Starting phenix.real_space_refine
on Sat Aug 23 04:53:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8bwq_16294/08_2025/8bwq_16294.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8bwq_16294/08_2025/8bwq_16294.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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8bwq_16294/08_2025/8bwq_16294.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8bwq_16294/08_2025/8bwq_16294.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8bwq_16294/08_2025/8bwq_16294.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8bwq_16294/08_2025/8bwq_16294.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.031
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      43      5.16       5
     C    6224      2.51       5
     N    1605      2.21       5
     O    1704      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9576
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9545
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1195, 9545
          Classifications: {'peptide': 1195}
          Link IDs: {'PTRANS': 37, 'TRANS': 1157}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'TTC': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 1.76, per 1000 atoms: 0.18
  Number of scatterers: 9576
  At special positions: 0
  Unit cell: (77.376, 108.16, 146.432, 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      43     16.00
     O    1704      8.00
     N    1605      7.00
     C    6224      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.76
  Conformation dependent library (CDL) restraints added in 214.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2266

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 4 sheets defined
      73.6% alpha, 6.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
    Processing helix  chain 'A' and resid 17 through 22
    Processing helix  chain 'A' and resid 24 through 26
      No H-bonds generated for 'chain 'A' and resid 24 through 26'
    Processing helix  chain 'A' and resid 27 through 37
      removed outlier: 3.808A  pdb=" N   PHE A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 51
    Processing helix  chain 'A' and resid 52 through 74
      removed outlier: 4.301A  pdb=" N   LYS A  66 " --> pdb=" O   GLY A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 122
      removed outlier: 4.916A  pdb=" N   LYS A  90 " --> pdb=" O   LYS A  86 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   SER A  91 " --> pdb=" O   CYS A  87 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   VAL A  94 " --> pdb=" O   LYS A  90 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU A  95 " --> pdb=" O   SER A  91 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLY A  96 " --> pdb=" O   TYR A  92 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   PHE A  98 " --> pdb=" O   VAL A  94 " (cutoff:3.500A)
      Proline residue:  A 110  - end of helix
      removed outlier: 4.111A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 116 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 127 through 150
    Processing helix  chain 'A' and resid 150 through 181
      removed outlier: 4.027A  pdb=" N   LEU A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 182 through 188
    Processing helix  chain 'A' and resid 190 through 200
      removed outlier: 3.608A  pdb=" N   ILE A 194 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 210
      removed outlier: 4.475A  pdb=" N   GLN A 207 " --> pdb=" O   ASN A 203 " (cutoff:3.500A)
      removed outlier: 3.779A  pdb=" N   THR A 209 " --> pdb=" O   PHE A 205 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   VAL A 210 " --> pdb=" O   ASP A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 234
      Proline residue:  A 219  - end of helix
    Processing helix  chain 'A' and resid 235 through 290
      removed outlier: 3.897A  pdb=" N   ALA A 239 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   GLY A 240 " --> pdb=" O   SER A 236 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   LEU A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      Proline residue:  A 249  - end of helix
      removed outlier: 3.723A  pdb=" N   THR A 267 " --> pdb=" O   SER A 263 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   PHE A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 5.605A  pdb=" N   ARG A 284 " --> pdb=" O   ILE A 280 " (cutoff:3.500A)
      removed outlier: 6.228A  pdb=" N   ILE A 285 " --> pdb=" O   THR A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 342
      removed outlier: 3.797A  pdb=" N   LEU A 316 " --> pdb=" O   ARG A 312 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   LEU A 321 " --> pdb=" O   ARG A 317 " (cutoff:3.500A)
      removed outlier: 5.108A  pdb=" N   SER A 328 " --> pdb=" O   PHE A 324 " (cutoff:3.500A)
      removed outlier: 4.856A  pdb=" N   LYS A 329 " --> pdb=" O   PHE A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 367
      removed outlier: 3.868A  pdb=" N   ALA A 354 " --> pdb=" O   ARG A 350 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   LEU A 363 " --> pdb=" O   GLY A 359 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   THR A 364 " --> pdb=" O   ALA A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 391
      removed outlier: 3.522A  pdb=" N   GLU A 374 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 459
    Processing helix  chain 'A' and resid 488 through 495
    Processing helix  chain 'A' and resid 500 through 511
    Processing helix  chain 'A' and resid 512 through 522
      removed outlier: 4.163A  pdb=" N   ASP A 516 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   ASP A 522 " --> pdb=" O   GLN A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 533
    Processing helix  chain 'A' and resid 536 through 552
      removed outlier: 3.631A  pdb=" N   ARG A 542 " --> pdb=" O   GLY A 538 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   ASN A 544 " --> pdb=" O   LYS A 540 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU A 545 " --> pdb=" O   ALA A 541 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ASP A 552 " --> pdb=" O   ALA A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 576
      removed outlier: 4.688A  pdb=" N   PHE A 574 " --> pdb=" O   SER A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 581
    Processing helix  chain 'A' and resid 582 through 585
    Processing helix  chain 'A' and resid 593 through 600
    Processing helix  chain 'A' and resid 616 through 620
    Processing helix  chain 'A' and resid 697 through 707
      removed outlier: 4.080A  pdb=" N   TYR A 701 " --> pdb=" O   GLY A 697 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 710 through 745
      removed outlier: 3.532A  pdb=" N   PHE A 714 " --> pdb=" O   HIS A 710 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ASP A 732 " --> pdb=" O   TYR A 728 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A 745 " --> pdb=" O   LYS A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 807
      removed outlier: 3.929A  pdb=" N   PHE A 787 " --> pdb=" O   SER A 783 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   SER A 804 " --> pdb=" O   LYS A 800 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 816
      removed outlier: 3.851A  pdb=" N   PHE A 813 " --> pdb=" O   PRO A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 817 through 827
      removed outlier: 3.957A  pdb=" N   ARG A 824 " --> pdb=" O   ARG A 820 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   PHE A 825 " --> pdb=" O   ILE A 821 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 827 through 835
    Processing helix  chain 'A' and resid 835 through 861
    Processing helix  chain 'A' and resid 864 through 910
      removed outlier: 4.163A  pdb=" N   VAL A 869 " --> pdb=" O   ALA A 865 " (cutoff:3.500A)
      Proline residue:  A 870  - end of helix
      removed outlier: 4.078A  pdb=" N   THR A 885 " --> pdb=" O   TYR A 881 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   ASP A 888 " --> pdb=" O   GLU A 884 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ARG A 891 " --> pdb=" O   ARG A 887 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   SER A 898 " --> pdb=" O   SER A 894 " (cutoff:3.500A)
      Proline residue:  A 899  - end of helix
    Processing helix  chain 'A' and resid 910 through 917
    Processing helix  chain 'A' and resid 919 through 970
      removed outlier: 4.016A  pdb=" N   GLU A 925 " --> pdb=" O   GLU A 921 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   ARG A 951 " --> pdb=" O   TRP A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 975 through 1007
      removed outlier: 3.660A  pdb=" N   THR A 988 " --> pdb=" O   SER A 984 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   MET A 990 " --> pdb=" O   ALA A 986 " (cutoff:3.500A)
      removed outlier: 4.922A  pdb=" N   GLY A 991 " --> pdb=" O   LEU A 987 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   MET A 992 " --> pdb=" O   THR A 988 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   GLN A 994 " --> pdb=" O   MET A 990 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   TRP A 995 " --> pdb=" O   GLY A 991 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1007 through 1018
      removed outlier: 3.880A  pdb=" N   ASP A1018 " --> pdb=" O   ILE A1014 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1082 through 1089
    Processing helix  chain 'A' and resid 1106 through 1108
      No H-bonds generated for 'chain 'A' and resid 1106 through 1108'
    Processing helix  chain 'A' and resid 1109 through 1115
    Processing helix  chain 'A' and resid 1130 through 1136
    Processing helix  chain 'A' and resid 1142 through 1153
    Processing helix  chain 'A' and resid 1154 through 1159
      removed outlier: 3.972A  pdb=" N   GLU A1157 " --> pdb=" O   GLN A1154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1168
    Processing helix  chain 'A' and resid 1171 through 1175
    Processing helix  chain 'A' and resid 1178 through 1194
    Processing helix  chain 'A' and resid 1203 through 1207
    Processing helix  chain 'A' and resid 1208 through 1223
    Processing helix  chain 'A' and resid 1234 through 1238
    Processing helix  chain 'A' and resid 1257 through 1264
    Processing helix  chain 'A' and resid 1267 through 1275
    Processing helix  chain 'A' and resid 1276 through 1278
      No H-bonds generated for 'chain 'A' and resid 1276 through 1278'
    Processing helix  chain 'A' and resid 1279 through 1291
      removed outlier: 3.785A  pdb=" N   ALA A1283 " --> pdb=" O   ALA A1279 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL A1291 " --> pdb=" O   THR A1287 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 435
      removed outlier: 6.684A  pdb=" N   GLN A 429 " --> pdb=" O   THR A 416 " (cutoff:3.500A)
      removed outlier: 6.259A  pdb=" N   THR A 416 " --> pdb=" O   GLN A 429 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   LEU A 431 " --> pdb=" O   ASP A 414 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   PHE A 415 " --> pdb=" O   HIS A 466 " (cutoff:3.500A)
      removed outlier: 6.851A  pdb=" N   HIS A 466 " --> pdb=" O   PHE A 415 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 475 through 478
      removed outlier: 6.976A  pdb=" N   ILE A 605 " --> pdb=" O   VAL A 612 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1065
      removed outlier: 5.848A  pdb=" N   LYS A1059 " --> pdb=" O   PHE A1048 " (cutoff:3.500A)
      removed outlier: 7.528A  pdb=" N   PHE A1048 " --> pdb=" O   LYS A1059 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ALA A1063 " --> pdb=" O   ASP A1044 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   ASP A1044 " --> pdb=" O   ALA A1063 " (cutoff:3.500A)
      removed outlier: 7.070A  pdb=" N   ILE A1065 " --> pdb=" O   ILE A1042 " (cutoff:3.500A)
      removed outlier: 5.431A  pdb=" N   ILE A1042 " --> pdb=" O   ILE A1065 " (cutoff:3.500A)
      removed outlier: 5.420A  pdb=" N   PHE A1043 " --> pdb=" O   TRP A1099 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   TRP A1099 " --> pdb=" O   PHE A1043 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   ASN A1045 " --> pdb=" O   LYS A1097 " (cutoff:3.500A)
      removed outlier: 4.870A  pdb=" N   LYS A1097 " --> pdb=" O   ASN A1045 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1197 through 1201
      removed outlier: 6.162A  pdb=" N   LYS A1070 " --> pdb=" O   LYS A1243 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   MET A1245 " --> pdb=" O   LYS A1070 " (cutoff:3.500A)
      removed outlier: 6.308A  pdb=" N   GLY A1072 " --> pdb=" O   MET A1245 " (cutoff:3.500A)
      removed outlier: 7.693A  pdb=" N   LEU A1247 " --> pdb=" O   GLY A1072 " (cutoff:3.500A)
      removed outlier: 6.388A  pdb=" N   VAL A1074 " --> pdb=" O   LEU A1247 " (cutoff:3.500A)
      removed outlier: 6.613A  pdb=" N   ILE A1244 " --> pdb=" O   TYR A1255 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR A1255 " --> pdb=" O   ILE A1244 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   VAL A1246 " --> pdb=" O   LYS A1253 " (cutoff:3.500A)

    634 hydrogen bonds defined for protein.
    1815 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: 1.48

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1729
        1.32 -     1.45: 2420
        1.45 -     1.57: 5563
        1.57 -     1.69: 2
        1.69 -     1.81: 70
  Bond restraints: 9784
  Sorted by residual:
  bond pdb=" C14 TTC A1401 "
       pdb=" N12 TTC A1401 "
    ideal  model  delta    sigma   weight residual
    1.375  1.479 -0.104 2.00e-02 2.50e+03 2.68e+01
  bond pdb=" C11 TTC A1401 "
       pdb=" N12 TTC A1401 "
    ideal  model  delta    sigma   weight residual
    1.463  1.533 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" C13 TTC A1401 "
       pdb=" C9  TTC A1401 "
    ideal  model  delta    sigma   weight residual
    1.456  1.523 -0.067 2.00e-02 2.50e+03 1.14e+01
  bond pdb=" C14 TTC A1401 "
       pdb=" C15 TTC A1401 "
    ideal  model  delta    sigma   weight residual
    1.441  1.508 -0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" C20 TTC A1401 "
       pdb=" O22 TTC A1401 "
    ideal  model  delta    sigma   weight residual
    1.320  1.381 -0.061 2.00e-02 2.50e+03 9.20e+00
  ... (remaining 9779 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 12425
        1.63 -     3.27: 701
        3.27 -     4.90: 99
        4.90 -     6.54: 33
        6.54 -     8.17: 10
  Bond angle restraints: 13268
  Sorted by residual:
  angle pdb=" CA  TYR A 985 "
        pdb=" CB  TYR A 985 "
        pdb=" CG  TYR A 985 "
      ideal   model   delta    sigma   weight residual
     113.90  108.55    5.35 1.80e+00 3.09e-01 8.82e+00
  angle pdb=" C   LEU A 341 "
        pdb=" N   LEU A 342 "
        pdb=" CA  LEU A 342 "
      ideal   model   delta    sigma   weight residual
     122.31  116.79    5.52 2.00e+00 2.50e-01 7.62e+00
  angle pdb=" N   PHE A 205 "
        pdb=" CA  PHE A 205 "
        pdb=" C   PHE A 205 "
      ideal   model   delta    sigma   weight residual
     112.38  115.65   -3.27 1.22e+00 6.72e-01 7.20e+00
  angle pdb=" C   CYS A 161 "
        pdb=" N   ALA A 162 "
        pdb=" CA  ALA A 162 "
      ideal   model   delta    sigma   weight residual
     120.28  116.84    3.44 1.34e+00 5.57e-01 6.58e+00
  angle pdb=" C   LEU A 730 "
        pdb=" N   GLN A 731 "
        pdb=" CA  GLN A 731 "
      ideal   model   delta    sigma   weight residual
     120.44  117.20    3.24 1.30e+00 5.92e-01 6.22e+00
  ... (remaining 13263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.60: 5419
       17.60 -    35.21: 340
       35.21 -    52.81: 61
       52.81 -    70.41: 10
       70.41 -    88.02: 13
  Dihedral angle restraints: 5843
    sinusoidal: 2349
      harmonic: 3494
  Sorted by residual:
  dihedral pdb=" CA  ASP A 834 "
           pdb=" C   ASP A 834 "
           pdb=" N   LEU A 835 "
           pdb=" CA  LEU A 835 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -150.62  -29.38     0      5.00e+00 4.00e-02 3.45e+01
  dihedral pdb=" CA  ARG A  37 "
           pdb=" C   ARG A  37 "
           pdb=" N   ARG A  38 "
           pdb=" CA  ARG A  38 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.94   28.06     0      5.00e+00 4.00e-02 3.15e+01
  dihedral pdb=" CA  GLN A1154 "
           pdb=" C   GLN A1154 "
           pdb=" N   LEU A1155 "
           pdb=" CA  LEU A1155 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.96  -28.04     0      5.00e+00 4.00e-02 3.15e+01
  ... (remaining 5840 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 915
       0.041 -    0.081: 441
       0.081 -    0.122: 138
       0.122 -    0.163: 42
       0.163 -    0.204: 2
  Chirality restraints: 1538
  Sorted by residual:
  chirality pdb=" CA  HIS A 158 "
            pdb=" N   HIS A 158 "
            pdb=" C   HIS A 158 "
            pdb=" CB  HIS A 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  PHE A 205 "
            pdb=" N   PHE A 205 "
            pdb=" C   PHE A 205 "
            pdb=" CB  PHE A 205 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 8.28e-01
  chirality pdb=" CA  LYS A1102 "
            pdb=" N   LYS A1102 "
            pdb=" C   LYS A1102 "
            pdb=" CB  LYS A1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.61e-01
  ... (remaining 1535 not shown)

  Planarity restraints: 1642
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1  TTC A1401 "   -0.016 2.00e-02 2.50e+03   2.61e-02 3.75e+01
        pdb=" C11 TTC A1401 "    0.036 2.00e-02 2.50e+03
        pdb=" C13 TTC A1401 "    0.041 2.00e-02 2.50e+03
        pdb=" C14 TTC A1401 "   -0.019 2.00e-02 2.50e+03
        pdb=" C15 TTC A1401 "   -0.018 2.00e-02 2.50e+03
        pdb=" C16 TTC A1401 "   -0.002 2.00e-02 2.50e+03
        pdb=" C17 TTC A1401 "    0.029 2.00e-02 2.50e+03
        pdb=" C19 TTC A1401 "   -0.054 2.00e-02 2.50e+03
        pdb=" C2  TTC A1401 "   -0.019 2.00e-02 2.50e+03
        pdb=" C21 TTC A1401 "   -0.010 2.00e-02 2.50e+03
        pdb=" C27 TTC A1401 "   -0.009 2.00e-02 2.50e+03
        pdb=" C3  TTC A1401 "   -0.018 2.00e-02 2.50e+03
        pdb=" C4  TTC A1401 "   -0.005 2.00e-02 2.50e+03
        pdb=" C5  TTC A1401 "    0.004 2.00e-02 2.50e+03
        pdb=" C6  TTC A1401 "    0.005 2.00e-02 2.50e+03
        pdb=" C7  TTC A1401 "    0.016 2.00e-02 2.50e+03
        pdb=" C8  TTC A1401 "    0.030 2.00e-02 2.50e+03
        pdb=" C9  TTC A1401 "    0.046 2.00e-02 2.50e+03
        pdb=" N10 TTC A1401 "    0.018 2.00e-02 2.50e+03
        pdb=" N12 TTC A1401 "    0.014 2.00e-02 2.50e+03
        pdb=" O18 TTC A1401 "   -0.035 2.00e-02 2.50e+03
        pdb=" O26 TTC A1401 "   -0.037 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 917 "    0.002 2.00e-02 2.50e+03   1.90e-02 7.25e+00
        pdb=" CG  TYR A 917 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 917 "    0.030 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 917 "    0.003 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 917 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 917 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 917 "   -0.026 2.00e-02 2.50e+03
        pdb=" OH  TYR A 917 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 157 "    0.003 2.00e-02 2.50e+03   1.80e-02 6.46e+00
        pdb=" CG  TYR A 157 "   -0.004 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 157 "    0.025 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 157 "    0.000 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 157 "   -0.025 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 157 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 157 "   -0.024 2.00e-02 2.50e+03
        pdb=" OH  TYR A 157 "    0.026 2.00e-02 2.50e+03
  ... (remaining 1639 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1914
        2.77 -     3.30: 10627
        3.30 -     3.84: 15887
        3.84 -     4.37: 19330
        4.37 -     4.90: 31439
  Nonbonded interactions: 79197
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 521 "
            pdb=" OG1 THR A 526 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" ND1 HIS A  35 "
            pdb=" OE1 GLU A 884 "
     model   vdw
     2.246 3.120
  nonbonded pdb=" O   GLN A1068 "
            pdb=" NZ  LYS A1070 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" O   SER A 563 "
            pdb=" NE2 GLN A 593 "
     model   vdw
     2.362 3.120
  nonbonded pdb=" NH1 ARG A1220 "
            pdb=" OD2 ASP A1240 "
     model   vdw
     2.365 3.120
  ... (remaining 79192 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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=0.00 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:             5.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.150
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.120
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
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   0.104   9784  Z= 0.406
  Angle     :  0.890   8.171  13268  Z= 0.478
  Chirality :  0.052   0.204   1538
  Planarity :  0.008   0.087   1642
  Dihedral  : 13.092  88.017   3577
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 4.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.15 %
    Favored  : 98.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.22), residues: 1187
  helix: -1.06 (0.16), residues: 770
  sheet: -0.45 (0.50), residues: 72
  loop :  0.16 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.002   ARG A  37 
 TYR   0.030   0.006   TYR A 917 
 PHE   0.026   0.003   PHE A 418 
 TRP   0.026   0.003   TRP A  89 
 HIS   0.007   0.002   HIS A 798 

Details of bonding type rmsd
  covalent geometry    : bond        0.00918 ( 9784)
  covalent geometry    : angle       0.88977 (13268)
  hydrogen bonds       : bond        0.21707 (  634)
  hydrogen bonds       : angle       8.41699 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 0.341 
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: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8134 (mt) cc_final: 0.7857 (tt)
REVERT: A   63 PHE cc_start: 0.8844 (m-80) cc_final: 0.8610 (m-10)
REVERT: A  142 THR cc_start: 0.9443 (m) cc_final: 0.9205 (p)
REVERT: A  241 MET cc_start: 0.8749 (mmm) cc_final: 0.8411 (mpp)
REVERT: A  333 PHE cc_start: 0.8903 (t80) cc_final: 0.8355 (t80)
REVERT: A  337 THR cc_start: 0.9118 (m) cc_final: 0.8832 (m)
REVERT: A  388 THR cc_start: 0.9039 (m) cc_final: 0.8625 (m)
REVERT: A  415 PHE cc_start: 0.8862 (t80) cc_final: 0.8562 (t80)
REVERT: A  558 LEU cc_start: 0.8099 (mt) cc_final: 0.7780 (tt)
REVERT: A  577 CYS cc_start: 0.7907 (t) cc_final: 0.7463 (t)
REVERT: A 1025 TRP cc_start: 0.8416 (m-10) cc_final: 0.7852 (m-10)
REVERT: A 1043 PHE cc_start: 0.8570 (m-80) cc_final: 0.8199 (m-80)
REVERT: A 1048 PHE cc_start: 0.7964 (t80) cc_final: 0.7509 (t80)
REVERT: A 1069 GLU cc_start: 0.7876 (tt0) cc_final: 0.7650 (tp30)
REVERT: A 1112 ASP cc_start: 0.7089 (m-30) cc_final: 0.6567 (m-30)
REVERT: A 1120 ILE cc_start: 0.9253 (mt) cc_final: 0.8989 (mm)
REVERT: A 1131 MET cc_start: 0.8803 (mmm) cc_final: 0.8588 (mmm)
REVERT: A 1191 ILE cc_start: 0.9088 (mt) cc_final: 0.8851 (mt)
REVERT: A 1201 ASP cc_start: 0.7276 (t0) cc_final: 0.7055 (t70)
REVERT: A 1230 THR cc_start: 0.9250 (m) cc_final: 0.8920 (p)
REVERT: A 1241 SER cc_start: 0.8639 (m) cc_final: 0.8382 (p)
REVERT: A 1251 ARG cc_start: 0.8333 (mtt-85) cc_final: 0.7563 (mtt-85)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.0845
  time to fit residues: 27.1514
Evaluate side-chains
  161 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:   10.0000
   chunk 117 optimal weight:    4.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 122 ASN
A 183 ASN
A 399 ASN
A 572 HIS
A 602 GLN
A 703 ASN
A 903 HIS
A1263 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.129963 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.093042 restraints weight = 22226.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.096292 restraints weight = 11373.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.098420 restraints weight = 7334.913|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.099663 restraints weight = 5508.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.100567 restraints weight = 4626.256|
|-----------------------------------------------------------------------------|
r_work (final): 0.3478
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.2573

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9784  Z= 0.198
  Angle     :  0.687   6.760  13268  Z= 0.367
  Chirality :  0.044   0.164   1538
  Planarity :  0.005   0.067   1642
  Dihedral  :  8.363  72.422   1308
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  :  8.54 %
    Favored  : 89.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.46 (0.24), residues: 1187
  helix:  0.45 (0.18), residues: 792
  sheet: -0.18 (0.55), residues: 68
  loop :  0.46 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 490 
 TYR   0.024   0.002   TYR A 499 
 PHE   0.031   0.002   PHE A 258 
 TRP   0.031   0.002   TRP A  89 
 HIS   0.009   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 ( 9784)
  covalent geometry    : angle       0.68718 (13268)
  hydrogen bonds       : bond        0.05724 (  634)
  hydrogen bonds       : angle       5.19945 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 198
  time to evaluate  : 0.226 
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: symmetry clash
REVERT: A   13 LEU cc_start: 0.8153 (mt) cc_final: 0.7914 (tt)
REVERT: A   43 ASP cc_start: 0.7818 (m-30) cc_final: 0.7527 (m-30)
REVERT: A  241 MET cc_start: 0.8889 (mmm) cc_final: 0.8636 (tpp)
REVERT: A  289 TYR cc_start: 0.8102 (m-10) cc_final: 0.7735 (m-80)
REVERT: A  415 PHE cc_start: 0.8736 (t80) cc_final: 0.8466 (t80)
REVERT: A  418 PHE cc_start: 0.7777 (OUTLIER) cc_final: 0.7202 (m-80)
REVERT: A  462 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.6880 (mt)
REVERT: A  550 TYR cc_start: 0.7774 (t80) cc_final: 0.7089 (t80)
REVERT: A  558 LEU cc_start: 0.8275 (mt) cc_final: 0.7713 (tt)
REVERT: A  589 LEU cc_start: 0.8570 (tp) cc_final: 0.8303 (tp)
REVERT: A  728 TYR cc_start: 0.9334 (t80) cc_final: 0.9098 (t80)
REVERT: A  990 MET cc_start: 0.8197 (tpp) cc_final: 0.7916 (tpp)
REVERT: A 1046 VAL cc_start: 0.9278 (OUTLIER) cc_final: 0.8940 (p)
REVERT: A 1069 GLU cc_start: 0.8036 (tt0) cc_final: 0.7629 (tp30)
REVERT: A 1111 HIS cc_start: 0.7530 (m170) cc_final: 0.7301 (m170)
REVERT: A 1120 ILE cc_start: 0.9362 (mt) cc_final: 0.9135 (mm)
REVERT: A 1128 THR cc_start: 0.7743 (m) cc_final: 0.7323 (m)
REVERT: A 1141 HIS cc_start: 0.8356 (m-70) cc_final: 0.8085 (m90)
REVERT: A 1166 MET cc_start: 0.7538 (mmt) cc_final: 0.7272 (mmt)
REVERT: A 1201 ASP cc_start: 0.7115 (t0) cc_final: 0.6863 (t70)
REVERT: A 1229 LEU cc_start: 0.8888 (mp) cc_final: 0.8686 (tt)
REVERT: A 1235 LEU cc_start: 0.9199 (mp) cc_final: 0.8850 (tt)
  outliers start: 22
  outliers final: 15
  residues processed: 209
  average time/residue: 0.0853
  time to fit residues: 24.9660
Evaluate side-chains
  172 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 154
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1046 VAL
Chi-restraints excluded: chain A residue 1108 ILE
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1276 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 111 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   chunk 110 optimal weight:    0.5980
   chunk 113 optimal weight:    6.9990
   chunk 45 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 79 optimal weight:    3.9990
   chunk 95 optimal weight:    3.9990
   overall best weight:    1.0384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3931 r_free = 0.3931 target = 0.130216 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.093378 restraints weight = 22340.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.096625 restraints weight = 11499.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.098706 restraints weight = 7392.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.100088 restraints weight = 5558.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.100826 restraints weight = 4650.064|
|-----------------------------------------------------------------------------|
r_work (final): 0.3479
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8272
moved from start:          0.3268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9784  Z= 0.167
  Angle     :  0.627   7.185  13268  Z= 0.331
  Chirality :  0.042   0.154   1538
  Planarity :  0.004   0.041   1642
  Dihedral  :  7.462  71.889   1308
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 13.15 %
    Favored  : 84.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.24), residues: 1187
  helix:  0.81 (0.18), residues: 785
  sheet:  0.25 (0.53), residues: 78
  loop :  0.64 (0.38), residues: 324

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1220 
 TYR   0.022   0.002   TYR A1016 
 PHE   0.029   0.002   PHE A 258 
 TRP   0.024   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9784)
  covalent geometry    : angle       0.62738 (13268)
  hydrogen bonds       : bond        0.05129 (  634)
  hydrogen bonds       : angle       4.82033 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 183
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.8148 (mt) cc_final: 0.7912 (tt)
REVERT: A  241 MET cc_start: 0.8839 (mmm) cc_final: 0.8511 (mpp)
REVERT: A  292 GLU cc_start: 0.8339 (mt-10) cc_final: 0.6408 (mt-10)
REVERT: A  418 PHE cc_start: 0.7687 (OUTLIER) cc_final: 0.7280 (m-80)
REVERT: A  495 PHE cc_start: 0.7695 (OUTLIER) cc_final: 0.7323 (m-80)
REVERT: A  550 TYR cc_start: 0.7976 (t80) cc_final: 0.7282 (t80)
REVERT: A  558 LEU cc_start: 0.8207 (mt) cc_final: 0.7678 (tt)
REVERT: A  589 LEU cc_start: 0.8511 (tp) cc_final: 0.8275 (tp)
REVERT: A  990 MET cc_start: 0.8335 (tpp) cc_final: 0.8029 (tpp)
REVERT: A 1025 TRP cc_start: 0.8127 (m-10) cc_final: 0.7608 (m-10)
REVERT: A 1043 PHE cc_start: 0.8254 (m-80) cc_final: 0.7936 (m-80)
REVERT: A 1069 GLU cc_start: 0.8027 (tt0) cc_final: 0.7710 (tp30)
REVERT: A 1120 ILE cc_start: 0.9356 (mt) cc_final: 0.9140 (mm)
REVERT: A 1201 ASP cc_start: 0.7563 (t0) cc_final: 0.7262 (t70)
REVERT: A 1216 GLN cc_start: 0.9009 (mm-40) cc_final: 0.8775 (tp-100)
REVERT: A 1229 LEU cc_start: 0.8796 (mp) cc_final: 0.8595 (tt)
REVERT: A 1248 ASP cc_start: 0.8242 (t0) cc_final: 0.7730 (t70)
  outliers start: 25
  outliers final: 18
  residues processed: 197
  average time/residue: 0.0742
  time to fit residues: 21.4466
Evaluate side-chains
  177 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 157
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  495 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  866 ILE
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1119 ILE
Chi-restraints excluded: chain A residue 1211 THR
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Chi-restraints excluded: chain A residue 1244 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 41 optimal weight:   10.0000
   chunk 72 optimal weight:    0.8980
   chunk 91 optimal weight:    0.7980
   chunk 101 optimal weight:    3.9990
   chunk 49 optimal weight:    7.9990
   chunk 25 optimal weight:    0.8980
   chunk 103 optimal weight:    0.1980
   chunk 45 optimal weight:    7.9990
   chunk 81 optimal weight:    0.7980
   chunk 47 optimal weight:    8.9990
   chunk 5 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 725 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3944 r_free = 0.3944 target = 0.130917 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.096882 restraints weight = 22753.775|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.100091 restraints weight = 11581.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.102147 restraints weight = 7363.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.103445 restraints weight = 5487.328|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.104141 restraints weight = 4556.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.3706

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9784  Z= 0.138
  Angle     :  0.615  11.594  13268  Z= 0.316
  Chirality :  0.041   0.145   1538
  Planarity :  0.004   0.031   1642
  Dihedral  :  6.754  65.898   1308
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.40 %
    Favored  : 82.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.16 (0.24), residues: 1187
  helix:  1.03 (0.18), residues: 786
  sheet:  0.34 (0.54), residues: 79
  loop :  0.53 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1251 
 TYR   0.030   0.002   TYR A 289 
 PHE   0.027   0.002   PHE A 258 
 TRP   0.024   0.001   TRP A  89 
 HIS   0.009   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 9784)
  covalent geometry    : angle       0.61488 (13268)
  hydrogen bonds       : bond        0.04700 (  634)
  hydrogen bonds       : angle       4.67111 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 173
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.7915 (tm-30)
REVERT: A  418 PHE cc_start: 0.7580 (OUTLIER) cc_final: 0.7220 (m-80)
REVERT: A  495 PHE cc_start: 0.7595 (OUTLIER) cc_final: 0.7326 (m-80)
REVERT: A  550 TYR cc_start: 0.7967 (t80) cc_final: 0.7278 (t80)
REVERT: A  558 LEU cc_start: 0.8273 (mt) cc_final: 0.7801 (tt)
REVERT: A 1043 PHE cc_start: 0.8169 (m-80) cc_final: 0.7781 (m-80)
REVERT: A 1069 GLU cc_start: 0.7918 (tt0) cc_final: 0.7539 (tp30)
REVERT: A 1120 ILE cc_start: 0.9397 (mt) cc_final: 0.9190 (mm)
REVERT: A 1201 ASP cc_start: 0.7676 (t0) cc_final: 0.7232 (t70)
REVERT: A 1216 GLN cc_start: 0.8961 (mm-40) cc_final: 0.8758 (tp-100)
  outliers start: 31
  outliers final: 18
  residues processed: 196
  average time/residue: 0.0655
  time to fit residues: 19.2475
Evaluate side-chains
  170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  495 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  923 CYS
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1211 THR
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Chi-restraints excluded: chain A residue 1244 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 6 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 80 optimal weight:    0.7980
   chunk 60 optimal weight:    4.9990
   chunk 78 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 112 optimal weight:    4.9990
   chunk 48 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0870
   chunk 49 optimal weight:    3.9990
   overall best weight:    1.7562

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

Flipped N/Q/H residues before XYZ refinement:
A 200 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.128407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3375 r_free = 0.3375 target = 0.093921 restraints weight = 22808.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.095432 restraints weight = 11443.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.096757 restraints weight = 7671.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.097243 restraints weight = 6266.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.097689 restraints weight = 5697.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3418
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.3821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   9784  Z= 0.221
  Angle     :  0.669   8.307  13268  Z= 0.341
  Chirality :  0.043   0.164   1538
  Planarity :  0.004   0.030   1642
  Dihedral  :  6.575  66.289   1308
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 15.55 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.13 (0.24), residues: 1187
  helix:  0.97 (0.18), residues: 787
  sheet:  0.49 (0.54), residues: 79
  loop :  0.59 (0.38), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  21 
 TYR   0.019   0.002   TYR A 339 
 PHE   0.026   0.002   PHE A 258 
 TRP   0.021   0.001   TRP A  89 
 HIS   0.007   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00499 ( 9784)
  covalent geometry    : angle       0.66920 (13268)
  hydrogen bonds       : bond        0.04837 (  634)
  hydrogen bonds       : angle       4.79156 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 156
  time to evaluate  : 0.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 GLU cc_start: 0.7619 (pp20) cc_final: 0.7368 (pp20)
REVERT: A  418 PHE cc_start: 0.7635 (OUTLIER) cc_final: 0.7199 (m-80)
REVERT: A  495 PHE cc_start: 0.7841 (OUTLIER) cc_final: 0.7478 (m-80)
REVERT: A  550 TYR cc_start: 0.8141 (t80) cc_final: 0.7424 (t80)
REVERT: A  558 LEU cc_start: 0.8261 (mt) cc_final: 0.7693 (tt)
REVERT: A 1043 PHE cc_start: 0.8493 (m-80) cc_final: 0.8061 (m-80)
REVERT: A 1046 VAL cc_start: 0.9267 (OUTLIER) cc_final: 0.9067 (m)
REVERT: A 1069 GLU cc_start: 0.8224 (tt0) cc_final: 0.7762 (tp30)
REVERT: A 1090 ARG cc_start: 0.8583 (mtp180) cc_final: 0.8111 (mmm160)
REVERT: A 1120 ILE cc_start: 0.9354 (mt) cc_final: 0.9120 (mm)
REVERT: A 1201 ASP cc_start: 0.7724 (t0) cc_final: 0.7231 (t70)
REVERT: A 1216 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8969 (tp-100)
REVERT: A 1280 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8686 (mp0)
  outliers start: 37
  outliers final: 24
  residues processed: 179
  average time/residue: 0.0693
  time to fit residues: 18.5686
Evaluate side-chains
  178 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 150
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   43 ASP
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue   97 ILE
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  221 GLN
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  495 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  923 CYS
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1017 THR
Chi-restraints excluded: chain A residue 1046 VAL
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Chi-restraints excluded: chain A residue 1244 ILE
Chi-restraints excluded: chain A residue 1280 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 67 optimal weight:    0.6980
   chunk 114 optimal weight:    7.9990
   chunk 57 optimal weight:   10.0000
   chunk 88 optimal weight:    0.6980
   chunk 27 optimal weight:    0.9980
   chunk 102 optimal weight:    0.3980
   chunk 45 optimal weight:   10.0000
   chunk 35 optimal weight:    0.5980
   chunk 117 optimal weight:    4.9990
   chunk 10 optimal weight:    0.5980
   chunk 31 optimal weight:    0.9980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A1274 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.130977 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.098974 restraints weight = 22110.145|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.100716 restraints weight = 11046.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.102331 restraints weight = 7029.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.102750 restraints weight = 5718.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.102822 restraints weight = 4931.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3502
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9784  Z= 0.130
  Angle     :  0.612   8.606  13268  Z= 0.307
  Chirality :  0.040   0.158   1538
  Planarity :  0.004   0.037   1642
  Dihedral  :  6.100  53.489   1308
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.02 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 17.47 %
    Favored  : 79.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.25), residues: 1187
  helix:  1.26 (0.18), residues: 787
  sheet:  0.68 (0.54), residues: 79
  loop :  0.60 (0.38), residues: 321

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  70 
 TYR   0.025   0.001   TYR A 289 
 PHE   0.024   0.001   PHE A 258 
 TRP   0.020   0.001   TRP A  89 
 HIS   0.007   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9784)
  covalent geometry    : angle       0.61238 (13268)
  hydrogen bonds       : bond        0.04495 (  634)
  hydrogen bonds       : angle       4.51310 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 176
  time to evaluate  : 0.279 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 SER cc_start: 0.8495 (m) cc_final: 0.8269 (m)
REVERT: A  289 TYR cc_start: 0.7733 (m-80) cc_final: 0.7510 (m-80)
REVERT: A  409 MET cc_start: 0.4246 (pmm) cc_final: 0.3194 (mmt)
REVERT: A  418 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.7167 (m-80)
REVERT: A  495 PHE cc_start: 0.7677 (OUTLIER) cc_final: 0.7388 (m-80)
REVERT: A  550 TYR cc_start: 0.8090 (t80) cc_final: 0.7395 (t80)
REVERT: A  558 LEU cc_start: 0.8247 (mt) cc_final: 0.7739 (tt)
REVERT: A  987 LEU cc_start: 0.9095 (OUTLIER) cc_final: 0.8860 (mt)
REVERT: A 1069 GLU cc_start: 0.8058 (tt0) cc_final: 0.7749 (tp30)
REVERT: A 1120 ILE cc_start: 0.9435 (mt) cc_final: 0.9205 (mm)
REVERT: A 1201 ASP cc_start: 0.7613 (t0) cc_final: 0.7187 (t70)
  outliers start: 27
  outliers final: 20
  residues processed: 195
  average time/residue: 0.0687
  time to fit residues: 19.7163
Evaluate side-chains
  180 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 157
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  495 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  923 CYS
Chi-restraints excluded: chain A residue  961 ILE
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Chi-restraints excluded: chain A residue 1244 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 38 optimal weight:    2.9990
   chunk 87 optimal weight:    7.9990
   chunk 77 optimal weight:    0.9980
   chunk 29 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9990
   chunk 96 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 99 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 7 optimal weight:    0.0870
   overall best weight:    1.0162

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.130338 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.095876 restraints weight = 22428.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.097526 restraints weight = 11957.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.098732 restraints weight = 7732.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.099505 restraints weight = 6454.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.099552 restraints weight = 5747.473|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8319
moved from start:          0.4341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9784  Z= 0.158
  Angle     :  0.651   9.898  13268  Z= 0.325
  Chirality :  0.041   0.187   1538
  Planarity :  0.004   0.040   1642
  Dihedral  :  5.990  54.448   1308
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  3.65 %
    Allowed  : 18.62 %
    Favored  : 77.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.47 (0.24), residues: 1187
  helix:  1.25 (0.18), residues: 788
  sheet:  0.82 (0.54), residues: 80
  loop :  0.62 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 262 
 TYR   0.018   0.002   TYR A1259 
 PHE   0.023   0.002   PHE A 258 
 TRP   0.019   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 9784)
  covalent geometry    : angle       0.65057 (13268)
  hydrogen bonds       : bond        0.04442 (  634)
  hydrogen bonds       : angle       4.54968 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 158
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  236 SER cc_start: 0.8570 (m) cc_final: 0.8357 (m)
REVERT: A  409 MET cc_start: 0.4397 (pmm) cc_final: 0.3552 (mmt)
REVERT: A  418 PHE cc_start: 0.7593 (OUTLIER) cc_final: 0.7252 (m-80)
REVERT: A  495 PHE cc_start: 0.7793 (OUTLIER) cc_final: 0.7467 (m-80)
REVERT: A  550 TYR cc_start: 0.8211 (t80) cc_final: 0.7501 (t80)
REVERT: A  558 LEU cc_start: 0.8211 (mt) cc_final: 0.7712 (tt)
REVERT: A 1043 PHE cc_start: 0.8486 (m-80) cc_final: 0.8182 (m-80)
REVERT: A 1061 LEU cc_start: 0.8863 (tt) cc_final: 0.8471 (mm)
REVERT: A 1069 GLU cc_start: 0.8264 (tt0) cc_final: 0.7847 (tp30)
REVERT: A 1120 ILE cc_start: 0.9395 (mt) cc_final: 0.9160 (mm)
REVERT: A 1201 ASP cc_start: 0.7622 (t0) cc_final: 0.7159 (t70)
REVERT: A 1210 ARG cc_start: 0.8509 (ptt-90) cc_final: 0.8044 (tmm-80)
  outliers start: 38
  outliers final: 27
  residues processed: 187
  average time/residue: 0.0731
  time to fit residues: 20.2557
Evaluate side-chains
  181 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 152
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  495 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  783 SER
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  883 LEU
Chi-restraints excluded: chain A residue  923 CYS
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1046 VAL
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Chi-restraints excluded: chain A residue 1244 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 23 optimal weight:    3.9990
   chunk 85 optimal weight:    0.3980
   chunk 63 optimal weight:    2.9990
   chunk 90 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9980
   chunk 52 optimal weight:    7.9990
   chunk 12 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 109 optimal weight:    5.9990
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 583 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.129488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.094343 restraints weight = 21934.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.096072 restraints weight = 11632.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.097041 restraints weight = 7510.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.098085 restraints weight = 6347.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.098021 restraints weight = 5602.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3427
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8341
moved from start:          0.4447

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9784  Z= 0.194
  Angle     :  0.672  10.146  13268  Z= 0.338
  Chirality :  0.043   0.164   1538
  Planarity :  0.004   0.042   1642
  Dihedral  :  6.080  55.813   1308
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.77 %
    Favored  : 77.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.24), residues: 1187
  helix:  1.23 (0.18), residues: 785
  sheet:  0.49 (0.54), residues: 80
  loop :  0.66 (0.38), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1210 
 TYR   0.015   0.002   TYR A 339 
 PHE   0.027   0.002   PHE A1269 
 TRP   0.019   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00439 ( 9784)
  covalent geometry    : angle       0.67203 (13268)
  hydrogen bonds       : bond        0.04610 (  634)
  hydrogen bonds       : angle       4.66493 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 152
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 PHE cc_start: 0.7663 (OUTLIER) cc_final: 0.7264 (m-80)
REVERT: A  495 PHE cc_start: 0.7867 (OUTLIER) cc_final: 0.7536 (m-80)
REVERT: A  550 TYR cc_start: 0.8205 (t80) cc_final: 0.7501 (t80)
REVERT: A  558 LEU cc_start: 0.8208 (mt) cc_final: 0.7690 (tt)
REVERT: A  835 LEU cc_start: 0.9002 (tp) cc_final: 0.8701 (tp)
REVERT: A 1069 GLU cc_start: 0.8330 (tt0) cc_final: 0.7853 (tp30)
REVERT: A 1120 ILE cc_start: 0.9389 (mt) cc_final: 0.9149 (mm)
REVERT: A 1201 ASP cc_start: 0.7581 (t0) cc_final: 0.7169 (t70)
REVERT: A 1210 ARG cc_start: 0.8469 (ptt-90) cc_final: 0.8000 (tmm-80)
  outliers start: 31
  outliers final: 26
  residues processed: 175
  average time/residue: 0.0734
  time to fit residues: 19.3244
Evaluate side-chains
  174 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 146
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   39 LEU
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  183 ASN
Chi-restraints excluded: chain A residue  191 THR
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  365 VAL
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  427 THR
Chi-restraints excluded: chain A residue  495 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  783 SER
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  923 CYS
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1046 VAL
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 109 optimal weight:    6.9990
   chunk 77 optimal weight:    0.9990
   chunk 98 optimal weight:    3.9990
   chunk 89 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 110 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9990
   chunk 57 optimal weight:    8.9990
   chunk 44 optimal weight:    0.0870
   chunk 29 optimal weight:    0.9980
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
** A 994 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 = 0.3954 r_free = 0.3954 target = 0.131622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.094980 restraints weight = 21929.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.098117 restraints weight = 11101.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.100161 restraints weight = 7134.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.101469 restraints weight = 5377.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 17)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.101958 restraints weight = 4517.006|
|-----------------------------------------------------------------------------|
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.4665

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9784  Z= 0.139
  Angle     :  0.654  11.390  13268  Z= 0.325
  Chirality :  0.042   0.182   1538
  Planarity :  0.004   0.040   1642
  Dihedral  :  5.878  50.240   1308
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.35 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.55 (0.25), residues: 1187
  helix:  1.37 (0.18), residues: 784
  sheet:  0.65 (0.55), residues: 80
  loop :  0.52 (0.37), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 262 
 TYR   0.014   0.001   TYR A1255 
 PHE   0.021   0.002   PHE A 258 
 TRP   0.019   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9784)
  covalent geometry    : angle       0.65424 (13268)
  hydrogen bonds       : bond        0.04462 (  634)
  hydrogen bonds       : angle       4.54093 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 163
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  409 MET cc_start: 0.4132 (pmm) cc_final: 0.3366 (mmt)
REVERT: A  418 PHE cc_start: 0.7499 (OUTLIER) cc_final: 0.7218 (m-80)
REVERT: A  495 PHE cc_start: 0.7692 (OUTLIER) cc_final: 0.7489 (m-80)
REVERT: A  550 TYR cc_start: 0.8131 (t80) cc_final: 0.7459 (t80)
REVERT: A  558 LEU cc_start: 0.8189 (mt) cc_final: 0.7701 (tt)
REVERT: A  801 MET cc_start: 0.9345 (tmm) cc_final: 0.9142 (tmm)
REVERT: A  835 LEU cc_start: 0.8989 (tp) cc_final: 0.8735 (tp)
REVERT: A  874 ILE cc_start: 0.8886 (mt) cc_final: 0.8598 (mm)
REVERT: A  994 GLN cc_start: 0.7962 (mt0) cc_final: 0.7740 (mt0)
REVERT: A 1061 LEU cc_start: 0.8651 (tt) cc_final: 0.8359 (mm)
REVERT: A 1069 GLU cc_start: 0.8114 (tt0) cc_final: 0.7693 (tp30)
REVERT: A 1120 ILE cc_start: 0.9403 (mt) cc_final: 0.9179 (mm)
REVERT: A 1147 TRP cc_start: 0.8556 (m100) cc_final: 0.7835 (m100)
REVERT: A 1201 ASP cc_start: 0.7565 (t0) cc_final: 0.7190 (t70)
REVERT: A 1210 ARG cc_start: 0.8213 (ptt-90) cc_final: 0.7885 (tmm-80)
REVERT: A 1234 ARG cc_start: 0.8213 (ptm160) cc_final: 0.7889 (ptm160)
REVERT: A 1269 PHE cc_start: 0.8673 (t80) cc_final: 0.8347 (t80)
  outliers start: 28
  outliers final: 22
  residues processed: 184
  average time/residue: 0.0739
  time to fit residues: 20.5242
Evaluate side-chains
  176 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 152
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue   85 ILE
Chi-restraints excluded: chain A residue   89 TRP
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  495 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  783 SER
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  923 CYS
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1046 VAL
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 47 optimal weight:    2.9990
   chunk 7 optimal weight:    0.6980
   chunk 41 optimal weight:    6.9990
   chunk 66 optimal weight:    0.0050
   chunk 21 optimal weight:    0.9990
   chunk 43 optimal weight:    5.9990
   chunk 92 optimal weight:    0.0020
   chunk 77 optimal weight:    0.8980
   chunk 88 optimal weight:    0.5980
   chunk 72 optimal weight:    2.9990
   chunk 57 optimal weight:    6.9990
   overall best weight:    0.4402

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

Flipped N/Q/H residues before XYZ refinement:
** A 994 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 = 0.3961 r_free = 0.3961 target = 0.131765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.095710 restraints weight = 21732.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.098651 restraints weight = 11430.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.100632 restraints weight = 7525.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.101722 restraints weight = 5703.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.102576 restraints weight = 4845.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3519
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.4875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9784  Z= 0.132
  Angle     :  0.668  11.231  13268  Z= 0.331
  Chirality :  0.042   0.177   1538
  Planarity :  0.004   0.039   1642
  Dihedral  :  5.652  53.304   1308
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.50 %
    Allowed  : 21.11 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.61 (0.25), residues: 1187
  helix:  1.39 (0.18), residues: 788
  sheet:  0.88 (0.56), residues: 80
  loop :  0.55 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 262 
 TYR   0.016   0.001   TYR A1255 
 PHE   0.020   0.001   PHE A1269 
 TRP   0.017   0.001   TRP A  89 
 HIS   0.006   0.001   HIS A1141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 9784)
  covalent geometry    : angle       0.66842 (13268)
  hydrogen bonds       : bond        0.04370 (  634)
  hydrogen bonds       : angle       4.52445 ( 1815)

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

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

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2374 Ramachandran restraints generated.
    1187 Oldfield, 0 Emsley, 1187 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 156
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  418 PHE cc_start: 0.7446 (OUTLIER) cc_final: 0.7203 (m-80)
REVERT: A  550 TYR cc_start: 0.8095 (t80) cc_final: 0.7437 (t80)
REVERT: A  558 LEU cc_start: 0.8226 (mt) cc_final: 0.7806 (tt)
REVERT: A  874 ILE cc_start: 0.8843 (mt) cc_final: 0.8593 (mm)
REVERT: A 1061 LEU cc_start: 0.8506 (tt) cc_final: 0.8278 (mm)
REVERT: A 1120 ILE cc_start: 0.9407 (mt) cc_final: 0.9172 (mm)
REVERT: A 1147 TRP cc_start: 0.8316 (m100) cc_final: 0.7613 (m100)
REVERT: A 1201 ASP cc_start: 0.7507 (t0) cc_final: 0.7118 (t70)
REVERT: A 1210 ARG cc_start: 0.8049 (ptt-90) cc_final: 0.7789 (tmm-80)
REVERT: A 1245 MET cc_start: 0.8323 (mmm) cc_final: 0.8077 (tpp)
REVERT: A 1269 PHE cc_start: 0.8730 (t80) cc_final: 0.8288 (t80)
  outliers start: 26
  outliers final: 20
  residues processed: 175
  average time/residue: 0.0714
  time to fit residues: 18.7764
Evaluate side-chains
  170 residues out of total 1042 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 149
  time to evaluate  : 0.380 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   81 THR
Chi-restraints excluded: chain A residue  104 SER
Chi-restraints excluded: chain A residue  107 VAL
Chi-restraints excluded: chain A residue  148 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  418 PHE
Chi-restraints excluded: chain A residue  729 VAL
Chi-restraints excluded: chain A residue  767 ILE
Chi-restraints excluded: chain A residue  783 SER
Chi-restraints excluded: chain A residue  826 SER
Chi-restraints excluded: chain A residue  923 CYS
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1015 GLU
Chi-restraints excluded: chain A residue 1046 VAL
Chi-restraints excluded: chain A residue 1058 LEU
Chi-restraints excluded: chain A residue 1213 GLU
Chi-restraints excluded: chain A residue 1230 THR
Chi-restraints excluded: chain A residue 1231 ILE
Chi-restraints excluded: chain A residue 1233 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 51 optimal weight:    9.9990
   chunk 61 optimal weight:    0.9990
   chunk 113 optimal weight:    3.9990
   chunk 86 optimal weight:    0.7980
   chunk 19 optimal weight:    0.5980
   chunk 77 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 60 optimal weight:    6.9990
   chunk 94 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 994 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 = 0.3954 r_free = 0.3954 target = 0.131358 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.095309 restraints weight = 21901.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.098229 restraints weight = 11573.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.100197 restraints weight = 7588.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.101384 restraints weight = 5800.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3517 r_free = 0.3517 target = 0.102177 restraints weight = 4897.185|
|-----------------------------------------------------------------------------|
r_work (final): 0.3509
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.4965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9784  Z= 0.140
  Angle     :  0.680  12.356  13268  Z= 0.339
  Chirality :  0.042   0.194   1538
  Planarity :  0.004   0.040   1642
  Dihedral  :  5.566  55.434   1308
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.27 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 21.79 %
    Favored  : 75.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.25), residues: 1187
  helix:  1.37 (0.18), residues: 788
  sheet:  0.92 (0.56), residues: 80
  loop :  0.55 (0.38), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 262 
 TYR   0.016   0.001   TYR A1259 
 PHE   0.027   0.002   PHE A1048 
 TRP   0.007   0.001   TRP A 863 
 HIS   0.005   0.001   HIS A 153 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 9784)
  covalent geometry    : angle       0.67960 (13268)
  hydrogen bonds       : bond        0.04371 (  634)
  hydrogen bonds       : angle       4.53156 ( 1815)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1493.46 seconds
wall clock time: 26 minutes 32.08 seconds (1592.08 seconds total)