT: B  902 ASP cc_start: 0.7996 (m-30) cc_final: 0.7672 (t0)
REVERT: B  903 ARG cc_start: 0.6968 (mmm-85) cc_final: 0.6595 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7736 (pptt) cc_final: 0.7452 (tttm)
REVERT: B 1037 ASP cc_start: 0.6486 (t0) cc_final: 0.5978 (t0)
  outliers start: 11
  outliers final: 9
  residues processed: 115
  average time/residue: 0.2311
  time to fit residues: 35.8615
Evaluate side-chains
  113 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 103
  time to evaluate  : 0.936 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  177 MET
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  690 ASN
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1144 VAL
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.0050
   chunk 55 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   chunk 82 optimal weight:    0.2980
   chunk 54 optimal weight:    0.5980
   chunk 97 optimal weight:    8.9990
   chunk 60 optimal weight:   10.0000
   chunk 59 optimal weight:    5.9990
   chunk 44 optimal weight:    0.7980
   chunk 38 optimal weight:    0.6980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.4794

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7199
moved from start:          0.2525

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042   8371  Z= 0.142
  Angle     :  0.436   5.129  11319  Z= 0.241
  Chirality :  0.041   0.169   1243
  Planarity :  0.003   0.033   1426
  Dihedral  :  4.387  36.768   1205
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 6.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 10.81 %
    Favored  : 87.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.27), residues: 1006
  helix:  2.12 (0.26), residues: 410
  sheet:  1.01 (0.44), residues: 147
  loop : -0.97 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 974 
 HIS   0.001   0.000   HIS A 331 
 PHE   0.022   0.001   PHE A 497 
 TYR   0.010   0.001   TYR A 306 
 ARG   0.004   0.000   ARG B 996 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 113
  time to evaluate  : 0.848 
Fit side-chains
REVERT: A  142 ARG cc_start: 0.6912 (ttm170) cc_final: 0.6690 (mtt180)
REVERT: A  513 ASN cc_start: 0.7810 (t0) cc_final: 0.7263 (t0)
REVERT: A  533 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6998 (mp0)
REVERT: A  568 ASN cc_start: 0.7841 (t0) cc_final: 0.7497 (t0)
REVERT: A  732 LYS cc_start: 0.6259 (mmtt) cc_final: 0.5995 (mttm)
REVERT: B  902 ASP cc_start: 0.8060 (m-30) cc_final: 0.7741 (t0)
REVERT: B  903 ARG cc_start: 0.6997 (mmm-85) cc_final: 0.6672 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7746 (pptt) cc_final: 0.7387 (tttm)
REVERT: B 1037 ASP cc_start: 0.6540 (t0) cc_final: 0.5950 (t0)
REVERT: B 1206 LEU cc_start: 0.6521 (mp) cc_final: 0.6252 (mp)
  outliers start: 11
  outliers final: 8
  residues processed: 122
  average time/residue: 0.2402
  time to fit residues: 39.3036
Evaluate side-chains
  116 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 107
  time to evaluate  : 0.965 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1144 VAL
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 19 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 61 optimal weight:    8.9990
   chunk 66 optimal weight:    0.9990
   chunk 48 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 76 optimal weight:    1.9990
   chunk 88 optimal weight:    9.9990
   chunk 93 optimal weight:    8.9990
   chunk 85 optimal weight:    0.7980
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7222
moved from start:          0.2594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8371  Z= 0.195
  Angle     :  0.466   5.528  11319  Z= 0.255
  Chirality :  0.042   0.173   1243
  Planarity :  0.003   0.034   1426
  Dihedral  :  4.415  36.982   1205
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 10.92 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.27), residues: 1006
  helix:  2.09 (0.26), residues: 410
  sheet:  1.02 (0.43), residues: 148
  loop : -1.02 (0.28), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 333 
 HIS   0.002   0.000   HIS A 331 
 PHE   0.021   0.001   PHE A 497 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.004   0.000   ARG B 996 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 0.862 
Fit side-chains
REVERT: A  513 ASN cc_start: 0.7814 (t0) cc_final: 0.7224 (t0)
REVERT: A  533 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7085 (mp0)
REVERT: A  568 ASN cc_start: 0.7841 (t0) cc_final: 0.7495 (t0)
REVERT: A  732 LYS cc_start: 0.6294 (mmtt) cc_final: 0.6060 (mttm)
REVERT: B  902 ASP cc_start: 0.8123 (m-30) cc_final: 0.7831 (t0)
REVERT: B  903 ARG cc_start: 0.7066 (mmm-85) cc_final: 0.6702 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7755 (pptt) cc_final: 0.7463 (tttm)
REVERT: B 1037 ASP cc_start: 0.6549 (t0) cc_final: 0.6015 (t0)
  outliers start: 15
  outliers final: 12
  residues processed: 120
  average time/residue: 0.2265
  time to fit residues: 36.7279
Evaluate side-chains
  119 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  690 ASN
Chi-restraints excluded: chain A residue  727 SER
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1144 VAL
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    0.3980
   chunk 93 optimal weight:    6.9990
   chunk 54 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 71 optimal weight:    0.6980
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   chunk 85 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 95 optimal weight:    4.9990
   chunk 58 optimal weight:    0.2980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7206
moved from start:          0.2676

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8371  Z= 0.162
  Angle     :  0.453   5.186  11319  Z= 0.250
  Chirality :  0.042   0.178   1243
  Planarity :  0.003   0.033   1426
  Dihedral  :  4.360  36.920   1205
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 6.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.49 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 10.69 %
    Favored  : 87.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.97 (0.27), residues: 1006
  helix:  2.14 (0.26), residues: 410
  sheet:  1.07 (0.44), residues: 147
  loop : -0.98 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 333 
 HIS   0.001   0.000   HIS A 331 
 PHE   0.022   0.001   PHE A 497 
 TYR   0.021   0.001   TYR B1191 
 ARG   0.004   0.000   ARG A 570 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 110
  time to evaluate  : 0.894 
Fit side-chains
REVERT: A  513 ASN cc_start: 0.7804 (t0) cc_final: 0.7185 (t0)
REVERT: A  533 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7098 (mp0)
REVERT: A  568 ASN cc_start: 0.7829 (t0) cc_final: 0.7485 (t0)
REVERT: A  732 LYS cc_start: 0.6307 (mmtt) cc_final: 0.6071 (mttm)
REVERT: B  902 ASP cc_start: 0.8103 (m-30) cc_final: 0.7829 (t0)
REVERT: B  903 ARG cc_start: 0.7074 (mmm-85) cc_final: 0.6711 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7800 (pptt) cc_final: 0.7448 (tttm)
REVERT: B 1037 ASP cc_start: 0.6597 (t0) cc_final: 0.6086 (t0)
  outliers start: 14
  outliers final: 11
  residues processed: 122
  average time/residue: 0.2414
  time to fit residues: 39.3414
Evaluate side-chains
  118 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  690 ASN
Chi-restraints excluded: chain A residue  727 SER
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1144 VAL
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 92 optimal weight:    5.9990
   chunk 80 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 49 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 85 optimal weight:    0.9990
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.9380

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.2720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   8371  Z= 0.203
  Angle     :  0.466   5.298  11319  Z= 0.257
  Chirality :  0.042   0.180   1243
  Planarity :  0.003   0.033   1426
  Dihedral  :  4.380  37.733   1205
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 11.15 %
    Favored  : 87.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.27), residues: 1006
  helix:  2.06 (0.25), residues: 409
  sheet:  1.07 (0.43), residues: 148
  loop : -1.02 (0.28), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 467 
 HIS   0.002   0.000   HIS A 331 
 PHE   0.023   0.001   PHE A 497 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.004   0.000   ARG A 570 

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

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

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2012 Ramachandran restraints generated.
    1006 Oldfield, 0 Emsley, 1006 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 106
  time to evaluate  : 0.831 
Fit side-chains
REVERT: A  533 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7144 (mp0)
REVERT: A  568 ASN cc_start: 0.7833 (t0) cc_final: 0.7483 (t0)
REVERT: A  732 LYS cc_start: 0.6244 (mmtt) cc_final: 0.6016 (mttm)
REVERT: B  903 ARG cc_start: 0.7062 (mmm-85) cc_final: 0.6726 (mmp-170)
REVERT: B 1000 LYS cc_start: 0.7814 (pptt) cc_final: 0.7447 (tttm)
REVERT: B 1037 ASP cc_start: 0.6645 (t0) cc_final: 0.6135 (t0)
  outliers start: 12
  outliers final: 11
  residues processed: 117
  average time/residue: 0.2384
  time to fit residues: 37.4070
Evaluate side-chains
  116 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 104
  time to evaluate  : 0.919 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  276 VAL
Chi-restraints excluded: chain A residue  482 SER
Chi-restraints excluded: chain A residue  530 LEU
Chi-restraints excluded: chain A residue  533 GLU
Chi-restraints excluded: chain A residue  544 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  690 ASN
Chi-restraints excluded: chain A residue  727 SER
Chi-restraints excluded: chain B residue 1105 LEU
Chi-restraints excluded: chain B residue 1143 VAL
Chi-restraints excluded: chain B residue 1144 VAL
Chi-restraints excluded: chain B residue 1294 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 11 optimal weight:    0.5980
   chunk 22 optimal weight:    0.0270
   chunk 80 optimal weight:    9.9990
   chunk 33 optimal weight:    0.8980
   chunk 82 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.213782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.138412 restraints weight = 8590.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3566 rms_B_bonded: 2.58
r_work: 0.3419 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.3255 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2796

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.041   8371  Z= 0.154
  Angle     :  0.450   5.188  11319  Z= 0.248
  Chirality :  0.041   0.186   1243
  Planarity :  0.003   0.033   1426
  Dihedral  :  4.296  37.149   1205
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.26 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.03 (0.27), residues: 1006
  helix:  2.16 (0.26), residues: 409
  sheet:  1.10 (0.43), residues: 147
  loop : -0.90 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 333 
 HIS   0.001   0.000   HIS A 331 
 PHE   0.022   0.001   PHE A 497 
 TYR   0.014   0.001   TYR B1191 
 ARG   0.004   0.000   ARG A 570 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2157.84 seconds
wall clock time: 40 minutes 2.10 seconds (2402.10 seconds total)