Starting phenix.real_space_refine
on Thu Mar 13 10:46:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6dmb_7963/03_2025/6dmb_7963.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6dmb_7963/03_2025/6dmb_7963.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6dmb_7963/03_2025/6dmb_7963.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6dmb_7963/03_2025/6dmb_7963.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6dmb_7963/03_2025/6dmb_7963.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6dmb_7963/03_2025/6dmb_7963.cif"
  }
  resolution = 3.9
  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=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 768 atoms to isotropic.
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      42      5.16       5
     C    5189      2.51       5
     N    1290      2.21       5
     O    1424      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7945
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 7777
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 990, 7777
          Classifications: {'peptide': 990}
          Incomplete info: {'truncation_to_alanine': 19}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 946}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 82
          Unresolved non-hydrogen dihedrals: 50
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 1, 'ASN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 140
          Unusual residues: {'NAG': 5, 'Y01': 2}
          Classifications: {'undetermined': 7}
          Link IDs: {None: 6}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 4.71, per 1000 atoms: 0.59
  Number of scatterers: 7945
  At special positions: 0
  Unit cell: (94.917, 77.461, 141.83, 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      42     16.00
     O    1424      8.00
     N    1290      7.00
     C    5189      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 203 " - pdb=" SG  CYS A 226 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 234 " - pdb=" SG  CYS A 327 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 296 " - pdb=" SG  CYS A 304 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A1801 " - " ASN A 312 "
      " NAG A1802 " - " ASN A 349 "
      " NAG A1803 " - " ASN A 414 "
      " NAG A1804 " - " ASN A 875 "
      " NAG A1807 " - " ASN A 141 "
      " NAG B   1 " - " ASN A1000 "
  Time building additional restraints: 2.05
  Conformation dependent library (CDL) restraints added in 877.0 milliseconds
  

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1856

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 5 sheets defined
      60.1% alpha, 3.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 96
      removed outlier: 4.175A  pdb=" N   TRP A  78 " --> pdb=" O   LYS A  74 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   PHE A  83 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 97 through 115
      removed outlier: 3.807A  pdb=" N   PHE A 101 " --> pdb=" O   ASN A  97 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   LEU A 102 " --> pdb=" O   CYS A  98 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   GLY A 110 " --> pdb=" O   LEU A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 119
    Processing helix  chain 'A' and resid 124 through 129
      removed outlier: 3.649A  pdb=" N   TRP A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 136 through 147
    Processing helix  chain 'A' and resid 171 through 185
    Processing helix  chain 'A' and resid 216 through 222
    Processing helix  chain 'A' and resid 230 through 234
      removed outlier: 3.685A  pdb=" N   ASP A 233 " --> pdb=" O   THR A 230 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   CYS A 234 " --> pdb=" O   PRO A 231 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 230 through 234'
    Processing helix  chain 'A' and resid 236 through 240
    Processing helix  chain 'A' and resid 255 through 259
      removed outlier: 3.534A  pdb=" N   ASN A 258 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   PHE A 259 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 255 through 259'
    Processing helix  chain 'A' and resid 260 through 271
      removed outlier: 4.069A  pdb=" N   ILE A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 277 through 285
      removed outlier: 3.751A  pdb=" N   ALA A 285 " --> pdb=" O   MET A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 343
      removed outlier: 3.790A  pdb=" N   ILE A 342 " --> pdb=" O   GLN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 376
    Processing helix  chain 'A' and resid 388 through 411
      removed outlier: 3.657A  pdb=" N   GLU A 405 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   VAL A 411 " --> pdb=" O   VAL A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 436
    Processing helix  chain 'A' and resid 439 through 457
      removed outlier: 3.661A  pdb=" N   LEU A 455 " --> pdb=" O   ALA A 451 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   MET A 457 " --> pdb=" O   ALA A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 491
      removed outlier: 3.842A  pdb=" N   LEU A 475 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 3.964A  pdb=" N   LEU A 476 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLY A 486 " --> pdb=" O   ALA A 482 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   SER A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   LEU A 490 " --> pdb=" O   GLY A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 503
    Processing helix  chain 'A' and resid 506 through 526
      removed outlier: 3.688A  pdb=" N   VAL A 510 " --> pdb=" O   LEU A 506 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   THR A 525 " --> pdb=" O   ALA A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 539 through 564
      removed outlier: 3.890A  pdb=" N   THR A 544 " --> pdb=" O   CYS A 540 " (cutoff:3.500A)
      removed outlier: 5.505A  pdb=" N   ALA A 546 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 5.367A  pdb=" N   SER A 547 " --> pdb=" O   ARG A 543 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A 558 " --> pdb=" O   SER A 554 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 605
      removed outlier: 4.022A  pdb=" N   GLN A 576 " --> pdb=" O   ALA A 572 " (cutoff:3.500A)
      Proline residue:  A 593  - end of helix
      removed outlier: 4.147A  pdb=" N   SER A 597 " --> pdb=" O   PRO A 593 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   ASP A 605 " --> pdb=" O   TYR A 601 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 732 through 741
      removed outlier: 3.713A  pdb=" N   LYS A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 745
      removed outlier: 3.619A  pdb=" N   LEU A 745 " --> pdb=" O   PRO A 742 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 742 through 745'
    Processing helix  chain 'A' and resid 746 through 749
    Processing helix  chain 'A' and resid 750 through 770
      removed outlier: 4.205A  pdb=" N   ILE A 754 " --> pdb=" O   LYS A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 785 through 798
    Processing helix  chain 'A' and resid 815 through 828
      removed outlier: 3.654A  pdb=" N   TYR A 820 " --> pdb=" O   GLN A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 843 through 863
      removed outlier: 3.688A  pdb=" N   TYR A 847 " --> pdb=" O   MET A 843 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 877 through 888
      removed outlier: 3.707A  pdb=" N   VAL A 881 " --> pdb=" O   SER A 877 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   LEU A 882 " --> pdb=" O   ASP A 878 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA A 883 " --> pdb=" O   ASP A 879 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   VAL A 888 " --> pdb=" O   TYR A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 899 through 903
    Processing helix  chain 'A' and resid 919 through 930
      removed outlier: 3.565A  pdb=" N   LEU A 923 " --> pdb=" O   PHE A 919 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   THR A 924 " --> pdb=" O   TYR A 920 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ALA A 925 " --> pdb=" O   ILE A 921 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 930 through 937
      removed outlier: 3.861A  pdb=" N   SER A 937 " --> pdb=" O   ALA A 933 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 1004
      removed outlier: 3.760A  pdb=" N   ILE A 997 " --> pdb=" O   LYS A 993 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER A1003 " --> pdb=" O   SER A 999 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU A1004 " --> pdb=" O   ASN A1000 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1018
    Processing helix  chain 'A' and resid 1019 through 1022
    Processing helix  chain 'A' and resid 1026 through 1046
      removed outlier: 3.510A  pdb=" N   PHE A1040 " --> pdb=" O   LEU A1036 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1052 through 1075
      removed outlier: 3.796A  pdb=" N   GLY A1075 " --> pdb=" O   MET A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1080 through 1106
      removed outlier: 3.556A  pdb=" N   VAL A1084 " --> pdb=" O   ALA A1080 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   ILE A1085 " --> pdb=" O   VAL A1081 " (cutoff:3.500A)
      removed outlier: 4.820A  pdb=" N   GLU A1095 " --> pdb=" O   GLY A1091 " (cutoff:3.500A)
      removed outlier: 4.684A  pdb=" N   PHE A1096 " --> pdb=" O   ILE A1092 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   THR A1097 " --> pdb=" O   GLY A1093 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1112 through 1122
      removed outlier: 3.525A  pdb=" N   ALA A1118 " --> pdb=" O   ARG A1114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1123 through 1138
    Processing helix  chain 'A' and resid 1146 through 1155
    Processing helix  chain 'A' and resid 1155 through 1178
      Proline residue:  A1172  - end of helix
    Processing sheet with id=AA1, first strand: chain 'A' and resid 360 through 363
    Processing sheet with id=AA2, first strand: chain 'A' and resid 190 through 191
    Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 331
      removed outlier: 4.751A  pdb=" N   SER A 331 " --> pdb=" O   MET A 335 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 347 through 348
      removed outlier: 7.242A  pdb=" N   VAL A 347 " --> pdb=" O   VAL A 355 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 975 through 978
      removed outlier: 3.738A  pdb=" N   TYR A 804 " --> pdb=" O   ASN A1011 " (cutoff:3.500A)

    389 hydrogen bonds defined for protein.
    1134 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: 1.96

  Time building geometry restraints manager: 2.42 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2419
        1.34 -     1.46: 1964
        1.46 -     1.59: 3690
        1.59 -     1.71: 0
        1.71 -     1.83: 69
  Bond restraints: 8142
  Sorted by residual:
  bond pdb=" CAY Y01 A1809 "
       pdb=" OAW Y01 A1809 "
    ideal  model  delta    sigma   weight residual
    1.332  1.462 -0.130 2.00e-02 2.50e+03 4.22e+01
  bond pdb=" CAY Y01 A1808 "
       pdb=" OAW Y01 A1808 "
    ideal  model  delta    sigma   weight residual
    1.332  1.452 -0.120 2.00e-02 2.50e+03 3.60e+01
  bond pdb=" C   ASP A 293 "
       pdb=" N   ARG A 294 "
    ideal  model  delta    sigma   weight residual
    1.331  1.252  0.079 1.59e-02 3.96e+03 2.47e+01
  bond pdb=" CAX Y01 A1808 "
       pdb=" OAH Y01 A1808 "
    ideal  model  delta    sigma   weight residual
    1.248  1.328 -0.080 2.00e-02 2.50e+03 1.61e+01
  bond pdb=" CAX Y01 A1809 "
       pdb=" OAH Y01 A1809 "
    ideal  model  delta    sigma   weight residual
    1.248  1.328 -0.080 2.00e-02 2.50e+03 1.60e+01
  ... (remaining 8137 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.01: 10629
        3.01 -     6.01: 359
        6.01 -     9.02: 83
        9.02 -    12.02: 10
       12.02 -    15.03: 4
  Bond angle restraints: 11085
  Sorted by residual:
  angle pdb=" C   LEU A 458 "
        pdb=" N   ARG A 459 "
        pdb=" CA  ARG A 459 "
      ideal   model   delta    sigma   weight residual
     121.54  132.51  -10.97 1.91e+00 2.74e-01 3.30e+01
  angle pdb=" N   VAL A 908 "
        pdb=" CA  VAL A 908 "
        pdb=" C   VAL A 908 "
      ideal   model   delta    sigma   weight residual
     113.53  108.53    5.00 9.80e-01 1.04e+00 2.60e+01
  angle pdb=" C   GLU A 836 "
        pdb=" N   ASN A 837 "
        pdb=" CA  ASN A 837 "
      ideal   model   delta    sigma   weight residual
     121.54  130.85   -9.31 1.91e+00 2.74e-01 2.37e+01
  angle pdb=" C   LEU A1048 "
        pdb=" N   ASN A1049 "
        pdb=" CA  ASN A1049 "
      ideal   model   delta    sigma   weight residual
     121.80  133.18  -11.38 2.44e+00 1.68e-01 2.18e+01
  angle pdb=" N   GLU A 947 "
        pdb=" CA  GLU A 947 "
        pdb=" C   GLU A 947 "
      ideal   model   delta    sigma   weight residual
     110.91  116.30   -5.39 1.17e+00 7.31e-01 2.12e+01
  ... (remaining 11080 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.57: 4738
       24.57 -    49.14: 227
       49.14 -    73.71: 23
       73.71 -    98.28: 6
       98.28 -   122.85: 3
  Dihedral angle restraints: 4997
    sinusoidal: 2111
      harmonic: 2886
  Sorted by residual:
  dihedral pdb=" CA  ASN A1049 "
           pdb=" C   ASN A1049 "
           pdb=" N   PRO A1050 "
           pdb=" CA  PRO A1050 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -120.68  -59.32     0      5.00e+00 4.00e-02 1.41e+02
  dihedral pdb=" CA  LYS A 867 "
           pdb=" C   LYS A 867 "
           pdb=" N   ILE A 868 "
           pdb=" CA  ILE A 868 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -132.90  -47.10     0      5.00e+00 4.00e-02 8.87e+01
  dihedral pdb=" CB  CYS A 296 "
           pdb=" SG  CYS A 296 "
           pdb=" SG  CYS A 304 "
           pdb=" CB  CYS A 304 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.11  -73.11     1      1.00e+01 1.00e-02 6.81e+01
  ... (remaining 4994 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 1079
       0.091 -    0.182: 193
       0.182 -    0.273: 14
       0.273 -    0.363: 2
       0.363 -    0.454: 1
  Chirality restraints: 1289
  Sorted by residual:
  chirality pdb=" C1  NAG A1804 "
            pdb=" ND2 ASN A 875 "
            pdb=" C2  NAG A1804 "
            pdb=" O5  NAG A1804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.95   -0.45 2.00e-01 2.50e+01 5.16e+00
  chirality pdb=" CB  ILE A 531 "
            pdb=" CA  ILE A 531 "
            pdb=" CG1 ILE A 531 "
            pdb=" CG2 ILE A 531 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.33 2.00e-01 2.50e+01 2.75e+00
  chirality pdb=" C1  NAG A1801 "
            pdb=" ND2 ASN A 312 "
            pdb=" C2  NAG A1801 "
            pdb=" O5  NAG A1801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.13   -0.27 2.00e-01 2.50e+01 1.87e+00
  ... (remaining 1286 not shown)

  Planarity restraints: 1380
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A 869 "   -0.063 5.00e-02 4.00e+02   9.52e-02 1.45e+01
        pdb=" N   PRO A 870 "    0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO A 870 "   -0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO A 870 "   -0.055 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 812 "    0.051 5.00e-02 4.00e+02   7.72e-02 9.54e+00
        pdb=" N   PRO A 813 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO A 813 "    0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO A 813 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A1081 "    0.051 5.00e-02 4.00e+02   7.58e-02 9.20e+00
        pdb=" N   PRO A1082 "   -0.131 5.00e-02 4.00e+02
        pdb=" CA  PRO A1082 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A1082 "    0.043 5.00e-02 4.00e+02
  ... (remaining 1377 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.79: 1940
        2.79 -     3.32: 7486
        3.32 -     3.85: 12883
        3.85 -     4.37: 13993
        4.37 -     4.90: 23612
  Nonbonded interactions: 59914
  Sorted by model distance:
  nonbonded pdb=" O   MET A 956 "
            pdb=" OG1 THR A 959 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" O   GLY A 774 "
            pdb=" OH  TYR A1021 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   CYS A 998 "
            pdb=" OG1 THR A1002 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   TYR A 452 "
            pdb=" OG1 THR A 456 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   ASN A 120 "
            pdb=" OG  SER A 494 "
     model   vdw
     2.338 3.040
  ... (remaining 59909 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:             0.720
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     20.040
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
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      :  0.009   0.130   8142  Z= 0.572
  Angle     :  1.362  15.028  11085  Z= 0.690
  Chirality :  0.068   0.454   1289
  Planarity :  0.009   0.095   1374
  Dihedral  : 13.898 122.852   3132
  Min Nonbonded Distance : 2.266

Molprobity Statistics.
  All-atom Clashscore : 6.34
  Ramachandran Plot:
    Outliers :  0.61 %
    Allowed  : 13.18 %
    Favored  : 86.21 %
  Rotamer:
    Outliers :  1.94 %
    Allowed  :  8.74 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 4.65 %
    Twisted General : 0.63 %

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: -4.55 (0.21), residues: 986
  helix: -2.31 (0.17), residues: 525
  sheet: -3.36 (0.56), residues: 52
  loop : -3.90 (0.26), residues: 409

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.004   TRP A 337 
 HIS   0.011   0.002   HIS A 520 
 PHE   0.045   0.004   PHE A1015 
 TYR   0.032   0.003   TYR A 222 
 ARG   0.008   0.001   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 215
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  129 TRP cc_start: 0.7803 (m100) cc_final: 0.7107 (m-10)
REVERT: A  183 LEU cc_start: 0.9037 (tp) cc_final: 0.8744 (tt)
REVERT: A  374 GLU cc_start: 0.8120 (mm-30) cc_final: 0.7873 (mm-30)
REVERT: A  416 THR cc_start: 0.8533 (p) cc_final: 0.8249 (t)
REVERT: A  455 LEU cc_start: 0.8678 (mm) cc_final: 0.8429 (tt)
REVERT: A  490 LEU cc_start: 0.8894 (mm) cc_final: 0.8401 (tt)
REVERT: A  550 LEU cc_start: 0.9214 (tp) cc_final: 0.8872 (tp)
REVERT: A  598 MET cc_start: 0.8044 (mmm) cc_final: 0.7783 (tmm)
REVERT: A  988 VAL cc_start: 0.9322 (t) cc_final: 0.8278 (m)
REVERT: A 1029 LEU cc_start: 0.8798 (tt) cc_final: 0.8478 (mm)
REVERT: A 1076 ILE cc_start: 0.9051 (mm) cc_final: 0.8837 (mm)
REVERT: A 1128 ASP cc_start: 0.7284 (m-30) cc_final: 0.6996 (m-30)
REVERT: A 1146 ASP cc_start: 0.7669 (t0) cc_final: 0.7237 (t0)
REVERT: A 1165 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8641 (mt)
  outliers start: 16
  outliers final: 4
  residues processed: 226
  average time/residue: 0.2024
  time to fit residues: 62.9723
Evaluate side-chains
  117 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 112
  time to evaluate  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1165 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 83 optimal weight:    1.9990
   chunk 75 optimal weight:    6.9990
   chunk 41 optimal weight:    6.9990
   chunk 25 optimal weight:    2.9990
   chunk 50 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    7.9990
   chunk 89 optimal weight:    0.9980
   overall best weight:    1.7986

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

Flipped N/Q/H residues before XYZ refinement:
A  84 GLN
A  95 GLN
A 178 HIS
** A 289 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 324 ASN
A 375 HIS
A 409 GLN
A 496 ASN
A 584 ASN
A 802 ASN
A 828 ASN
A 846 HIS
A 853 GLN
A 856 GLN
A 929 ASN
A1099 HIS
A1112 ASN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.109388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.092675 restraints weight = 19562.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.095095 restraints weight = 11349.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.096796 restraints weight = 7884.860|
|-----------------------------------------------------------------------------|
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7875
moved from start:          0.2822

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8142  Z= 0.249
  Angle     :  0.860  11.366  11085  Z= 0.422
  Chirality :  0.045   0.251   1289
  Planarity :  0.006   0.071   1374
  Dihedral  :  9.173  59.089   1368
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 10.99
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.07 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  6.07 %
    Allowed  : 14.81 %
    Favored  : 79.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.32 %

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: -2.88 (0.25), residues: 986
  helix: -0.71 (0.21), residues: 567
  sheet: -2.70 (0.70), residues: 46
  loop : -3.75 (0.28), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 236 
 HIS   0.005   0.001   HIS A 817 
 PHE   0.029   0.002   PHE A 800 
 TYR   0.021   0.002   TYR A 740 
 ARG   0.005   0.000   ARG A 603 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 133
  time to evaluate  : 0.807 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  374 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7781 (mm-30)
REVERT: A  432 LYS cc_start: 0.9031 (tmtt) cc_final: 0.8579 (tmtt)
REVERT: A  455 LEU cc_start: 0.8311 (mm) cc_final: 0.8091 (tt)
REVERT: A  456 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.7886 (t)
REVERT: A  490 LEU cc_start: 0.8578 (mm) cc_final: 0.8143 (tt)
REVERT: A  988 VAL cc_start: 0.9337 (t) cc_final: 0.8760 (m)
  outliers start: 50
  outliers final: 22
  residues processed: 169
  average time/residue: 0.1583
  time to fit residues: 38.8018
Evaluate side-chains
  125 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 102
  time to evaluate  : 0.797 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  402 THR
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  456 THR
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  950 HIS
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1098 VAL
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 95 optimal weight:    0.4980
   chunk 44 optimal weight:    4.9990
   chunk 41 optimal weight:    6.9990
   chunk 11 optimal weight:    9.9990
   chunk 0 optimal weight:    8.9990
   chunk 12 optimal weight:    6.9990
   chunk 9 optimal weight:    0.0670
   chunk 78 optimal weight:    3.9990
   chunk 38 optimal weight:    6.9990
   chunk 81 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.3124

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 289 HIS
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 856 GLN
A 872 ASN
A 889 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.107766 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.091366 restraints weight = 19913.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.093733 restraints weight = 11581.081|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.095454 restraints weight = 8004.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3464
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.3393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8142  Z= 0.262
  Angle     :  0.842  10.591  11085  Z= 0.410
  Chirality :  0.045   0.295   1289
  Planarity :  0.006   0.077   1374
  Dihedral  :  8.487  71.591   1364
  Min Nonbonded Distance : 2.372

Molprobity Statistics.
  All-atom Clashscore : 12.18
  Ramachandran Plot:
    Outliers :  0.30 %
    Allowed  : 12.27 %
    Favored  : 87.42 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 17.23 %
    Favored  : 76.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.32 %

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: -2.16 (0.27), residues: 986
  helix: -0.04 (0.22), residues: 569
  sheet: -2.09 (0.75), residues: 51
  loop : -3.68 (0.29), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  78 
 HIS   0.004   0.001   HIS A 520 
 PHE   0.023   0.002   PHE A1104 
 TYR   0.023   0.002   TYR A 740 
 ARG   0.005   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 109
  time to evaluate  : 0.902 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  198 LYS cc_start: 0.7589 (OUTLIER) cc_final: 0.7025 (mtmp)
REVERT: A  360 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8733 (pp)
REVERT: A  374 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7755 (mm-30)
REVERT: A  455 LEU cc_start: 0.8440 (mm) cc_final: 0.8195 (tt)
REVERT: A  490 LEU cc_start: 0.8620 (mm) cc_final: 0.8170 (tt)
REVERT: A  856 GLN cc_start: 0.8067 (OUTLIER) cc_final: 0.7739 (tm-30)
  outliers start: 52
  outliers final: 33
  residues processed: 148
  average time/residue: 0.1561
  time to fit residues: 34.0113
Evaluate side-chains
  134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 98
  time to evaluate  : 0.882 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  194 ASN
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  856 GLN
Chi-restraints excluded: chain A residue  875 ASN
Chi-restraints excluded: chain A residue  950 HIS
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1134 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 85 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 1 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 41 optimal weight:    0.0970
   chunk 72 optimal weight:    8.9990
   chunk 80 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 86 optimal weight:    1.9990
   chunk 53 optimal weight:    3.9990
   overall best weight:    1.3984

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

Flipped N/Q/H residues before XYZ refinement:
A 584 ASN
A 856 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.109373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.092927 restraints weight = 19593.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.095430 restraints weight = 11207.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.097186 restraints weight = 7669.484|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.3777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8142  Z= 0.208
  Angle     :  0.815  10.769  11085  Z= 0.388
  Chirality :  0.044   0.298   1289
  Planarity :  0.006   0.076   1374
  Dihedral  :  7.998  59.008   1364
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.37 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  4.73 %
    Allowed  : 20.75 %
    Favored  : 74.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

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 (0.27), residues: 986
  helix:  0.23 (0.22), residues: 576
  sheet: -1.96 (0.75), residues: 51
  loop : -3.65 (0.30), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A  78 
 HIS   0.003   0.001   HIS A 520 
 PHE   0.020   0.002   PHE A 800 
 TYR   0.022   0.001   TYR A 740 
 ARG   0.003   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 118
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  360 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8759 (pp)
REVERT: A  455 LEU cc_start: 0.8385 (mm) cc_final: 0.8152 (tt)
REVERT: A  490 LEU cc_start: 0.8568 (mm) cc_final: 0.8154 (tt)
REVERT: A  493 ILE cc_start: 0.6441 (OUTLIER) cc_final: 0.6129 (mm)
  outliers start: 39
  outliers final: 25
  residues processed: 143
  average time/residue: 0.1537
  time to fit residues: 32.7384
Evaluate side-chains
  134 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 107
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  803 MET
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  950 HIS
Chi-restraints excluded: chain A residue  992 GLU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 34 optimal weight:   10.0000
   chunk 38 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 33 optimal weight:    0.6980
   chunk 8 optimal weight:    2.9990
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 22 optimal weight:    6.9990
   overall best weight:    2.1388

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.108677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.091931 restraints weight = 19683.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.094390 restraints weight = 11472.736|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.096083 restraints weight = 7950.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3471
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.4074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   8142  Z= 0.251
  Angle     :  0.838  12.262  11085  Z= 0.397
  Chirality :  0.045   0.320   1289
  Planarity :  0.006   0.075   1374
  Dihedral  :  8.174  59.174   1362
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.78 %
    Favored  : 87.22 %
  Rotamer:
    Outliers :  6.31 %
    Allowed  : 20.02 %
    Favored  : 73.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

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: -1.66 (0.28), residues: 986
  helix:  0.45 (0.23), residues: 573
  sheet: -1.95 (0.75), residues: 51
  loop : -3.66 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 256 
 HIS   0.004   0.001   HIS A 520 
 PHE   0.021   0.002   PHE A 592 
 TYR   0.020   0.001   TYR A 740 
 ARG   0.003   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 118
  time to evaluate  : 0.874 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ASN cc_start: 0.8395 (m-40) cc_final: 0.6846 (p0)
REVERT: A  156 GLN cc_start: 0.8584 (mp-120) cc_final: 0.8030 (mp-120)
REVERT: A  198 LYS cc_start: 0.7454 (OUTLIER) cc_final: 0.7016 (mtmp)
REVERT: A  360 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8818 (pp)
REVERT: A  374 GLU cc_start: 0.7811 (mm-30) cc_final: 0.7581 (mm-30)
REVERT: A  455 LEU cc_start: 0.8295 (mm) cc_final: 0.8079 (tt)
REVERT: A  490 LEU cc_start: 0.8553 (mm) cc_final: 0.8113 (tt)
REVERT: A  493 ILE cc_start: 0.6558 (OUTLIER) cc_final: 0.6261 (mm)
REVERT: A  905 GLN cc_start: 0.6862 (tp-100) cc_final: 0.6574 (tp40)
REVERT: A 1048 LEU cc_start: 0.7867 (OUTLIER) cc_final: 0.7399 (tt)
REVERT: A 1076 ILE cc_start: 0.9113 (mm) cc_final: 0.8868 (mm)
  outliers start: 52
  outliers final: 33
  residues processed: 156
  average time/residue: 0.1548
  time to fit residues: 35.9511
Evaluate side-chains
  137 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 100
  time to evaluate  : 0.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  158 MET
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  254 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  763 VAL
Chi-restraints excluded: chain A residue  803 MET
Chi-restraints excluded: chain A residue  815 ILE
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  949 VAL
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 61 optimal weight:    0.6980
   chunk 14 optimal weight:    0.0970
   chunk 64 optimal weight:    5.9990
   chunk 47 optimal weight:    0.8980
   chunk 6 optimal weight:    0.5980
   chunk 38 optimal weight:    4.9990
   chunk 63 optimal weight:    0.1980
   chunk 88 optimal weight:    0.4980
   chunk 91 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 66 optimal weight:    4.9990
   overall best weight:    0.4178

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

Flipped N/Q/H residues before XYZ refinement:
A 496 ASN
** A 872 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3724 r_free = 0.3724 target = 0.111262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.094633 restraints weight = 19373.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.097155 restraints weight = 11117.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.098910 restraints weight = 7635.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3544
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7818
moved from start:          0.4391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   8142  Z= 0.180
  Angle     :  0.803  11.838  11085  Z= 0.378
  Chirality :  0.045   0.366   1289
  Planarity :  0.005   0.076   1374
  Dihedral  :  7.622  59.500   1362
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 9.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.16 %
    Favored  : 88.84 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 22.82 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

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: -1.40 (0.28), residues: 986
  helix:  0.63 (0.23), residues: 573
  sheet: -1.87 (0.75), residues: 51
  loop : -3.49 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 256 
 HIS   0.002   0.000   HIS A 739 
 PHE   0.018   0.001   PHE A 800 
 TYR   0.024   0.001   TYR A 740 
 ARG   0.003   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 123
  time to evaluate  : 0.878 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  154 ASN cc_start: 0.8414 (m110) cc_final: 0.7112 (p0)
REVERT: A  198 LYS cc_start: 0.7413 (OUTLIER) cc_final: 0.7006 (mtmp)
REVERT: A  346 THR cc_start: 0.8085 (m) cc_final: 0.7851 (p)
REVERT: A  360 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8653 (pp)
REVERT: A  374 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7536 (mm-30)
REVERT: A  455 LEU cc_start: 0.8131 (mm) cc_final: 0.7930 (tt)
REVERT: A  490 LEU cc_start: 0.8411 (mm) cc_final: 0.7911 (tt)
REVERT: A  493 ILE cc_start: 0.6461 (OUTLIER) cc_final: 0.6048 (mm)
REVERT: A 1048 LEU cc_start: 0.7719 (OUTLIER) cc_final: 0.7473 (tt)
REVERT: A 1076 ILE cc_start: 0.9162 (mm) cc_final: 0.8851 (mm)
REVERT: A 1077 LYS cc_start: 0.8021 (mppt) cc_final: 0.7684 (mtmt)
  outliers start: 35
  outliers final: 24
  residues processed: 150
  average time/residue: 0.1614
  time to fit residues: 35.6899
Evaluate side-chains
  139 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 111
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  803 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1135 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 22 optimal weight:    9.9990
   chunk 77 optimal weight:    0.0000
   chunk 4 optimal weight:    5.9990
   chunk 89 optimal weight:    0.9990
   chunk 3 optimal weight:    7.9990
   chunk 92 optimal weight:    5.9990
   chunk 48 optimal weight:    8.9990
   chunk 21 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    1.9590

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 365 GLN
A 496 ASN
** A 584 ASN ** 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 = 0.3686 r_free = 0.3686 target = 0.108864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.092186 restraints weight = 19682.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.094580 restraints weight = 11523.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.096271 restraints weight = 8050.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3482
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7905
moved from start:          0.4512

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   8142  Z= 0.240
  Angle     :  0.831  13.429  11085  Z= 0.390
  Chirality :  0.044   0.230   1289
  Planarity :  0.006   0.112   1374
  Dihedral  :  7.554  59.966   1362
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 12.37 %
    Favored  : 87.53 %
  Rotamer:
    Outliers :  4.61 %
    Allowed  : 23.54 %
    Favored  : 71.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

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: -1.24 (0.28), residues: 986
  helix:  0.84 (0.23), residues: 568
  sheet: -1.78 (0.76), residues: 51
  loop : -3.53 (0.30), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  78 
 HIS   0.004   0.001   HIS A 520 
 PHE   0.020   0.002   PHE A 592 
 TYR   0.024   0.001   TYR A 740 
 ARG   0.004   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.817 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 ASN cc_start: 0.8248 (m110) cc_final: 0.7520 (p0)
REVERT: A  156 GLN cc_start: 0.8556 (mp-120) cc_final: 0.8335 (mp10)
REVERT: A  198 LYS cc_start: 0.7409 (OUTLIER) cc_final: 0.7075 (mtmp)
REVERT: A  360 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8825 (pp)
REVERT: A  490 LEU cc_start: 0.8428 (mm) cc_final: 0.7957 (tt)
REVERT: A  493 ILE cc_start: 0.6649 (OUTLIER) cc_final: 0.6321 (mm)
REVERT: A  845 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8930 (tm)
REVERT: A 1048 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7469 (tt)
  outliers start: 38
  outliers final: 27
  residues processed: 132
  average time/residue: 0.1630
  time to fit residues: 31.2640
Evaluate side-chains
  126 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 94
  time to evaluate  : 0.857 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  831 TYR
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1048 LEU
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 53 optimal weight:   10.0000
   chunk 41 optimal weight:    0.7980
   chunk 23 optimal weight:   20.0000
   chunk 39 optimal weight:    7.9990
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 37 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 496 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.108867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.092329 restraints weight = 19830.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.094810 restraints weight = 11510.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.096532 restraints weight = 7935.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.4653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8142  Z= 0.218
  Angle     :  0.823  13.372  11085  Z= 0.388
  Chirality :  0.043   0.228   1289
  Planarity :  0.006   0.101   1374
  Dihedral  :  7.434  59.053   1362
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 10.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.76 %
    Favored  : 88.24 %
  Rotamer:
    Outliers :  5.22 %
    Allowed  : 23.06 %
    Favored  : 71.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

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: -1.21 (0.28), residues: 986
  helix:  0.81 (0.23), residues: 574
  sheet: -1.75 (0.76), residues: 51
  loop : -3.46 (0.31), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  78 
 HIS   0.006   0.001   HIS A 817 
 PHE   0.029   0.002   PHE A1104 
 TYR   0.024   0.001   TYR A 740 
 ARG   0.003   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 97
  time to evaluate  : 0.926 
Fit side-chains
   revert: symmetry clash
REVERT: A  154 ASN cc_start: 0.8319 (m110) cc_final: 0.7416 (p0)
REVERT: A  198 LYS cc_start: 0.7427 (OUTLIER) cc_final: 0.7120 (mtmp)
REVERT: A  360 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8789 (pp)
REVERT: A  490 LEU cc_start: 0.8413 (mm) cc_final: 0.7926 (tt)
REVERT: A  493 ILE cc_start: 0.6794 (OUTLIER) cc_final: 0.6362 (mm)
REVERT: A  845 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.8895 (tm)
  outliers start: 43
  outliers final: 28
  residues processed: 131
  average time/residue: 0.1596
  time to fit residues: 31.4217
Evaluate side-chains
  121 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 89
  time to evaluate  : 0.876 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  831 TYR
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 21 optimal weight:    9.9990
   chunk 60 optimal weight:    6.9990
   chunk 0 optimal weight:    8.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    5.9990
   chunk 13 optimal weight:    7.9990
   chunk 72 optimal weight:    0.2980
   chunk 4 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 55 optimal weight:    3.9990
   overall best weight:    2.6588

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 496 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.105894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.089542 restraints weight = 20151.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.091832 restraints weight = 11985.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.093485 restraints weight = 8399.621|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
moved from start:          0.4722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   8142  Z= 0.282
  Angle     :  0.863  13.667  11085  Z= 0.411
  Chirality :  0.045   0.222   1289
  Planarity :  0.006   0.095   1374
  Dihedral  :  7.613  56.974   1362
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 12.31
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 13.18 %
    Favored  : 86.71 %
  Rotamer:
    Outliers :  4.98 %
    Allowed  : 24.03 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

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: -1.19 (0.28), residues: 986
  helix:  0.85 (0.23), residues: 570
  sheet: -1.86 (0.74), residues: 51
  loop : -3.43 (0.30), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  78 
 HIS   0.006   0.001   HIS A 817 
 PHE   0.027   0.002   PHE A1104 
 TYR   0.025   0.002   TYR A 740 
 ARG   0.003   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 91
  time to evaluate  : 0.841 
Fit side-chains
REVERT: A  154 ASN cc_start: 0.8309 (m110) cc_final: 0.7586 (p0)
REVERT: A  198 LYS cc_start: 0.7533 (OUTLIER) cc_final: 0.7252 (mtmp)
REVERT: A  360 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8820 (pp)
REVERT: A  490 LEU cc_start: 0.8494 (mm) cc_final: 0.7971 (tt)
REVERT: A  493 ILE cc_start: 0.6723 (OUTLIER) cc_final: 0.6350 (mm)
REVERT: A  845 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8992 (tm)
  outliers start: 41
  outliers final: 33
  residues processed: 123
  average time/residue: 0.1712
  time to fit residues: 31.4872
Evaluate side-chains
  125 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 88
  time to evaluate  : 0.881 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   77 LEU
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  355 VAL
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  481 VAL
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  496 ASN
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  992 GLU
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 72 optimal weight:    0.0980
   chunk 30 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 90 optimal weight:    0.8980
   chunk 53 optimal weight:    7.9990
   chunk 22 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 48 optimal weight:    5.9990
   chunk 24 optimal weight:    0.3980
   chunk 39 optimal weight:    7.9990
   chunk 77 optimal weight:    2.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 496 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.110708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.093811 restraints weight = 19618.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.096317 restraints weight = 11561.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.098061 restraints weight = 8052.634|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.4919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8142  Z= 0.199
  Angle     :  0.838  13.862  11085  Z= 0.393
  Chirality :  0.043   0.224   1289
  Planarity :  0.006   0.092   1374
  Dihedral  :  7.314  57.833   1362
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.07 %
    Favored  : 87.93 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 24.64 %
    Favored  : 71.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.28), residues: 986
  helix:  0.98 (0.23), residues: 567
  sheet: -1.75 (0.76), residues: 51
  loop : -3.31 (0.31), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  78 
 HIS   0.005   0.001   HIS A 817 
 PHE   0.020   0.001   PHE A 800 
 TYR   0.025   0.001   TYR A 740 
 ARG   0.003   0.000   ARG A 255 

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

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

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1972 Ramachandran restraints generated.
    986 Oldfield, 0 Emsley, 986 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 93
  time to evaluate  : 0.883 
Fit side-chains
REVERT: A  154 ASN cc_start: 0.8186 (m110) cc_final: 0.7590 (p0)
REVERT: A  183 LEU cc_start: 0.8219 (tt) cc_final: 0.7911 (mt)
REVERT: A  198 LYS cc_start: 0.7395 (OUTLIER) cc_final: 0.7114 (mtmp)
REVERT: A  360 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8752 (pp)
REVERT: A  367 MET cc_start: 0.6892 (pmm) cc_final: 0.6109 (ptp)
REVERT: A  490 LEU cc_start: 0.8450 (mm) cc_final: 0.7947 (tt)
REVERT: A  493 ILE cc_start: 0.6509 (OUTLIER) cc_final: 0.6138 (mm)
REVERT: A  845 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8866 (tm)
  outliers start: 36
  outliers final: 29
  residues processed: 120
  average time/residue: 0.1699
  time to fit residues: 30.1265
Evaluate side-chains
  122 residues out of total 843 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 89
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  140 LEU
Chi-restraints excluded: chain A residue  157 LEU
Chi-restraints excluded: chain A residue  171 THR
Chi-restraints excluded: chain A residue  198 LYS
Chi-restraints excluded: chain A residue  230 THR
Chi-restraints excluded: chain A residue  265 LEU
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  322 VAL
Chi-restraints excluded: chain A residue  354 LEU
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  432 LYS
Chi-restraints excluded: chain A residue  458 LEU
Chi-restraints excluded: chain A residue  479 LEU
Chi-restraints excluded: chain A residue  493 ILE
Chi-restraints excluded: chain A residue  503 LEU
Chi-restraints excluded: chain A residue  517 LEU
Chi-restraints excluded: chain A residue  561 MET
Chi-restraints excluded: chain A residue  592 PHE
Chi-restraints excluded: chain A residue  600 LEU
Chi-restraints excluded: chain A residue  753 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  843 MET
Chi-restraints excluded: chain A residue  845 LEU
Chi-restraints excluded: chain A residue  992 GLU
Chi-restraints excluded: chain A residue 1008 SER
Chi-restraints excluded: chain A residue 1024 LEU
Chi-restraints excluded: chain A residue 1064 THR
Chi-restraints excluded: chain A residue 1073 LEU
Chi-restraints excluded: chain A residue 1105 LEU
Chi-restraints excluded: chain A residue 1137 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   chunk 23 optimal weight:   10.0000
   chunk 12 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 45 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   chunk 83 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 26 optimal weight:    5.9990
   chunk 24 optimal weight:   10.0000
   overall best weight:    3.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 400 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 496 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.104169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.087516 restraints weight = 20149.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.089838 restraints weight = 11924.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.091346 restraints weight = 8351.378|
|-----------------------------------------------------------------------------|
r_work (final): 0.3410
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.4886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   8142  Z= 0.338
  Angle     :  0.888  13.621  11085  Z= 0.427
  Chirality :  0.046   0.214   1289
  Planarity :  0.006   0.090   1374
  Dihedral  :  7.719  56.994   1362
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 13.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 13.89 %
    Favored  : 86.00 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 24.27 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.33 %
    Twisted General : 0.21 %

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: -1.11 (0.28), residues: 986
  helix:  0.97 (0.23), residues: 564
  sheet: -1.90 (0.73), residues: 51
  loop : -3.43 (0.30), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 129 
 HIS   0.006   0.001   HIS A 817 
 PHE   0.026   0.002   PHE A 592 
 TYR   0.026   0.002   TYR A 740 
 ARG   0.005   0.001   ARG A 536 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2351.35 seconds
wall clock time: 42 minutes 10.26 seconds (2530.26 seconds total)