Starting phenix.real_space_refine
on Wed Sep 17 17:56:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f76_50247/09_2025/9f76_50247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f76_50247/09_2025/9f76_50247.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9f76_50247/09_2025/9f76_50247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f76_50247/09_2025/9f76_50247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f76_50247/09_2025/9f76_50247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f76_50247/09_2025/9f76_50247.cif"
  }
  resolution = 3.1
  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=   0.001 sd=   0.026
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      65      5.16       5
     C    6596      2.51       5
     N    1733      2.21       5
     O    1785      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10179
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 10179
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1258, 10179
          Classifications: {'peptide': 1258}
          Link IDs: {'PTRANS': 67, 'TRANS': 1190}
          Chain breaks: 3
  Time building chain proxies: 2.16, per 1000 atoms: 0.21
  Number of scatterers: 10179
  At special positions: 0
  Unit cell: (105.625, 115.781, 131.016, 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      65     16.00
     O    1785      8.00
     N    1733      7.00
     C    6596      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: 0.88
  Conformation dependent library (CDL) restraints added in 375.2 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2418

  Finding SS restraints...
    Secondary structure from input PDB file:
      78 helices and 1 sheets defined
      74.0% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 70
      removed outlier: 3.515A  pdb=" N   GLN A  58 " --> pdb=" O   GLU A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 72 through 89
    Processing helix  chain 'A' and resid 93 through 104
    Processing helix  chain 'A' and resid 111 through 126
    Processing helix  chain 'A' and resid 127 through 129
      No H-bonds generated for 'chain 'A' and resid 127 through 129'
    Processing helix  chain 'A' and resid 130 through 147
      removed outlier: 3.747A  pdb=" N   THR A 147 " --> pdb=" O   GLU A 143 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 161 through 172
    Processing helix  chain 'A' and resid 179 through 191
      removed outlier: 3.617A  pdb=" N   ALA A 183 " --> pdb=" O   PRO A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 211
      removed outlier: 4.316A  pdb=" N   SER A 206 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 219
    Processing helix  chain 'A' and resid 223 through 227
    Processing helix  chain 'A' and resid 259 through 264
      removed outlier: 3.960A  pdb=" N   GLU A 264 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 276
    Processing helix  chain 'A' and resid 279 through 288
    Processing helix  chain 'A' and resid 297 through 316
    Processing helix  chain 'A' and resid 328 through 344
      removed outlier: 4.156A  pdb=" N   ILE A 339 " --> pdb=" O   SER A 335 " (cutoff:3.500A)
      removed outlier: 5.000A  pdb=" N   PHE A 340 " --> pdb=" O   SER A 336 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   PHE A 341 " --> pdb=" O   GLN A 337 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 348 through 361
    Processing helix  chain 'A' and resid 368 through 383
      removed outlier: 3.624A  pdb=" N   GLN A 378 " --> pdb=" O   TRP A 374 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   PHE A 379 " --> pdb=" O   VAL A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 392
    Processing helix  chain 'A' and resid 393 through 403
      removed outlier: 4.114A  pdb=" N   LYS A 397 " --> pdb=" O   LEU A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 423
      removed outlier: 4.012A  pdb=" N   HIS A 421 " --> pdb=" O   PRO A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 438
    Processing helix  chain 'A' and resid 451 through 464
    Processing helix  chain 'A' and resid 472 through 481
    Processing helix  chain 'A' and resid 488 through 501
      removed outlier: 4.338A  pdb=" N   THR A 498 " --> pdb=" O   ALA A 494 " (cutoff:3.500A)
      removed outlier: 4.591A  pdb=" N   ILE A 499 " --> pdb=" O   LEU A 495 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   GLY A 501 " --> pdb=" O   GLU A 497 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 524 through 531
    Processing helix  chain 'A' and resid 532 through 554
    Processing helix  chain 'A' and resid 560 through 571
    Processing helix  chain 'A' and resid 572 through 577
      removed outlier: 6.355A  pdb=" N   GLU A 575 " --> pdb=" O   VAL A 572 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ILE A 576 " --> pdb=" O   TYR A 573 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   GLU A 577 " --> pdb=" O   MET A 574 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 572 through 577'
    Processing helix  chain 'A' and resid 581 through 587
      removed outlier: 3.620A  pdb=" N   ILE A 585 " --> pdb=" O   ILE A 581 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 596
    Processing helix  chain 'A' and resid 599 through 612
      removed outlier: 3.926A  pdb=" N   MET A 612 " --> pdb=" O   PHE A 608 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 616 through 633
    Processing helix  chain 'A' and resid 638 through 655
    Processing helix  chain 'A' and resid 660 through 666
    Processing helix  chain 'A' and resid 667 through 669
      No H-bonds generated for 'chain 'A' and resid 667 through 669'
    Processing helix  chain 'A' and resid 671 through 675
    Processing helix  chain 'A' and resid 680 through 698
    Processing helix  chain 'A' and resid 711 through 723
      removed outlier: 3.968A  pdb=" N   ILE A 715 " --> pdb=" O   TRP A 711 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 733
    Processing helix  chain 'A' and resid 736 through 745
      removed outlier: 3.599A  pdb=" N   GLN A 745 " --> pdb=" O   ALA A 741 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 770
    Processing helix  chain 'A' and resid 772 through 781
      removed outlier: 3.816A  pdb=" N   ILE A 776 " --> pdb=" O   ASN A 772 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   ILE A 777 " --> pdb=" O   GLU A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 788 through 800
    Processing helix  chain 'A' and resid 804 through 815
      removed outlier: 3.660A  pdb=" N   TYR A 808 " --> pdb=" O   ASN A 804 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   GLY A 815 " --> pdb=" O   LEU A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 815 through 836
      removed outlier: 3.840A  pdb=" N   VAL A 820 " --> pdb=" O   ALA A 816 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   ALA A 821 " --> pdb=" O   ARG A 817 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   HIS A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ASP A 828 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 855
    Processing helix  chain 'A' and resid 861 through 871
    Processing helix  chain 'A' and resid 876 through 892
    Processing helix  chain 'A' and resid 894 through 907
    Processing helix  chain 'A' and resid 910 through 914
      removed outlier: 3.635A  pdb=" N   LEU A 913 " --> pdb=" O   GLU A 910 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLN A 914 " --> pdb=" O   HIS A 911 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 910 through 914'
    Processing helix  chain 'A' and resid 916 through 928
    Processing helix  chain 'A' and resid 934 through 941
    Processing helix  chain 'A' and resid 958 through 963
    Processing helix  chain 'A' and resid 963 through 977
    Processing helix  chain 'A' and resid 980 through 992
      removed outlier: 3.908A  pdb=" N   LEU A 984 " --> pdb=" O   VAL A 980 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   GLU A 985 " --> pdb=" O   SER A 981 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   THR A 986 " --> pdb=" O   LYS A 982 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 993 through 998
    Processing helix  chain 'A' and resid 1000 through 1012
    Processing helix  chain 'A' and resid 1019 through 1033
      removed outlier: 3.653A  pdb=" N   LYS A1023 " --> pdb=" O   ARG A1019 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   SER A1033 " --> pdb=" O   ALA A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1045 through 1052
    Processing helix  chain 'A' and resid 1064 through 1081
      removed outlier: 3.654A  pdb=" N   TYR A1068 " --> pdb=" O   ASP A1064 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   LEU A1075 " --> pdb=" O   LEU A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1091 through 1095
      removed outlier: 3.528A  pdb=" N   ASN A1095 " --> pdb=" O   TRP A1092 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1099 through 1115
      removed outlier: 3.534A  pdb=" N   HIS A1103 " --> pdb=" O   ASN A1099 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1118 through 1132
      removed outlier: 4.283A  pdb=" N   VAL A1130 " --> pdb=" O   LEU A1126 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1156
      removed outlier: 3.590A  pdb=" N   TRP A1145 " --> pdb=" O   ASN A1141 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1157 through 1162
      removed outlier: 3.633A  pdb=" N   TRP A1161 " --> pdb=" O   PRO A1157 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1162 through 1173
      removed outlier: 4.142A  pdb=" N   ASP A1166 " --> pdb=" O   ILE A1162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1174 through 1179
    Processing helix  chain 'A' and resid 1187 through 1191
      removed outlier: 3.777A  pdb=" N   LEU A1190 " --> pdb=" O   PRO A1187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1199 through 1219
      removed outlier: 3.631A  pdb=" N   HIS A1218 " --> pdb=" O   ALA A1214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1220 through 1225
    Processing helix  chain 'A' and resid 1226 through 1234
    Processing helix  chain 'A' and resid 1241 through 1253
    Processing helix  chain 'A' and resid 1255 through 1262
      removed outlier: 3.714A  pdb=" N   PHE A1259 " --> pdb=" O   PHE A1255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1285
      removed outlier: 3.995A  pdb=" N   ILE A1268 " --> pdb=" O   THR A1264 " (cutoff:3.500A)
      removed outlier: 3.686A  pdb=" N   GLU A1269 " --> pdb=" O   ARG A1265 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1290 through 1305
      removed outlier: 3.537A  pdb=" N   ILE A1294 " --> pdb=" O   TYR A1290 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1320
      removed outlier: 3.694A  pdb=" N   LYS A1316 " --> pdb=" O   GLU A1312 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   ILE A1317 " --> pdb=" O   GLN A1313 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ASN A1320 " --> pdb=" O   LYS A1316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1322 through 1329
    Processing sheet with id=AA1, first strand: chain 'A' and resid 506 through 508

    577 hydrogen bonds defined for protein.
    1692 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: 1.71

  Time building geometry restraints manager: 1.15 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 3235
        1.35 -     1.46: 2439
        1.46 -     1.58: 4674
        1.58 -     1.70: 0
        1.70 -     1.82: 99
  Bond restraints: 10447
  Sorted by residual:
  bond pdb=" N   MET A 796 "
       pdb=" CA  MET A 796 "
    ideal  model  delta    sigma   weight residual
    1.459  1.498 -0.040 1.28e-02 6.10e+03 9.67e+00
  bond pdb=" N   LEU A 797 "
       pdb=" CA  LEU A 797 "
    ideal  model  delta    sigma   weight residual
    1.456  1.482 -0.025 1.31e-02 5.83e+03 3.74e+00
  bond pdb=" N   LEU A 798 "
       pdb=" CA  LEU A 798 "
    ideal  model  delta    sigma   weight residual
    1.455  1.480 -0.025 1.37e-02 5.33e+03 3.41e+00
  bond pdb=" N   GLU A 799 "
       pdb=" CA  GLU A 799 "
    ideal  model  delta    sigma   weight residual
    1.458  1.480 -0.022 1.28e-02 6.10e+03 2.93e+00
  bond pdb=" C   PHE A 263 "
       pdb=" N   GLU A 264 "
    ideal  model  delta    sigma   weight residual
    1.333  1.376 -0.044 2.74e-02 1.33e+03 2.55e+00
  ... (remaining 10442 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 13938
        1.64 -     3.28: 192
        3.28 -     4.92: 55
        4.92 -     6.56: 11
        6.56 -     8.20: 3
  Bond angle restraints: 14199
  Sorted by residual:
  angle pdb=" N   LEU A 798 "
        pdb=" CA  LEU A 798 "
        pdb=" C   LEU A 798 "
      ideal   model   delta    sigma   weight residual
     113.72  107.75    5.97 1.30e+00 5.92e-01 2.11e+01
  angle pdb=" C   PRO A 404 "
        pdb=" N   GLU A 405 "
        pdb=" CA  GLU A 405 "
      ideal   model   delta    sigma   weight residual
     121.54  127.27   -5.73 1.91e+00 2.74e-01 9.00e+00
  angle pdb=" CG1 ILE A 576 "
        pdb=" CB  ILE A 576 "
        pdb=" CG2 ILE A 576 "
      ideal   model   delta    sigma   weight residual
     110.70  102.50    8.20 3.00e+00 1.11e-01 7.47e+00
  angle pdb=" O   LYS A 795 "
        pdb=" C   LYS A 795 "
        pdb=" N   MET A 796 "
      ideal   model   delta    sigma   weight residual
     122.27  119.09    3.18 1.23e+00 6.61e-01 6.70e+00
  angle pdb=" CA  GLU A 405 "
        pdb=" CB  GLU A 405 "
        pdb=" CG  GLU A 405 "
      ideal   model   delta    sigma   weight residual
     114.10  118.96   -4.86 2.00e+00 2.50e-01 5.92e+00
  ... (remaining 14194 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.80: 5694
       15.80 -    31.59: 447
       31.59 -    47.39: 87
       47.39 -    63.18: 14
       63.18 -    78.98: 11
  Dihedral angle restraints: 6253
    sinusoidal: 2535
      harmonic: 3718
  Sorted by residual:
  dihedral pdb=" CA  ASP A 942 "
           pdb=" C   ASP A 942 "
           pdb=" N   PRO A 943 "
           pdb=" CA  PRO A 943 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.94   19.06     0      5.00e+00 4.00e-02 1.45e+01
  dihedral pdb=" CA  LYS A 744 "
           pdb=" C   LYS A 744 "
           pdb=" N   GLN A 745 "
           pdb=" CA  GLN A 745 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  164.62   15.38     0      5.00e+00 4.00e-02 9.46e+00
  dihedral pdb=" CG  LYS A 195 "
           pdb=" CD  LYS A 195 "
           pdb=" CE  LYS A 195 "
           pdb=" NZ  LYS A 195 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -180.00 -126.19  -53.81     3      1.50e+01 4.44e-03 9.23e+00
  ... (remaining 6250 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1220
       0.041 -    0.083: 299
       0.083 -    0.124: 84
       0.124 -    0.166: 3
       0.166 -    0.207: 2
  Chirality restraints: 1608
  Sorted by residual:
  chirality pdb=" CG  LEU A1034 "
            pdb=" CB  LEU A1034 "
            pdb=" CD1 LEU A1034 "
            pdb=" CD2 LEU A1034 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.38   -0.21 2.00e-01 2.50e+01 1.07e+00
  chirality pdb=" CB  ILE A 576 "
            pdb=" CA  ILE A 576 "
            pdb=" CG1 ILE A 576 "
            pdb=" CG2 ILE A 576 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.85   -0.20 2.00e-01 2.50e+01 1.04e+00
  chirality pdb=" CA  LEU A 798 "
            pdb=" N   LEU A 798 "
            pdb=" C   LEU A 798 "
            pdb=" CB  LEU A 798 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.66e-01
  ... (remaining 1605 not shown)

  Planarity restraints: 1784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 249 "   -0.221 9.50e-02 1.11e+02   9.94e-02 6.25e+00
        pdb=" NE  ARG A 249 "    0.011 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 249 "    0.010 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 249 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 249 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 213 "   -0.186 9.50e-02 1.11e+02   8.41e-02 5.35e+00
        pdb=" NE  ARG A 213 "    0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 213 "   -0.016 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 213 "    0.008 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 213 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 403 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO A 404 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 404 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 404 "    0.030 5.00e-02 4.00e+02
  ... (remaining 1781 not shown)

  Histogram of nonbonded interaction distances:
        2.24 -     2.77: 1714
        2.77 -     3.30: 9788
        3.30 -     3.83: 16108
        3.83 -     4.37: 18789
        4.37 -     4.90: 32915
  Nonbonded interactions: 79314
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 729 "
            pdb=" OE1 GLU A 875 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" NH2 ARG A 188 "
            pdb=" OE1 GLU A 193 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" O   ILE A 777 "
            pdb=" OG  SER A 781 "
     model   vdw
     2.271 3.040
  nonbonded pdb=" OE2 GLU A 935 "
            pdb=" OH  TYR A 951 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" NH2 ARG A 620 "
            pdb=" OE1 GLU A 660 "
     model   vdw
     2.292 3.120
  ... (remaining 79309 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=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.280
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     10.230
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.220
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
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      :  0.002   0.044  10447  Z= 0.105
  Angle     :  0.532   8.200  14199  Z= 0.261
  Chirality :  0.038   0.207   1608
  Planarity :  0.006   0.099   1784
  Dihedral  : 12.283  78.981   3835
  Min Nonbonded Distance : 2.235

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.18 %
    Favored  : 99.65 %
  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:  1.12 (0.24), residues: 1250
  helix:  1.54 (0.18), residues: 827
  sheet:  None (None), residues: 0
  loop : -0.84 (0.29), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 213 
 TYR   0.009   0.001   TYR A 764 
 PHE   0.023   0.001   PHE A 834 
 TRP   0.015   0.001   TRP A1183 
 HIS   0.005   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00217 (10447)
  covalent geometry    : angle       0.53188 (14199)
  hydrogen bonds       : bond        0.14009 (  577)
  hydrogen bonds       : angle       5.10651 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 263
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 MET cc_start: 0.7725 (tpt) cc_final: 0.7425 (tpt)
REVERT: A  111 ARG cc_start: 0.7406 (mmm160) cc_final: 0.7075 (mmm160)
REVERT: A  120 LYS cc_start: 0.8829 (mttt) cc_final: 0.8380 (mtpp)
REVERT: A  302 ASP cc_start: 0.7712 (m-30) cc_final: 0.7037 (m-30)
REVERT: A  306 ASP cc_start: 0.8150 (m-30) cc_final: 0.7875 (m-30)
REVERT: A  413 ASP cc_start: 0.7941 (t0) cc_final: 0.7669 (t0)
REVERT: A  415 ASN cc_start: 0.8509 (m-40) cc_final: 0.8141 (m110)
REVERT: A  545 THR cc_start: 0.8625 (m) cc_final: 0.8412 (m)
REVERT: A  554 LYS cc_start: 0.8293 (tppp) cc_final: 0.8010 (tppp)
REVERT: A  659 SER cc_start: 0.8377 (p) cc_final: 0.7897 (t)
REVERT: A  711 TRP cc_start: 0.8495 (p-90) cc_final: 0.8196 (p-90)
REVERT: A  761 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7380 (mm-30)
REVERT: A  766 LYS cc_start: 0.8485 (tppp) cc_final: 0.8196 (ttmm)
REVERT: A  806 ILE cc_start: 0.8008 (mm) cc_final: 0.7788 (mm)
REVERT: A  845 LYS cc_start: 0.8121 (tttm) cc_final: 0.7869 (ttmm)
REVERT: A  884 PHE cc_start: 0.8696 (t80) cc_final: 0.8417 (t80)
REVERT: A  887 GLN cc_start: 0.8354 (tt0) cc_final: 0.8076 (tt0)
REVERT: A  905 LYS cc_start: 0.8578 (ttpp) cc_final: 0.8360 (ttpp)
REVERT: A  945 VAL cc_start: 0.8382 (p) cc_final: 0.8077 (p)
REVERT: A  982 LYS cc_start: 0.8355 (tppp) cc_final: 0.8135 (tppp)
REVERT: A  989 ASP cc_start: 0.8035 (t0) cc_final: 0.7806 (t0)
REVERT: A 1229 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8324 (ttmm)
REVERT: A 1296 ASP cc_start: 0.8560 (m-30) cc_final: 0.8082 (m-30)
  outliers start: 2
  outliers final: 2
  residues processed: 264
  average time/residue: 0.1109
  time to fit residues: 38.9769
Evaluate side-chains
  230 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 228
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  797 LEU
Chi-restraints excluded: chain A residue  799 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    0.4980
   chunk 49 optimal weight:    0.5980
   chunk 97 optimal weight:    0.2980
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0040
   chunk 123 optimal weight:    2.9990
   chunk 65 optimal weight:    0.1980
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.3192

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

Flipped N/Q/H residues before XYZ refinement:
A 418 GLN
A 596 HIS
A 618 HIS
A 759 ASN
A1134 GLN
A1261 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.123532 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.100300 restraints weight = 14774.779|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.01
r_work: 0.3060 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.1188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023  10447  Z= 0.105
  Angle     :  0.514   8.534  14199  Z= 0.254
  Chirality :  0.038   0.159   1608
  Planarity :  0.004   0.042   1784
  Dihedral  :  4.154  67.029   1363
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 4.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  6.41 %
    Favored  : 92.62 %
  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:  1.69 (0.24), residues: 1250
  helix:  2.05 (0.18), residues: 831
  sheet:  None (None), residues: 0
  loop : -0.81 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.009   0.001   TYR A 181 
 PHE   0.011   0.001   PHE A 488 
 TRP   0.020   0.001   TRP A 199 
 HIS   0.006   0.001   HIS A  68 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 (10447)
  covalent geometry    : angle       0.51387 (14199)
  hydrogen bonds       : bond        0.03666 (  577)
  hydrogen bonds       : angle       3.80521 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 227
  time to evaluate  : 0.428 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7738 (tpt) cc_final: 0.7429 (tpt)
REVERT: A  111 ARG cc_start: 0.7367 (mmm160) cc_final: 0.7048 (mmm160)
REVERT: A  120 LYS cc_start: 0.8826 (mttt) cc_final: 0.8391 (mtpp)
REVERT: A  302 ASP cc_start: 0.7749 (m-30) cc_final: 0.7309 (m-30)
REVERT: A  306 ASP cc_start: 0.8199 (m-30) cc_final: 0.7906 (m-30)
REVERT: A  367 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8061 (mtmm)
REVERT: A  413 ASP cc_start: 0.7940 (t0) cc_final: 0.7734 (t0)
REVERT: A  415 ASN cc_start: 0.8557 (m-40) cc_final: 0.8136 (m110)
REVERT: A  457 PHE cc_start: 0.8549 (t80) cc_final: 0.8271 (t80)
REVERT: A  484 ASN cc_start: 0.7968 (t0) cc_final: 0.7745 (t0)
REVERT: A  659 SER cc_start: 0.8337 (p) cc_final: 0.7820 (t)
REVERT: A  711 TRP cc_start: 0.8503 (p-90) cc_final: 0.8153 (p-90)
REVERT: A  761 GLU cc_start: 0.7645 (mm-30) cc_final: 0.7369 (mm-30)
REVERT: A  764 TYR cc_start: 0.8215 (t80) cc_final: 0.7986 (t80)
REVERT: A  765 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7627 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8291 (tppp) cc_final: 0.8062 (ttmm)
REVERT: A  806 ILE cc_start: 0.7948 (mm) cc_final: 0.7744 (mm)
REVERT: A  905 LYS cc_start: 0.8538 (ttpp) cc_final: 0.8256 (ttpp)
REVERT: A  945 VAL cc_start: 0.8436 (p) cc_final: 0.7912 (m)
REVERT: A  982 LYS cc_start: 0.8360 (tppp) cc_final: 0.8144 (tppp)
REVERT: A  989 ASP cc_start: 0.8065 (t0) cc_final: 0.7766 (t0)
REVERT: A 1038 ARG cc_start: 0.8341 (mtt90) cc_final: 0.8037 (mtt180)
REVERT: A 1229 LYS cc_start: 0.8574 (ttmm) cc_final: 0.8235 (ttmm)
REVERT: A 1267 MET cc_start: 0.7558 (mtp) cc_final: 0.7205 (mtm)
REVERT: A 1296 ASP cc_start: 0.8510 (m-30) cc_final: 0.7995 (m-30)
  outliers start: 11
  outliers final: 8
  residues processed: 231
  average time/residue: 0.1209
  time to fit residues: 37.0434
Evaluate side-chains
  225 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 217
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  952 LEU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1090 CYS
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 99 optimal weight:    1.9990
   chunk 102 optimal weight:    1.9990
   chunk 14 optimal weight:    7.9990
   chunk 48 optimal weight:    0.7980
   chunk 119 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 4 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 62 optimal weight:    0.5980
   chunk 84 optimal weight:    0.0270
   chunk 114 optimal weight:    0.6980
   overall best weight:    0.5638

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

Flipped N/Q/H residues before XYZ refinement:
A 303 GLN
A 618 HIS
A1261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.121203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097429 restraints weight = 14862.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.06
r_work: 0.3024 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.1412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10447  Z= 0.123
  Angle     :  0.505   8.522  14199  Z= 0.252
  Chirality :  0.038   0.154   1608
  Planarity :  0.004   0.043   1784
  Dihedral  :  3.536  19.812   1358
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  7.82 %
    Favored  : 90.95 %
  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:  1.83 (0.25), residues: 1250
  helix:  2.16 (0.18), residues: 831
  sheet:  None (None), residues: 0
  loop : -0.78 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 363 
 TYR   0.009   0.001   TYR A 131 
 PHE   0.015   0.001   PHE A 608 
 TRP   0.011   0.001   TRP A 115 
 HIS   0.006   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 (10447)
  covalent geometry    : angle       0.50531 (14199)
  hydrogen bonds       : bond        0.04203 (  577)
  hydrogen bonds       : angle       3.74320 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  236 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 222
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7743 (tpt) cc_final: 0.7459 (tpt)
REVERT: A  111 ARG cc_start: 0.7355 (mmm160) cc_final: 0.7108 (mmm160)
REVERT: A  120 LYS cc_start: 0.8839 (mttt) cc_final: 0.8411 (mtpp)
REVERT: A  302 ASP cc_start: 0.7830 (m-30) cc_final: 0.7342 (m-30)
REVERT: A  306 ASP cc_start: 0.8236 (m-30) cc_final: 0.7943 (m-30)
REVERT: A  367 LYS cc_start: 0.8567 (mmmm) cc_final: 0.8054 (mtmm)
REVERT: A  408 TYR cc_start: 0.8506 (m-10) cc_final: 0.8304 (m-10)
REVERT: A  413 ASP cc_start: 0.7985 (t0) cc_final: 0.7725 (t0)
REVERT: A  415 ASN cc_start: 0.8573 (m-40) cc_final: 0.8121 (m110)
REVERT: A  484 ASN cc_start: 0.7937 (t0) cc_final: 0.7589 (t0)
REVERT: A  596 HIS cc_start: 0.8424 (m170) cc_final: 0.8206 (m170)
REVERT: A  659 SER cc_start: 0.8355 (p) cc_final: 0.7847 (t)
REVERT: A  711 TRP cc_start: 0.8507 (p-90) cc_final: 0.8135 (p-90)
REVERT: A  761 GLU cc_start: 0.7676 (mm-30) cc_final: 0.7397 (mm-30)
REVERT: A  764 TYR cc_start: 0.8376 (t80) cc_final: 0.7965 (t80)
REVERT: A  765 ARG cc_start: 0.8092 (ttp80) cc_final: 0.7730 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8317 (tppp) cc_final: 0.8067 (ttmm)
REVERT: A  905 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8309 (ttpp)
REVERT: A  945 VAL cc_start: 0.8497 (p) cc_final: 0.8036 (m)
REVERT: A  982 LYS cc_start: 0.8288 (tppp) cc_final: 0.8080 (tppp)
REVERT: A  989 ASP cc_start: 0.8135 (t0) cc_final: 0.7807 (t0)
REVERT: A 1038 ARG cc_start: 0.8387 (mtt90) cc_final: 0.8082 (mtt180)
REVERT: A 1267 MET cc_start: 0.7626 (mtp) cc_final: 0.7255 (ttm)
REVERT: A 1296 ASP cc_start: 0.8449 (m-30) cc_final: 0.7975 (m-30)
  outliers start: 14
  outliers final: 11
  residues processed: 229
  average time/residue: 0.1161
  time to fit residues: 35.3876
Evaluate side-chains
  234 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 223
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 3 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 106 optimal weight:    2.9990
   chunk 0 optimal weight:   10.0000
   chunk 71 optimal weight:    0.1980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS
A 618 HIS
A1089 ASN
A1261 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.119460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.095733 restraints weight = 14884.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3122 rms_B_bonded: 2.04
r_work: 0.2985 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7976
moved from start:          0.1663

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  10447  Z= 0.170
  Angle     :  0.543   9.733  14199  Z= 0.272
  Chirality :  0.040   0.150   1608
  Planarity :  0.005   0.049   1784
  Dihedral  :  3.721  20.903   1358
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 4.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  :  8.88 %
    Favored  : 89.63 %
  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:  1.73 (0.24), residues: 1250
  helix:  2.08 (0.18), residues: 831
  sheet:  None (None), residues: 0
  loop : -0.81 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 363 
 TYR   0.012   0.001   TYR A 131 
 PHE   0.014   0.001   PHE A 608 
 TRP   0.013   0.002   TRP A 115 
 HIS   0.006   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (10447)
  covalent geometry    : angle       0.54267 (14199)
  hydrogen bonds       : bond        0.05103 (  577)
  hydrogen bonds       : angle       3.83523 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 232
  time to evaluate  : 0.383 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7729 (tpt) cc_final: 0.7490 (tpt)
REVERT: A  111 ARG cc_start: 0.7370 (mmm160) cc_final: 0.7101 (mmm160)
REVERT: A  120 LYS cc_start: 0.8852 (mttt) cc_final: 0.8417 (mtpp)
REVERT: A  302 ASP cc_start: 0.7835 (m-30) cc_final: 0.7312 (m-30)
REVERT: A  306 ASP cc_start: 0.8236 (m-30) cc_final: 0.7952 (m-30)
REVERT: A  413 ASP cc_start: 0.7969 (t0) cc_final: 0.7708 (t0)
REVERT: A  415 ASN cc_start: 0.8609 (m-40) cc_final: 0.8127 (m110)
REVERT: A  433 ASN cc_start: 0.7656 (t0) cc_final: 0.7202 (t0)
REVERT: A  484 ASN cc_start: 0.7996 (t0) cc_final: 0.7690 (t0)
REVERT: A  596 HIS cc_start: 0.8438 (m170) cc_final: 0.8227 (m170)
REVERT: A  659 SER cc_start: 0.8383 (p) cc_final: 0.7880 (t)
REVERT: A  711 TRP cc_start: 0.8512 (p-90) cc_final: 0.8152 (p-90)
REVERT: A  761 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7362 (mm-30)
REVERT: A  764 TYR cc_start: 0.8467 (t80) cc_final: 0.8067 (t80)
REVERT: A  765 ARG cc_start: 0.8073 (ttp80) cc_final: 0.7843 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8423 (tppp) cc_final: 0.8098 (ttmm)
REVERT: A  813 ARG cc_start: 0.8362 (mtp-110) cc_final: 0.8046 (ttm110)
REVERT: A  945 VAL cc_start: 0.8532 (p) cc_final: 0.8113 (m)
REVERT: A  989 ASP cc_start: 0.8144 (t0) cc_final: 0.7795 (t0)
REVERT: A 1038 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8139 (mtt180)
REVERT: A 1267 MET cc_start: 0.7691 (mtp) cc_final: 0.7402 (ttm)
REVERT: A 1292 ASP cc_start: 0.7954 (m-30) cc_final: 0.7508 (m-30)
REVERT: A 1296 ASP cc_start: 0.8485 (m-30) cc_final: 0.8115 (m-30)
  outliers start: 17
  outliers final: 10
  residues processed: 240
  average time/residue: 0.1056
  time to fit residues: 34.2091
Evaluate side-chains
  237 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 227
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 LEU
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 111 optimal weight:    0.0570
   chunk 57 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 23 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   chunk 121 optimal weight:    0.6980
   chunk 99 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.0980
   overall best weight:    0.4898

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

Flipped N/Q/H residues before XYZ refinement:
A 618 HIS
A1134 GLN
A1261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.120892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.097146 restraints weight = 14804.622|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.05
r_work: 0.3017 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10447  Z= 0.114
  Angle     :  0.500   8.949  14199  Z= 0.249
  Chirality :  0.038   0.147   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.601  20.477   1358
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 10.72 %
    Favored  : 87.70 %
  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:  1.86 (0.24), residues: 1250
  helix:  2.21 (0.18), residues: 825
  sheet:  None (None), residues: 0
  loop : -0.75 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 363 
 TYR   0.010   0.001   TYR A 310 
 PHE   0.015   0.001   PHE A 457 
 TRP   0.021   0.001   TRP A 429 
 HIS   0.006   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10447)
  covalent geometry    : angle       0.50042 (14199)
  hydrogen bonds       : bond        0.03873 (  577)
  hydrogen bonds       : angle       3.67985 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 223
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7715 (tpt) cc_final: 0.7441 (tpt)
REVERT: A  111 ARG cc_start: 0.7254 (mmm160) cc_final: 0.6993 (mmm160)
REVERT: A  120 LYS cc_start: 0.8845 (mttt) cc_final: 0.8383 (mtpp)
REVERT: A  302 ASP cc_start: 0.7799 (m-30) cc_final: 0.7293 (m-30)
REVERT: A  306 ASP cc_start: 0.8252 (m-30) cc_final: 0.7971 (m-30)
REVERT: A  367 LYS cc_start: 0.8585 (mmmm) cc_final: 0.8208 (mtmt)
REVERT: A  408 TYR cc_start: 0.8457 (m-10) cc_final: 0.8221 (m-10)
REVERT: A  413 ASP cc_start: 0.7981 (t0) cc_final: 0.7765 (t0)
REVERT: A  415 ASN cc_start: 0.8592 (m-40) cc_final: 0.8132 (m110)
REVERT: A  484 ASN cc_start: 0.7946 (t0) cc_final: 0.7592 (t0)
REVERT: A  532 THR cc_start: 0.8374 (p) cc_final: 0.8130 (p)
REVERT: A  659 SER cc_start: 0.8348 (p) cc_final: 0.7833 (t)
REVERT: A  711 TRP cc_start: 0.8493 (p-90) cc_final: 0.8122 (p-90)
REVERT: A  761 GLU cc_start: 0.7685 (mm-30) cc_final: 0.7394 (mm-30)
REVERT: A  764 TYR cc_start: 0.8439 (t80) cc_final: 0.8043 (t80)
REVERT: A  765 ARG cc_start: 0.8068 (ttp80) cc_final: 0.7845 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8378 (tppp) cc_final: 0.8062 (ttmm)
REVERT: A  945 VAL cc_start: 0.8482 (p) cc_final: 0.8099 (m)
REVERT: A  989 ASP cc_start: 0.8144 (t0) cc_final: 0.7798 (t0)
REVERT: A 1038 ARG cc_start: 0.8426 (mtt90) cc_final: 0.8102 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8233 (t) cc_final: 0.7988 (p)
REVERT: A 1267 MET cc_start: 0.7539 (mtp) cc_final: 0.7325 (ttm)
REVERT: A 1296 ASP cc_start: 0.8463 (m-30) cc_final: 0.8102 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 232
  average time/residue: 0.1139
  time to fit residues: 35.3558
Evaluate side-chains
  236 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 223
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1099 ASN
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 121 optimal weight:    0.0770
   chunk 83 optimal weight:    0.9990
   chunk 24 optimal weight:    0.6980
   chunk 119 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 68 optimal weight:    3.9990
   chunk 86 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 18 optimal weight:    0.2980
   chunk 76 optimal weight:    0.8980
   chunk 59 optimal weight:    0.0270
   overall best weight:    0.3996

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS
A 596 HIS
A 618 HIS
A1134 GLN
A1261 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.122018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.098383 restraints weight = 14898.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3164 rms_B_bonded: 2.04
r_work: 0.3030 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2857 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10447  Z= 0.104
  Angle     :  0.490   8.602  14199  Z= 0.242
  Chirality :  0.037   0.147   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.500  20.021   1358
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.25 %
    Favored  : 87.43 %
  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:  1.97 (0.24), residues: 1250
  helix:  2.28 (0.18), residues: 825
  sheet:  None (None), residues: 0
  loop : -0.69 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 363 
 TYR   0.009   0.001   TYR A 310 
 PHE   0.013   0.001   PHE A 457 
 TRP   0.017   0.001   TRP A 429 
 HIS   0.006   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (10447)
  covalent geometry    : angle       0.48962 (14199)
  hydrogen bonds       : bond        0.03597 (  577)
  hydrogen bonds       : angle       3.59476 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 220
  time to evaluate  : 0.378 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7694 (tpt) cc_final: 0.7414 (tpt)
REVERT: A  111 ARG cc_start: 0.7213 (mmm160) cc_final: 0.6994 (mmm160)
REVERT: A  120 LYS cc_start: 0.8842 (mttt) cc_final: 0.8385 (mtpp)
REVERT: A  302 ASP cc_start: 0.7787 (m-30) cc_final: 0.7295 (m-30)
REVERT: A  306 ASP cc_start: 0.8239 (m-30) cc_final: 0.7971 (m-30)
REVERT: A  367 LYS cc_start: 0.8586 (mmmm) cc_final: 0.8218 (mmmm)
REVERT: A  402 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8256 (mp)
REVERT: A  408 TYR cc_start: 0.8439 (m-10) cc_final: 0.8212 (m-10)
REVERT: A  413 ASP cc_start: 0.8005 (t0) cc_final: 0.7794 (t0)
REVERT: A  415 ASN cc_start: 0.8581 (m-40) cc_final: 0.8087 (m110)
REVERT: A  433 ASN cc_start: 0.7738 (t0) cc_final: 0.7285 (t0)
REVERT: A  484 ASN cc_start: 0.7928 (t0) cc_final: 0.7556 (t0)
REVERT: A  532 THR cc_start: 0.8336 (p) cc_final: 0.8121 (p)
REVERT: A  659 SER cc_start: 0.8348 (p) cc_final: 0.7834 (t)
REVERT: A  711 TRP cc_start: 0.8481 (p-90) cc_final: 0.8104 (p-90)
REVERT: A  761 GLU cc_start: 0.7666 (mm-30) cc_final: 0.7369 (mm-30)
REVERT: A  764 TYR cc_start: 0.8425 (t80) cc_final: 0.7987 (t80)
REVERT: A  765 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7815 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8363 (tppp) cc_final: 0.8036 (ttmm)
REVERT: A  945 VAL cc_start: 0.8480 (p) cc_final: 0.8112 (m)
REVERT: A  989 ASP cc_start: 0.8152 (t0) cc_final: 0.7803 (t0)
REVERT: A 1038 ARG cc_start: 0.8433 (mtt90) cc_final: 0.8097 (mtt180)
REVERT: A 1134 GLN cc_start: 0.7756 (OUTLIER) cc_final: 0.7340 (tt0)
REVERT: A 1267 MET cc_start: 0.7511 (mtp) cc_final: 0.7281 (ttm)
REVERT: A 1296 ASP cc_start: 0.8433 (m-30) cc_final: 0.8077 (m-30)
  outliers start: 15
  outliers final: 11
  residues processed: 229
  average time/residue: 0.1195
  time to fit residues: 37.0488
Evaluate side-chains
  233 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 220
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1099 ASN
Chi-restraints excluded: chain A residue 1134 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 41 optimal weight:    0.0040
   chunk 7 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 97 optimal weight:    3.9990
   chunk 37 optimal weight:    0.0980
   chunk 113 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 64 optimal weight:    0.3980
   chunk 71 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.4592

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

Flipped N/Q/H residues before XYZ refinement:
A 449 HIS
A 596 HIS
A 759 ASN
A1261 GLN
A1280 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.121508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3165 r_free = 0.3165 target = 0.097756 restraints weight = 14707.798|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.05
r_work: 0.3028 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1782

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10447  Z= 0.108
  Angle     :  0.505  10.366  14199  Z= 0.246
  Chirality :  0.038   0.148   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.494  19.995   1358
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.98 %
    Favored  : 87.52 %
  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:  2.01 (0.24), residues: 1250
  helix:  2.31 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.65 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 249 
 TYR   0.016   0.001   TYR A 191 
 PHE   0.016   0.001   PHE A 457 
 TRP   0.016   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10447)
  covalent geometry    : angle       0.50468 (14199)
  hydrogen bonds       : bond        0.03687 (  577)
  hydrogen bonds       : angle       3.57901 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 222
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7706 (tpt) cc_final: 0.7402 (tpt)
REVERT: A  111 ARG cc_start: 0.7181 (mmm160) cc_final: 0.6960 (mmm160)
REVERT: A  120 LYS cc_start: 0.8821 (mttt) cc_final: 0.8362 (mtpp)
REVERT: A  302 ASP cc_start: 0.7781 (m-30) cc_final: 0.7286 (m-30)
REVERT: A  306 ASP cc_start: 0.8250 (m-30) cc_final: 0.7974 (m-30)
REVERT: A  402 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8295 (mp)
REVERT: A  413 ASP cc_start: 0.8000 (t0) cc_final: 0.7760 (t0)
REVERT: A  415 ASN cc_start: 0.8584 (m-40) cc_final: 0.8083 (m110)
REVERT: A  433 ASN cc_start: 0.7727 (t0) cc_final: 0.7276 (t0)
REVERT: A  484 ASN cc_start: 0.7906 (t0) cc_final: 0.7522 (t0)
REVERT: A  532 THR cc_start: 0.8339 (p) cc_final: 0.8126 (p)
REVERT: A  659 SER cc_start: 0.8346 (p) cc_final: 0.7830 (t)
REVERT: A  761 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7394 (mm-30)
REVERT: A  764 TYR cc_start: 0.8418 (t80) cc_final: 0.7929 (t80)
REVERT: A  765 ARG cc_start: 0.8040 (ttp80) cc_final: 0.7809 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8358 (tppp) cc_final: 0.8030 (ttmm)
REVERT: A  945 VAL cc_start: 0.8457 (p) cc_final: 0.8098 (m)
REVERT: A  989 ASP cc_start: 0.8143 (t0) cc_final: 0.7804 (t0)
REVERT: A 1038 ARG cc_start: 0.8450 (mtt90) cc_final: 0.8168 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8167 (t) cc_final: 0.7917 (p)
REVERT: A 1267 MET cc_start: 0.7525 (mtp) cc_final: 0.7291 (ttm)
REVERT: A 1296 ASP cc_start: 0.8467 (m-30) cc_final: 0.8100 (m-30)
  outliers start: 17
  outliers final: 14
  residues processed: 231
  average time/residue: 0.1157
  time to fit residues: 35.7892
Evaluate side-chains
  239 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 224
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  811 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1099 ASN
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 61 optimal weight:    0.8980
   chunk 67 optimal weight:    1.9990
   chunk 91 optimal weight:    0.8980
   chunk 87 optimal weight:    0.0020
   chunk 101 optimal weight:    0.9980
   chunk 27 optimal weight:    0.6980
   chunk 103 optimal weight:    0.5980
   chunk 72 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0980
   chunk 123 optimal weight:    3.9990
   overall best weight:    0.4588

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

Flipped N/Q/H residues before XYZ refinement:
A 596 HIS
A1134 GLN
A1261 GLN
A1280 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.121877 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.098192 restraints weight = 14788.379|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.04
r_work: 0.3026 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.1833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10447  Z= 0.108
  Angle     :  0.510  10.609  14199  Z= 0.247
  Chirality :  0.038   0.147   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.474  19.914   1358
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  : 11.07 %
    Favored  : 87.26 %
  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:  2.03 (0.24), residues: 1250
  helix:  2.32 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.64 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 249 
 TYR   0.015   0.001   TYR A 191 
 PHE   0.015   0.001   PHE A 457 
 TRP   0.015   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 (10447)
  covalent geometry    : angle       0.50971 (14199)
  hydrogen bonds       : bond        0.03683 (  577)
  hydrogen bonds       : angle       3.58373 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 220
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7698 (tpt) cc_final: 0.7382 (tpt)
REVERT: A  111 ARG cc_start: 0.7180 (mmm160) cc_final: 0.6973 (mmm160)
REVERT: A  120 LYS cc_start: 0.8837 (mttt) cc_final: 0.8370 (mtpp)
REVERT: A  302 ASP cc_start: 0.7780 (m-30) cc_final: 0.7061 (m-30)
REVERT: A  306 ASP cc_start: 0.8263 (m-30) cc_final: 0.7901 (m-30)
REVERT: A  402 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8306 (mp)
REVERT: A  413 ASP cc_start: 0.8010 (t0) cc_final: 0.7769 (t0)
REVERT: A  415 ASN cc_start: 0.8585 (m-40) cc_final: 0.8085 (m110)
REVERT: A  484 ASN cc_start: 0.7902 (t0) cc_final: 0.7556 (t0)
REVERT: A  532 THR cc_start: 0.8343 (p) cc_final: 0.8120 (p)
REVERT: A  659 SER cc_start: 0.8352 (p) cc_final: 0.7840 (t)
REVERT: A  761 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7423 (mm-30)
REVERT: A  764 TYR cc_start: 0.8427 (t80) cc_final: 0.7920 (t80)
REVERT: A  765 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7788 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8361 (tppp) cc_final: 0.8050 (ttmm)
REVERT: A  849 ILE cc_start: 0.8633 (mm) cc_final: 0.8433 (mt)
REVERT: A  945 VAL cc_start: 0.8422 (p) cc_final: 0.8079 (m)
REVERT: A  989 ASP cc_start: 0.8153 (t0) cc_final: 0.7814 (t0)
REVERT: A 1038 ARG cc_start: 0.8449 (mtt90) cc_final: 0.8144 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8224 (t) cc_final: 0.7978 (p)
REVERT: A 1267 MET cc_start: 0.7570 (mtp) cc_final: 0.7328 (ttm)
REVERT: A 1296 ASP cc_start: 0.8426 (m-30) cc_final: 0.8073 (m-30)
  outliers start: 19
  outliers final: 15
  residues processed: 231
  average time/residue: 0.1191
  time to fit residues: 36.8860
Evaluate side-chains
  233 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 217
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  576 ILE
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1099 ASN
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 75 optimal weight:    0.7980
   chunk 122 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9990
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0670
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A 596 HIS
A1134 GLN
A1261 GLN
A1280 ASN
A1289 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.121325 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097687 restraints weight = 14723.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.03
r_work: 0.3017 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2845 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
moved from start:          0.1875

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10447  Z= 0.118
  Angle     :  0.518  10.884  14199  Z= 0.252
  Chirality :  0.038   0.148   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.507  19.988   1358
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.34 %
    Favored  : 87.17 %
  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:  2.00 (0.24), residues: 1250
  helix:  2.30 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.66 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 249 
 TYR   0.016   0.001   TYR A 191 
 PHE   0.017   0.001   PHE A 457 
 TRP   0.028   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 (10447)
  covalent geometry    : angle       0.51816 (14199)
  hydrogen bonds       : bond        0.03908 (  577)
  hydrogen bonds       : angle       3.60919 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 217
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 MET cc_start: 0.7714 (tpt) cc_final: 0.7398 (tpt)
REVERT: A  111 ARG cc_start: 0.7189 (mmm160) cc_final: 0.6989 (mmm160)
REVERT: A  120 LYS cc_start: 0.8842 (mttt) cc_final: 0.8375 (mtpp)
REVERT: A  213 ARG cc_start: 0.8197 (mpt180) cc_final: 0.7824 (mpt180)
REVERT: A  302 ASP cc_start: 0.7786 (m-30) cc_final: 0.7061 (m-30)
REVERT: A  306 ASP cc_start: 0.8263 (m-30) cc_final: 0.7901 (m-30)
REVERT: A  402 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8283 (mp)
REVERT: A  413 ASP cc_start: 0.8001 (t0) cc_final: 0.7761 (t0)
REVERT: A  415 ASN cc_start: 0.8588 (m-40) cc_final: 0.8082 (m110)
REVERT: A  484 ASN cc_start: 0.7902 (t0) cc_final: 0.7562 (t0)
REVERT: A  659 SER cc_start: 0.8353 (p) cc_final: 0.7841 (t)
REVERT: A  761 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7434 (mm-30)
REVERT: A  764 TYR cc_start: 0.8433 (t80) cc_final: 0.7912 (t80)
REVERT: A  765 ARG cc_start: 0.8022 (ttp80) cc_final: 0.7791 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8378 (tppp) cc_final: 0.8065 (ttmm)
REVERT: A  945 VAL cc_start: 0.8407 (p) cc_final: 0.8083 (m)
REVERT: A  989 ASP cc_start: 0.8148 (t0) cc_final: 0.7815 (t0)
REVERT: A 1038 ARG cc_start: 0.8476 (mtt90) cc_final: 0.8164 (mtt180)
REVERT: A 1267 MET cc_start: 0.7589 (mtp) cc_final: 0.7345 (ttm)
REVERT: A 1296 ASP cc_start: 0.8423 (m-30) cc_final: 0.8069 (m-30)
REVERT: A 1315 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7859 (mt-10)
  outliers start: 17
  outliers final: 14
  residues processed: 227
  average time/residue: 0.1207
  time to fit residues: 37.0793
Evaluate side-chains
  232 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 217
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue  987 LEU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1099 ASN
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 29 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 69 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9980
   chunk 83 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 5 optimal weight:    7.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 596 HIS
** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1261 GLN
A1280 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.118221 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.094461 restraints weight = 14619.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3107 rms_B_bonded: 2.03
r_work: 0.2971 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2797 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7982
moved from start:          0.2028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  10447  Z= 0.194
  Angle     :  0.584  10.930  14199  Z= 0.286
  Chirality :  0.041   0.148   1608
  Planarity :  0.005   0.047   1784
  Dihedral  :  3.760  20.991   1358
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.78 %
    Favored  : 86.91 %
  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:  1.75 (0.24), residues: 1250
  helix:  2.09 (0.18), residues: 830
  sheet:  None (None), residues: 0
  loop : -0.77 (0.30), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.022   0.002   TYR A 191 
 PHE   0.017   0.002   PHE A 457 
 TRP   0.025   0.002   TRP A 429 
 HIS   0.005   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00477 (10447)
  covalent geometry    : angle       0.58363 (14199)
  hydrogen bonds       : bond        0.05299 (  577)
  hydrogen bonds       : angle       3.79659 ( 1692)

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

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

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2500 Ramachandran restraints generated.
    1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 223
  time to evaluate  : 0.441 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7759 (tpt) cc_final: 0.7483 (tpt)
REVERT: A  111 ARG cc_start: 0.7289 (mmm160) cc_final: 0.7072 (mmm160)
REVERT: A  120 LYS cc_start: 0.8847 (mttt) cc_final: 0.8364 (mtpp)
REVERT: A  213 ARG cc_start: 0.8192 (mpt180) cc_final: 0.7744 (mpt180)
REVERT: A  302 ASP cc_start: 0.7794 (m-30) cc_final: 0.7293 (m-30)
REVERT: A  306 ASP cc_start: 0.8258 (m-30) cc_final: 0.7964 (m-30)
REVERT: A  413 ASP cc_start: 0.8033 (t0) cc_final: 0.7780 (t0)
REVERT: A  415 ASN cc_start: 0.8645 (m-40) cc_final: 0.8166 (m110)
REVERT: A  433 ASN cc_start: 0.7670 (t0) cc_final: 0.7292 (t0)
REVERT: A  484 ASN cc_start: 0.7985 (t0) cc_final: 0.7645 (t0)
REVERT: A  532 THR cc_start: 0.8482 (p) cc_final: 0.8232 (p)
REVERT: A  659 SER cc_start: 0.8385 (p) cc_final: 0.7888 (t)
REVERT: A  761 GLU cc_start: 0.7650 (mm-30) cc_final: 0.7391 (mm-30)
REVERT: A  764 TYR cc_start: 0.8489 (t80) cc_final: 0.7949 (t80)
REVERT: A  765 ARG cc_start: 0.8042 (ttp80) cc_final: 0.7780 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8425 (tppp) cc_final: 0.8108 (ttmm)
REVERT: A  813 ARG cc_start: 0.8332 (mtp-110) cc_final: 0.7997 (ttm110)
REVERT: A  945 VAL cc_start: 0.8492 (p) cc_final: 0.8181 (m)
REVERT: A  989 ASP cc_start: 0.8174 (t0) cc_final: 0.7846 (t0)
REVERT: A 1267 MET cc_start: 0.7710 (mtp) cc_final: 0.7444 (ttm)
REVERT: A 1292 ASP cc_start: 0.7953 (m-30) cc_final: 0.7749 (m-30)
  outliers start: 15
  outliers final: 14
  residues processed: 230
  average time/residue: 0.1106
  time to fit residues: 34.2320
Evaluate side-chains
  233 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 219
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  176 CYS
Chi-restraints excluded: chain A residue  280 ARG
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  366 ILE
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  601 LEU
Chi-restraints excluded: chain A residue  721 SER
Chi-restraints excluded: chain A residue  788 LEU
Chi-restraints excluded: chain A residue  792 LEU
Chi-restraints excluded: chain A residue  806 ILE
Chi-restraints excluded: chain A residue  906 GLU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1099 ASN
Chi-restraints excluded: chain A residue 1154 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 111 optimal weight:    0.1980
   chunk 53 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 54 optimal weight:    0.7980
   chunk 110 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 357 HIS
A 596 HIS
A 759 ASN
** A1134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1261 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.119702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.095943 restraints weight = 14716.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3127 rms_B_bonded: 2.04
r_work: 0.2991 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.2008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  10447  Z= 0.145
  Angle     :  0.548  10.977  14199  Z= 0.268
  Chirality :  0.039   0.147   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.675  20.865   1358
  Min Nonbonded Distance : 2.601

Molprobity Statistics.
  All-atom Clashscore : 3.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.65 %
    Favored  : 86.20 %
  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:  1.86 (0.24), residues: 1250
  helix:  2.18 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.68 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.018   0.001   TYR A 191 
 PHE   0.015   0.001   PHE A 457 
 TRP   0.027   0.002   TRP A 429 
 HIS   0.005   0.001   HIS A 618 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 (10447)
  covalent geometry    : angle       0.54771 (14199)
  hydrogen bonds       : bond        0.04434 (  577)
  hydrogen bonds       : angle       3.72244 ( 1692)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2687.25 seconds
wall clock time: 46 minutes 42.30 seconds (2802.30 seconds total)