Starting phenix.real_space_refine
on Mon Jun  9 03:35:51 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9f76_50247/06_2025/9f76_50247.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9f76_50247/06_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_50247/06_2025/9f76_50247.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9f76_50247/06_2025/9f76_50247.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9f76_50247/06_2025/9f76_50247.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9f76_50247/06_2025/9f76_50247.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 5.91, per 1000 atoms: 0.58
  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: 2.45
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.42
  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: 3.14

  Time building geometry restraints manager: 2.94 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:             1.180
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.080
  Set scattering table:                    0.090
  Process input model:                     25.280
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.080
-------------------------------------------------------------------------------
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 : 5.77
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (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
 TRP   0.015   0.001   TRP A1183 
 HIS   0.005   0.001   HIS A  68 
 PHE   0.023   0.001   PHE A 834 
 TYR   0.009   0.001   TYR A 764 
 ARG   0.018   0.001   ARG A 213 

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

*********************** 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  : 1.051 
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: 0.2716
  time to fit residues: 95.0631
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  : 1.616 
-------------------------------------------------------------------------------
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 105 optimal weight:    0.0370
   chunk 94 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0470
   chunk 32 optimal weight:    0.5980
   chunk 63 optimal weight:    0.0470
   chunk 50 optimal weight:    1.9990
   chunk 97 optimal weight:    0.2980
   chunk 37 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 113 optimal weight:    0.9980
   overall best weight:    0.2054

-------------------------------------------------------------------------------
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 = 0.3566 r_free = 0.3566 target = 0.123825 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.100619 restraints weight = 14700.669|
|-----------------------------------------------------------------------------|
r_work (start): 0.3207 rms_B_bonded: 2.01
r_work: 0.3076 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.2908 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7895
moved from start:          0.1200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  10447  Z= 0.097
  Angle     :  0.507   8.266  14199  Z= 0.249
  Chirality :  0.037   0.160   1608
  Planarity :  0.004   0.042   1784
  Dihedral  :  4.135  67.377   1363
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.88 %
    Allowed  :  6.50 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.24), residues: 1250
  helix:  2.05 (0.18), residues: 831
  sheet:  None (None), residues: 0
  loop : -0.79 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 199 
 HIS   0.006   0.001   HIS A  68 
 PHE   0.010   0.001   PHE A 488 
 TYR   0.010   0.001   TYR A 181 
 ARG   0.003   0.000   ARG A1167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03561 (  577)
  hydrogen bonds       : angle       3.80334 ( 1692)
  covalent geometry    : bond        0.00207 (10447)
  covalent geometry    : angle       0.50661 (14199)

*********************** 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
  235 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 225
  time to evaluate  : 1.125 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7713 (tpt) cc_final: 0.7406 (tpt)
REVERT: A  111 ARG cc_start: 0.7340 (mmm160) cc_final: 0.7046 (mmm160)
REVERT: A  120 LYS cc_start: 0.8828 (mttt) cc_final: 0.8393 (mtpp)
REVERT: A  302 ASP cc_start: 0.7748 (m-30) cc_final: 0.7304 (m-30)
REVERT: A  306 ASP cc_start: 0.8199 (m-30) cc_final: 0.7971 (m-30)
REVERT: A  367 LYS cc_start: 0.8541 (mmmm) cc_final: 0.8057 (mtmm)
REVERT: A  413 ASP cc_start: 0.7897 (t0) cc_final: 0.7693 (t0)
REVERT: A  415 ASN cc_start: 0.8546 (m-40) cc_final: 0.8135 (m110)
REVERT: A  457 PHE cc_start: 0.8543 (t80) cc_final: 0.8261 (t80)
REVERT: A  484 ASN cc_start: 0.7945 (t0) cc_final: 0.7734 (t0)
REVERT: A  659 SER cc_start: 0.8328 (p) cc_final: 0.7811 (t)
REVERT: A  711 TRP cc_start: 0.8495 (p-90) cc_final: 0.8150 (p-90)
REVERT: A  761 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7385 (mm-30)
REVERT: A  764 TYR cc_start: 0.8203 (t80) cc_final: 0.7985 (t80)
REVERT: A  765 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7612 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8286 (tppp) cc_final: 0.8061 (ttmm)
REVERT: A  806 ILE cc_start: 0.7933 (mm) cc_final: 0.7728 (mm)
REVERT: A  905 LYS cc_start: 0.8533 (ttpp) cc_final: 0.8248 (ttpp)
REVERT: A  945 VAL cc_start: 0.8414 (p) cc_final: 0.7879 (m)
REVERT: A  982 LYS cc_start: 0.8339 (tppp) cc_final: 0.8123 (tppp)
REVERT: A  989 ASP cc_start: 0.8061 (t0) cc_final: 0.7763 (t0)
REVERT: A 1038 ARG cc_start: 0.8322 (mtt90) cc_final: 0.8097 (mtt180)
REVERT: A 1229 LYS cc_start: 0.8573 (ttmm) cc_final: 0.8236 (ttmm)
REVERT: A 1267 MET cc_start: 0.7506 (mtp) cc_final: 0.7158 (mtm)
REVERT: A 1296 ASP cc_start: 0.8509 (m-30) cc_final: 0.8003 (m-30)
  outliers start: 10
  outliers final: 7
  residues processed: 229
  average time/residue: 0.2637
  time to fit residues: 80.4490
Evaluate side-chains
  225 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 218
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 3 optimal weight:    0.1980
   chunk 70 optimal weight:    0.7980
   chunk 88 optimal weight:    0.6980
   chunk 111 optimal weight:    0.5980
   chunk 47 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 2 optimal weight:    0.4980
   chunk 57 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3531 r_free = 0.3531 target = 0.121306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097466 restraints weight = 14950.465|
|-----------------------------------------------------------------------------|
r_work (start): 0.3159 rms_B_bonded: 2.07
r_work: 0.3025 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2852 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2852
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.1423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10447  Z= 0.123
  Angle     :  0.507   8.489  14199  Z= 0.253
  Chirality :  0.038   0.154   1608
  Planarity :  0.004   0.043   1784
  Dihedral  :  3.519  19.727   1358
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  :  8.00 %
    Favored  : 91.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.84 (0.25), residues: 1250
  helix:  2.17 (0.18), residues: 831
  sheet:  None (None), residues: 0
  loop : -0.78 (0.30), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 115 
 HIS   0.006   0.001   HIS A 618 
 PHE   0.015   0.001   PHE A 608 
 TYR   0.009   0.001   TYR A 181 
 ARG   0.004   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04223 (  577)
  hydrogen bonds       : angle       3.73972 ( 1692)
  covalent geometry    : bond        0.00288 (10447)
  covalent geometry    : angle       0.50744 (14199)

*********************** 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
  233 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 222
  time to evaluate  : 1.075 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7725 (tpt) cc_final: 0.7444 (tpt)
REVERT: A  111 ARG cc_start: 0.7348 (mmm160) cc_final: 0.7109 (mmm160)
REVERT: A  120 LYS cc_start: 0.8843 (mttt) cc_final: 0.8415 (mtpp)
REVERT: A  302 ASP cc_start: 0.7828 (m-30) cc_final: 0.7319 (m-30)
REVERT: A  306 ASP cc_start: 0.8239 (m-30) cc_final: 0.7961 (m-30)
REVERT: A  367 LYS cc_start: 0.8538 (mmmm) cc_final: 0.8054 (mtmm)
REVERT: A  408 TYR cc_start: 0.8501 (m-10) cc_final: 0.8295 (m-10)
REVERT: A  413 ASP cc_start: 0.7992 (t0) cc_final: 0.7732 (t0)
REVERT: A  415 ASN cc_start: 0.8565 (m-40) cc_final: 0.8111 (m110)
REVERT: A  484 ASN cc_start: 0.7926 (t0) cc_final: 0.7577 (t0)
REVERT: A  596 HIS cc_start: 0.8428 (m170) cc_final: 0.8204 (m170)
REVERT: A  659 SER cc_start: 0.8357 (p) cc_final: 0.7851 (t)
REVERT: A  711 TRP cc_start: 0.8508 (p-90) cc_final: 0.8134 (p-90)
REVERT: A  761 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7409 (mm-30)
REVERT: A  764 TYR cc_start: 0.8375 (t80) cc_final: 0.7949 (t80)
REVERT: A  765 ARG cc_start: 0.8081 (ttp80) cc_final: 0.7648 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8309 (tppp) cc_final: 0.8026 (ttmm)
REVERT: A  905 LYS cc_start: 0.8573 (ttpp) cc_final: 0.8311 (ttpp)
REVERT: A  945 VAL cc_start: 0.8483 (p) cc_final: 0.8036 (m)
REVERT: A  982 LYS cc_start: 0.8281 (tppp) cc_final: 0.8065 (tppp)
REVERT: A  989 ASP cc_start: 0.8146 (t0) cc_final: 0.7816 (t0)
REVERT: A 1038 ARG cc_start: 0.8391 (mtt90) cc_final: 0.8088 (mtt180)
REVERT: A 1267 MET cc_start: 0.7638 (mtp) cc_final: 0.7266 (ttm)
REVERT: A 1296 ASP cc_start: 0.8449 (m-30) cc_final: 0.7976 (m-30)
  outliers start: 11
  outliers final: 9
  residues processed: 228
  average time/residue: 0.3153
  time to fit residues: 96.4282
Evaluate side-chains
  228 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 219
  time to evaluate  : 1.076 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 68 optimal weight:    0.6980
   chunk 104 optimal weight:    0.0770
   chunk 114 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 109 optimal weight:    1.9990
   chunk 75 optimal weight:    0.5980
   chunk 10 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.5538

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.121711 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.098072 restraints weight = 14770.343|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.04
r_work: 0.3023 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2851 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1559

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= 0.119
  Angle     :  0.495   8.649  14199  Z= 0.247
  Chirality :  0.038   0.149   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.522  20.002   1358
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.88 %
    Favored  : 97.12 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  :  8.70 %
    Favored  : 89.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.93 (0.24), residues: 1250
  helix:  2.24 (0.18), residues: 826
  sheet:  None (None), residues: 0
  loop : -0.71 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 115 
 HIS   0.006   0.001   HIS A 618 
 PHE   0.013   0.001   PHE A 608 
 TYR   0.009   0.001   TYR A 181 
 ARG   0.003   0.000   ARG A1167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03979 (  577)
  hydrogen bonds       : angle       3.67190 ( 1692)
  covalent geometry    : bond        0.00281 (10447)
  covalent geometry    : angle       0.49549 (14199)

*********************** 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
  238 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 220
  time to evaluate  : 1.132 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 MET cc_start: 0.7706 (tpt) cc_final: 0.7433 (tpt)
REVERT: A  111 ARG cc_start: 0.7253 (mmm160) cc_final: 0.7008 (mmm160)
REVERT: A  120 LYS cc_start: 0.8835 (mttt) cc_final: 0.8381 (mtpp)
REVERT: A  302 ASP cc_start: 0.7809 (m-30) cc_final: 0.7307 (m-30)
REVERT: A  306 ASP cc_start: 0.8233 (m-30) cc_final: 0.7947 (m-30)
REVERT: A  402 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8202 (mp)
REVERT: A  413 ASP cc_start: 0.7963 (t0) cc_final: 0.7725 (t0)
REVERT: A  415 ASN cc_start: 0.8585 (m-40) cc_final: 0.8116 (m110)
REVERT: A  484 ASN cc_start: 0.7918 (t0) cc_final: 0.7594 (t0)
REVERT: A  659 SER cc_start: 0.8359 (p) cc_final: 0.7852 (t)
REVERT: A  711 TRP cc_start: 0.8502 (p-90) cc_final: 0.8127 (p-90)
REVERT: A  761 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7379 (mm-30)
REVERT: A  764 TYR cc_start: 0.8418 (t80) cc_final: 0.8064 (t80)
REVERT: A  765 ARG cc_start: 0.8089 (ttp80) cc_final: 0.7851 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8347 (tppp) cc_final: 0.8029 (ttmm)
REVERT: A  905 LYS cc_start: 0.8571 (ttpp) cc_final: 0.8315 (ttpp)
REVERT: A  945 VAL cc_start: 0.8479 (p) cc_final: 0.8036 (m)
REVERT: A  989 ASP cc_start: 0.8151 (t0) cc_final: 0.7817 (t0)
REVERT: A 1038 ARG cc_start: 0.8421 (mtt90) cc_final: 0.8117 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8224 (t) cc_final: 0.7972 (p)
REVERT: A 1231 LEU cc_start: 0.8517 (mp) cc_final: 0.8307 (mt)
REVERT: A 1267 MET cc_start: 0.7616 (mtp) cc_final: 0.7262 (ttm)
REVERT: A 1296 ASP cc_start: 0.8481 (m-30) cc_final: 0.8121 (m-30)
  outliers start: 18
  outliers final: 13
  residues processed: 230
  average time/residue: 0.2716
  time to fit residues: 83.6112
Evaluate side-chains
  231 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 217
  time to evaluate  : 1.177 
-------------------------------------------------------------------------------
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  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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 119 optimal weight:    0.1980
   chunk 0 optimal weight:   10.0000
   chunk 104 optimal weight:    0.0770
   chunk 58 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 77 optimal weight:    0.9980
   chunk 17 optimal weight:    1.9990
   chunk 111 optimal weight:    0.0970
   chunk 51 optimal weight:    0.1980
   chunk 97 optimal weight:    0.0470
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.1234

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

Flipped N/Q/H residues before XYZ refinement:
A 596 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 = 0.3584 r_free = 0.3584 target = 0.125277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.101929 restraints weight = 14838.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3218 rms_B_bonded: 2.05
r_work: 0.3087 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.2918 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.1764

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025  10447  Z= 0.086
  Angle     :  0.468   8.077  14199  Z= 0.229
  Chirality :  0.036   0.145   1608
  Planarity :  0.004   0.043   1784
  Dihedral  :  3.332  18.870   1358
  Min Nonbonded Distance : 2.615

Molprobity Statistics.
  All-atom Clashscore : 3.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 10.90 %
    Favored  : 88.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.25), residues: 1250
  helix:  2.34 (0.18), residues: 826
  sheet:  None (None), residues: 0
  loop : -0.57 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 429 
 HIS   0.006   0.001   HIS A 618 
 PHE   0.011   0.001   PHE A1193 
 TYR   0.008   0.001   TYR A 310 
 ARG   0.002   0.000   ARG A 314 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02654 (  577)
  hydrogen bonds       : angle       3.50447 ( 1692)
  covalent geometry    : bond        0.00180 (10447)
  covalent geometry    : angle       0.46836 (14199)

*********************** 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
  235 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 224
  time to evaluate  : 1.192 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7676 (tpt) cc_final: 0.7394 (tpt)
REVERT: A  120 LYS cc_start: 0.8817 (mttt) cc_final: 0.8354 (mtpp)
REVERT: A  302 ASP cc_start: 0.7742 (m-30) cc_final: 0.7253 (m-30)
REVERT: A  306 ASP cc_start: 0.8171 (m-30) cc_final: 0.7900 (m-30)
REVERT: A  367 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8188 (mmmm)
REVERT: A  415 ASN cc_start: 0.8570 (m-40) cc_final: 0.8094 (m110)
REVERT: A  484 ASN cc_start: 0.7818 (t0) cc_final: 0.7434 (t0)
REVERT: A  532 THR cc_start: 0.8112 (p) cc_final: 0.7896 (p)
REVERT: A  659 SER cc_start: 0.8344 (p) cc_final: 0.7820 (t)
REVERT: A  691 LEU cc_start: 0.8338 (tt) cc_final: 0.7931 (tp)
REVERT: A  761 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7422 (mm-30)
REVERT: A  764 TYR cc_start: 0.8373 (t80) cc_final: 0.7994 (t80)
REVERT: A  765 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7795 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8317 (tppp) cc_final: 0.7981 (ttmm)
REVERT: A  849 ILE cc_start: 0.8582 (mm) cc_final: 0.8354 (mt)
REVERT: A  905 LYS cc_start: 0.8542 (ttpp) cc_final: 0.8281 (ttpp)
REVERT: A  945 VAL cc_start: 0.8345 (p) cc_final: 0.7972 (m)
REVERT: A  989 ASP cc_start: 0.8156 (t0) cc_final: 0.7815 (t0)
REVERT: A 1038 ARG cc_start: 0.8383 (mtt90) cc_final: 0.8067 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8084 (t) cc_final: 0.7834 (p)
REVERT: A 1229 LYS cc_start: 0.8545 (ttmm) cc_final: 0.8189 (tttp)
REVERT: A 1231 LEU cc_start: 0.8322 (mp) cc_final: 0.8119 (mp)
REVERT: A 1267 MET cc_start: 0.7375 (mtp) cc_final: 0.7133 (ttm)
REVERT: A 1287 HIS cc_start: 0.7769 (p90) cc_final: 0.7507 (p-80)
REVERT: A 1296 ASP cc_start: 0.8462 (m-30) cc_final: 0.7980 (m-30)
  outliers start: 11
  outliers final: 10
  residues processed: 232
  average time/residue: 0.3173
  time to fit residues: 100.2048
Evaluate side-chains
  229 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 219
  time to evaluate  : 1.633 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 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  952 LEU
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 118 optimal weight:    1.9990
   chunk 20 optimal weight:    0.6980
   chunk 70 optimal weight:    0.0770
   chunk 14 optimal weight:    2.9990
   chunk 26 optimal weight:    3.9990
   chunk 106 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0980
   chunk 24 optimal weight:    0.5980
   chunk 10 optimal weight:    3.9990
   chunk 51 optimal weight:    0.0670
   chunk 124 optimal weight:    2.9990
   overall best weight:    0.3076

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

Flipped N/Q/H residues before XYZ refinement:
A 596 HIS
A1037 ASN
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 = 0.3559 r_free = 0.3559 target = 0.123248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.099647 restraints weight = 14863.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3191 rms_B_bonded: 2.05
r_work: 0.3060 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.2889 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7908
moved from start:          0.1800

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  10447  Z= 0.094
  Angle     :  0.479   7.956  14199  Z= 0.234
  Chirality :  0.037   0.146   1608
  Planarity :  0.004   0.043   1784
  Dihedral  :  3.315  18.897   1358
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 3.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 11.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.25), residues: 1250
  helix:  2.42 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.58 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 618 
 PHE   0.015   0.001   PHE A 608 
 TYR   0.009   0.001   TYR A 181 
 ARG   0.002   0.000   ARG A 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03163 (  577)
  hydrogen bonds       : angle       3.48172 ( 1692)
  covalent geometry    : bond        0.00210 (10447)
  covalent geometry    : angle       0.47852 (14199)

*********************** 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
  230 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 219
  time to evaluate  : 1.198 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7669 (tpt) cc_final: 0.7386 (tpt)
REVERT: A  120 LYS cc_start: 0.8824 (mttt) cc_final: 0.8364 (mtpp)
REVERT: A  302 ASP cc_start: 0.7755 (m-30) cc_final: 0.7259 (m-30)
REVERT: A  306 ASP cc_start: 0.8185 (m-30) cc_final: 0.7916 (m-30)
REVERT: A  415 ASN cc_start: 0.8480 (m-40) cc_final: 0.8223 (m110)
REVERT: A  484 ASN cc_start: 0.7799 (t0) cc_final: 0.7424 (t0)
REVERT: A  532 THR cc_start: 0.8239 (p) cc_final: 0.8010 (p)
REVERT: A  659 SER cc_start: 0.8354 (p) cc_final: 0.7842 (t)
REVERT: A  761 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7432 (mm-30)
REVERT: A  764 TYR cc_start: 0.8408 (t80) cc_final: 0.7949 (t80)
REVERT: A  765 ARG cc_start: 0.8063 (ttp80) cc_final: 0.7810 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8321 (tppp) cc_final: 0.7987 (ttmm)
REVERT: A  905 LYS cc_start: 0.8551 (ttpp) cc_final: 0.8301 (ttpp)
REVERT: A  945 VAL cc_start: 0.8387 (p) cc_final: 0.8025 (m)
REVERT: A  989 ASP cc_start: 0.8165 (t0) cc_final: 0.7787 (t0)
REVERT: A 1038 ARG cc_start: 0.8412 (mtt90) cc_final: 0.8068 (mtt180)
REVERT: A 1229 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8310 (tttp)
REVERT: A 1267 MET cc_start: 0.7518 (mtp) cc_final: 0.7278 (ttm)
REVERT: A 1287 HIS cc_start: 0.7765 (p90) cc_final: 0.7495 (p-80)
REVERT: A 1296 ASP cc_start: 0.8435 (m-30) cc_final: 0.8079 (m-30)
  outliers start: 11
  outliers final: 11
  residues processed: 227
  average time/residue: 0.2743
  time to fit residues: 83.3135
Evaluate side-chains
  227 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 216
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 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  952 LEU
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 86 optimal weight:    0.7980
   chunk 61 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 114 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 107 optimal weight:    0.9980
   chunk 77 optimal weight:    0.8980
   chunk 57 optimal weight:    0.7980
   chunk 71 optimal weight:    0.0570
   overall best weight:    0.7098

-------------------------------------------------------------------------------
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
A1261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.120516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.096648 restraints weight = 14927.532|
|-----------------------------------------------------------------------------|
r_work (start): 0.3145 rms_B_bonded: 2.05
r_work: 0.3011 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2838 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2838
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.1835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10447  Z= 0.139
  Angle     :  0.525   8.791  14199  Z= 0.260
  Chirality :  0.039   0.146   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.516  19.799   1358
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 11.07 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.24), residues: 1250
  helix:  2.33 (0.18), residues: 825
  sheet:  None (None), residues: 0
  loop : -0.65 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 429 
 HIS   0.005   0.001   HIS A 618 
 PHE   0.035   0.001   PHE A 608 
 TYR   0.015   0.001   TYR A 191 
 ARG   0.003   0.000   ARG A 249 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04374 (  577)
  hydrogen bonds       : angle       3.64662 ( 1692)
  covalent geometry    : bond        0.00336 (10447)
  covalent geometry    : angle       0.52511 (14199)

*********************** 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
  240 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 223
  time to evaluate  : 1.186 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7713 (tpt) cc_final: 0.7438 (tpt)
REVERT: A  120 LYS cc_start: 0.8848 (mttt) cc_final: 0.8389 (mtpp)
REVERT: A  302 ASP cc_start: 0.7793 (m-30) cc_final: 0.7304 (m-30)
REVERT: A  306 ASP cc_start: 0.8273 (m-30) cc_final: 0.8012 (m-30)
REVERT: A  397 LYS cc_start: 0.8530 (mtmt) cc_final: 0.8220 (mtpp)
REVERT: A  402 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8274 (mp)
REVERT: A  408 TYR cc_start: 0.8472 (m-10) cc_final: 0.8238 (m-10)
REVERT: A  484 ASN cc_start: 0.7903 (t0) cc_final: 0.7575 (t0)
REVERT: A  532 THR cc_start: 0.8411 (p) cc_final: 0.8188 (p)
REVERT: A  659 SER cc_start: 0.8368 (p) cc_final: 0.7860 (t)
REVERT: A  711 TRP cc_start: 0.8496 (p-90) cc_final: 0.8125 (p-90)
REVERT: A  761 GLU cc_start: 0.7691 (mm-30) cc_final: 0.7417 (mm-30)
REVERT: A  764 TYR cc_start: 0.8462 (t80) cc_final: 0.7916 (t80)
REVERT: A  765 ARG cc_start: 0.8047 (ttp80) cc_final: 0.7805 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8382 (tppp) cc_final: 0.8073 (ttmm)
REVERT: A  813 ARG cc_start: 0.8294 (mtp-110) cc_final: 0.7965 (ttm110)
REVERT: A  905 LYS cc_start: 0.8587 (ttpp) cc_final: 0.8337 (ttpp)
REVERT: A  945 VAL cc_start: 0.8479 (p) cc_final: 0.8112 (m)
REVERT: A  989 ASP cc_start: 0.8175 (t0) cc_final: 0.7778 (t0)
REVERT: A 1038 ARG cc_start: 0.8454 (mtt90) cc_final: 0.8085 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8240 (t) cc_final: 0.7996 (p)
REVERT: A 1231 LEU cc_start: 0.8469 (mp) cc_final: 0.8184 (mt)
REVERT: A 1267 MET cc_start: 0.7608 (mtp) cc_final: 0.7319 (ttm)
REVERT: A 1287 HIS cc_start: 0.7807 (p90) cc_final: 0.7578 (p-80)
REVERT: A 1296 ASP cc_start: 0.8453 (m-30) cc_final: 0.8102 (m-30)
  outliers start: 17
  outliers final: 9
  residues processed: 232
  average time/residue: 0.2873
  time to fit residues: 89.3676
Evaluate side-chains
  226 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 216
  time to evaluate  : 1.218 
-------------------------------------------------------------------------------
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  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 1065 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 27 optimal weight:    1.9990
   chunk 84 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0010
   chunk 67 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 93 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0170
   overall best weight:    0.4824

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

Flipped N/Q/H residues before XYZ refinement:
A 415 ASN
A 449 HIS
A 596 HIS
A1261 GLN
A1289 ASN

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 = 0.121992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.098301 restraints weight = 14876.074|
|-----------------------------------------------------------------------------|
r_work (start): 0.3161 rms_B_bonded: 2.05
r_work: 0.3027 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.2856 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.2856
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.1854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10447  Z= 0.112
  Angle     :  0.507   8.595  14199  Z= 0.249
  Chirality :  0.038   0.146   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.476  19.868   1358
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 3.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 11.60 %
    Favored  : 87.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.09 (0.24), residues: 1250
  helix:  2.36 (0.18), residues: 824
  sheet:  None (None), residues: 0
  loop : -0.60 (0.30), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 618 
 PHE   0.026   0.001   PHE A 608 
 TYR   0.015   0.001   TYR A 191 
 ARG   0.002   0.000   ARG A 363 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03731 (  577)
  hydrogen bonds       : angle       3.58689 ( 1692)
  covalent geometry    : bond        0.00264 (10447)
  covalent geometry    : angle       0.50708 (14199)

*********************** 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
  230 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 215
  time to evaluate  : 1.176 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7720 (tpt) cc_final: 0.7409 (tpt)
REVERT: A  120 LYS cc_start: 0.8825 (mttt) cc_final: 0.8366 (mtpp)
REVERT: A  302 ASP cc_start: 0.7777 (m-30) cc_final: 0.7288 (m-30)
REVERT: A  306 ASP cc_start: 0.8187 (m-30) cc_final: 0.7923 (m-30)
REVERT: A  397 LYS cc_start: 0.8486 (mtmt) cc_final: 0.8192 (mtpp)
REVERT: A  402 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8215 (mp)
REVERT: A  408 TYR cc_start: 0.8416 (m-10) cc_final: 0.8191 (m-10)
REVERT: A  484 ASN cc_start: 0.7902 (t0) cc_final: 0.7574 (t0)
REVERT: A  532 THR cc_start: 0.8351 (p) cc_final: 0.8126 (p)
REVERT: A  576 ILE cc_start: 0.7912 (OUTLIER) cc_final: 0.7701 (pt)
REVERT: A  659 SER cc_start: 0.8353 (p) cc_final: 0.7842 (t)
REVERT: A  711 TRP cc_start: 0.8477 (p-90) cc_final: 0.8105 (p-90)
REVERT: A  761 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7429 (mm-30)
REVERT: A  764 TYR cc_start: 0.8433 (t80) cc_final: 0.7898 (t80)
REVERT: A  765 ARG cc_start: 0.8027 (ttp80) cc_final: 0.7789 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8384 (tppp) cc_final: 0.8083 (ttmm)
REVERT: A  905 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8310 (ttpp)
REVERT: A  945 VAL cc_start: 0.8469 (p) cc_final: 0.8112 (m)
REVERT: A  989 ASP cc_start: 0.8158 (t0) cc_final: 0.7757 (t0)
REVERT: A 1038 ARG cc_start: 0.8442 (mtt90) cc_final: 0.8143 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8194 (t) cc_final: 0.7948 (p)
REVERT: A 1231 LEU cc_start: 0.8456 (mp) cc_final: 0.8207 (mt)
REVERT: A 1267 MET cc_start: 0.7535 (mtp) cc_final: 0.7280 (ttm)
REVERT: A 1296 ASP cc_start: 0.8428 (m-30) cc_final: 0.8067 (m-30)
  outliers start: 15
  outliers final: 13
  residues processed: 225
  average time/residue: 0.2805
  time to fit residues: 84.4984
Evaluate side-chains
  228 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 213
  time to evaluate  : 1.114 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  338 LEU
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  445 ILE
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  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 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Chi-restraints excluded: chain A residue 1099 ASN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 57 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 94 optimal weight:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 114 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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
A1261 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.120155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.096472 restraints weight = 14833.038|
|-----------------------------------------------------------------------------|
r_work (start): 0.3132 rms_B_bonded: 2.04
r_work: 0.2997 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2824 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2824
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7962
moved from start:          0.1929

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= 0.151
  Angle     :  0.548  10.178  14199  Z= 0.268
  Chirality :  0.039   0.146   1608
  Planarity :  0.004   0.045   1784
  Dihedral  :  3.602  20.355   1358
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 3.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 11.78 %
    Favored  : 86.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.98 (0.24), residues: 1250
  helix:  2.30 (0.18), residues: 825
  sheet:  None (None), residues: 0
  loop : -0.70 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.002   TRP A 429 
 HIS   0.005   0.001   HIS A 618 
 PHE   0.023   0.001   PHE A 608 
 TYR   0.017   0.001   TYR A 191 
 ARG   0.002   0.000   ARG A1167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04574 (  577)
  hydrogen bonds       : angle       3.69256 ( 1692)
  covalent geometry    : bond        0.00370 (10447)
  covalent geometry    : angle       0.54783 (14199)

*********************** 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
  232 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 218
  time to evaluate  : 1.208 
Fit side-chains
REVERT: A   85 MET cc_start: 0.7746 (tpt) cc_final: 0.7456 (tpt)
REVERT: A  120 LYS cc_start: 0.8834 (mttt) cc_final: 0.8375 (mtpp)
REVERT: A  302 ASP cc_start: 0.7810 (m-30) cc_final: 0.7315 (m-30)
REVERT: A  306 ASP cc_start: 0.8277 (m-30) cc_final: 0.8018 (m-30)
REVERT: A  397 LYS cc_start: 0.8521 (mtmt) cc_final: 0.8223 (mtpp)
REVERT: A  433 ASN cc_start: 0.7691 (t0) cc_final: 0.7240 (t0)
REVERT: A  484 ASN cc_start: 0.7926 (t0) cc_final: 0.7648 (t0)
REVERT: A  659 SER cc_start: 0.8360 (p) cc_final: 0.7860 (t)
REVERT: A  711 TRP cc_start: 0.8491 (p-90) cc_final: 0.8119 (p-90)
REVERT: A  761 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7408 (mm-30)
REVERT: A  764 TYR cc_start: 0.8465 (t80) cc_final: 0.7895 (t80)
REVERT: A  765 ARG cc_start: 0.8033 (ttp80) cc_final: 0.7787 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8407 (tppp) cc_final: 0.8092 (ttmm)
REVERT: A  813 ARG cc_start: 0.8300 (mtp-110) cc_final: 0.7954 (ttm110)
REVERT: A  905 LYS cc_start: 0.8556 (ttpp) cc_final: 0.8294 (ttpp)
REVERT: A  945 VAL cc_start: 0.8467 (p) cc_final: 0.8130 (m)
REVERT: A  989 ASP cc_start: 0.8170 (t0) cc_final: 0.7764 (t0)
REVERT: A 1038 ARG cc_start: 0.8485 (mtt90) cc_final: 0.8187 (mtt180)
REVERT: A 1267 MET cc_start: 0.7664 (mtp) cc_final: 0.7392 (ttm)
REVERT: A 1296 ASP cc_start: 0.8405 (m-30) cc_final: 0.8002 (m-30)
  outliers start: 14
  outliers final: 11
  residues processed: 226
  average time/residue: 0.2833
  time to fit residues: 85.2119
Evaluate side-chains
  227 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 216
  time to evaluate  : 0.923 
-------------------------------------------------------------------------------
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  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 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 65 optimal weight:    0.6980
   chunk 38 optimal weight:    1.9990
   chunk 42 optimal weight:    0.2980
   chunk 85 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   chunk 13 optimal weight:    0.3980
   chunk 104 optimal weight:    0.9990
   chunk 4 optimal weight:    0.9980
   chunk 81 optimal weight:    0.6980
   chunk 93 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   overall best weight:    0.4980

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.121420 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.097735 restraints weight = 14779.914|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 2.05
r_work: 0.3019 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.2847 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.1928

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= 0.116
  Angle     :  0.531  11.439  14199  Z= 0.258
  Chirality :  0.038   0.146   1608
  Planarity :  0.004   0.044   1784
  Dihedral  :  3.540  20.101   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 :  0.79 %
    Allowed  : 12.57 %
    Favored  : 86.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.02 (0.24), residues: 1250
  helix:  2.32 (0.18), residues: 825
  sheet:  None (None), residues: 0
  loop : -0.67 (0.30), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.001   TRP A 429 
 HIS   0.004   0.001   HIS A 618 
 PHE   0.026   0.001   PHE A 608 
 TYR   0.016   0.001   TYR A 191 
 ARG   0.002   0.000   ARG A 213 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03848 (  577)
  hydrogen bonds       : angle       3.62969 ( 1692)
  covalent geometry    : bond        0.00275 (10447)
  covalent geometry    : angle       0.53107 (14199)

********************** 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
  224 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 215
  time to evaluate  : 1.049 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 MET cc_start: 0.7729 (tpt) cc_final: 0.7413 (tpt)
REVERT: A  120 LYS cc_start: 0.8833 (mttt) cc_final: 0.8353 (mtpp)
REVERT: A  213 ARG cc_start: 0.8205 (mpt180) cc_final: 0.7802 (mpt180)
REVERT: A  302 ASP cc_start: 0.7784 (m-30) cc_final: 0.7289 (m-30)
REVERT: A  306 ASP cc_start: 0.8260 (m-30) cc_final: 0.7995 (m-30)
REVERT: A  397 LYS cc_start: 0.8511 (mtmt) cc_final: 0.8222 (mtpp)
REVERT: A  408 TYR cc_start: 0.8445 (m-80) cc_final: 0.8207 (m-10)
REVERT: A  484 ASN cc_start: 0.7903 (t0) cc_final: 0.7624 (t0)
REVERT: A  532 THR cc_start: 0.8353 (p) cc_final: 0.8129 (p)
REVERT: A  659 SER cc_start: 0.8353 (p) cc_final: 0.7840 (t)
REVERT: A  761 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7430 (mm-30)
REVERT: A  764 TYR cc_start: 0.8445 (t80) cc_final: 0.7890 (t80)
REVERT: A  765 ARG cc_start: 0.8024 (ttp80) cc_final: 0.7789 (ttp-170)
REVERT: A  766 LYS cc_start: 0.8393 (tppp) cc_final: 0.8096 (ttmm)
REVERT: A  905 LYS cc_start: 0.8561 (ttpp) cc_final: 0.8297 (ttpp)
REVERT: A  945 VAL cc_start: 0.8442 (p) cc_final: 0.8111 (m)
REVERT: A  989 ASP cc_start: 0.8144 (t0) cc_final: 0.7748 (t0)
REVERT: A 1038 ARG cc_start: 0.8477 (mtt90) cc_final: 0.8176 (mtt180)
REVERT: A 1117 VAL cc_start: 0.8216 (t) cc_final: 0.7975 (p)
REVERT: A 1267 MET cc_start: 0.7594 (mtp) cc_final: 0.7329 (ttm)
REVERT: A 1296 ASP cc_start: 0.8408 (m-30) cc_final: 0.7991 (m-30)
  outliers start: 9
  outliers final: 8
  residues processed: 220
  average time/residue: 0.2911
  time to fit residues: 84.5980
Evaluate side-chains
  222 residues out of total 1138 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 214
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  906 GLU
Chi-restraints excluded: chain A residue 1034 LEU
Chi-restraints excluded: chain A residue 1065 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1891 > 50:
  distance: 71 - 101:   3.668
  distance: 77 - 108:   5.517
  distance: 79 - 82:   3.097
  distance: 80 - 90:   3.450
  distance: 81 - 116:   3.856
  distance: 82 - 83:   3.693
  distance: 83 - 85:   3.440
  distance: 84 - 86:   4.353
  distance: 85 - 87:   4.599
  distance: 86 - 88:   3.117
  distance: 87 - 88:   3.583
  distance: 88 - 89:   3.116
  distance: 93 - 125:   5.379
  distance: 94 - 95:   4.803
  distance: 95 - 96:   3.431
  distance: 102 - 103:   4.808
  distance: 102 - 105:   4.321
  distance: 103 - 104:   3.650
  distance: 103 - 108:   4.852
  distance: 104 - 136:  10.129
  distance: 105 - 106:   3.643
  distance: 105 - 107:   4.463
  distance: 108 - 109:   3.016
  distance: 109 - 110:   4.049
  distance: 109 - 112:   4.281
  distance: 112 - 113:   3.674
  distance: 113 - 114:   3.304
  distance: 113 - 115:   3.322
  distance: 118 - 119:   3.699
  distance: 120 - 121:   4.956
  distance: 122 - 124:   3.511
  distance: 125 - 126:   3.748
  distance: 126 - 127:   4.485
  distance: 126 - 129:   6.908
  distance: 127 - 128:   5.044
  distance: 127 - 136:   5.228
  distance: 129 - 130:   4.847
  distance: 130 - 131:   5.409
  distance: 131 - 132:   4.155
  distance: 133 - 134:  10.795
  distance: 133 - 135:   4.454
  distance: 136 - 137:   5.090
  distance: 137 - 138:  14.724
  distance: 137 - 140:   3.559
  distance: 138 - 139:  19.836
  distance: 138 - 144:  33.680
  distance: 140 - 142:   9.202
  distance: 141 - 143:   6.869
  distance: 144 - 145:   3.615
  distance: 145 - 146:  18.447
  distance: 146 - 147:   7.157
  distance: 146 - 148:  15.028
  distance: 147 - 169:   6.695
  distance: 148 - 149:  10.113
  distance: 149 - 150:   5.877
  distance: 149 - 152:   3.761
  distance: 150 - 151:   5.297
  distance: 150 - 153:   4.245
  distance: 153 - 154:   3.985
  distance: 154 - 157:   3.685
  distance: 155 - 156:   7.200
  distance: 155 - 164:   5.193
  distance: 157 - 158:   5.801
  distance: 158 - 159:   4.343
  distance: 159 - 160:   4.856
  distance: 160 - 161:   7.882
  distance: 161 - 162:   8.230
  distance: 161 - 163:   8.314