Starting phenix.real_space_refine
on Sun Aug  4 04:44:10 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi2_37555/08_2024/8wi2_37555.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi2_37555/08_2024/8wi2_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi2_37555/08_2024/8wi2_37555.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi2_37555/08_2024/8wi2_37555.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi2_37555/08_2024/8wi2_37555.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wi2_37555/08_2024/8wi2_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
    Residue "A ASP  352": "OD1" <-> "OD2"
    Residue "A TYR  371": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A GLU  393": "OE1" <-> "OE2"
    Residue "A PHE  452": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR  627": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  702": "OD1" <-> "OD2"
    Residue "A TYR  746": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE  866": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A ASP  949": "OD1" <-> "OD2"
    Residue "A PHE 1001": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1014": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1050": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A TYR 1077": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1088": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "A PHE 1280": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 5.65, per 1000 atoms: 0.59
  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  - 3.50
        Amino acid           : False - 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: 3.90
  Conformation dependent library (CDL) restraints added in 1.6 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: 1.11
  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: 3.08

  Time building geometry restraints manager: 4.29 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:
       96.35 -   103.92: 106
      103.92 -   111.48: 4459
      111.48 -   119.05: 3526
      119.05 -   126.61: 4939
      126.61 -   134.18: 124
  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:             1.590
  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:         0.060
  Set scattering table:                    0.080
  Process input model:                     28.800
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.540
-------------------------------------------------------------------------------
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 fitting.
    rotamer outliers: 7
    poor density    : 105
  time to evaluate  : 0.979 
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: 0.1764
  time to fit residues: 29.7072
Evaluate side-chains
  105 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 101
  time to evaluate  : 1.098 
-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
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 fitting.
    rotamer outliers: 1
    poor density    : 145
  time to evaluate  : 1.117 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9039 (mmm) cc_final: 0.8606 (tpp)
REVERT: A  257 MET cc_start: 0.9295 (tpp) cc_final: 0.8929 (tmm)
REVERT: A  747 LEU cc_start: 0.7834 (mp) cc_final: 0.7501 (mt)
REVERT: A  771 MET cc_start: 0.5397 (mpp) cc_final: 0.5104 (mpp)
REVERT: A  885 LYS cc_start: 0.9399 (tmtt) cc_final: 0.9079 (tttt)
REVERT: A 1103 ASP cc_start: 0.7993 (t0) cc_final: 0.7758 (t0)
REVERT: A 1238 MET cc_start: 0.9020 (mpp) cc_final: 0.8688 (mpp)
REVERT: A 1272 ILE cc_start: 0.9420 (pt) cc_final: 0.9112 (mm)
REVERT: A 1389 HIS cc_start: 0.8782 (m90) cc_final: 0.8481 (m90)
  outliers start: 1
  outliers final: 1
  residues processed: 146
  average time/residue: 0.1993
  time to fit residues: 42.0945
Evaluate side-chains
  97 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.961 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 61 optimal weight:   10.0000
   chunk 34 optimal weight:    2.9990
   chunk 91 optimal weight:    0.4980
   chunk 74 optimal weight:   10.0000
   chunk 30 optimal weight:    1.9990
   chunk 110 optimal weight:    8.9990
   chunk 118 optimal weight:    7.9990
   chunk 98 optimal weight:    7.9990
   chunk 109 optimal weight:    7.9990
   chunk 37 optimal weight:    2.9990
   chunk 88 optimal weight:    2.9990
   overall best weight:    2.2988

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7884
moved from start:          0.2332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9719  Z= 0.227
  Angle     :  0.586   8.176  13154  Z= 0.310
  Chirality :  0.041   0.187   1544
  Planarity :  0.004   0.057   1645
  Dihedral  :  3.866  16.512   1305
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  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:  1.86 (0.25), residues: 1202
  helix:  1.88 (0.18), residues: 763
  sheet:  1.84 (0.64), residues: 72
  loop : -0.23 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A 722 
 PHE   0.018   0.002   PHE A1050 
 TYR   0.028   0.001   TYR A 918 
 ARG   0.004   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
  123 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 123
  time to evaluate  : 0.974 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9037 (mmm) cc_final: 0.8669 (tpp)
REVERT: A  257 MET cc_start: 0.9298 (tpp) cc_final: 0.8954 (tmm)
REVERT: A  310 TYR cc_start: 0.8600 (t80) cc_final: 0.8339 (t80)
REVERT: A  387 GLU cc_start: 0.8945 (tm-30) cc_final: 0.8486 (tm-30)
REVERT: A  771 MET cc_start: 0.5312 (mpp) cc_final: 0.5082 (mpp)
REVERT: A  885 LYS cc_start: 0.9407 (tmtt) cc_final: 0.9050 (tttt)
REVERT: A  911 MET cc_start: 0.8532 (ppp) cc_final: 0.8058 (ppp)
REVERT: A 1103 ASP cc_start: 0.8041 (t0) cc_final: 0.7787 (t0)
REVERT: A 1238 MET cc_start: 0.9063 (mpp) cc_final: 0.8716 (mpp)
REVERT: A 1308 MET cc_start: 0.8383 (tpp) cc_final: 0.6995 (tpp)
REVERT: A 1389 HIS cc_start: 0.8771 (m90) cc_final: 0.8482 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 123
  average time/residue: 0.1783
  time to fit residues: 32.9405
Evaluate side-chains
  97 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.072 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 82 optimal weight:    3.9990
   chunk 57 optimal weight:    9.9990
   chunk 12 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 73 optimal weight:    2.9990
   chunk 110 optimal weight:    6.9990
   chunk 116 optimal weight:    0.6980
   chunk 104 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   overall best weight:    2.5388

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7912
moved from start:          0.2646

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9719  Z= 0.237
  Angle     :  0.591   7.554  13154  Z= 0.313
  Chirality :  0.040   0.174   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.933  17.412   1305
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 9.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.16 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.87 %
    Favored  : 97.04 %
  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: 759
  sheet:  1.65 (0.64), residues: 72
  loop : -0.27 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A1065 
 PHE   0.023   0.002   PHE A 288 
 TYR   0.019   0.001   TYR A 918 
 ARG   0.004   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
  122 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 1.005 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9093 (mmm) cc_final: 0.8773 (tpp)
REVERT: A  310 TYR cc_start: 0.8728 (t80) cc_final: 0.8255 (t80)
REVERT: A  612 MET cc_start: -0.0178 (tpt) cc_final: -0.0764 (tpt)
REVERT: A  747 LEU cc_start: 0.7969 (mp) cc_final: 0.7623 (mt)
REVERT: A  771 MET cc_start: 0.5161 (mpp) cc_final: 0.4853 (mpp)
REVERT: A  885 LYS cc_start: 0.9441 (tmtt) cc_final: 0.9063 (tttt)
REVERT: A  911 MET cc_start: 0.8568 (ppp) cc_final: 0.8118 (ppp)
REVERT: A 1103 ASP cc_start: 0.8146 (t0) cc_final: 0.7894 (t0)
REVERT: A 1238 MET cc_start: 0.9093 (mpp) cc_final: 0.8744 (mpp)
REVERT: A 1389 HIS cc_start: 0.8788 (m90) cc_final: 0.8495 (m90)
  outliers start: 1
  outliers final: 0
  residues processed: 122
  average time/residue: 0.1642
  time to fit residues: 30.6395
Evaluate side-chains
  93 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 1 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    6.9990
   chunk 99 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 0 optimal weight:   20.0000
   chunk 59 optimal weight:    7.9990
   chunk 104 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 39 optimal weight:    9.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 611 GLN
A 910 HIS
A 996 ASN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1386 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.3320

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065   9719  Z= 0.354
  Angle     :  0.696   6.481  13154  Z= 0.373
  Chirality :  0.043   0.229   1544
  Planarity :  0.005   0.056   1645
  Dihedral  :  4.343  18.703   1305
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 12.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.49 %
    Favored  : 95.32 %
  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:  1.23 (0.24), residues: 1202
  helix:  1.41 (0.18), residues: 758
  sheet:  1.03 (0.61), residues: 77
  loop : -0.39 (0.34), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 883 
 HIS   0.006   0.001   HIS A1065 
 PHE   0.023   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
  114 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 1.130 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9073 (mmm) cc_final: 0.8770 (tpp)
REVERT: A  310 TYR cc_start: 0.8874 (t80) cc_final: 0.8283 (t80)
REVERT: A  353 GLU cc_start: 0.9385 (tp30) cc_final: 0.8820 (mt-10)
REVERT: A  771 MET cc_start: 0.5133 (mpp) cc_final: 0.4848 (mpp)
REVERT: A  885 LYS cc_start: 0.9491 (tmtt) cc_final: 0.9083 (tttt)
REVERT: A  911 MET cc_start: 0.8542 (ppp) cc_final: 0.8340 (ppp)
REVERT: A 1103 ASP cc_start: 0.8226 (t0) cc_final: 0.7982 (t0)
REVERT: A 1238 MET cc_start: 0.9212 (mpp) cc_final: 0.8854 (mpp)
REVERT: A 1389 HIS cc_start: 0.8950 (m90) cc_final: 0.8690 (m90)
  outliers start: 2
  outliers final: 0
  residues processed: 114
  average time/residue: 0.1740
  time to fit residues: 30.3748
Evaluate side-chains
  89 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 105 optimal weight:    6.9990
   chunk 23 optimal weight:    4.9990
   chunk 68 optimal weight:    1.9990
   chunk 28 optimal weight:    1.9990
   chunk 117 optimal weight:   10.0000
   chunk 97 optimal weight:    6.9990
   chunk 54 optimal weight:    8.9990
   chunk 9 optimal weight:    3.9990
   chunk 38 optimal weight:    8.9990
   chunk 61 optimal weight:    9.9990
   chunk 112 optimal weight:    0.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 973 ASN
A 996 ASN
** A1336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7973
moved from start:          0.3400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9719  Z= 0.259
  Angle     :  0.641   6.740  13154  Z= 0.337
  Chirality :  0.041   0.174   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  4.218  18.860   1305
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.20 %
    Favored  : 97.80 %
  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:  1.39 (0.24), residues: 1202
  helix:  1.61 (0.18), residues: 754
  sheet:  0.81 (0.60), residues: 77
  loop : -0.40 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 240 
 HIS   0.004   0.001   HIS A1065 
 PHE   0.024   0.002   PHE A 988 
 TYR   0.035   0.002   TYR A 918 
 ARG   0.004   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
  116 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 116
  time to evaluate  : 1.104 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9085 (mmm) cc_final: 0.8755 (tpp)
REVERT: A  240 TRP cc_start: 0.8442 (m100) cc_final: 0.8071 (m-10)
REVERT: A  310 TYR cc_start: 0.8870 (t80) cc_final: 0.8139 (t80)
REVERT: A  353 GLU cc_start: 0.9385 (tp30) cc_final: 0.8843 (mt-10)
REVERT: A  708 LEU cc_start: 0.8891 (tt) cc_final: 0.7932 (mp)
REVERT: A  771 MET cc_start: 0.5239 (mpp) cc_final: 0.4913 (mpp)
REVERT: A  885 LYS cc_start: 0.9473 (tmtt) cc_final: 0.9196 (tmtt)
REVERT: A  960 MET cc_start: 0.8702 (mtm) cc_final: 0.8344 (mtm)
REVERT: A 1103 ASP cc_start: 0.8253 (t0) cc_final: 0.8022 (t0)
REVERT: A 1238 MET cc_start: 0.9181 (mpp) cc_final: 0.8817 (mpp)
REVERT: A 1389 HIS cc_start: 0.8928 (m90) cc_final: 0.8669 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 116
  average time/residue: 0.1792
  time to fit residues: 31.8542
Evaluate side-chains
  93 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 93
  time to evaluate  : 1.254 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 85 optimal weight:    3.9990
   chunk 98 optimal weight:    6.9990
   chunk 65 optimal weight:    0.7980
   chunk 116 optimal weight:   30.0000
   chunk 72 optimal weight:    6.9990
   chunk 71 optimal weight:    0.9990
   chunk 53 optimal weight:    9.9990
   chunk 46 optimal weight:    6.9990
   chunk 69 optimal weight:    0.5980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7878
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9719  Z= 0.171
  Angle     :  0.608   8.583  13154  Z= 0.306
  Chirality :  0.040   0.193   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.963  17.149   1305
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  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:  1.76 (0.25), residues: 1202
  helix:  1.88 (0.18), residues: 760
  sheet:  1.21 (0.63), residues: 72
  loop : -0.29 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A 477 
 PHE   0.017   0.001   PHE A 988 
 TYR   0.023   0.001   TYR A 918 
 ARG   0.003   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
  127 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 1.084 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9097 (mmm) cc_final: 0.8748 (tpp)
REVERT: A  240 TRP cc_start: 0.8291 (m100) cc_final: 0.7996 (m-10)
REVERT: A  353 GLU cc_start: 0.9362 (tp30) cc_final: 0.8790 (mt-10)
REVERT: A  480 LYS cc_start: 0.8147 (mttt) cc_final: 0.7788 (tppt)
REVERT: A  708 LEU cc_start: 0.8757 (tt) cc_final: 0.7785 (mp)
REVERT: A  747 LEU cc_start: 0.8110 (mp) cc_final: 0.7838 (mt)
REVERT: A  771 MET cc_start: 0.5076 (mpp) cc_final: 0.4723 (mpp)
REVERT: A  885 LYS cc_start: 0.9367 (tmtt) cc_final: 0.8940 (tttt)
REVERT: A  960 MET cc_start: 0.8699 (mtm) cc_final: 0.8010 (mtm)
REVERT: A 1095 MET cc_start: 0.7439 (ttm) cc_final: 0.7043 (ttm)
REVERT: A 1103 ASP cc_start: 0.8169 (t0) cc_final: 0.7894 (t0)
REVERT: A 1308 MET cc_start: 0.8224 (tpp) cc_final: 0.7008 (tpp)
REVERT: A 1389 HIS cc_start: 0.8899 (m90) cc_final: 0.8617 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1782
  time to fit residues: 34.0056
Evaluate side-chains
  105 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.987 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 35 optimal weight:    0.8980
   chunk 22 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   chunk 79 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 10 optimal weight:    0.8980
   chunk 91 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 111 optimal weight:    5.9990
   chunk 101 optimal weight:    8.9990
   chunk 108 optimal weight:    3.9990
   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  99 HIS
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 996 ASN
A1336 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.3301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9719  Z= 0.167
  Angle     :  0.597   8.325  13154  Z= 0.299
  Chirality :  0.040   0.172   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.886  16.403   1305
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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:  1.85 (0.25), residues: 1202
  helix:  1.95 (0.18), residues: 760
  sheet:  1.21 (0.63), residues: 72
  loop : -0.25 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A 477 
 PHE   0.021   0.001   PHE A 988 
 TYR   0.025   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
  124 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.985 
Fit side-chains
REVERT: A  130 MET cc_start: 0.9086 (mmm) cc_final: 0.8739 (tpp)
REVERT: A  240 TRP cc_start: 0.8255 (m100) cc_final: 0.7935 (m-10)
REVERT: A  353 GLU cc_start: 0.9342 (tp30) cc_final: 0.9008 (tt0)
REVERT: A  480 LYS cc_start: 0.8136 (mttt) cc_final: 0.7794 (tppt)
REVERT: A  708 LEU cc_start: 0.8751 (tt) cc_final: 0.7767 (mp)
REVERT: A  747 LEU cc_start: 0.8087 (mp) cc_final: 0.7792 (mt)
REVERT: A  756 MET cc_start: 0.8639 (ptt) cc_final: 0.8055 (ppp)
REVERT: A  771 MET cc_start: 0.5024 (mpp) cc_final: 0.4654 (mpp)
REVERT: A  885 LYS cc_start: 0.9265 (tmtt) cc_final: 0.8827 (tttt)
REVERT: A  960 MET cc_start: 0.8401 (mtm) cc_final: 0.7860 (mtm)
REVERT: A 1103 ASP cc_start: 0.8184 (t0) cc_final: 0.7899 (t0)
REVERT: A 1238 MET cc_start: 0.8973 (mpp) cc_final: 0.8262 (mpp)
REVERT: A 1308 MET cc_start: 0.8330 (tpp) cc_final: 0.7157 (tpp)
REVERT: A 1336 GLN cc_start: 0.9276 (mp10) cc_final: 0.8816 (tp-100)
REVERT: A 1389 HIS cc_start: 0.8904 (m90) cc_final: 0.8626 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1709
  time to fit residues: 31.7238
Evaluate side-chains
  106 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 0.982 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 65 optimal weight:    0.8980
   chunk 47 optimal weight:    2.9990
   chunk 85 optimal weight:    6.9990
   chunk 33 optimal weight:   10.0000
   chunk 98 optimal weight:    0.0270
   chunk 102 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 114 optimal weight:    9.9990
   chunk 70 optimal weight:    0.5980
   overall best weight:    1.5042

-------------------------------------------------------------------------------
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
A1085 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.3394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9719  Z= 0.189
  Angle     :  0.608   7.788  13154  Z= 0.305
  Chirality :  0.040   0.172   1544
  Planarity :  0.004   0.054   1645
  Dihedral  :  3.854  16.539   1305
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.76 %
    Favored  : 99.24 %
  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:  1.90 (0.25), residues: 1202
  helix:  2.02 (0.18), residues: 756
  sheet:  1.22 (0.62), residues: 72
  loop : -0.26 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 114 
 HIS   0.003   0.001   HIS A 477 
 PHE   0.015   0.002   PHE A 645 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.004   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 fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.082 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9081 (mmm) cc_final: 0.8737 (tpp)
REVERT: A  240 TRP cc_start: 0.8276 (m100) cc_final: 0.7968 (m-10)
REVERT: A  353 GLU cc_start: 0.9359 (tp30) cc_final: 0.9025 (tt0)
REVERT: A  480 LYS cc_start: 0.8145 (mttt) cc_final: 0.7806 (tppt)
REVERT: A  708 LEU cc_start: 0.8815 (tt) cc_final: 0.7849 (mp)
REVERT: A  747 LEU cc_start: 0.8041 (mp) cc_final: 0.7747 (mt)
REVERT: A  756 MET cc_start: 0.8613 (ptt) cc_final: 0.7951 (ppp)
REVERT: A  885 LYS cc_start: 0.9322 (tmtt) cc_final: 0.8859 (tttt)
REVERT: A  960 MET cc_start: 0.8462 (mtm) cc_final: 0.7909 (mtm)
REVERT: A 1103 ASP cc_start: 0.8207 (t0) cc_final: 0.7914 (t0)
REVERT: A 1238 MET cc_start: 0.8984 (mpp) cc_final: 0.8318 (mpp)
REVERT: A 1389 HIS cc_start: 0.8911 (m90) cc_final: 0.8643 (m90)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1791
  time to fit residues: 33.8462
Evaluate side-chains
  103 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 1.036 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 54 optimal weight:    8.9990
   chunk 79 optimal weight:    3.9990
   chunk 120 optimal weight:    0.8980
   chunk 110 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0770
   chunk 9 optimal weight:    2.9990
   chunk 74 optimal weight:    1.9990
   chunk 58 optimal weight:   20.0000
   chunk 76 optimal weight:    0.9990
   chunk 102 optimal weight:    0.7980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.7340

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7825
moved from start:          0.3423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9719  Z= 0.161
  Angle     :  0.605   8.782  13154  Z= 0.300
  Chirality :  0.040   0.195   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.818  15.935   1305
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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:  1.89 (0.25), residues: 1202
  helix:  2.04 (0.19), residues: 756
  sheet:  1.30 (0.62), residues: 72
  loop : -0.36 (0.34), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 240 
 HIS   0.003   0.001   HIS A 477 
 PHE   0.025   0.001   PHE A 988 
 TYR   0.015   0.001   TYR A 342 
 ARG   0.004   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
  126 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 1.008 
Fit side-chains
   revert: symmetry clash
REVERT: A  130 MET cc_start: 0.9098 (mmm) cc_final: 0.8747 (tpp)
REVERT: A  240 TRP cc_start: 0.8225 (m100) cc_final: 0.7884 (m-10)
REVERT: A  353 GLU cc_start: 0.9337 (tp30) cc_final: 0.9033 (tt0)
REVERT: A  480 LYS cc_start: 0.8181 (mttt) cc_final: 0.7861 (tppt)
REVERT: A  708 LEU cc_start: 0.8773 (tt) cc_final: 0.7821 (mp)
REVERT: A  747 LEU cc_start: 0.8010 (mp) cc_final: 0.7713 (mt)
REVERT: A  756 MET cc_start: 0.8579 (ptt) cc_final: 0.8024 (ppp)
REVERT: A  885 LYS cc_start: 0.9262 (tmtt) cc_final: 0.8805 (tttt)
REVERT: A  960 MET cc_start: 0.8384 (mtm) cc_final: 0.8183 (ptp)
REVERT: A 1001 PHE cc_start: 0.8246 (t80) cc_final: 0.7974 (t80)
REVERT: A 1103 ASP cc_start: 0.8122 (t0) cc_final: 0.7818 (t0)
REVERT: A 1238 MET cc_start: 0.8943 (mpp) cc_final: 0.8249 (mpp)
REVERT: A 1308 MET cc_start: 0.8278 (tpp) cc_final: 0.7041 (tpp)
REVERT: A 1324 MET cc_start: 0.8622 (pmm) cc_final: 0.8379 (pmm)
REVERT: A 1336 GLN cc_start: 0.9274 (mp10) cc_final: 0.8780 (tp-100)
REVERT: A 1389 HIS cc_start: 0.8891 (m90) cc_final: 0.8613 (m90)
REVERT: B   59 LEU cc_start: 0.7391 (mm) cc_final: 0.7145 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1715
  time to fit residues: 32.4902
Evaluate side-chains
  108 residues out of total 1047 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 108
  time to evaluate  : 0.986 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 121
   random chunks:
   chunk 88 optimal weight:    2.9990
   chunk 14 optimal weight:    1.9990
   chunk 26 optimal weight:    5.9990
   chunk 96 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 12 optimal weight:    4.9990
   chunk 17 optimal weight:    6.9990
   chunk 84 optimal weight:    2.9990
   chunk 5 optimal weight:    8.9990
   chunk 69 optimal weight:    0.7980
   overall best weight:    1.5184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.085844 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.071547 restraints weight = 48504.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.073303 restraints weight = 27026.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.074494 restraints weight = 17628.376|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.3499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9719  Z= 0.186
  Angle     :  0.603   7.820  13154  Z= 0.301
  Chirality :  0.040   0.172   1544
  Planarity :  0.004   0.055   1645
  Dihedral  :  3.780  16.148   1305
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.64
  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:  1.93 (0.25), residues: 1202
  helix:  2.08 (0.19), residues: 755
  sheet:  1.27 (0.63), residues: 72
  loop : -0.35 (0.34), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 114 
 HIS   0.002   0.001   HIS A 477 
 PHE   0.024   0.001   PHE A 988 
 TYR   0.014   0.001   TYR A 342 
 ARG   0.007   0.000   ARG B  55 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1739.72 seconds
wall clock time: 32 minutes 2.88 seconds (1922.88 seconds total)