Starting phenix.real_space_refine
on Wed Feb  4 19:10:27 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9waa_65810/02_2026/9waa_65810.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9waa_65810/02_2026/9waa_65810.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.17
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9waa_65810/02_2026/9waa_65810.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9waa_65810/02_2026/9waa_65810.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9waa_65810/02_2026/9waa_65810.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9waa_65810/02_2026/9waa_65810.cif"
  }
  resolution = 4.17
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.032
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: 5
    Type Number    sf(0)   Gaussians
     P     147      5.49       5
     S      18      5.16       5
     C    7313      2.51       5
     N    2178      2.21       5
     O    2703      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

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

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12359
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9201
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1129, 9201
          Classifications: {'peptide': 1129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 30, 'TRANS': 1098}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 761
          Classifications: {'DNA': 37}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 36}
    Chain: "C"
      Number of atoms: 286
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 286
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 13}
    Chain: "D"
      Number of atoms: 2111
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 99, 2111
          Classifications: {'RNA': 99}
          Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 5, 'rna3p_pur': 49, 'rna3p_pyr': 39}
          Link IDs: {'rna2p': 11, 'rna3p': 87}
  Time building chain proxies: 3.29, per 1000 atoms: 0.27
  Number of scatterers: 12359
  At special positions: 0
  Unit cell: (136.398, 115.992, 111.696, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      18     16.00
     P     147     15.00
     O    2703      8.00
     N    2178      7.00
     C    7313      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: 1.14
  Conformation dependent library (CDL) restraints added in 512.7 milliseconds
  

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2146

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 7 sheets defined
      55.4% alpha, 8.0% beta
      59 base pairs and 85 stacking pairs defined.
    Time for finding SS restraints: 1.96
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 92
      removed outlier: 4.695A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.376A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   ALA A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 103
    Processing helix  chain 'A' and resid 104 through 106
      No H-bonds generated for 'chain 'A' and resid 104 through 106'
    Processing helix  chain 'A' and resid 121 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 3.589A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
      removed outlier: 3.504A  pdb=" N   ILE A 154 " --> pdb=" O   ASP A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 180 through 196
      removed outlier: 3.604A  pdb=" N   LEU A 184 " --> pdb=" O   ASP A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 213
    Processing helix  chain 'A' and resid 217 through 228
    Processing helix  chain 'A' and resid 236 through 247
    Processing helix  chain 'A' and resid 252 through 257
      removed outlier: 3.874A  pdb=" N   PHE A 256 " --> pdb=" O   PHE A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 283
      removed outlier: 4.600A  pdb=" N   ASP A 273 " --> pdb=" O   ASP A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 305
      removed outlier: 3.585A  pdb=" N   PHE A 290 " --> pdb=" O   TYR A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
    Processing helix  chain 'A' and resid 346 through 352
    Processing helix  chain 'A' and resid 358 through 365
    Processing helix  chain 'A' and resid 368 through 382
      Proline residue:  A 378  - end of helix
    Processing helix  chain 'A' and resid 386 through 395
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.696A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 405 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ILE A 410 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.329A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
    Processing helix  chain 'A' and resid 436 through 446
    Processing helix  chain 'A' and resid 483 through 495
      removed outlier: 4.182A  pdb=" N   MET A 495 " --> pdb=" O   PHE A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 526
      removed outlier: 3.859A  pdb=" N   LYS A 526 " --> pdb=" O   ASN A 522 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 552
    Processing helix  chain 'A' and resid 560 through 568
    Processing helix  chain 'A' and resid 591 through 601
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 612 through 626
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 4.481A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 654
    Processing helix  chain 'A' and resid 664 through 668
    Processing helix  chain 'A' and resid 678 through 685
    Processing helix  chain 'A' and resid 692 through 699
    Processing helix  chain 'A' and resid 703 through 712
    Processing helix  chain 'A' and resid 719 through 726
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.512A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 959 through 970
      removed outlier: 3.957A  pdb=" N   VAL A 963 " --> pdb=" O   LYS A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 980 through 999
      removed outlier: 4.433A  pdb=" N   ALA A 984 " --> pdb=" O   ASN A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1077 through 1088
    Processing helix  chain 'A' and resid 1127 through 1132
    Processing helix  chain 'A' and resid 1170 through 1177
    Processing helix  chain 'A' and resid 1177 through 1185
    Processing helix  chain 'A' and resid 1191 through 1195
    Processing helix  chain 'A' and resid 1207 through 1209
      No H-bonds generated for 'chain 'A' and resid 1207 through 1209'
    Processing helix  chain 'A' and resid 1229 through 1241
    Processing helix  chain 'A' and resid 1248 through 1262
      removed outlier: 3.563A  pdb=" N   HIS A1262 " --> pdb=" O   PHE A1258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1281
    Processing helix  chain 'A' and resid 1283 through 1297
    Processing helix  chain 'A' and resid 1301 through 1311
      removed outlier: 3.704A  pdb=" N   HIS A1311 " --> pdb=" O   GLU A1307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1312 through 1317
      removed outlier: 3.923A  pdb=" N   THR A1316 " --> pdb=" O   LEU A1312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1340 through 1344
      removed outlier: 4.208A  pdb=" N   ASP A1344 " --> pdb=" O   GLU A1341 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 954 through 957
      removed outlier: 6.653A  pdb=" N   ILE A   7 " --> pdb=" O   VAL A 760 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL A1095 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 29 through 33
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 36
      removed outlier: 6.585A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 8.364A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 4.257A  pdb=" N   SER A1202 " --> pdb=" O   LEU A1214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 507 through 509
      removed outlier: 4.812A  pdb=" N   LEU A 508 " --> pdb=" O   GLY A 660 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 538 through 539
      removed outlier: 3.588A  pdb=" N   TYR A 529 " --> pdb=" O   ALA A 538 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1167
      removed outlier: 5.728A  pdb=" N   LYS A1156 " --> pdb=" O   GLU A1150 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   GLU A1150 " --> pdb=" O   LYS A1156 " (cutoff:3.500A)
      removed outlier: 5.696A  pdb=" N   LYS A1158 " --> pdb=" O   LYS A1148 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   LYS A1148 " --> pdb=" O   LYS A1158 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL A1160 " --> pdb=" O   VAL A1146 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   VAL A1146 " --> pdb=" O   VAL A1160 " (cutoff:3.500A)
      removed outlier: 7.398A  pdb=" N   GLU A1162 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
      removed outlier: 5.411A  pdb=" N   LEU A1144 " --> pdb=" O   GLU A1162 " (cutoff:3.500A)
      removed outlier: 7.247A  pdb=" N   LEU A1164 " --> pdb=" O   SER A1142 " (cutoff:3.500A)
      removed outlier: 5.589A  pdb=" N   SER A1142 " --> pdb=" O   LEU A1164 " (cutoff:3.500A)
      removed outlier: 6.811A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1326

    434 hydrogen bonds defined for protein.
    1263 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      150 hydrogen bonds
      296 hydrogen bond angles
      0 basepair planarities
      59 basepair parallelities
      85 stacking parallelities
  Total time for adding SS restraints: 3.50

  Time building geometry restraints manager: 1.48 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2866
        1.33 -     1.45: 3252
        1.45 -     1.57: 6458
        1.57 -     1.69: 294
        1.69 -     1.81: 34
  Bond restraints: 12904
  Sorted by residual:
  bond pdb=" CG  LEU A 301 "
       pdb=" CD2 LEU A 301 "
    ideal  model  delta    sigma   weight residual
    1.521  1.489  0.032 3.30e-02 9.18e+02 9.63e-01
  bond pdb=" C4'  DG B  32 "
       pdb=" C3'  DG B  32 "
    ideal  model  delta    sigma   weight residual
    1.523  1.504  0.019 2.00e-02 2.50e+03 8.81e-01
  bond pdb=" C3'  DG B   7 "
       pdb=" O3'  DG B   7 "
    ideal  model  delta    sigma   weight residual
    1.422  1.447 -0.025 3.00e-02 1.11e+03 6.87e-01
  bond pdb=" C2'  DG B  32 "
       pdb=" C1'  DG B  32 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 2.00e-02 2.50e+03 6.77e-01
  bond pdb=" CA  LEU A 306 "
       pdb=" C   LEU A 306 "
    ideal  model  delta    sigma   weight residual
    1.532  1.525  0.008 9.60e-03 1.09e+04 6.49e-01
  ... (remaining 12899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.47: 17989
        2.47 -     4.94: 91
        4.94 -     7.40: 0
        7.40 -     9.87: 0
        9.87 -    12.34: 1
  Bond angle restraints: 18081
  Sorted by residual:
  angle pdb=" CA  LEU A 301 "
        pdb=" CB  LEU A 301 "
        pdb=" CG  LEU A 301 "
      ideal   model   delta    sigma   weight residual
     116.30  128.64  -12.34 3.50e+00 8.16e-02 1.24e+01
  angle pdb=" N   ILE A 410 "
        pdb=" CA  ILE A 410 "
        pdb=" C   ILE A 410 "
      ideal   model   delta    sigma   weight residual
     107.76  110.32   -2.56 1.01e+00 9.80e-01 6.45e+00
  angle pdb=" C   PHE A 164 "
        pdb=" N   ARG A 165 "
        pdb=" CA  ARG A 165 "
      ideal   model   delta    sigma   weight residual
     120.60  124.19   -3.59 1.60e+00 3.91e-01 5.03e+00
  angle pdb=" N   VAL A1280 "
        pdb=" CA  VAL A1280 "
        pdb=" C   VAL A1280 "
      ideal   model   delta    sigma   weight residual
     109.34  113.99   -4.65 2.08e+00 2.31e-01 4.99e+00
  angle pdb=" N   ILE A 312 "
        pdb=" CA  ILE A 312 "
        pdb=" C   ILE A 312 "
      ideal   model   delta    sigma   weight residual
     107.51  110.70   -3.19 1.49e+00 4.50e-01 4.57e+00
  ... (remaining 18076 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.04: 7367
       30.04 -    60.09: 353
       60.09 -    90.13: 78
       90.13 -   120.18: 1
      120.18 -   150.22: 1
  Dihedral angle restraints: 7800
    sinusoidal: 4485
      harmonic: 3315
  Sorted by residual:
  dihedral pdb=" C4'  DG B   7 "
           pdb=" C3'  DG B   7 "
           pdb=" O3'  DG B   7 "
           pdb=" P    DA B   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
     220.00   69.78  150.22     1      3.50e+01 8.16e-04 1.46e+01
  dihedral pdb=" CG  ARG A1359 "
           pdb=" CD  ARG A1359 "
           pdb=" NE  ARG A1359 "
           pdb=" CZ  ARG A1359 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -90.00 -134.87   44.87     2      1.50e+01 4.44e-03 1.06e+01
  dihedral pdb=" N   LYS A1158 "
           pdb=" CA  LYS A1158 "
           pdb=" CB  LYS A1158 "
           pdb=" CG  LYS A1158 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -116.25   56.25     3      1.50e+01 4.44e-03 9.39e+00
  ... (remaining 7797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.032: 1548
       0.032 -    0.064: 399
       0.064 -    0.097: 96
       0.097 -    0.129: 42
       0.129 -    0.161: 3
  Chirality restraints: 2088
  Sorted by residual:
  chirality pdb=" CA  ILE A 305 "
            pdb=" N   ILE A 305 "
            pdb=" C   ILE A 305 "
            pdb=" CB  ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.49e-01
  chirality pdb=" CA  VAL A  27 "
            pdb=" N   VAL A  27 "
            pdb=" C   VAL A  27 "
            pdb=" CB  VAL A  27 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.45e-01
  chirality pdb=" C1'   A D  36 "
            pdb=" O4'   A D  36 "
            pdb=" C2'   A D  36 "
            pdb=" N9    A D  36 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.46    2.33    0.13 2.00e-01 2.50e+01 4.25e-01
  ... (remaining 2085 not shown)

  Planarity restraints: 1762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 653 "    0.173 9.50e-02 1.11e+02   7.76e-02 3.70e+00
        pdb=" NE  ARG A 653 "   -0.010 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 653 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 653 "   -0.002 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 653 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  44 "    0.024 2.00e-02 2.50e+03   1.08e-02 3.18e+00
        pdb=" N9    A D  44 "   -0.025 2.00e-02 2.50e+03
        pdb=" C8    A D  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" N7    A D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    A D  44 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  44 "    0.001 2.00e-02 2.50e+03
        pdb=" N6    A D  44 "    0.007 2.00e-02 2.50e+03
        pdb=" N1    A D  44 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A D  44 "   -0.002 2.00e-02 2.50e+03
        pdb=" N3    A D  44 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  44 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A D  36 "    0.020 2.00e-02 2.50e+03   9.26e-03 2.36e+00
        pdb=" N9    A D  36 "   -0.023 2.00e-02 2.50e+03
        pdb=" C8    A D  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" N7    A D  36 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A D  36 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    A D  36 "    0.003 2.00e-02 2.50e+03
        pdb=" N6    A D  36 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A D  36 "    0.001 2.00e-02 2.50e+03
        pdb=" C2    A D  36 "   -0.001 2.00e-02 2.50e+03
        pdb=" N3    A D  36 "   -0.003 2.00e-02 2.50e+03
        pdb=" C4    A D  36 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1759 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 5
        2.02 -     2.74: 990
        2.74 -     3.46: 17070
        3.46 -     4.18: 31229
        4.18 -     4.90: 49602
  Nonbonded interactions: 98896
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS A 742 "
            pdb=" OP1   C D  69 "
     model   vdw
     1.296 3.120
  nonbonded pdb=" NZ  LYS A1340 "
            pdb=" OP2  DA B   8 "
     model   vdw
     1.297 3.120
  nonbonded pdb=" NH1 ARG A  71 "
            pdb=" N4    C D  20 "
     model   vdw
     1.352 3.200
  nonbonded pdb=" CA  GLY A 582 "
            pdb=" OP1  DC B  34 "
     model   vdw
     1.375 3.440
  nonbonded pdb=" N   GLY A 582 "
            pdb=" OP1  DC B  34 "
     model   vdw
     1.920 3.120
  ... (remaining 98891 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.640
  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:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     16.270
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.770
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7533
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   0.032  12904  Z= 0.125
  Angle     :  0.517  12.340  18081  Z= 0.307
  Chirality :  0.034   0.161   2088
  Planarity :  0.004   0.078   1762
  Dihedral  : 16.334 150.220   5654
  Min Nonbonded Distance : 1.296

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.03 %
    Favored  : 96.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.26), residues: 1123
  helix:  1.87 (0.23), residues: 577
  sheet:  1.65 (0.64), residues: 71
  loop : -0.08 (0.28), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  71 
 TYR   0.010   0.001   TYR A1356 
 PHE   0.009   0.001   PHE A 432 
 TRP   0.010   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 328 

Details of bonding type rmsd
  covalent geometry    : bond        0.00236 (12904)
  covalent geometry    : angle       0.51694 (18081)
  hydrogen bonds       : bond        0.14587 (  584)
  hydrogen bonds       : angle       5.47416 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 205
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  310 THR cc_start: 0.7978 (p) cc_final: 0.7563 (t)
REVERT: A  517 TYR cc_start: 0.8645 (m-80) cc_final: 0.8406 (m-80)
REVERT: A  667 ILE cc_start: 0.9265 (mt) cc_final: 0.8732 (mt)
REVERT: A  668 ASN cc_start: 0.9382 (t0) cc_final: 0.9161 (m110)
REVERT: A 1135 ASP cc_start: 0.7374 (t0) cc_final: 0.7017 (t70)
  outliers start: 0
  outliers final: 0
  residues processed: 205
  average time/residue: 0.1666
  time to fit residues: 44.6724
Evaluate side-chains
  115 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 115
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    9.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:   30.0000
   chunk 113 optimal weight:   10.0000
   chunk 53 optimal weight:    9.9990
   chunk 5 optimal weight:   20.0000
   chunk 33 optimal weight:    9.9990
   chunk 123 optimal weight:   20.0000
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    1.9990
   chunk 51 optimal weight:    9.9990
   overall best weight:    6.5988

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

Flipped N/Q/H residues before XYZ refinement:
A  41 HIS
A 415 HIS
A 556 ASN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1101 GLN
A1264 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.047960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2984 r_free = 0.2984 target = 0.035376 restraints weight = 115709.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3015 r_free = 0.3015 target = 0.036377 restraints weight = 70057.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.037014 restraints weight = 50664.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.037472 restraints weight = 40934.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.037754 restraints weight = 35238.558|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12904  Z= 0.226
  Angle     :  0.659   7.409  18081  Z= 0.351
  Chirality :  0.039   0.182   2088
  Planarity :  0.005   0.054   1762
  Dihedral  : 18.974 152.589   3276
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 12.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.78 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.97 (0.24), residues: 1123
  helix:  1.44 (0.21), residues: 578
  sheet:  1.17 (0.65), residues: 61
  loop : -0.35 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 557 
 TYR   0.032   0.002   TYR A1201 
 PHE   0.027   0.002   PHE A 626 
 TRP   0.012   0.002   TRP A 476 
 HIS   0.007   0.002   HIS A 167 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (12904)
  covalent geometry    : angle       0.65922 (18081)
  hydrogen bonds       : bond        0.05256 (  584)
  hydrogen bonds       : angle       4.66213 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 123
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.9724 (pm20) cc_final: 0.9408 (pm20)
REVERT: A   75 ARG cc_start: 0.9766 (ttp-170) cc_final: 0.9431 (mmt-90)
REVERT: A  415 HIS cc_start: 0.9496 (m-70) cc_final: 0.9062 (m90)
REVERT: A  517 TYR cc_start: 0.9074 (m-80) cc_final: 0.8813 (m-80)
REVERT: A  518 PHE cc_start: 0.9669 (t80) cc_final: 0.9141 (t80)
REVERT: A  534 MET cc_start: 0.6063 (ttt) cc_final: 0.5781 (ttt)
REVERT: A  596 ASP cc_start: 0.8975 (m-30) cc_final: 0.8714 (m-30)
REVERT: A  631 MET cc_start: 0.9166 (ptp) cc_final: 0.8630 (ptp)
REVERT: A  667 ILE cc_start: 0.9515 (mt) cc_final: 0.8663 (mt)
REVERT: A  668 ASN cc_start: 0.9587 (t0) cc_final: 0.9280 (m-40)
REVERT: A  724 ILE cc_start: 0.9397 (mt) cc_final: 0.9054 (tt)
REVERT: A  751 MET cc_start: 0.9077 (mmp) cc_final: 0.8734 (mmm)
REVERT: A  926 GLN cc_start: 0.9403 (mm-40) cc_final: 0.9100 (mt0)
REVERT: A  943 TYR cc_start: 0.9448 (p90) cc_final: 0.9221 (p90)
REVERT: A 1126 TRP cc_start: 0.9153 (m-10) cc_final: 0.8767 (m-10)
REVERT: A 1170 GLU cc_start: 0.9403 (tp30) cc_final: 0.9137 (tm-30)
REVERT: A 1171 ARG cc_start: 0.9656 (ttt180) cc_final: 0.9339 (ttm170)
  outliers start: 1
  outliers final: 0
  residues processed: 124
  average time/residue: 0.1488
  time to fit residues: 24.8137
Evaluate side-chains
  86 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 50 optimal weight:    7.9990
   chunk 31 optimal weight:    8.9990
   chunk 4 optimal weight:   20.0000
   chunk 14 optimal weight:   10.0000
   chunk 36 optimal weight:   20.0000
   chunk 41 optimal weight:   10.0000
   chunk 67 optimal weight:   20.0000
   chunk 6 optimal weight:    5.9990
   chunk 115 optimal weight:   10.0000
   chunk 40 optimal weight:    6.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    6.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 129 HIS
A 328 HIS
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.063198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.052708 restraints weight = 136133.972|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.053843 restraints weight = 68095.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.054514 restraints weight = 43496.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.055016 restraints weight = 32934.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.055244 restraints weight = 27147.100|
|-----------------------------------------------------------------------------|
r_work (final): 0.2956
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.5000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  12904  Z= 0.196
  Angle     :  0.589   6.411  18081  Z= 0.321
  Chirality :  0.037   0.162   2088
  Planarity :  0.005   0.053   1762
  Dihedral  : 19.372 157.483   3276
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.20 %
    Allowed  :  2.28 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.25), residues: 1123
  helix:  1.43 (0.21), residues: 583
  sheet:  0.79 (0.57), residues: 78
  loop : -0.42 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1303 
 TYR   0.016   0.002   TYR A 639 
 PHE   0.015   0.002   PHE A 351 
 TRP   0.015   0.002   TRP A 476 
 HIS   0.006   0.002   HIS A 721 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 (12904)
  covalent geometry    : angle       0.58897 (18081)
  hydrogen bonds       : bond        0.04528 (  584)
  hydrogen bonds       : angle       4.48338 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 111
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 GLU cc_start: 0.9646 (pm20) cc_final: 0.9384 (pm20)
REVERT: A  158 LEU cc_start: 0.9805 (tp) cc_final: 0.9420 (tp)
REVERT: A  415 HIS cc_start: 0.9363 (m-70) cc_final: 0.8925 (m90)
REVERT: A  517 TYR cc_start: 0.9182 (m-80) cc_final: 0.8924 (m-80)
REVERT: A  518 PHE cc_start: 0.9650 (t80) cc_final: 0.9134 (t80)
REVERT: A  534 MET cc_start: 0.5689 (ttt) cc_final: 0.5241 (ttt)
REVERT: A  596 ASP cc_start: 0.8927 (m-30) cc_final: 0.8638 (m-30)
REVERT: A  628 ASP cc_start: 0.9684 (t70) cc_final: 0.9428 (t70)
REVERT: A  667 ILE cc_start: 0.9587 (mt) cc_final: 0.8775 (mt)
REVERT: A  668 ASN cc_start: 0.9666 (t0) cc_final: 0.9318 (m-40)
REVERT: A  724 ILE cc_start: 0.9449 (mt) cc_final: 0.9166 (tt)
REVERT: A  751 MET cc_start: 0.9122 (mmp) cc_final: 0.8850 (mmm)
REVERT: A  943 TYR cc_start: 0.9410 (p90) cc_final: 0.9098 (p90)
REVERT: A 1089 MET cc_start: 0.9026 (tpt) cc_final: 0.8209 (tpt)
REVERT: A 1126 TRP cc_start: 0.9017 (m-10) cc_final: 0.8785 (m-10)
REVERT: A 1170 GLU cc_start: 0.9099 (tp30) cc_final: 0.8657 (tp30)
REVERT: A 1171 ARG cc_start: 0.9573 (ttt180) cc_final: 0.9302 (ttm170)
  outliers start: 2
  outliers final: 1
  residues processed: 112
  average time/residue: 0.1485
  time to fit residues: 22.7593
Evaluate side-chains
  84 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 83
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 73 optimal weight:   10.0000
   chunk 54 optimal weight:   30.0000
   chunk 44 optimal weight:    0.9990
   chunk 115 optimal weight:   10.0000
   chunk 3 optimal weight:    0.0970
   chunk 1 optimal weight:    7.9990
   chunk 39 optimal weight:    8.9990
   chunk 75 optimal weight:    7.9990
   chunk 108 optimal weight:   20.0000
   chunk 9 optimal weight:    6.9990
   overall best weight:    4.8186

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

Flipped N/Q/H residues before XYZ refinement:
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.062663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.052229 restraints weight = 136676.683|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.053401 restraints weight = 68848.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.054090 restraints weight = 43250.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.054567 restraints weight = 32498.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.054824 restraints weight = 26885.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.2934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.5671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12904  Z= 0.163
  Angle     :  0.540   6.684  18081  Z= 0.295
  Chirality :  0.036   0.155   2088
  Planarity :  0.004   0.051   1762
  Dihedral  : 19.246 157.009   3276
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 12.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.45 %
    Favored  : 95.55 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.68 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.96 (0.25), residues: 1123
  helix:  1.49 (0.21), residues: 583
  sheet:  0.70 (0.55), residues: 89
  loop : -0.47 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A1303 
 TYR   0.014   0.001   TYR A 271 
 PHE   0.012   0.001   PHE A 351 
 TRP   0.009   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (12904)
  covalent geometry    : angle       0.53985 (18081)
  hydrogen bonds       : bond        0.04175 (  584)
  hydrogen bonds       : angle       4.28804 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    1 MET cc_start: 0.6412 (ttp) cc_final: 0.5988 (tmm)
REVERT: A   60 GLU cc_start: 0.9649 (pm20) cc_final: 0.9365 (pm20)
REVERT: A  271 TYR cc_start: 0.9557 (t80) cc_final: 0.9285 (t80)
REVERT: A  399 LEU cc_start: 0.9613 (mp) cc_final: 0.9411 (mt)
REVERT: A  415 HIS cc_start: 0.9474 (m-70) cc_final: 0.8980 (m90)
REVERT: A  518 PHE cc_start: 0.9600 (t80) cc_final: 0.9167 (t80)
REVERT: A  534 MET cc_start: 0.5314 (ttt) cc_final: 0.4855 (ttt)
REVERT: A  668 ASN cc_start: 0.9633 (t0) cc_final: 0.9431 (m110)
REVERT: A  724 ILE cc_start: 0.9557 (mt) cc_final: 0.9281 (tt)
REVERT: A  943 TYR cc_start: 0.9370 (p90) cc_final: 0.9019 (p90)
REVERT: A 1089 MET cc_start: 0.8912 (tpt) cc_final: 0.8385 (tpt)
REVERT: A 1126 TRP cc_start: 0.8989 (m-10) cc_final: 0.8771 (m-10)
REVERT: A 1170 GLU cc_start: 0.9124 (tp30) cc_final: 0.8507 (tp30)
REVERT: A 1171 ARG cc_start: 0.9568 (ttt180) cc_final: 0.9283 (ttm170)
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.1408
  time to fit residues: 20.4121
Evaluate side-chains
  76 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 121 optimal weight:   20.0000
   chunk 60 optimal weight:   20.0000
   chunk 6 optimal weight:   10.0000
   chunk 44 optimal weight:    9.9990
   chunk 89 optimal weight:   20.0000
   chunk 1 optimal weight:   30.0000
   chunk 17 optimal weight:    0.0370
   chunk 110 optimal weight:    6.9990
   chunk 14 optimal weight:   20.0000
   chunk 93 optimal weight:    5.9990
   overall best weight:    6.2066

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

Flipped N/Q/H residues before XYZ refinement:
A 277 ASN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 754 HIS
A1305 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.058699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.048703 restraints weight = 142061.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.049773 restraints weight = 71026.182|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.050462 restraints weight = 44675.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.050865 restraints weight = 33294.791|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.051080 restraints weight = 27854.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.2900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.6806

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12904  Z= 0.204
  Angle     :  0.595   5.746  18081  Z= 0.326
  Chirality :  0.038   0.181   2088
  Planarity :  0.004   0.051   1762
  Dihedral  : 19.528 158.712   3276
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.55 (0.24), residues: 1123
  helix:  1.14 (0.21), residues: 582
  sheet:  0.27 (0.55), residues: 90
  loop : -0.57 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 653 
 TYR   0.015   0.002   TYR A 347 
 PHE   0.028   0.002   PHE A1204 
 TRP   0.008   0.002   TRP A 476 
 HIS   0.007   0.002   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 (12904)
  covalent geometry    : angle       0.59472 (18081)
  hydrogen bonds       : bond        0.04872 (  584)
  hydrogen bonds       : angle       4.46211 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 TYR cc_start: 0.9472 (t80) cc_final: 0.9157 (t80)
REVERT: A  415 HIS cc_start: 0.9416 (m-70) cc_final: 0.8973 (m90)
REVERT: A  534 MET cc_start: 0.5339 (ttt) cc_final: 0.4871 (ttt)
REVERT: A  648 MET cc_start: 0.9385 (mmp) cc_final: 0.9100 (mmm)
REVERT: A  724 ILE cc_start: 0.9620 (mt) cc_final: 0.9384 (tt)
REVERT: A  943 TYR cc_start: 0.9341 (p90) cc_final: 0.8971 (p90)
REVERT: A 1089 MET cc_start: 0.9071 (tpt) cc_final: 0.8628 (tpt)
REVERT: A 1170 GLU cc_start: 0.9083 (tp30) cc_final: 0.8468 (tp30)
REVERT: A 1171 ARG cc_start: 0.9610 (ttt180) cc_final: 0.9370 (ttm170)
REVERT: A 1213 MET cc_start: 0.9341 (mmm) cc_final: 0.8765 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 94
  average time/residue: 0.1277
  time to fit residues: 17.0982
Evaluate side-chains
  64 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 31 optimal weight:    9.9990
   chunk 21 optimal weight:   50.0000
   chunk 23 optimal weight:   50.0000
   chunk 69 optimal weight:    9.9990
   chunk 24 optimal weight:    8.9990
   chunk 93 optimal weight:    5.9990
   chunk 51 optimal weight:   10.0000
   chunk 101 optimal weight:   10.0000
   chunk 120 optimal weight:   20.0000
   chunk 70 optimal weight:    8.9990
   chunk 113 optimal weight:   10.0000
   overall best weight:    8.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 113 HIS
A 394 ASN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 758 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.041528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.2742 r_free = 0.2742 target = 0.030673 restraints weight = 143736.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.031555 restraints weight = 86213.598|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.032086 restraints weight = 61600.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 58)----------------|
| r_work = 0.2799 r_free = 0.2799 target = 0.032445 restraints weight = 49714.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2806 r_free = 0.2806 target = 0.032657 restraints weight = 43031.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.2748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.7886

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  12904  Z= 0.262
  Angle     :  0.681   8.196  18081  Z= 0.373
  Chirality :  0.040   0.172   2088
  Planarity :  0.005   0.052   1762
  Dihedral  : 19.955 162.414   3276
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 19.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.23), residues: 1123
  helix:  0.43 (0.20), residues: 590
  sheet:  0.35 (0.58), residues: 71
  loop : -0.89 (0.27), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A  71 
 TYR   0.018   0.002   TYR A 347 
 PHE   0.019   0.002   PHE A1276 
 TRP   0.009   0.002   TRP A 476 
 HIS   0.008   0.002   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00515 (12904)
  covalent geometry    : angle       0.68105 (18081)
  hydrogen bonds       : bond        0.05710 (  584)
  hydrogen bonds       : angle       4.82090 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   90 MET cc_start: 0.9080 (tpt) cc_final: 0.8869 (tpp)
REVERT: A  271 TYR cc_start: 0.9331 (t80) cc_final: 0.9012 (t80)
REVERT: A  399 LEU cc_start: 0.9836 (pp) cc_final: 0.9600 (tt)
REVERT: A  415 HIS cc_start: 0.9419 (m-70) cc_final: 0.9015 (m90)
REVERT: A  498 PHE cc_start: 0.9231 (m-80) cc_final: 0.8983 (m-80)
REVERT: A  515 TYR cc_start: 0.9343 (t80) cc_final: 0.9043 (t80)
REVERT: A  534 MET cc_start: 0.5731 (ttt) cc_final: 0.5344 (ttt)
REVERT: A  631 MET cc_start: 0.9655 (ptp) cc_final: 0.9446 (ptp)
REVERT: A  943 TYR cc_start: 0.9361 (p90) cc_final: 0.9107 (p90)
REVERT: A 1126 TRP cc_start: 0.9148 (m-10) cc_final: 0.8868 (m-10)
REVERT: A 1170 GLU cc_start: 0.9056 (tp30) cc_final: 0.8536 (tp30)
REVERT: A 1171 ARG cc_start: 0.9618 (ttt180) cc_final: 0.9334 (ttm170)
REVERT: A 1213 MET cc_start: 0.9322 (mmm) cc_final: 0.8972 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1020
  time to fit residues: 12.8189
Evaluate side-chains
  65 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 29 optimal weight:   20.0000
   chunk 36 optimal weight:    9.9990
   chunk 115 optimal weight:   10.0000
   chunk 81 optimal weight:    0.7980
   chunk 124 optimal weight:   20.0000
   chunk 110 optimal weight:    8.9990
   chunk 26 optimal weight:   40.0000
   chunk 119 optimal weight:   20.0000
   chunk 64 optimal weight:   10.0000
   chunk 42 optimal weight:    8.9990
   chunk 43 optimal weight:    8.9990
   overall best weight:    7.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 420 HIS
A 497 ASN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 933 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.040424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2727 r_free = 0.2727 target = 0.029203 restraints weight = 133216.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2755 r_free = 0.2755 target = 0.030050 restraints weight = 80470.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.030602 restraints weight = 57764.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2783 r_free = 0.2783 target = 0.030849 restraints weight = 46386.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2791 r_free = 0.2791 target = 0.031115 restraints weight = 41082.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.2742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.8303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  12904  Z= 0.228
  Angle     :  0.623   7.447  18081  Z= 0.342
  Chirality :  0.039   0.178   2088
  Planarity :  0.004   0.050   1762
  Dihedral  : 19.955 166.634   3276
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 18.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.25 %
    Favored  : 94.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.24), residues: 1123
  helix:  0.58 (0.20), residues: 587
  sheet:  0.24 (0.60), residues: 71
  loop : -0.95 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 653 
 TYR   0.014   0.002   TYR A 347 
 PHE   0.021   0.002   PHE A1204 
 TRP   0.007   0.001   TRP A 464 
 HIS   0.007   0.002   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 (12904)
  covalent geometry    : angle       0.62318 (18081)
  hydrogen bonds       : bond        0.05109 (  584)
  hydrogen bonds       : angle       4.70397 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 TYR cc_start: 0.9304 (t80) cc_final: 0.8873 (t80)
REVERT: A  415 HIS cc_start: 0.9436 (m-70) cc_final: 0.9022 (m90)
REVERT: A  515 TYR cc_start: 0.9380 (t80) cc_final: 0.9073 (t80)
REVERT: A  518 PHE cc_start: 0.9584 (t80) cc_final: 0.9280 (t80)
REVERT: A  534 MET cc_start: 0.5687 (ttt) cc_final: 0.5282 (ttt)
REVERT: A  631 MET cc_start: 0.9671 (ptp) cc_final: 0.9470 (ptp)
REVERT: A  943 TYR cc_start: 0.9360 (p90) cc_final: 0.9098 (p90)
REVERT: A 1170 GLU cc_start: 0.9031 (tp30) cc_final: 0.8488 (tp30)
REVERT: A 1171 ARG cc_start: 0.9627 (ttt180) cc_final: 0.9333 (ttm170)
REVERT: A 1204 PHE cc_start: 0.9372 (m-80) cc_final: 0.8944 (m-80)
REVERT: A 1213 MET cc_start: 0.9373 (mmm) cc_final: 0.8776 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.0952
  time to fit residues: 11.6368
Evaluate side-chains
  57 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 47 optimal weight:    9.9990
   chunk 66 optimal weight:    9.9990
   chunk 102 optimal weight:   10.0000
   chunk 0 optimal weight:   30.0000
   chunk 23 optimal weight:   10.0000
   chunk 15 optimal weight:   10.0000
   chunk 41 optimal weight:    5.9990
   chunk 61 optimal weight:    5.9990
   chunk 88 optimal weight:   20.0000
   chunk 19 optimal weight:    5.9990
   chunk 98 optimal weight:    7.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 990 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.040092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2722 r_free = 0.2722 target = 0.029027 restraints weight = 134876.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2752 r_free = 0.2752 target = 0.029883 restraints weight = 81164.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2770 r_free = 0.2770 target = 0.030414 restraints weight = 58126.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2781 r_free = 0.2781 target = 0.030745 restraints weight = 46855.909|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.030981 restraints weight = 40902.852|
|-----------------------------------------------------------------------------|
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.8714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12904  Z= 0.223
  Angle     :  0.624   8.357  18081  Z= 0.341
  Chirality :  0.039   0.170   2088
  Planarity :  0.004   0.046   1762
  Dihedral  : 20.016 172.106   3276
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.79 %
    Favored  : 94.21 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.22 (0.24), residues: 1123
  helix:  0.57 (0.20), residues: 579
  sheet: -0.36 (0.55), residues: 90
  loop : -0.94 (0.28), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 653 
 TYR   0.014   0.002   TYR A1237 
 PHE   0.018   0.002   PHE A1276 
 TRP   0.010   0.001   TRP A 659 
 HIS   0.006   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (12904)
  covalent geometry    : angle       0.62371 (18081)
  hydrogen bonds       : bond        0.05139 (  584)
  hydrogen bonds       : angle       4.70965 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.316 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 TYR cc_start: 0.9266 (t80) cc_final: 0.8831 (t80)
REVERT: A  371 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9121 (mt-10)
REVERT: A  415 HIS cc_start: 0.9418 (m-70) cc_final: 0.9029 (m90)
REVERT: A  513 LEU cc_start: 0.9351 (mt) cc_final: 0.8917 (pp)
REVERT: A  515 TYR cc_start: 0.9436 (t80) cc_final: 0.9169 (t80)
REVERT: A  518 PHE cc_start: 0.9548 (t80) cc_final: 0.9247 (t80)
REVERT: A  534 MET cc_start: 0.5439 (ttt) cc_final: 0.5045 (ttt)
REVERT: A  943 TYR cc_start: 0.9340 (p90) cc_final: 0.9079 (p90)
REVERT: A 1171 ARG cc_start: 0.9511 (ttt180) cc_final: 0.9249 (ttm170)
REVERT: A 1204 PHE cc_start: 0.9352 (m-80) cc_final: 0.8938 (m-10)
REVERT: A 1213 MET cc_start: 0.9357 (mmm) cc_final: 0.8827 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1112
  time to fit residues: 13.2534
Evaluate side-chains
  61 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 61
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 33 optimal weight:   30.0000
   chunk 84 optimal weight:    6.9990
   chunk 78 optimal weight:    4.9990
   chunk 61 optimal weight:   10.0000
   chunk 77 optimal weight:   20.0000
   chunk 116 optimal weight:   30.0000
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 105 optimal weight:   10.0000
   chunk 121 optimal weight:   20.0000
   chunk 67 optimal weight:   20.0000
   overall best weight:    4.8990

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN
A 394 ASN
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 990 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.040792 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2746 r_free = 0.2746 target = 0.029582 restraints weight = 133180.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2776 r_free = 0.2776 target = 0.030461 restraints weight = 79558.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.031006 restraints weight = 56904.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.031364 restraints weight = 46014.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2813 r_free = 0.2813 target = 0.031605 restraints weight = 39775.594|
|-----------------------------------------------------------------------------|
r_work (final): 0.2761
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.8828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  12904  Z= 0.166
  Angle     :  0.559   8.494  18081  Z= 0.305
  Chirality :  0.037   0.167   2088
  Planarity :  0.004   0.050   1762
  Dihedral  : 19.940 176.518   3276
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 13.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.18 (0.24), residues: 1123
  helix:  0.95 (0.21), residues: 579
  sheet: -0.29 (0.55), residues: 90
  loop : -0.81 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1303 
 TYR   0.026   0.002   TYR A 517 
 PHE   0.024   0.001   PHE A1276 
 TRP   0.008   0.001   TRP A 659 
 HIS   0.005   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 (12904)
  covalent geometry    : angle       0.55894 (18081)
  hydrogen bonds       : bond        0.04269 (  584)
  hydrogen bonds       : angle       4.51351 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 TYR cc_start: 0.9214 (t80) cc_final: 0.8811 (t80)
REVERT: A  371 GLU cc_start: 0.9398 (mt-10) cc_final: 0.9161 (mt-10)
REVERT: A  415 HIS cc_start: 0.9404 (m-70) cc_final: 0.9025 (m90)
REVERT: A  513 LEU cc_start: 0.9336 (mt) cc_final: 0.9125 (mt)
REVERT: A  517 TYR cc_start: 0.8934 (m-80) cc_final: 0.8583 (m-80)
REVERT: A  518 PHE cc_start: 0.9617 (t80) cc_final: 0.9351 (t80)
REVERT: A  534 MET cc_start: 0.5355 (ttt) cc_final: 0.4954 (ttt)
REVERT: A  648 MET cc_start: 0.9433 (mtm) cc_final: 0.9057 (mpp)
REVERT: A  943 TYR cc_start: 0.9378 (p90) cc_final: 0.9108 (p90)
REVERT: A 1204 PHE cc_start: 0.9387 (m-80) cc_final: 0.8984 (m-10)
REVERT: A 1213 MET cc_start: 0.9412 (mmm) cc_final: 0.8904 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1007
  time to fit residues: 12.0301
Evaluate side-chains
  57 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 46 optimal weight:   10.0000
   chunk 70 optimal weight:   30.0000
   chunk 109 optimal weight:    6.9990
   chunk 59 optimal weight:   20.0000
   chunk 12 optimal weight:    9.9990
   chunk 20 optimal weight:    3.9990
   chunk 29 optimal weight:   50.0000
   chunk 50 optimal weight:   10.0000
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:    9.9990
   chunk 37 optimal weight:    7.9990
   overall best weight:    7.1990

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

Flipped N/Q/H residues before XYZ refinement:
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.039659 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2713 r_free = 0.2713 target = 0.028551 restraints weight = 136855.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2741 r_free = 0.2741 target = 0.029370 restraints weight = 82463.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2759 r_free = 0.2759 target = 0.029877 restraints weight = 59448.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2772 r_free = 0.2772 target = 0.030254 restraints weight = 48101.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.030476 restraints weight = 41574.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.2730
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.9330

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12904  Z= 0.225
  Angle     :  0.623   9.038  18081  Z= 0.340
  Chirality :  0.039   0.169   2088
  Planarity :  0.004   0.046   1762
  Dihedral  : 20.156 179.725   3276
  Min Nonbonded Distance : 2.319

Molprobity Statistics.
  All-atom Clashscore : 18.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.24), residues: 1123
  helix:  0.62 (0.20), residues: 583
  sheet:  0.06 (0.64), residues: 61
  loop : -1.01 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 653 
 TYR   0.028   0.002   TYR A 517 
 PHE   0.022   0.002   PHE A1276 
 TRP   0.008   0.002   TRP A 659 
 HIS   0.010   0.001   HIS A 698 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 (12904)
  covalent geometry    : angle       0.62288 (18081)
  hydrogen bonds       : bond        0.05102 (  584)
  hydrogen bonds       : angle       4.70752 ( 1559)

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

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

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2246 Ramachandran restraints generated.
    1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.435 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  271 TYR cc_start: 0.9158 (t80) cc_final: 0.8842 (t80)
REVERT: A  371 GLU cc_start: 0.9395 (mt-10) cc_final: 0.9159 (mt-10)
REVERT: A  415 HIS cc_start: 0.9414 (m-70) cc_final: 0.9000 (m90)
REVERT: A  517 TYR cc_start: 0.8919 (m-80) cc_final: 0.8662 (m-80)
REVERT: A  518 PHE cc_start: 0.9580 (t80) cc_final: 0.9270 (t80)
REVERT: A  534 MET cc_start: 0.5439 (ttt) cc_final: 0.5082 (ttt)
REVERT: A  648 MET cc_start: 0.9371 (mtm) cc_final: 0.9157 (ptp)
REVERT: A  943 TYR cc_start: 0.9376 (p90) cc_final: 0.9116 (p90)
REVERT: A 1135 ASP cc_start: 0.9387 (m-30) cc_final: 0.9187 (t70)
REVERT: A 1204 PHE cc_start: 0.9328 (m-80) cc_final: 0.8906 (m-10)
REVERT: A 1213 MET cc_start: 0.9379 (mmm) cc_final: 0.8964 (tpp)
REVERT: A 1271 GLU cc_start: 0.9743 (tt0) cc_final: 0.9468 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.1100
  time to fit residues: 12.7430
Evaluate side-chains
  58 residues out of total 1009 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.354 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 61 optimal weight:    3.9990
   chunk 85 optimal weight:   30.0000
   chunk 76 optimal weight:   20.0000
   chunk 121 optimal weight:   20.0000
   chunk 16 optimal weight:    6.9990
   chunk 27 optimal weight:    8.9990
   chunk 88 optimal weight:   20.0000
   chunk 119 optimal weight:   20.0000
   chunk 32 optimal weight:    9.9990
   chunk 18 optimal weight:    6.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 723 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 990 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.040025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2719 r_free = 0.2719 target = 0.028818 restraints weight = 133045.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2748 r_free = 0.2748 target = 0.029650 restraints weight = 80394.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2767 r_free = 0.2767 target = 0.030183 restraints weight = 57972.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.2778 r_free = 0.2778 target = 0.030542 restraints weight = 46847.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2784 r_free = 0.2784 target = 0.030704 restraints weight = 40660.922|
|-----------------------------------------------------------------------------|
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.9484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12904  Z= 0.176
  Angle     :  0.562   9.315  18081  Z= 0.306
  Chirality :  0.037   0.168   2088
  Planarity :  0.004   0.047   1762
  Dihedral  : 20.051 176.924   3276
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 14.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.40 %
    Favored  : 99.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.08 (0.24), residues: 1123
  helix:  0.92 (0.21), residues: 585
  sheet: -0.63 (0.56), residues: 87
  loop : -0.89 (0.29), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 467 
 TYR   0.023   0.002   TYR A 517 
 PHE   0.023   0.002   PHE A1276 
 TRP   0.006   0.001   TRP A 659 
 HIS   0.004   0.001   HIS A 930 

Details of bonding type rmsd
  covalent geometry    : bond        0.00353 (12904)
  covalent geometry    : angle       0.56222 (18081)
  hydrogen bonds       : bond        0.04339 (  584)
  hydrogen bonds       : angle       4.50098 ( 1559)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2067.10 seconds
wall clock time: 36 minutes 43.91 seconds (2203.91 seconds total)