Starting phenix.real_space_refine
on Sat Dec 28 09:30:44 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8js8_36616/12_2024/8js8_36616.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8js8_36616/12_2024/8js8_36616.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8js8_36616/12_2024/8js8_36616.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8js8_36616/12_2024/8js8_36616.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8js8_36616/12_2024/8js8_36616.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8js8_36616/12_2024/8js8_36616.cif"
  }
  resolution = 2.88
  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=   1.121
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    5291      2.51       5
     N    1362      2.21       5
     O    1489      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 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: 8189
  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: "F"
      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: 40
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 40
          Unusual residues: {'NAG': 2, 'UKX': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 5.24, per 1000 atoms: 0.64
  Number of scatterers: 8189
  At special positions: 0
  Unit cell: (88.81, 84.66, 147.74, 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    1489      8.00
     N    1362      7.00
     C    5291      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 F   1 " - " NAG F   2 "
    BETA1-6
      " NAG F   1 " - " FUC F   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 F   1 " - " ASN A 573 "
  Time building additional restraints: 2.55
  Conformation dependent library (CDL) restraints added in 963.8 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:
      27 helices and 10 sheets defined
      43.7% alpha, 23.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 137 through 160
    Processing helix  chain 'A' and resid 162 through 183
      removed outlier: 3.734A  pdb=" N   ASP A 179 " --> pdb=" O   ALA A 175 " (cutoff:3.500A)
      removed outlier: 3.804A  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: 4.327A  pdb=" N   LYS A 195 " --> pdb=" O   PRO A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 230
      removed outlier: 4.554A  pdb=" N   VAL A 211 " --> pdb=" O   LEU A 207 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   TYR A 212 " --> pdb=" O   GLY A 208 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   PHE A 220 " --> pdb=" O   MET A 216 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ASP A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 4.383A  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 271
      removed outlier: 4.339A  pdb=" N   GLY A 271 " --> pdb=" O   VAL A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 282
      removed outlier: 3.712A  pdb=" N   ILE A 275 " --> pdb=" O   GLY A 271 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLU A 282 " --> pdb=" O   SER A 278 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 284
      No H-bonds generated for 'chain 'A' and resid 283 through 284'
    Processing helix  chain 'A' and resid 285 through 288
      removed outlier: 3.782A  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: 3.969A  pdb=" N   MET A 301 " --> pdb=" O   CYS A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.741A  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: 3.578A  pdb=" N   PHE A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 386
    Processing helix  chain 'A' and resid 419 through 439
      removed outlier: 3.521A  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 593 through 619
      removed outlier: 3.777A  pdb=" N   VAL A 597 " --> pdb=" O   GLY A 593 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL A 608 " --> pdb=" O   GLY A 604 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   LEU A 609 " --> pdb=" O   THR A 605 " (cutoff:3.500A)
      Proline residue:  A 610  - end of helix
      removed outlier: 3.516A  pdb=" N   ILE A 613 " --> pdb=" O   LEU A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 641
      removed outlier: 3.628A  pdb=" N   MET A 634 " --> pdb=" O   GLY A 630 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 642 through 644
      No H-bonds generated for 'chain 'A' and resid 642 through 644'
    Processing helix  chain 'A' and resid 647 through 676
      removed outlier: 3.812A  pdb=" N   ILE A 663 " --> pdb=" O   GLY A 659 " (cutoff:3.500A)
      removed outlier: 5.195A  pdb=" N   ALA A 664 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
      removed outlier: 4.477A  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
      removed outlier: 3.925A  pdb=" N   ILE A 716 " --> pdb=" O   LYS A 712 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 929 through 933
      removed outlier: 3.854A  pdb=" N   VAL B 933 " --> pdb=" O   ASN B 930 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 958
    Processing helix  chain 'B' and resid 1080 through 1092
    Processing helix  chain 'B' and resid 1265 through 1273
    Processing sheet with id=AA1, first strand: chain 'A' and resid 485 through 492
      removed outlier: 6.247A  pdb=" N   GLY A 509 " --> pdb=" O   GLY A 489 " (cutoff:3.500A)
      removed outlier: 6.886A  pdb=" N   ARG A 491 " --> pdb=" O   GLY A 509 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   TYR A 511 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   THR A 500 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU A 521 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   GLU A 502 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   SER A 523 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 515 through 527
    current: chain 'A' and resid 550 through 552
      removed outlier: 6.242A  pdb=" N   PHE A 551 " --> pdb=" O   ILE A 572 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 566 through 567
      removed outlier: 6.031A  pdb=" N   PHE A 546 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   PHE A 545 " --> pdb=" O   VAL A 524 " (cutoff:3.500A)
      removed outlier: 7.065A  pdb=" N   THR A 500 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 7.018A  pdb=" N   LEU A 521 " --> pdb=" O   THR A 500 " (cutoff:3.500A)
      removed outlier: 7.126A  pdb=" N   GLU A 502 " --> pdb=" O   LEU A 521 " (cutoff:3.500A)
      removed outlier: 6.905A  pdb=" N   SER A 523 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 500 through 512
    current: chain 'A' and resid 555 through 559
    Processing sheet with id=AA3, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.556A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU B1074 " --> pdb=" O   ILE B 878 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   SER B 880 " --> pdb=" O   PHE B1072 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   PHE B1072 " --> pdb=" O   SER B 880 " (cutoff:3.500A)
      removed outlier: 8.807A  pdb=" N   VAL B 882 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 10.596A  pdb=" N   LYS B1070 " --> pdb=" O   VAL B 882 " (cutoff:3.500A)
      removed outlier: 16.599A  pdb=" N   LYS B 884 " --> pdb=" O   MET B1068 " (cutoff:3.500A)
      removed outlier: 18.261A  pdb=" N   MET B1068 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 887 through 890
      removed outlier: 3.556A  pdb=" N   ASP B 887 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
      removed outlier: 6.617A  pdb=" N   LEU B1074 " --> pdb=" O   ILE B 878 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   SER B 880 " --> pdb=" O   PHE B1072 " (cutoff:3.500A)
      removed outlier: 6.951A  pdb=" N   PHE B1072 " --> pdb=" O   SER B 880 " (cutoff:3.500A)
      removed outlier: 8.807A  pdb=" N   VAL B 882 " --> pdb=" O   LYS B1070 " (cutoff:3.500A)
      removed outlier: 10.596A  pdb=" N   LYS B1070 " --> pdb=" O   VAL B 882 " (cutoff:3.500A)
      removed outlier: 16.599A  pdb=" N   LYS B 884 " --> pdb=" O   MET B1068 " (cutoff:3.500A)
      removed outlier: 18.261A  pdb=" N   MET B1068 " --> pdb=" O   LYS B 884 " (cutoff:3.500A)
      removed outlier: 5.555A  pdb=" N   ILE B1069 " --> pdb=" O   LYS B 948 " (cutoff:3.500A)
      removed outlier: 7.071A  pdb=" N   LYS B 948 " --> pdb=" O   ILE B1069 " (cutoff:3.500A)
      removed outlier: 5.507A  pdb=" N   TYR B1071 " --> pdb=" O   TRP B 946 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   TRP B 946 " --> pdb=" O   TYR B1071 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASP B1037 " --> pdb=" O   ILE B1029 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ILE B1031 " --> pdb=" O   LEU B1035 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   LEU B1035 " --> pdb=" O   ILE B1031 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 897 through 900
    Processing sheet with id=AA6, first strand: chain 'B' and resid 962 through 968
      removed outlier: 6.839A  pdb=" N   VAL B 976 " --> pdb=" O   ILE B 964 " (cutoff:3.500A)
      removed outlier: 5.127A  pdb=" N   ASN B 966 " --> pdb=" O   TRP B 974 " (cutoff:3.500A)
      removed outlier: 7.165A  pdb=" N   TRP B 974 " --> pdb=" O   ASN B 966 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 1112 through 1115
    Processing sheet with id=AA8, first strand: chain 'B' and resid 1122 through 1125
    Processing sheet with id=AA9, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 3.977A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 5.521A  pdb=" N   LYS B1226 " --> pdb=" O   LYS B1234 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   LYS B1234 " --> pdb=" O   LYS B1226 " (cutoff:3.500A)
      removed outlier: 27.362A  pdb=" N   ASN B1233 " --> pdb=" O   LEU B1254 " (cutoff:3.500A)
      removed outlier: 23.576A  pdb=" N   LEU B1254 " --> pdb=" O   ASN B1233 " (cutoff:3.500A)
      removed outlier: 16.011A  pdb=" N   CYS B1235 " --> pdb=" O   PHE B1252 " (cutoff:3.500A)
      removed outlier: 11.284A  pdb=" N   PHE B1252 " --> pdb=" O   CYS B1235 " (cutoff:3.500A)
      removed outlier: 5.436A  pdb=" N   MET B1237 " --> pdb=" O   ILE B1250 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   LYS B1204 " --> pdb=" O   ALA B1263 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 1159 through 1164
      removed outlier: 3.977A  pdb=" N   LYS B1159 " --> pdb=" O   VAL B1185 " (cutoff:3.500A)
      removed outlier: 5.735A  pdb=" N   ILE B1182 " --> pdb=" O   LEU B1193 " (cutoff:3.500A)

    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: 3.21

  Time building geometry restraints manager: 2.73 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2017
        1.33 -     1.45: 1766
        1.45 -     1.57: 4524
        1.57 -     1.69: 0
        1.69 -     1.81: 76
  Bond restraints: 8383
  Sorted by residual:
  bond pdb=" C5  UKX A 803 "
       pdb=" N2  UKX A 803 "
    ideal  model  delta    sigma   weight residual
    1.340  1.390 -0.050 2.00e-02 2.50e+03 6.20e+00
  bond pdb=" C1  UKX A 803 "
       pdb=" N1  UKX A 803 "
    ideal  model  delta    sigma   weight residual
    1.353  1.396 -0.043 2.00e-02 2.50e+03 4.58e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.444 -0.038 2.00e-02 2.50e+03 3.60e+00
  bond pdb=" C   ILE A 315 "
       pdb=" N   PRO A 316 "
    ideal  model  delta    sigma   weight residual
    1.335  1.357 -0.022 1.19e-02 7.06e+03 3.39e+00
  bond pdb=" C6  UKX A 803 "
       pdb=" C7  UKX A 803 "
    ideal  model  delta    sigma   weight residual
    1.523  1.548 -0.025 2.00e-02 2.50e+03 1.57e+00
  ... (remaining 8378 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 11146
        1.94 -     3.89: 153
        3.89 -     5.83: 27
        5.83 -     7.77: 8
        7.77 -     9.72: 1
  Bond angle restraints: 11335
  Sorted by residual:
  angle pdb=" N   GLY B1157 "
        pdb=" CA  GLY B1157 "
        pdb=" C   GLY B1157 "
      ideal   model   delta    sigma   weight residual
     111.56  115.41   -3.85 1.01e+00 9.80e-01 1.45e+01
  angle pdb=" CA  ARG A 141 "
        pdb=" CB  ARG A 141 "
        pdb=" CG  ARG A 141 "
      ideal   model   delta    sigma   weight residual
     114.10  121.52   -7.42 2.00e+00 2.50e-01 1.38e+01
  angle pdb=" C   GLU B1210 "
        pdb=" N   ILE B1211 "
        pdb=" CA  ILE B1211 "
      ideal   model   delta    sigma   weight residual
     120.33  123.10   -2.77 8.00e-01 1.56e+00 1.20e+01
  angle pdb=" CB  ARG A 141 "
        pdb=" CG  ARG A 141 "
        pdb=" CD  ARG A 141 "
      ideal   model   delta    sigma   weight residual
     111.30  118.74   -7.44 2.30e+00 1.89e-01 1.05e+01
  angle pdb=" CA  ARG A 491 "
        pdb=" CB  ARG A 491 "
        pdb=" CG  ARG A 491 "
      ideal   model   delta    sigma   weight residual
     114.10  120.20   -6.10 2.00e+00 2.50e-01 9.30e+00
  ... (remaining 11330 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.39: 4278
       16.39 -    32.78: 468
       32.78 -    49.17: 173
       49.17 -    65.55: 31
       65.55 -    81.94: 14
  Dihedral angle restraints: 4964
    sinusoidal: 2041
      harmonic: 2923
  Sorted by residual:
  dihedral pdb=" CA  MET B 937 "
           pdb=" C   MET B 937 "
           pdb=" N   TYR B 938 "
           pdb=" CA  TYR B 938 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.32   21.68     0      5.00e+00 4.00e-02 1.88e+01
  dihedral pdb=" CA  GLN B1219 "
           pdb=" C   GLN B1219 "
           pdb=" N   VAL B1220 "
           pdb=" CA  VAL B1220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.94  -20.06     0      5.00e+00 4.00e-02 1.61e+01
  dihedral pdb=" CA  PHE A 497 "
           pdb=" C   PHE A 497 "
           pdb=" N   ASN A 498 "
           pdb=" CA  ASN A 498 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.81   19.19     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 4961 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 1035
       0.057 -    0.113: 186
       0.113 -    0.170: 18
       0.170 -    0.226: 2
       0.226 -    0.283: 3
  Chirality restraints: 1244
  Sorted by residual:
  chirality pdb=" C1  NAG A 801 "
            pdb=" ND2 ASN A 498 "
            pdb=" C2  NAG A 801 "
            pdb=" O5  NAG A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.12   -0.28 2.00e-01 2.50e+01 2.00e+00
  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   -2.16   -0.24 2.00e-01 2.50e+01 1.50e+00
  chirality pdb=" C6  UKX A 803 "
            pdb=" C5  UKX A 803 "
            pdb=" C7  UKX A 803 "
            pdb=" N1  UKX A 803 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.45    2.69   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 1241 not shown)

  Planarity restraints: 1431
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE B1117 "   -0.007 2.00e-02 2.50e+03   1.46e-02 2.12e+00
        pdb=" C   PHE B1117 "    0.025 2.00e-02 2.50e+03
        pdb=" O   PHE B1117 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP B1118 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 938 "    0.008 2.00e-02 2.50e+03   9.69e-03 1.88e+00
        pdb=" CG  TYR B 938 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 938 "    0.006 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 938 "    0.011 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 938 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 938 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 938 "   -0.002 2.00e-02 2.50e+03
        pdb=" OH  TYR B 938 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 602 "    0.007 2.00e-02 2.50e+03   1.36e-02 1.85e+00
        pdb=" C   PHE A 602 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   PHE A 602 "    0.009 2.00e-02 2.50e+03
        pdb=" N   LEU A 603 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1428 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 410
        2.73 -     3.27: 8086
        3.27 -     3.82: 13720
        3.82 -     4.36: 16679
        4.36 -     4.90: 29111
  Nonbonded interactions: 68006
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 279 "
            pdb=" O   PRO A 355 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" NE2 GLN A 323 "
            pdb=" O   GLY A 325 "
     model   vdw
     2.232 3.120
  nonbonded pdb=" ND2 ASN B 918 "
            pdb=" O   ASP B1062 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" NH2 ARG A 145 "
            pdb=" O   GLN A 742 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" O   TRP B1266 "
            pdb=" NE2 GLN B1270 "
     model   vdw
     2.268 3.120
  ... (remaining 68001 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:             1.720
  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:          0.330
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     23.090
  Find NCS groups from input model:        0.090
  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:             0.010
  Load rotamer database and sin/cos tables:14.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8082
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8383  Z= 0.205
  Angle     :  0.613   9.718  11335  Z= 0.338
  Chirality :  0.045   0.283   1244
  Planarity :  0.003   0.041   1428
  Dihedral  : 16.363  81.943   3098
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 19.45 %
    Favored  : 78.27 %
  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:  0.62 (0.27), residues: 1006
  helix:  1.75 (0.25), residues: 408
  sheet:  0.32 (0.35), residues: 239
  loop : -1.08 (0.32), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 300 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.017   0.001   PHE A 512 
 TYR   0.023   0.001   TYR B 938 
 ARG   0.011   0.001   ARG B1064 

*********************** 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
  147 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 127
  time to evaluate  : 0.858 
Fit side-chains
REVERT: A  379 ASP cc_start: 0.7003 (m-30) cc_final: 0.6546 (p0)
REVERT: B  937 MET cc_start: 0.4649 (OUTLIER) cc_final: 0.4298 (pp-130)
REVERT: B 1058 ASP cc_start: 0.6456 (OUTLIER) cc_final: 0.5889 (m-30)
  outliers start: 20
  outliers final: 15
  residues processed: 142
  average time/residue: 1.2304
  time to fit residues: 186.6355
Evaluate side-chains
  144 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  353 THR
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain A residue  706 SER
Chi-restraints excluded: chain B residue  908 SER
Chi-restraints excluded: chain B residue  921 SER
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1058 ASP
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain B residue 1218 SER
Chi-restraints excluded: chain B residue 1247 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 85 optimal weight:    0.8980
   chunk 76 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 26 optimal weight:    6.9990
   chunk 51 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 91 optimal weight:    0.6980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 378 HIS
A 387 HIS
A 434 ASN
A 568 ASN
** B 960 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 970 ASN
B1038 GLN
B1091 GLN
B1093 ASN
B1199 GLN
B1257 ASN
B1265 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.0743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8383  Z= 0.204
  Angle     :  0.529   6.263  11335  Z= 0.285
  Chirality :  0.044   0.277   1244
  Planarity :  0.003   0.030   1428
  Dihedral  :  6.829  57.696   1249
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 17.86 %
    Favored  : 79.52 %
  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:  2.16 (0.25), residues: 412
  sheet:  0.27 (0.34), residues: 244
  loop : -0.99 (0.33), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 494 
 PHE   0.013   0.001   PHE A 512 
 TYR   0.015   0.001   TYR B 938 
 ARG   0.004   0.000   ARG B1064 

*********************** 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
  163 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A  473 ARG cc_start: 0.7470 (OUTLIER) cc_final: 0.7208 (mtm-85)
REVERT: A  515 LYS cc_start: 0.7858 (ptpp) cc_final: 0.7566 (ptpp)
REVERT: B  937 MET cc_start: 0.4777 (OUTLIER) cc_final: 0.4548 (pp-130)
REVERT: B 1022 ASN cc_start: 0.8020 (t0) cc_final: 0.7663 (t0)
  outliers start: 23
  outliers final: 13
  residues processed: 151
  average time/residue: 1.2277
  time to fit residues: 197.6316
Evaluate side-chains
  144 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 129
  time to evaluate  : 1.855 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  473 ARG
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  540 THR
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  634 MET
Chi-restraints excluded: chain A residue  646 ASN
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  907 ASP
Chi-restraints excluded: chain B residue  923 THR
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 50 optimal weight:    0.9980
   chunk 28 optimal weight:    0.9990
   chunk 76 optimal weight:   10.0000
   chunk 62 optimal weight:    0.3980
   chunk 25 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   chunk 99 optimal weight:    3.9990
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 73 optimal weight:    5.9990
   chunk 90 optimal weight:    0.0870
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
B 970 ASN
B1003 GLN
B1038 GLN
B1093 ASN
B1199 GLN
B1257 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.0993

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8383  Z= 0.182
  Angle     :  0.497   5.738  11335  Z= 0.269
  Chirality :  0.043   0.265   1244
  Planarity :  0.003   0.031   1428
  Dihedral  :  5.669  49.287   1231
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 5.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 17.63 %
    Favored  : 78.84 %
  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:  2.29 (0.25), residues: 412
  sheet:  0.24 (0.35), residues: 240
  loop : -0.93 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.008   0.001   PHE A 459 
 TYR   0.021   0.001   TYR B1181 
 ARG   0.009   0.001   ARG B1064 

*********************** 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
  173 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 142
  time to evaluate  : 0.967 
Fit side-chains
REVERT: A  619 MET cc_start: 0.8108 (mmt) cc_final: 0.7716 (tpt)
REVERT: B 1037 ASP cc_start: 0.8345 (t0) cc_final: 0.7605 (m-30)
REVERT: B 1052 LYS cc_start: 0.7411 (OUTLIER) cc_final: 0.7084 (ttpp)
REVERT: B 1083 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7295 (mt-10)
  outliers start: 31
  outliers final: 11
  residues processed: 163
  average time/residue: 1.1602
  time to fit residues: 201.7840
Evaluate side-chains
  148 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 136
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  907 ASP
Chi-restraints excluded: chain B residue  923 THR
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1052 LYS
Chi-restraints excluded: chain B residue 1209 LEU
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:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 61 optimal weight:    0.9980
   chunk 92 optimal weight:    0.1980
   chunk 97 optimal weight:    1.9990
   chunk 48 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0870
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.4558

-------------------------------------------------------------------------------
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**
B 970 ASN
B1003 GLN
B1093 ASN
B1233 ASN
B1257 ASN
B1270 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8383  Z= 0.153
  Angle     :  0.477   6.320  11335  Z= 0.258
  Chirality :  0.042   0.257   1244
  Planarity :  0.003   0.030   1428
  Dihedral  :  5.058  40.475   1224
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 17.97 %
    Favored  : 78.27 %
  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:  1.14 (0.27), residues: 1006
  helix:  2.39 (0.25), residues: 413
  sheet:  0.14 (0.35), residues: 230
  loop : -0.74 (0.33), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 467 
 HIS   0.004   0.001   HIS A 494 
 PHE   0.015   0.001   PHE A 512 
 TYR   0.019   0.001   TYR B1181 
 ARG   0.009   0.000   ARG B1064 

*********************** 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
  170 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 137
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ASP cc_start: 0.8321 (m-30) cc_final: 0.8030 (m-30)
REVERT: A  619 MET cc_start: 0.8039 (mmt) cc_final: 0.7712 (tpt)
REVERT: B 1026 LYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7688 (ttpt)
REVERT: B 1028 LYS cc_start: 0.8334 (OUTLIER) cc_final: 0.7979 (mttp)
REVERT: B 1037 ASP cc_start: 0.8234 (t0) cc_final: 0.7531 (m-30)
REVERT: B 1052 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7092 (ttpp)
REVERT: B 1083 GLU cc_start: 0.7723 (mt-10) cc_final: 0.7296 (mt-10)
REVERT: B 1165 TYR cc_start: 0.6927 (t80) cc_final: 0.6643 (t80)
  outliers start: 33
  outliers final: 14
  residues processed: 160
  average time/residue: 1.1909
  time to fit residues: 203.7689
Evaluate side-chains
  141 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 124
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  907 ASP
Chi-restraints excluded: chain B residue  911 LYS
Chi-restraints excluded: chain B residue  923 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1026 LYS
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1052 LYS
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1247 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 55 optimal weight:    0.3980
   chunk 1 optimal weight:    0.6980
   chunk 72 optimal weight:    0.3980
   chunk 40 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 67 optimal weight:    4.9990
   chunk 0 optimal weight:    5.9990
   chunk 49 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
A 253 GLN
B 960 ASN
B 970 ASN
B1003 GLN
B1093 ASN
B1219 GLN
B1257 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8383  Z= 0.231
  Angle     :  0.516   5.572  11335  Z= 0.277
  Chirality :  0.044   0.310   1244
  Planarity :  0.003   0.036   1428
  Dihedral  :  5.097  40.700   1224
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 19.00 %
    Favored  : 77.02 %
  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:  0.99 (0.27), residues: 1006
  helix:  2.29 (0.25), residues: 412
  sheet:  0.14 (0.35), residues: 230
  loop : -0.91 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.003   0.001   HIS A 494 
 PHE   0.011   0.001   PHE A 184 
 TYR   0.017   0.001   TYR A 306 
 ARG   0.010   0.000   ARG B1064 

*********************** 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
  171 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 136
  time to evaluate  : 0.961 
Fit side-chains
REVERT: A  252 VAL cc_start: 0.6500 (OUTLIER) cc_final: 0.6295 (p)
REVERT: A  619 MET cc_start: 0.8099 (mmt) cc_final: 0.7728 (tpt)
REVERT: A  634 MET cc_start: 0.7760 (OUTLIER) cc_final: 0.7549 (mmm)
REVERT: B  882 VAL cc_start: 0.7714 (m) cc_final: 0.7491 (p)
REVERT: B 1026 LYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7832 (ttpt)
REVERT: B 1028 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.8008 (mttp)
REVERT: B 1052 LYS cc_start: 0.7420 (OUTLIER) cc_final: 0.7100 (ttpp)
REVERT: B 1058 ASP cc_start: 0.6716 (OUTLIER) cc_final: 0.6131 (m-30)
REVERT: B 1083 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7347 (mt-10)
REVERT: B 1165 TYR cc_start: 0.6930 (t80) cc_final: 0.6630 (t80)
  outliers start: 35
  outliers final: 16
  residues processed: 158
  average time/residue: 1.1893
  time to fit residues: 200.4958
Evaluate side-chains
  156 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 134
  time to evaluate  : 0.921 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  634 MET
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  907 ASP
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1026 LYS
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1052 LYS
Chi-restraints excluded: chain B residue 1058 ASP
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1125 VAL
Chi-restraints excluded: chain B residue 1204 LYS
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 87 optimal weight:    0.9980
   chunk 19 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 97 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9980
   chunk 94 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 513 ASN
B 970 ASN
B1003 GLN
B1093 ASN
B1199 GLN
B1219 GLN
B1257 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8383  Z= 0.251
  Angle     :  0.529   6.669  11335  Z= 0.283
  Chirality :  0.045   0.301   1244
  Planarity :  0.003   0.034   1428
  Dihedral  :  5.145  43.293   1224
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  4.78 %
    Allowed  : 19.00 %
    Favored  : 76.22 %
  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:  0.90 (0.27), residues: 1006
  helix:  2.20 (0.25), residues: 411
  sheet:  0.09 (0.35), residues: 230
  loop : -0.93 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.018   0.001   PHE A 512 
 TYR   0.016   0.001   TYR A 306 
 ARG   0.010   0.001   ARG B1064 

*********************** 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
  180 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 138
  time to evaluate  : 0.945 
Fit side-chains
   revert: symmetry clash
REVERT: A  517 ILE cc_start: 0.9183 (OUTLIER) cc_final: 0.8830 (mm)
REVERT: A  619 MET cc_start: 0.8111 (mmt) cc_final: 0.7688 (tpt)
REVERT: B  882 VAL cc_start: 0.7708 (m) cc_final: 0.7470 (p)
REVERT: B 1028 LYS cc_start: 0.8367 (OUTLIER) cc_final: 0.7982 (mttp)
REVERT: B 1037 ASP cc_start: 0.8334 (t0) cc_final: 0.8016 (t70)
REVERT: B 1052 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7144 (ttpp)
REVERT: B 1083 GLU cc_start: 0.7782 (mt-10) cc_final: 0.7331 (mt-10)
REVERT: B 1165 TYR cc_start: 0.6877 (t80) cc_final: 0.6558 (t80)
  outliers start: 42
  outliers final: 20
  residues processed: 168
  average time/residue: 1.1938
  time to fit residues: 213.9776
Evaluate side-chains
  157 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 134
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  583 CYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  907 ASP
Chi-restraints excluded: chain B residue  911 LYS
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1052 LYS
Chi-restraints excluded: chain B residue 1125 VAL
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain B residue 1204 LYS
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 11 optimal weight:    0.9990
   chunk 55 optimal weight:    0.8980
   chunk 71 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   chunk 54 optimal weight:    0.5980
   chunk 97 optimal weight:    3.9990
   chunk 60 optimal weight:    0.3980
   chunk 59 optimal weight:    0.9990
   chunk 44 optimal weight:    0.0870
   chunk 38 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
B 970 ASN
B1003 GLN
B1219 GLN
B1257 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.1638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8383  Z= 0.168
  Angle     :  0.498   8.429  11335  Z= 0.267
  Chirality :  0.043   0.285   1244
  Planarity :  0.003   0.041   1428
  Dihedral  :  4.995  42.325   1224
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.16 %
    Favored  : 75.31 %
  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:  1.02 (0.27), residues: 1006
  helix:  2.35 (0.25), residues: 412
  sheet:  0.08 (0.35), residues: 229
  loop : -0.88 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.008   0.001   PHE A 459 
 TYR   0.012   0.001   TYR A 306 
 ARG   0.011   0.000   ARG B1064 

*********************** 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
  168 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
REVERT: A  382 MET cc_start: 0.7092 (mmt) cc_final: 0.6816 (mpt)
REVERT: A  493 GLU cc_start: 0.7126 (OUTLIER) cc_final: 0.6833 (pm20)
REVERT: A  517 ILE cc_start: 0.9147 (OUTLIER) cc_final: 0.8813 (mm)
REVERT: A  619 MET cc_start: 0.8070 (mmt) cc_final: 0.7703 (tpt)
REVERT: B  882 VAL cc_start: 0.7690 (m) cc_final: 0.7465 (p)
REVERT: B  925 GLU cc_start: 0.5949 (mm-30) cc_final: 0.5662 (tp30)
REVERT: B  937 MET cc_start: 0.4887 (OUTLIER) cc_final: 0.4677 (pp-130)
REVERT: B 1026 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7656 (ttmt)
REVERT: B 1028 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.7946 (mttp)
REVERT: B 1037 ASP cc_start: 0.8236 (t0) cc_final: 0.7861 (t70)
REVERT: B 1038 GLN cc_start: 0.8534 (pt0) cc_final: 0.8119 (pt0)
REVERT: B 1052 LYS cc_start: 0.7429 (OUTLIER) cc_final: 0.6605 (ttpp)
REVERT: B 1083 GLU cc_start: 0.7774 (mt-10) cc_final: 0.7348 (mt-10)
REVERT: B 1165 TYR cc_start: 0.6830 (t80) cc_final: 0.6555 (t80)
  outliers start: 31
  outliers final: 18
  residues processed: 159
  average time/residue: 1.1877
  time to fit residues: 201.0977
Evaluate side-chains
  157 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 133
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  583 CYS
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  911 LYS
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  990 ASN
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1026 LYS
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1052 LYS
Chi-restraints excluded: chain B residue 1125 VAL
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain B residue 1204 LYS
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1247 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0170
   chunk 61 optimal weight:    8.9990
   chunk 66 optimal weight:    0.3980
   chunk 48 optimal weight:    3.9990
   chunk 9 optimal weight:    2.9990
   chunk 76 optimal weight:   10.0000
   chunk 88 optimal weight:    0.6980
   chunk 93 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.8020

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 513 ASN
B 970 ASN
B1003 GLN
B1199 GLN
B1257 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.1740

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8383  Z= 0.198
  Angle     :  0.508   6.995  11335  Z= 0.271
  Chirality :  0.044   0.280   1244
  Planarity :  0.003   0.044   1428
  Dihedral  :  4.921  41.305   1223
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.75 %
    Allowed  : 21.39 %
    Favored  : 74.86 %
  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:  1.04 (0.27), residues: 1006
  helix:  2.34 (0.25), residues: 413
  sheet:  0.07 (0.35), residues: 229
  loop : -0.83 (0.32), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.018   0.001   PHE A 512 
 TYR   0.014   0.001   TYR A 306 
 ARG   0.012   0.001   ARG B1064 

*********************** 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
  164 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 131
  time to evaluate  : 0.997 
Fit side-chains
   revert: symmetry clash
REVERT: A  493 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6829 (pm20)
REVERT: A  517 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8831 (mm)
REVERT: A  619 MET cc_start: 0.8085 (mmt) cc_final: 0.7690 (tpt)
REVERT: B  882 VAL cc_start: 0.7713 (m) cc_final: 0.7484 (p)
REVERT: B 1028 LYS cc_start: 0.8374 (OUTLIER) cc_final: 0.8011 (mttp)
REVERT: B 1037 ASP cc_start: 0.8273 (t0) cc_final: 0.7942 (t70)
REVERT: B 1038 GLN cc_start: 0.8565 (pt0) cc_final: 0.8082 (pt0)
REVERT: B 1052 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7224 (ttpp)
REVERT: B 1083 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7352 (mt-10)
REVERT: B 1165 TYR cc_start: 0.6854 (t80) cc_final: 0.6586 (t80)
  outliers start: 33
  outliers final: 20
  residues processed: 154
  average time/residue: 1.1785
  time to fit residues: 193.5494
Evaluate side-chains
  154 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 130
  time to evaluate  : 0.928 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  583 CYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  899 ASN
Chi-restraints excluded: chain B residue  911 LYS
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  990 ASN
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1052 LYS
Chi-restraints excluded: chain B residue 1125 VAL
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain B residue 1204 LYS
Chi-restraints excluded: chain B residue 1247 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 90 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 39 optimal weight:    4.9990
   chunk 71 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 59 optimal weight:    5.9990
   chunk 95 optimal weight:    0.9990
   chunk 58 optimal weight:    0.1980
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 513 ASN
B 970 ASN
B1257 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.1810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8383  Z= 0.215
  Angle     :  0.517   6.891  11335  Z= 0.277
  Chirality :  0.044   0.280   1244
  Planarity :  0.003   0.041   1428
  Dihedral  :  4.940  41.002   1223
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 5.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 21.73 %
    Favored  : 74.74 %
  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:  2.33 (0.25), residues: 411
  sheet: -0.04 (0.34), residues: 239
  loop : -0.86 (0.33), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.009   0.001   PHE A 459 
 TYR   0.022   0.001   TYR B1133 
 ARG   0.011   0.000   ARG B1064 

*********************** 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
  162 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 0.938 
Fit side-chains
REVERT: A  382 MET cc_start: 0.7046 (mmt) cc_final: 0.6722 (mpt)
REVERT: A  493 GLU cc_start: 0.7144 (OUTLIER) cc_final: 0.6822 (pm20)
REVERT: A  517 ILE cc_start: 0.9191 (OUTLIER) cc_final: 0.8862 (mm)
REVERT: A  619 MET cc_start: 0.8107 (mmt) cc_final: 0.7718 (tpt)
REVERT: B  882 VAL cc_start: 0.7731 (m) cc_final: 0.7507 (p)
REVERT: B  925 GLU cc_start: 0.6037 (mm-30) cc_final: 0.5819 (tp30)
REVERT: B 1026 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7554 (ttmt)
REVERT: B 1028 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.8010 (mttp)
REVERT: B 1037 ASP cc_start: 0.8215 (t0) cc_final: 0.7863 (t70)
REVERT: B 1038 GLN cc_start: 0.8550 (pt0) cc_final: 0.8069 (pt0)
REVERT: B 1083 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7350 (mt-10)
REVERT: B 1165 TYR cc_start: 0.6831 (t80) cc_final: 0.6535 (t80)
  outliers start: 31
  outliers final: 21
  residues processed: 151
  average time/residue: 1.2451
  time to fit residues: 200.3201
Evaluate side-chains
  153 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.959 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  583 CYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue  990 ASN
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1026 LYS
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain B residue 1204 LYS
Chi-restraints excluded: chain B residue 1209 LEU
Chi-restraints excluded: chain B residue 1247 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 45 optimal weight:    0.6980
   chunk 66 optimal weight:    0.5980
   chunk 100 optimal weight:    2.9990
   chunk 92 optimal weight:    0.4980
   chunk 80 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 49 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 85 optimal weight:    0.8980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 513 ASN
B 970 ASN
B1257 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8128
moved from start:          0.1862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8383  Z= 0.192
  Angle     :  0.511   7.168  11335  Z= 0.271
  Chirality :  0.043   0.273   1244
  Planarity :  0.003   0.040   1428
  Dihedral  :  4.860  40.692   1223
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.07 %
    Favored  : 74.52 %
  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:  1.01 (0.27), residues: 1006
  helix:  2.34 (0.25), residues: 413
  sheet: -0.03 (0.34), residues: 239
  loop : -0.83 (0.33), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.005   0.001   HIS A 387 
 PHE   0.019   0.001   PHE A 512 
 TYR   0.018   0.001   TYR B1133 
 ARG   0.011   0.001   ARG B1064 

********************** 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
  158 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  382 MET cc_start: 0.7021 (mmt) cc_final: 0.6745 (mpt)
REVERT: A  493 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6822 (pm20)
REVERT: A  517 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8847 (mm)
REVERT: A  619 MET cc_start: 0.8100 (mmt) cc_final: 0.7706 (tpt)
REVERT: B  882 VAL cc_start: 0.7729 (m) cc_final: 0.7500 (p)
REVERT: B 1026 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7478 (ttmt)
REVERT: B 1028 LYS cc_start: 0.8348 (OUTLIER) cc_final: 0.7987 (mttp)
REVERT: B 1037 ASP cc_start: 0.8196 (t0) cc_final: 0.7831 (t70)
REVERT: B 1038 GLN cc_start: 0.8578 (pt0) cc_final: 0.8024 (pt0)
REVERT: B 1083 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7350 (mt-10)
REVERT: B 1165 TYR cc_start: 0.6927 (t80) cc_final: 0.6654 (t80)
  outliers start: 30
  outliers final: 21
  residues processed: 148
  average time/residue: 1.2303
  time to fit residues: 193.8247
Evaluate side-chains
  153 residues out of total 879 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 128
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  206 MET
Chi-restraints excluded: chain A residue  369 GLU
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  493 GLU
Chi-restraints excluded: chain A residue  517 ILE
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 GLU
Chi-restraints excluded: chain A residue  583 CYS
Chi-restraints excluded: chain A residue  588 THR
Chi-restraints excluded: chain A residue  608 VAL
Chi-restraints excluded: chain A residue  655 LEU
Chi-restraints excluded: chain A residue  665 SER
Chi-restraints excluded: chain A residue  674 VAL
Chi-restraints excluded: chain B residue  899 ASN
Chi-restraints excluded: chain B residue  907 ASP
Chi-restraints excluded: chain B residue  937 MET
Chi-restraints excluded: chain B residue  943 THR
Chi-restraints excluded: chain B residue  977 SER
Chi-restraints excluded: chain B residue 1018 THR
Chi-restraints excluded: chain B residue 1026 LYS
Chi-restraints excluded: chain B residue 1028 LYS
Chi-restraints excluded: chain B residue 1074 LEU
Chi-restraints excluded: chain B residue 1158 THR
Chi-restraints excluded: chain B residue 1204 LYS
Chi-restraints excluded: chain B residue 1209 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 73 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0980
   chunk 22 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 33 optimal weight:    0.2980
   chunk 82 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 70 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9990
   chunk 57 optimal weight:    2.9990
   overall best weight:    0.6182

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
A 513 ASN
B 970 ASN
B1003 GLN
B1093 ASN
B1257 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.175118 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.134852 restraints weight = 9017.943|
|-----------------------------------------------------------------------------|
r_work (start): 0.3412 rms_B_bonded: 2.15
r_work: 0.3241 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work: 0.3095 rms_B_bonded: 4.74 restraints_weight: 0.2500
r_work (final): 0.3095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.1925

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8383  Z= 0.175
  Angle     :  0.505   6.820  11335  Z= 0.270
  Chirality :  0.043   0.264   1244
  Planarity :  0.003   0.040   1428
  Dihedral  :  4.805  39.872   1223
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 22.30 %
    Favored  : 74.29 %
  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:  1.06 (0.27), residues: 1006
  helix:  2.41 (0.25), residues: 412
  sheet: -0.02 (0.34), residues: 239
  loop : -0.83 (0.33), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 467 
 HIS   0.006   0.001   HIS A 387 
 PHE   0.009   0.001   PHE A 459 
 TYR   0.018   0.001   TYR B1133 
 ARG   0.010   0.000   ARG B1064 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3740.10 seconds
wall clock time: 67 minutes 42.05 seconds (4062.05 seconds total)