Starting phenix.real_space_refine
on Fri Mar 14 06:55:20 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wi2_37555/03_2025/8wi2_37555.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wi2_37555/03_2025/8wi2_37555.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.06
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wi2_37555/03_2025/8wi2_37555.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wi2_37555/03_2025/8wi2_37555.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wi2_37555/03_2025/8wi2_37555.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wi2_37555/03_2025/8wi2_37555.cif"
  }
  resolution = 4.06
  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=   0.003 sd=   0.035
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      57      5.16       5
     C    6131      2.51       5
     N    1621      2.21       5
     O    1728      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9537
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1200, 9439
          Classifications: {'peptide': 1200}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 1163}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 98
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 98
          Classifications: {'peptide': 14}
          Link IDs: {'TRANS': 13}
  Time building chain proxies: 5.46, per 1000 atoms: 0.57
  Number of scatterers: 9537
  At special positions: 0
  Unit cell: (76.95, 113.715, 153.9, 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      57     16.00
     O    1728      8.00
     N    1621      7.00
     C    6131      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.29
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2286

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 7 sheets defined
      69.6% alpha, 6.5% 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 105 through 112
    Processing helix  chain 'A' and resid 112 through 126
    Processing helix  chain 'A' and resid 129 through 133
      removed outlier: 3.725A  pdb=" N   VAL A 133 " --> pdb=" O   MET A 130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 140
    Processing helix  chain 'A' and resid 141 through 161
    Processing helix  chain 'A' and resid 166 through 210
      removed outlier: 3.644A  pdb=" N   VAL A 170 " --> pdb=" O   SER A 166 " (cutoff:3.500A)
      removed outlier: 5.436A  pdb=" N   THR A 177 " --> pdb=" O   ILE A 173 " (cutoff:3.500A)
      removed outlier: 6.257A  pdb=" N   ARG A 178 " --> pdb=" O   PHE A 174 " (cutoff:3.500A)
      Proline residue:  A 197  - end of helix
    Processing helix  chain 'A' and resid 214 through 264
      removed outlier: 3.729A  pdb=" N   SER A 218 " --> pdb=" O   ASN A 214 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU A 220 " --> pdb=" O   GLN A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 279
    Processing helix  chain 'A' and resid 282 through 298
    Processing helix  chain 'A' and resid 300 through 316
    Processing helix  chain 'A' and resid 318 through 324
      removed outlier: 4.174A  pdb=" N   GLY A 322 " --> pdb=" O   THR A 318 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 364
      Proline residue:  A 331  - end of helix
      removed outlier: 3.763A  pdb=" N   ALA A 349 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   TYR A 364 " --> pdb=" O   GLU A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 370
    Processing helix  chain 'A' and resid 373 through 402
      removed outlier: 3.937A  pdb=" N   PHE A 377 " --> pdb=" O   TRP A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 424
      removed outlier: 4.195A  pdb=" N   ILE A 408 " --> pdb=" O   GLY A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 429 through 470
      Proline residue:  A 451  - end of helix
    Processing helix  chain 'A' and resid 600 through 610
    Processing helix  chain 'A' and resid 638 through 645
      removed outlier: 3.708A  pdb=" N   ASN A 642 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ILE A 643 " --> pdb=" O   LEU A 639 " (cutoff:3.500A)
      removed outlier: 4.106A  pdb=" N   LEU A 644 " --> pdb=" O   ARG A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 651 through 661
    Processing helix  chain 'A' and resid 663 through 670
      removed outlier: 3.535A  pdb=" N   LEU A 670 " --> pdb=" O   ASP A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 672 through 676
      removed outlier: 3.632A  pdb=" N   THR A 676 " --> pdb=" O   SER A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 702
      removed outlier: 3.688A  pdb=" N   ASP A 702 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 728
    Processing helix  chain 'A' and resid 744 through 748
      removed outlier: 3.731A  pdb=" N   LEU A 747 " --> pdb=" O   LEU A 744 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   VAL A 748 " --> pdb=" O   GLN A 745 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 744 through 748'
    Processing helix  chain 'A' and resid 766 through 773
    Processing helix  chain 'A' and resid 775 through 786
      removed outlier: 3.758A  pdb=" N   THR A 779 " --> pdb=" O   GLY A 775 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ASN A 783 " --> pdb=" O   THR A 779 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   LEU A 784 " --> pdb=" O   ILE A 780 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU A 785 " --> pdb=" O   PHE A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 842 through 854
      removed outlier: 4.119A  pdb=" N   TYR A 846 " --> pdb=" O   PRO A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 855 through 887
      removed outlier: 3.982A  pdb=" N   PHE A 859 " --> pdb=" O   GLY A 855 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLY A 887 " --> pdb=" O   TRP A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 908
    Processing helix  chain 'A' and resid 910 through 956
    Processing helix  chain 'A' and resid 959 through 966
      removed outlier: 4.406A  pdb=" N   PHE A 963 " --> pdb=" O   PRO A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 967 through 1011
      removed outlier: 4.167A  pdb=" N   ILE A 971 " --> pdb=" O   PRO A 967 " (cutoff:3.500A)
      removed outlier: 4.075A  pdb=" N   ASP A 978 " --> pdb=" O   ARG A 974 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   MET A 979 " --> pdb=" O   PHE A 975 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP A 980 " --> pdb=" O   SER A 976 " (cutoff:3.500A)
      Proline residue:  A 987  - end of helix
    Processing helix  chain 'A' and resid 1011 through 1060
      removed outlier: 3.800A  pdb=" N   LEU A1015 " --> pdb=" O   PHE A1011 " (cutoff:3.500A)
      Proline residue:  A1020  - end of helix
      Proline residue:  A1049  - end of helix
      removed outlier: 3.771A  pdb=" N   GLY A1060 " --> pdb=" O   SER A1056 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1060 through 1068
    Processing helix  chain 'A' and resid 1069 through 1120
      removed outlier: 3.549A  pdb=" N   PHE A1073 " --> pdb=" O   LYS A1069 " (cutoff:3.500A)
      Proline residue:  A1087  - end of helix
      removed outlier: 3.892A  pdb=" N   MET A1120 " --> pdb=" O   MET A1116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1125 through 1139
      removed outlier: 3.505A  pdb=" N   ALA A1129 " --> pdb=" O   PRO A1125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1169
    Processing helix  chain 'A' and resid 1234 through 1241
      removed outlier: 4.026A  pdb=" N   MET A1238 " --> pdb=" O   SER A1234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1261
      No H-bonds generated for 'chain 'A' and resid 1259 through 1261'
    Processing helix  chain 'A' and resid 1262 through 1268
    Processing helix  chain 'A' and resid 1284 through 1289
    Processing helix  chain 'A' and resid 1295 through 1307
    Processing helix  chain 'A' and resid 1308 through 1312
    Processing helix  chain 'A' and resid 1324 through 1328
      removed outlier: 3.721A  pdb=" N   ASP A1328 " --> pdb=" O   GLU A1325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1331 through 1345
    Processing helix  chain 'A' and resid 1363 through 1376
      removed outlier: 3.585A  pdb=" N   PHE A1376 " --> pdb=" O   ILE A1372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1387 through 1392
      removed outlier: 3.518A  pdb=" N   VAL A1391 " --> pdb=" O   ARG A1387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1410 through 1416
    Processing helix  chain 'A' and resid 1420 through 1424
    Processing helix  chain 'B' and resid 50 through 59
      removed outlier: 3.761A  pdb=" N   ALA B  54 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   ARG B  55 " --> pdb=" O   GLU B  51 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLU B  57 " --> pdb=" O   ALA B  53 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   GLY B  58 " --> pdb=" O   ALA B  54 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 576 through 585
      removed outlier: 6.902A  pdb=" N   LEU A 497 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
      removed outlier: 5.095A  pdb=" N   HIS A 579 " --> pdb=" O   ALA A 495 " (cutoff:3.500A)
      removed outlier: 7.251A  pdb=" N   ALA A 495 " --> pdb=" O   HIS A 579 " (cutoff:3.500A)
      removed outlier: 6.937A  pdb=" N   ILE A 581 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   LYS A 493 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
      removed outlier: 7.822A  pdb=" N   LEU A 583 " --> pdb=" O   GLU A 491 " (cutoff:3.500A)
      removed outlier: 5.676A  pdb=" N   GLU A 491 " --> pdb=" O   LEU A 583 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   SER A 618 " --> pdb=" O   LYS A 493 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 625 through 626
      removed outlier: 5.823A  pdb=" N   ALA A 626 " --> pdb=" O   ILE A 707 " (cutoff:3.500A)
      removed outlier: 7.578A  pdb=" N   ASP A 709 " --> pdb=" O   ALA A 626 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   TYR A 706 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   VAL A 740 " --> pdb=" O   TYR A 706 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   LEU A 708 " --> pdb=" O   VAL A 740 " (cutoff:3.500A)
      removed outlier: 6.294A  pdb=" N   VAL A 591 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   LEU A 590 " --> pdb=" O   GLU A 752 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   ILE A 754 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
      removed outlier: 6.133A  pdb=" N   GLY A 592 " --> pdb=" O   ILE A 754 " (cutoff:3.500A)
      removed outlier: 7.206A  pdb=" N   MET A 756 " --> pdb=" O   GLY A 592 " (cutoff:3.500A)
      removed outlier: 6.160A  pdb=" N   CYS A 594 " --> pdb=" O   MET A 756 " (cutoff:3.500A)
      removed outlier: 7.500A  pdb=" N   VAL A 753 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
      removed outlier: 5.235A  pdb=" N   ARG A 764 " --> pdb=" O   VAL A 753 " (cutoff:3.500A)
      removed outlier: 7.909A  pdb=" N   PHE A 755 " --> pdb=" O   THR A 762 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   THR A 762 " --> pdb=" O   PHE A 755 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LYS A 757 " --> pdb=" O   CYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 892 through 894
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1216 through 1217
      removed outlier: 3.504A  pdb=" N   VAL A1193 " --> pdb=" O   ILE A1217 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1200 through 1201
      removed outlier: 3.534A  pdb=" N   MET A1200 " --> pdb=" O   LEU A1210 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1270 through 1273
      removed outlier: 3.699A  pdb=" N   SER A1271 " --> pdb=" O   ILE A1350 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   ILE A1352 " --> pdb=" O   SER A1271 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   LEU A1351 " --> pdb=" O   THR A1380 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   LEU A1382 " --> pdb=" O   LEU A1351 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   ILE A1223 " --> pdb=" O   THR A1383 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LYS A1222 " --> pdb=" O   ARG A1396 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   MET A1398 " --> pdb=" O   LYS A1222 " (cutoff:3.500A)
      removed outlier: 6.188A  pdb=" N   GLY A1224 " --> pdb=" O   MET A1398 " (cutoff:3.500A)
      removed outlier: 7.453A  pdb=" N   LEU A1400 " --> pdb=" O   GLY A1224 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   VAL A1226 " --> pdb=" O   LEU A1400 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1282 through 1283

    610 hydrogen bonds defined for protein.
    1788 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: 3.24

  Time building geometry restraints manager: 2.72 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3073
        1.35 -     1.46: 2216
        1.46 -     1.58: 4334
        1.58 -     1.70: 0
        1.70 -     1.82: 96
  Bond restraints: 9719
  Sorted by residual:
  bond pdb=" CA  THR A 450 "
       pdb=" C   THR A 450 "
    ideal  model  delta    sigma   weight residual
    1.522  1.542 -0.021 1.26e-02 6.30e+03 2.65e+00
  bond pdb=" CG  MET A 370 "
       pdb=" SD  MET A 370 "
    ideal  model  delta    sigma   weight residual
    1.803  1.774  0.029 2.50e-02 1.60e+03 1.37e+00
  bond pdb=" CA  SER A1048 "
       pdb=" C   SER A1048 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 1.23e-02 6.61e+03 1.10e+00
  bond pdb=" CA  ILE A1384 "
       pdb=" CB  ILE A1384 "
    ideal  model  delta    sigma   weight residual
    1.540  1.526  0.014 1.36e-02 5.41e+03 1.04e+00
  bond pdb=" CB  ASP A 980 "
       pdb=" CG  ASP A 980 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 2.50e-02 1.60e+03 9.62e-01
  ... (remaining 9714 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 12841
        1.73 -     3.46: 233
        3.46 -     5.19: 48
        5.19 -     6.92: 21
        6.92 -     8.65: 11
  Bond angle restraints: 13154
  Sorted by residual:
  angle pdb=" N   MET A 443 "
        pdb=" CA  MET A 443 "
        pdb=" CB  MET A 443 "
      ideal   model   delta    sigma   weight residual
     110.28  116.35   -6.07 1.55e+00 4.16e-01 1.54e+01
  angle pdb=" C   LYS A 369 "
        pdb=" N   MET A 370 "
        pdb=" CA  MET A 370 "
      ideal   model   delta    sigma   weight residual
     121.94  114.99    6.95 2.00e+00 2.50e-01 1.21e+01
  angle pdb=" N   THR A 450 "
        pdb=" CA  THR A 450 "
        pdb=" C   THR A 450 "
      ideal   model   delta    sigma   weight residual
     113.16  117.62   -4.46 1.42e+00 4.96e-01 9.86e+00
  angle pdb=" C   SER A 442 "
        pdb=" N   MET A 443 "
        pdb=" CA  MET A 443 "
      ideal   model   delta    sigma   weight residual
     120.31  115.78    4.53 1.52e+00 4.33e-01 8.87e+00
  angle pdb=" N   GLY A1070 "
        pdb=" CA  GLY A1070 "
        pdb=" C   GLY A1070 "
      ideal   model   delta    sigma   weight residual
     112.73  115.90   -3.17 1.20e+00 6.94e-01 6.97e+00
  ... (remaining 13149 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.82: 4936
       17.82 -    35.64: 673
       35.64 -    53.45: 188
       53.45 -    71.27: 22
       71.27 -    89.09: 17
  Dihedral angle restraints: 5836
    sinusoidal: 2312
      harmonic: 3524
  Sorted by residual:
  dihedral pdb=" CA  THR A 450 "
           pdb=" C   THR A 450 "
           pdb=" N   PRO A 451 "
           pdb=" CA  PRO A 451 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.58  -18.42     0      5.00e+00 4.00e-02 1.36e+01
  dihedral pdb=" CA  ASP A1378 "
           pdb=" CB  ASP A1378 "
           pdb=" CG  ASP A1378 "
           pdb=" OD1 ASP A1378 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -89.83   59.83     1      2.00e+01 2.50e-03 1.19e+01
  dihedral pdb=" CA  ASP A 776 "
           pdb=" CB  ASP A 776 "
           pdb=" CG  ASP A 776 "
           pdb=" OD1 ASP A 776 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -86.88   56.88     1      2.00e+01 2.50e-03 1.09e+01
  ... (remaining 5833 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.046: 1221
       0.046 -    0.092: 258
       0.092 -    0.138: 60
       0.138 -    0.184: 4
       0.184 -    0.230: 1
  Chirality restraints: 1544
  Sorted by residual:
  chirality pdb=" CB  ILE A 180 "
            pdb=" CA  ILE A 180 "
            pdb=" CG1 ILE A 180 "
            pdb=" CG2 ILE A 180 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.41    0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" CA  THR A 450 "
            pdb=" N   THR A 450 "
            pdb=" C   THR A 450 "
            pdb=" CB  THR A 450 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.35    0.18 2.00e-01 2.50e+01 8.11e-01
  chirality pdb=" CA  MET A 443 "
            pdb=" N   MET A 443 "
            pdb=" C   MET A 443 "
            pdb=" CB  MET A 443 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.65e-01
  ... (remaining 1541 not shown)

  Planarity restraints: 1645
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 316 "    0.039 5.00e-02 4.00e+02   5.95e-02 5.67e+00
        pdb=" N   PRO A 317 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 317 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 317 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 330 "    0.039 5.00e-02 4.00e+02   5.93e-02 5.62e+00
        pdb=" N   PRO A 331 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 331 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 331 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 982 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.07e+00
        pdb=" C   VAL A 982 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   VAL A 982 "    0.011 2.00e-02 2.50e+03
        pdb=" N   ASP A 983 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1642 not shown)

  Histogram of nonbonded interaction distances:
        2.11 -     2.66: 160
        2.66 -     3.22: 9490
        3.22 -     3.78: 15817
        3.78 -     4.34: 18947
        4.34 -     4.90: 31029
  Nonbonded interactions: 75443
  Sorted by model distance:
  nonbonded pdb=" O   THR A 450 "
            pdb=" OG  SER A 453 "
     model   vdw
     2.106 3.040
  nonbonded pdb=" OG1 THR A 496 "
            pdb=" OE1 GLU A 616 "
     model   vdw
     2.151 3.040
  nonbonded pdb=" O   ASN A 359 "
            pdb=" OG1 THR A 363 "
     model   vdw
     2.226 3.040
  nonbonded pdb=" O   LEU A 186 "
            pdb=" OG1 THR A 189 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OG  SER A 137 "
            pdb=" OE1 GLU A 140 "
     model   vdw
     2.258 3.040
  ... (remaining 75438 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.660
  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:          0.380
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     23.620
  Find NCS groups from input model:        0.080
  Set up NCS constraints:                  0.050
  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:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
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   0.033   9719  Z= 0.177
  Angle     :  0.660   8.654  13154  Z= 0.344
  Chirality :  0.040   0.230   1544
  Planarity :  0.004   0.060   1645
  Dihedral  : 17.703  89.089   3550
  Min Nonbonded Distance : 2.106

Molprobity Statistics.
  All-atom Clashscore : 11.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 32.38 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.25), residues: 1202
  helix:  2.13 (0.19), residues: 753
  sheet:  2.30 (0.71), residues: 64
  loop : -0.07 (0.33), residues: 385

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 240 
 HIS   0.002   0.001   HIS A1165 
 PHE   0.019   0.001   PHE A1014 
 TYR   0.016   0.001   TYR A 397 
 ARG   0.002   0.000   ARG A 389 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  886 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8779 (tp40)
REVERT: A 1238 MET cc_start: 0.9115 (mpp) cc_final: 0.8861 (mpp)
  outliers start: 7
  outliers final: 3
  residues processed: 110
  average time/residue: 0.1759
  time to fit residues: 29.8753
Evaluate side-chains
  105 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 102 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 50 optimal weight:    0.1980
   chunk 31 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 48 optimal weight:    7.9990
   chunk 94 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 70 optimal weight:    4.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    2.6386

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

Flipped N/Q/H residues before XYZ refinement:
A  97 HIS
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 575 GLN
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 908 ASN
A 996 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3883 r_free = 0.3883 target = 0.087878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.073329 restraints weight = 49106.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.075154 restraints weight = 26562.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.076400 restraints weight = 17036.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.1957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   9719  Z= 0.263
  Angle     :  0.621   7.190  13154  Z= 0.328
  Chirality :  0.041   0.189   1544
  Planarity :  0.005   0.058   1645
  Dihedral  :  3.866  16.896   1305
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 10.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.87 %
    Favored  : 95.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.95 (0.25), residues: 1202
  helix:  1.97 (0.19), residues: 758
  sheet:  1.85 (0.64), residues: 74
  loop : -0.22 (0.33), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 114 
 HIS   0.006   0.001   HIS A1165 
 PHE   0.021   0.002   PHE A1145 
 TYR   0.023   0.002   TYR A 918 
 ARG   0.008   0.000   ARG A1148 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.081 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9344 (mmm) cc_final: 0.9014 (tpp)
REVERT: A  771 MET cc_start: 0.5377 (mpp) cc_final: 0.4994 (mpp)
REVERT: A 1103 ASP cc_start: 0.8033 (t0) cc_final: 0.7806 (t0)
REVERT: A 1238 MET cc_start: 0.8620 (mpp) cc_final: 0.8292 (mpp)
REVERT: A 1389 HIS cc_start: 0.8463 (m90) cc_final: 0.8111 (m90)
  outliers start: 1
  outliers final: 1
  residues processed: 146
  average time/residue: 0.2147
  time to fit residues: 46.1090
Evaluate side-chains
  95 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 1.003 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 93 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 19 optimal weight:    6.9990
   chunk 26 optimal weight:    9.9990
   chunk 82 optimal weight:    4.9990
   chunk 52 optimal weight:    8.9990
   chunk 120 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9990
   chunk 95 optimal weight:    0.3980
   chunk 37 optimal weight:    0.7980
   overall best weight:    1.6386

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 611 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 721 ASN
A 996 ASN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.086481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3531 r_free = 0.3531 target = 0.072029 restraints weight = 49134.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.073852 restraints weight = 26516.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.075101 restraints weight = 16913.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3598
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9719  Z= 0.193
  Angle     :  0.571   8.237  13154  Z= 0.299
  Chirality :  0.040   0.176   1544
  Planarity :  0.004   0.057   1645
  Dihedral  :  3.819  15.896   1305
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.01 %
    Favored  : 95.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.88 (0.25), residues: 1202
  helix:  1.93 (0.18), residues: 764
  sheet:  1.52 (0.64), residues: 74
  loop : -0.24 (0.34), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A  97 
 PHE   0.021   0.002   PHE A 975 
 TYR   0.021   0.001   TYR A 918 
 ARG   0.006   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 1.004 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9343 (mmm) cc_final: 0.9049 (tpp)
REVERT: A  387 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7859 (tm-30)
REVERT: A  771 MET cc_start: 0.5275 (mpp) cc_final: 0.5036 (mpp)
REVERT: A  911 MET cc_start: 0.7831 (ppp) cc_final: 0.7494 (ppp)
REVERT: A 1103 ASP cc_start: 0.8057 (t0) cc_final: 0.7835 (t0)
REVERT: A 1238 MET cc_start: 0.8539 (mpp) cc_final: 0.8205 (mpp)
REVERT: A 1308 MET cc_start: 0.7938 (tpp) cc_final: 0.6402 (tpp)
REVERT: A 1389 HIS cc_start: 0.8355 (m90) cc_final: 0.8023 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.1784
  time to fit residues: 34.1005
Evaluate side-chains
  96 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.009 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 60 optimal weight:   20.0000
   chunk 110 optimal weight:    0.9980
   chunk 115 optimal weight:    7.9990
   chunk 33 optimal weight:    0.0980
   chunk 55 optimal weight:    9.9990
   chunk 11 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9990
   chunk 120 optimal weight:    0.0670
   chunk 59 optimal weight:    6.9990
   chunk 45 optimal weight:    5.9990
   chunk 71 optimal weight:    2.9990
   overall best weight:    1.0322

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 611 GLN
A 973 ASN
A 996 ASN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.087031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.072931 restraints weight = 47643.593|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.074811 restraints weight = 25359.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.076057 restraints weight = 15968.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9719  Z= 0.169
  Angle     :  0.548   8.066  13154  Z= 0.283
  Chirality :  0.039   0.176   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.755  15.820   1305
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 8.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.00 %
    Favored  : 97.00 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.06 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.91 (0.25), residues: 1202
  helix:  1.96 (0.18), residues: 763
  sheet:  1.63 (0.63), residues: 72
  loop : -0.26 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 240 
 HIS   0.002   0.001   HIS A  97 
 PHE   0.018   0.002   PHE A 335 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.006   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 128
  time to evaluate  : 1.114 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9344 (mmm) cc_final: 0.9056 (tpp)
REVERT: A  771 MET cc_start: 0.5122 (mpp) cc_final: 0.4799 (mpp)
REVERT: A  911 MET cc_start: 0.7688 (ppp) cc_final: 0.7394 (ppp)
REVERT: A 1103 ASP cc_start: 0.8056 (t0) cc_final: 0.7805 (t0)
REVERT: A 1238 MET cc_start: 0.8583 (mpp) cc_final: 0.8237 (mpp)
REVERT: A 1308 MET cc_start: 0.8023 (tpp) cc_final: 0.6470 (tpp)
REVERT: A 1389 HIS cc_start: 0.8370 (m90) cc_final: 0.8033 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 129
  average time/residue: 0.1803
  time to fit residues: 36.2770
Evaluate side-chains
  96 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 96
  time to evaluate  : 1.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 27 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 112 optimal weight:    8.9990
   chunk 94 optimal weight:    9.9990
   chunk 97 optimal weight:   20.0000
   chunk 82 optimal weight:    1.9990
   chunk 62 optimal weight:    0.6980
   chunk 67 optimal weight:    3.9990
   chunk 75 optimal weight:    4.9990
   chunk 4 optimal weight:    5.9990
   chunk 91 optimal weight:    6.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
A 996 ASN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.084446 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.068987 restraints weight = 48172.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.070711 restraints weight = 27412.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.071871 restraints weight = 18014.415|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8012
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9719  Z= 0.268
  Angle     :  0.618   6.804  13154  Z= 0.325
  Chirality :  0.041   0.183   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.952  17.325   1305
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.73 (0.24), residues: 1202
  helix:  1.79 (0.18), residues: 758
  sheet:  1.51 (0.63), residues: 72
  loop : -0.20 (0.34), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 883 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.020   0.002   PHE A 434 
 TYR   0.029   0.002   TYR A 918 
 ARG   0.005   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.971 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9421 (mmm) cc_final: 0.9156 (tpp)
REVERT: A  310 TYR cc_start: 0.8696 (t80) cc_final: 0.8255 (t80)
REVERT: A  612 MET cc_start: 0.0689 (tpt) cc_final: -0.0138 (tpt)
REVERT: A  771 MET cc_start: 0.5015 (mpp) cc_final: 0.4701 (mpp)
REVERT: A  911 MET cc_start: 0.7961 (ppp) cc_final: 0.7687 (ppp)
REVERT: A 1103 ASP cc_start: 0.8199 (t0) cc_final: 0.7961 (t0)
REVERT: A 1238 MET cc_start: 0.8785 (mpp) cc_final: 0.8456 (mpp)
REVERT: A 1389 HIS cc_start: 0.8533 (m90) cc_final: 0.8205 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 117
  average time/residue: 0.1636
  time to fit residues: 29.8896
Evaluate side-chains
  97 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 65 optimal weight:    0.8980
   chunk 75 optimal weight:    1.9990
   chunk 108 optimal weight:    2.9990
   chunk 114 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 54 optimal weight:   30.0000
   chunk 88 optimal weight:    0.7980
   chunk 96 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 49 optimal weight:   10.0000
   chunk 3 optimal weight:    0.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1336 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.085777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.071179 restraints weight = 48750.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.072986 restraints weight = 26662.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.074183 restraints weight = 17219.644|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2830

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9719  Z= 0.190
  Angle     :  0.580   7.042  13154  Z= 0.300
  Chirality :  0.040   0.178   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.879  16.788   1305
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.83 (0.24), residues: 1202
  helix:  1.91 (0.18), residues: 759
  sheet:  1.43 (0.63), residues: 72
  loop : -0.23 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 240 
 HIS   0.002   0.001   HIS A1065 
 PHE   0.019   0.002   PHE A 988 
 TYR   0.022   0.001   TYR A 918 
 ARG   0.007   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 1.112 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9402 (mmm) cc_final: 0.9151 (tpp)
REVERT: A  771 MET cc_start: 0.4892 (mpp) cc_final: 0.4547 (mpp)
REVERT: A 1001 PHE cc_start: 0.7999 (t80) cc_final: 0.7676 (t80)
REVERT: A 1103 ASP cc_start: 0.8120 (t0) cc_final: 0.7880 (t0)
REVERT: A 1308 MET cc_start: 0.7806 (tpp) cc_final: 0.6416 (tpp)
REVERT: A 1389 HIS cc_start: 0.8468 (m90) cc_final: 0.8159 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1680
  time to fit residues: 31.7970
Evaluate side-chains
  100 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 75 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 30 optimal weight:    2.9990
   chunk 38 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9990
   chunk 32 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 61 optimal weight:    8.9990
   overall best weight:    1.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1336 GLN
A1386 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.085447 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.070727 restraints weight = 49200.099|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.072493 restraints weight = 27088.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.073727 restraints weight = 17607.697|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.2935

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9719  Z= 0.198
  Angle     :  0.589   7.020  13154  Z= 0.302
  Chirality :  0.040   0.176   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.868  16.631   1305
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    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:  1.88 (0.24), residues: 1202
  helix:  1.95 (0.18), residues: 759
  sheet:  1.38 (0.64), residues: 72
  loop : -0.22 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A 477 
 PHE   0.015   0.001   PHE A 418 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.005   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 1.153 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9418 (mmm) cc_final: 0.9159 (tpp)
REVERT: A  310 TYR cc_start: 0.8699 (t80) cc_final: 0.8219 (t80)
REVERT: A  771 MET cc_start: 0.4982 (mpp) cc_final: 0.4621 (mpp)
REVERT: A  960 MET cc_start: 0.7990 (mtm) cc_final: 0.7630 (mtm)
REVERT: A 1001 PHE cc_start: 0.8008 (t80) cc_final: 0.7737 (t80)
REVERT: A 1103 ASP cc_start: 0.8146 (t0) cc_final: 0.7905 (t0)
REVERT: A 1308 MET cc_start: 0.7936 (tpp) cc_final: 0.6530 (tpp)
REVERT: A 1389 HIS cc_start: 0.8530 (m90) cc_final: 0.8208 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 118
  average time/residue: 0.1700
  time to fit residues: 31.4492
Evaluate side-chains
  97 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 32 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0570
   chunk 104 optimal weight:    5.9990
   chunk 25 optimal weight:    4.9990
   chunk 96 optimal weight:    0.9980
   chunk 105 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 108 optimal weight:    5.9990
   chunk 60 optimal weight:   20.0000
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.7700

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
A1121 HIS
A1336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.087582 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.073439 restraints weight = 49122.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.075259 restraints weight = 26804.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.076480 restraints weight = 17273.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.3058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9719  Z= 0.162
  Angle     :  0.594   9.123  13154  Z= 0.296
  Chirality :  0.040   0.174   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.795  16.078   1305
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.03 (0.25), residues: 1202
  helix:  2.08 (0.18), residues: 757
  sheet:  1.33 (0.63), residues: 72
  loop : -0.14 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 883 
 HIS   0.003   0.001   HIS A 477 
 PHE   0.020   0.001   PHE A 988 
 TYR   0.020   0.001   TYR A 918 
 ARG   0.005   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.996 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9393 (mmm) cc_final: 0.9150 (tpp)
REVERT: A  310 TYR cc_start: 0.8637 (t80) cc_final: 0.8121 (t80)
REVERT: A  771 MET cc_start: 0.4857 (mpp) cc_final: 0.4461 (mpp)
REVERT: A  883 TRP cc_start: 0.7931 (t60) cc_final: 0.7705 (t60)
REVERT: A  960 MET cc_start: 0.7757 (mtm) cc_final: 0.7518 (mtm)
REVERT: A 1001 PHE cc_start: 0.7915 (t80) cc_final: 0.7687 (t80)
REVERT: A 1103 ASP cc_start: 0.8041 (t0) cc_final: 0.7837 (t0)
REVERT: A 1308 MET cc_start: 0.7851 (tpp) cc_final: 0.6499 (tpp)
REVERT: A 1324 MET cc_start: 0.8055 (pmm) cc_final: 0.7823 (pmm)
REVERT: A 1389 HIS cc_start: 0.8448 (m90) cc_final: 0.8141 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1688
  time to fit residues: 33.3435
Evaluate side-chains
  100 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.952 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 36 optimal weight:    0.9990
   chunk 67 optimal weight:   20.0000
   chunk 13 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 15 optimal weight:    8.9990
   chunk 66 optimal weight:    0.4980
   chunk 118 optimal weight:   10.0000
   chunk 21 optimal weight:    0.6980
   chunk 54 optimal weight:    9.9990
   chunk 4 optimal weight:    9.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
A1336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.087894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.073679 restraints weight = 49171.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.075489 restraints weight = 26993.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.076685 restraints weight = 17386.168|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9719  Z= 0.162
  Angle     :  0.587   8.241  13154  Z= 0.292
  Chirality :  0.039   0.176   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.735  15.410   1305
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.24), residues: 1202
  helix:  2.13 (0.18), residues: 750
  sheet:  1.10 (0.60), residues: 77
  loop : -0.16 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 114 
 HIS   0.002   0.001   HIS A 477 
 PHE   0.014   0.001   PHE A 335 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.009   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.021 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9409 (mmm) cc_final: 0.9163 (tpp)
REVERT: A  310 TYR cc_start: 0.8628 (t80) cc_final: 0.8115 (t80)
REVERT: A  747 LEU cc_start: 0.7909 (mt) cc_final: 0.7353 (tt)
REVERT: A 1001 PHE cc_start: 0.7918 (t80) cc_final: 0.7707 (t80)
REVERT: A 1308 MET cc_start: 0.7886 (tpp) cc_final: 0.6591 (tpp)
REVERT: A 1324 MET cc_start: 0.8052 (pmm) cc_final: 0.7847 (pmm)
REVERT: A 1336 GLN cc_start: 0.8852 (mp10) cc_final: 0.8484 (tp-100)
REVERT: A 1389 HIS cc_start: 0.8442 (m90) cc_final: 0.8136 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1631
  time to fit residues: 32.4748
Evaluate side-chains
  104 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 104
  time to evaluate  : 1.019 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 70 optimal weight:    0.9990
   chunk 72 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 27 optimal weight:    6.9990
   chunk 18 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 28 optimal weight:    2.9990
   chunk 103 optimal weight:    4.9990
   chunk 95 optimal weight:   30.0000
   overall best weight:    0.9986

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
A1085 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.087793 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3556 r_free = 0.3556 target = 0.073616 restraints weight = 48745.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.075415 restraints weight = 26659.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.076601 restraints weight = 17207.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9719  Z= 0.168
  Angle     :  0.607   8.233  13154  Z= 0.301
  Chirality :  0.040   0.173   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.747  15.479   1305
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.24 %
    Favored  : 96.76 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.24), residues: 1202
  helix:  2.10 (0.18), residues: 750
  sheet:  1.12 (0.59), residues: 77
  loop : -0.18 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 883 
 HIS   0.002   0.001   HIS A 477 
 PHE   0.017   0.001   PHE A 988 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.008   0.000   ARG B  55 

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

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

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2404 Ramachandran restraints generated.
    1202 Oldfield, 0 Emsley, 1202 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 1.015 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9419 (mmm) cc_final: 0.9173 (tpp)
REVERT: A  310 TYR cc_start: 0.8622 (t80) cc_final: 0.8119 (t80)
REVERT: A  747 LEU cc_start: 0.7814 (mt) cc_final: 0.7295 (tt)
REVERT: A  911 MET cc_start: 0.7550 (ppp) cc_final: 0.7161 (ppp)
REVERT: A  960 MET cc_start: 0.8039 (ptp) cc_final: 0.7664 (mtm)
REVERT: A 1001 PHE cc_start: 0.7977 (t80) cc_final: 0.7666 (t80)
REVERT: A 1095 MET cc_start: 0.7844 (ttm) cc_final: 0.7451 (ttm)
REVERT: A 1308 MET cc_start: 0.7904 (tpp) cc_final: 0.6628 (tpp)
REVERT: A 1389 HIS cc_start: 0.8398 (m90) cc_final: 0.8089 (m90)
REVERT: B   59 LEU cc_start: 0.8193 (mm) cc_final: 0.7547 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1847
  time to fit residues: 36.3315
Evaluate side-chains
  100 residues out of total 1047 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.100 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    5.9990
   chunk 34 optimal weight:    0.6980
   chunk 80 optimal weight:    6.9990
   chunk 117 optimal weight:    5.9990
   chunk 118 optimal weight:    6.9990
   chunk 50 optimal weight:    0.6980
   chunk 105 optimal weight:    0.0980
   chunk 33 optimal weight:    2.9990
   chunk 70 optimal weight:    0.8980
   chunk 113 optimal weight:    6.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 190 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1047 GLN
A1336 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.088937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.075047 restraints weight = 49054.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.076850 restraints weight = 26816.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.078070 restraints weight = 17275.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3297

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9719  Z= 0.158
  Angle     :  0.597   8.640  13154  Z= 0.292
  Chirality :  0.039   0.174   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.660  15.056   1305
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.24), residues: 1202
  helix:  2.17 (0.18), residues: 754
  sheet:  1.18 (0.59), residues: 77
  loop : -0.12 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 114 
 HIS   0.003   0.001   HIS A 477 
 PHE   0.021   0.001   PHE A 988 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.008   0.000   ARG B  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2771.85 seconds
wall clock time: 49 minutes 33.89 seconds (2973.89 seconds total)