Starting phenix.real_space_refine
on Wed Jul 30 13:51:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7s4v_24835/07_2025/7s4v_24835.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7s4v_24835/07_2025/7s4v_24835.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2025/7s4v_24835.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2025/7s4v_24835.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2025/7s4v_24835.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7s4v_24835/07_2025/7s4v_24835.cif"
  }
  resolution = 3.28
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.015
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     141      5.49       5
     S      18      5.16       5
     C    7249      2.51       5
     N    2149      2.21       5
     O    2658      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 12215
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 9167
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1122, 9167
          Classifications: {'peptide': 1122}
          Link IDs: {'PTRANS': 30, 'TRANS': 1091}
          Chain breaks: 5
    Chain: "B"
      Number of atoms: 2100
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 2100
          Classifications: {'RNA': 98}
          Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 52, 'rna3p_pyr': 33}
          Link IDs: {'rna2p': 13, 'rna3p': 84}
    Chain: "C"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 33, 665
          Classifications: {'DNA': 33}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 32}
    Chain: "D"
      Number of atoms: 283
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 283
          Inner-chain residues flagged as termini: ['pdbres=" DC D  30 "']
          Classifications: {'DNA': 14}
          Modifications used: {'5*END': 2}
          Link IDs: {'rna3p': 13}
  Time building chain proxies: 7.65, per 1000 atoms: 0.63
  Number of scatterers: 12215
  At special positions: 0
  Unit cell: (88, 143, 129.8, 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     141     15.00
     O    2658      8.00
     N    2149      7.00
     C    7249      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.92
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2140

  Finding SS restraints...
    Secondary structure from input PDB file:
      59 helices and 7 sheets defined
      54.2% alpha, 8.2% beta
      22 base pairs and 73 stacking pairs defined.
    Time for finding SS restraints: 3.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 59 through 94
      removed outlier: 3.673A  pdb=" N   ARG A  63 " --> pdb=" O   ALA A  59 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ARG A  74 " --> pdb=" O   ARG A  70 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ARG A  75 " --> pdb=" O   ARG A  71 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LYS A  76 " --> pdb=" O   TYR A  72 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASN A  77 " --> pdb=" O   THR A  73 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   LEU A  82 " --> pdb=" O   ARG A  78 " (cutoff:3.500A)
      removed outlier: 5.504A  pdb=" N   ASN A  88 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   GLU A  89 " --> pdb=" O   ILE A  85 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LYS A  92 " --> pdb=" O   ASN A  88 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   VAL A  93 " --> pdb=" O   GLU A  89 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ASP A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 96 through 104
    Processing helix  chain 'A' and resid 122 through 132
    Processing helix  chain 'A' and resid 134 through 145
      removed outlier: 4.059A  pdb=" N   LEU A 138 " --> pdb=" O   THR A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 164
    Processing helix  chain 'A' and resid 175 through 180
    Processing helix  chain 'A' and resid 181 through 183
      No H-bonds generated for 'chain 'A' and resid 181 through 183'
    Processing helix  chain 'A' and resid 184 through 196
    Processing helix  chain 'A' and resid 207 through 214
    Processing helix  chain 'A' and resid 217 through 229
      removed outlier: 3.928A  pdb=" N   GLU A 223 " --> pdb=" O   SER A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
      removed outlier: 3.571A  pdb=" N   PHE A 238 " --> pdb=" O   LYS A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 240 through 246
    Processing helix  chain 'A' and resid 270 through 275
    Processing helix  chain 'A' and resid 275 through 280
      removed outlier: 4.185A  pdb=" N   ALA A 280 " --> pdb=" O   ASP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
      removed outlier: 3.949A  pdb=" N   LYS A 294 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ASN A 295 " --> pdb=" O   LEU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 343
      removed outlier: 3.548A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 352
      removed outlier: 3.627A  pdb=" N   PHE A 352 " --> pdb=" O   LYS A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 364
    Processing helix  chain 'A' and resid 368 through 382
      Proline residue:  A 378  - end of helix
      removed outlier: 3.919A  pdb=" N   LYS A 382 " --> pdb=" O   PRO A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 394
      removed outlier: 3.500A  pdb=" N   ASN A 394 " --> pdb=" O   LEU A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 410
      removed outlier: 3.645A  pdb=" N   ASN A 407 " --> pdb=" O   THR A 404 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   SER A 409 " --> pdb=" O   ASP A 406 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE A 410 " --> pdb=" O   ASN A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 427
      removed outlier: 4.164A  pdb=" N   HIS A 415 " --> pdb=" O   PRO A 411 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY A 417 " --> pdb=" O   GLN A 413 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   GLN A 426 " --> pdb=" O   ILE A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 430 through 436
      removed outlier: 3.960A  pdb=" N   LYS A 434 " --> pdb=" O   TYR A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 445
      removed outlier: 3.649A  pdb=" N   ILE A 440 " --> pdb=" O   ASN A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 477 through 481
      removed outlier: 3.552A  pdb=" N   GLU A 480 " --> pdb=" O   ASN A 477 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 494
      removed outlier: 3.862A  pdb=" N   ILE A 492 " --> pdb=" O   ALA A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 512 through 525
    Processing helix  chain 'A' and resid 541 through 553
      removed outlier: 3.906A  pdb=" N   ASP A 550 " --> pdb=" O   LYS A 546 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 567
      removed outlier: 3.554A  pdb=" N   LEU A 564 " --> pdb=" O   THR A 560 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 568 through 572
      removed outlier: 4.053A  pdb=" N   LYS A 571 " --> pdb=" O   TYR A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 576
      removed outlier: 4.299A  pdb=" N   ASP A 576 " --> pdb=" O   GLU A 573 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 573 through 576'
    Processing helix  chain 'A' and resid 591 through 602
    Processing helix  chain 'A' and resid 604 through 609
    Processing helix  chain 'A' and resid 612 through 626
      removed outlier: 3.989A  pdb=" N   LEU A 621 " --> pdb=" O   GLU A 617 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU A 623 " --> pdb=" O   ILE A 619 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 637
    Processing helix  chain 'A' and resid 638 through 643
      removed outlier: 4.928A  pdb=" N   HIS A 641 " --> pdb=" O   THR A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 652
    Processing helix  chain 'A' and resid 663 through 668
      removed outlier: 3.814A  pdb=" N   ILE A 667 " --> pdb=" O   SER A 663 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 678 through 686
    Processing helix  chain 'A' and resid 692 through 698
    Processing helix  chain 'A' and resid 705 through 712
      removed outlier: 3.547A  pdb=" N   GLN A 709 " --> pdb=" O   LYS A 705 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 720 through 725
    Processing helix  chain 'A' and resid 730 through 751
      removed outlier: 3.579A  pdb=" N   LYS A 734 " --> pdb=" O   SER A 730 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   LYS A 742 " --> pdb=" O   LEU A 738 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   MET A 751 " --> pdb=" O   LEU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 926 through 940
    Processing helix  chain 'A' and resid 960 through 970
      removed outlier: 3.603A  pdb=" N   SER A 964 " --> pdb=" O   SER A 960 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A 970 " --> pdb=" O   PHE A 966 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 981 through 998
    Processing helix  chain 'A' and resid 1079 through 1088
      removed outlier: 4.028A  pdb=" N   VAL A1083 " --> pdb=" O   ASP A1079 " (cutoff:3.500A)
    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 1184
    Processing helix  chain 'A' and resid 1229 through 1240
      removed outlier: 3.627A  pdb=" N   SER A1240 " --> pdb=" O   LEU A1236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1248 through 1251
    Processing helix  chain 'A' and resid 1252 through 1262
      removed outlier: 3.533A  pdb=" N   GLN A1256 " --> pdb=" O   ASN A1252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1264 through 1280
      removed outlier: 4.380A  pdb=" N   GLU A1268 " --> pdb=" O   HIS A1264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1283 through 1296
    Processing helix  chain 'A' and resid 1301 through 1310
    Processing helix  chain 'A' and resid 1311 through 1316
      removed outlier: 3.766A  pdb=" N   THR A1314 " --> pdb=" O   HIS A1311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1339 through 1343
      removed outlier: 3.940A  pdb=" N   VAL A1342 " --> pdb=" O   THR A1339 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU A1343 " --> pdb=" O   LYS A1340 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1339 through 1343'
    Processing helix  chain 'A' and resid 1363 through 1365
      No H-bonds generated for 'chain 'A' and resid 1363 through 1365'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 956 through 957
      removed outlier: 6.144A  pdb=" N   ILE A 759 " --> pdb=" O   ILE A 956 " (cutoff:3.500A)
      removed outlier: 3.615A  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 32
    Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.114A  pdb=" N   LEU A  35 " --> pdb=" O   ARG A1359 " (cutoff:3.500A)
      removed outlier: 7.725A  pdb=" N   ASP A1361 " --> pdb=" O   LEU A  35 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   LEU A1203 " --> pdb=" O   ILE A1348 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ARG A1210 " --> pdb=" O   LEU A1206 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   GLU A1219 " --> pdb=" O   ALA A1215 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 530 through 531
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1162
      removed outlier: 3.648A  pdb=" N   LYS A1156 " --> pdb=" O   LYS A1151 " (cutoff:3.500A)
      removed outlier: 7.210A  pdb=" N   ILE A1166 " --> pdb=" O   ALA A1140 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1156 through 1162
      removed outlier: 3.648A  pdb=" N   LYS A1156 " --> pdb=" O   LYS A1151 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ILE A1196 " --> pdb=" O   LEU A1144 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 1324 through 1325
      removed outlier: 3.592A  pdb=" N   PHE A1324 " --> pdb=" O   ILE A1331 " (cutoff:3.500A)

    380 hydrogen bonds defined for protein.
    1101 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      57 hydrogen bonds
      110 hydrogen bond angles
      0 basepair planarities
      22 basepair parallelities
      73 stacking parallelities
  Total time for adding SS restraints: 5.23

  Time building geometry restraints manager: 3.50 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3053
        1.33 -     1.45: 3123
        1.45 -     1.58: 6250
        1.58 -     1.70: 282
        1.70 -     1.82: 34
  Bond restraints: 12742
  Sorted by residual:
  bond pdb=" CB  PRO A 503 "
       pdb=" CG  PRO A 503 "
    ideal  model  delta    sigma   weight residual
    1.492  1.563 -0.071 5.00e-02 4.00e+02 1.99e+00
  bond pdb=" CA  MET A 751 "
       pdb=" C   MET A 751 "
    ideal  model  delta    sigma   weight residual
    1.525  1.541 -0.016 1.38e-02 5.25e+03 1.31e+00
  bond pdb=" C3'  DG C  11 "
       pdb=" O3'  DG C  11 "
    ideal  model  delta    sigma   weight residual
    1.422  1.452 -0.030 3.00e-02 1.11e+03 1.00e+00
  bond pdb=" CD  GLU A1260 "
       pdb=" OE1 GLU A1260 "
    ideal  model  delta    sigma   weight residual
    1.249  1.230  0.019 1.90e-02 2.77e+03 9.75e-01
  bond pdb=" C3'  DC D   2 "
       pdb=" O3'  DC D   2 "
    ideal  model  delta    sigma   weight residual
    1.422  1.451 -0.029 3.00e-02 1.11e+03 9.53e-01
  ... (remaining 12737 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 17517
        1.73 -     3.45: 267
        3.45 -     5.18: 36
        5.18 -     6.90: 6
        6.90 -     8.63: 2
  Bond angle restraints: 17828
  Sorted by residual:
  angle pdb=" N   GLU A1260 "
        pdb=" CA  GLU A1260 "
        pdb=" CB  GLU A1260 "
      ideal   model   delta    sigma   weight residual
     110.16  115.21   -5.05 1.48e+00 4.57e-01 1.17e+01
  angle pdb=" N   VAL A 481 "
        pdb=" CA  VAL A 481 "
        pdb=" C   VAL A 481 "
      ideal   model   delta    sigma   weight residual
     111.62  109.03    2.59 7.90e-01 1.60e+00 1.08e+01
  angle pdb=" CA  MET A 751 "
        pdb=" CB  MET A 751 "
        pdb=" CG  MET A 751 "
      ideal   model   delta    sigma   weight residual
     114.10  119.97   -5.87 2.00e+00 2.50e-01 8.61e+00
  angle pdb=" C   MET A 534 "
        pdb=" CA  MET A 534 "
        pdb=" CB  MET A 534 "
      ideal   model   delta    sigma   weight residual
     110.79  115.49   -4.70 1.63e+00 3.76e-01 8.32e+00
  angle pdb=" CB  MET A 694 "
        pdb=" CG  MET A 694 "
        pdb=" SD  MET A 694 "
      ideal   model   delta    sigma   weight residual
     112.70  121.33   -8.63 3.00e+00 1.11e-01 8.27e+00
  ... (remaining 17823 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.01: 7237
       35.01 -    70.03: 436
       70.03 -   105.04: 29
      105.04 -   140.06: 1
      140.06 -   175.07: 7
  Dihedral angle restraints: 7710
    sinusoidal: 4411
      harmonic: 3299
  Sorted by residual:
  dihedral pdb=" O4'   C B  70 "
           pdb=" C1'   C B  70 "
           pdb=" N1    C B  70 "
           pdb=" C2    C B  70 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   54.05  145.95     1      1.50e+01 4.44e-03 7.80e+01
  dihedral pdb=" CA  LEU A 258 "
           pdb=" C   LEU A 258 "
           pdb=" N   ALA A 259 "
           pdb=" CA  ALA A 259 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.00   28.00     0      5.00e+00 4.00e-02 3.14e+01
  dihedral pdb=" C4'  DC D   2 "
           pdb=" C3'  DC D   2 "
           pdb=" O3'  DC D   2 "
           pdb=" P    DT D   3 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -140.00   35.07 -175.07     1      3.50e+01 8.16e-04 1.56e+01
  ... (remaining 7707 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 1649
       0.043 -    0.086: 343
       0.086 -    0.129: 57
       0.129 -    0.173: 10
       0.173 -    0.216: 2
  Chirality restraints: 2061
  Sorted by residual:
  chirality pdb=" CB  VAL A1259 "
            pdb=" CA  VAL A1259 "
            pdb=" CG1 VAL A1259 "
            pdb=" CG2 VAL A1259 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  GLU A1260 "
            pdb=" N   GLU A1260 "
            pdb=" C   GLU A1260 "
            pdb=" CB  GLU A1260 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" C3'   A B  38 "
            pdb=" C4'   A B  38 "
            pdb=" O3'   A B  38 "
            pdb=" C2'   A B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.31   -0.17 2.00e-01 2.50e+01 7.18e-01
  ... (remaining 2058 not shown)

  Planarity restraints: 1745
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 343 "   -0.044 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO A 344 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 344 "   -0.035 5.00e-02 4.00e+02
        pdb=" CD  PRO A 344 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B  69 "    0.031 2.00e-02 2.50e+03   1.43e-02 5.65e+00
        pdb=" N9    A B  69 "   -0.035 2.00e-02 2.50e+03
        pdb=" C8    A B  69 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    A B  69 "    0.001 2.00e-02 2.50e+03
        pdb=" C5    A B  69 "   -0.000 2.00e-02 2.50e+03
        pdb=" C6    A B  69 "    0.004 2.00e-02 2.50e+03
        pdb=" N6    A B  69 "    0.008 2.00e-02 2.50e+03
        pdb=" N1    A B  69 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    A B  69 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A B  69 "   -0.005 2.00e-02 2.50e+03
        pdb=" C4    A B  69 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 502 "   -0.030 5.00e-02 4.00e+02   4.51e-02 3.26e+00
        pdb=" N   PRO A 503 "    0.078 5.00e-02 4.00e+02
        pdb=" CA  PRO A 503 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 503 "   -0.025 5.00e-02 4.00e+02
  ... (remaining 1742 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1082
        2.74 -     3.28: 11247
        3.28 -     3.82: 19240
        3.82 -     4.36: 23326
        4.36 -     4.90: 37704
  Nonbonded interactions: 92599
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 515 "
            pdb=" OP1   C B   5 "
     model   vdw
     2.202 3.040
  nonbonded pdb=" OH  TYR A   5 "
            pdb=" O   HIS A 754 "
     model   vdw
     2.253 3.040
  nonbonded pdb=" N2    G B  73 "
            pdb=" OP2   A B  76 "
     model   vdw
     2.271 3.120
  nonbonded pdb=" OG  SER A 541 "
            pdb=" OE2 GLU A 543 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   GLY A 533 "
            pdb=" NH1 ARG A 535 "
     model   vdw
     2.309 3.120
  ... (remaining 92594 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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.470
  Check model and map are aligned:         0.070
  Set scattering table:                    0.110
  Process input model:                     32.530
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.760
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
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      :  0.003   0.071  12742  Z= 0.126
  Angle     :  0.537   8.627  17828  Z= 0.290
  Chirality :  0.037   0.216   2061
  Planarity :  0.004   0.067   1745
  Dihedral  : 19.694 175.071   5570
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.24), residues: 1110
  helix: -0.28 (0.23), residues: 518
  sheet: -0.79 (0.55), residues: 101
  loop : -1.71 (0.26), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A1262 
 PHE   0.010   0.001   PHE A  97 
 TYR   0.013   0.001   TYR A 325 
 ARG   0.007   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19746 (  430)
  hydrogen bonds       : angle       7.12044 ( 1211)
  covalent geometry    : bond        0.00268 (12742)
  covalent geometry    : angle       0.53670 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  540 LEU cc_start: 0.6211 (tp) cc_final: 0.5895 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.3161
  time to fit residues: 35.2045
Evaluate side-chains
  43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 105 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 63 optimal weight:    8.9990
   chunk 50 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0970
   chunk 59 optimal weight:    2.9990
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:    3.9990
   overall best weight:    1.5784

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

Flipped N/Q/H residues before XYZ refinement:
A 342 GLN
A 721 HIS
A1256 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.097800 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.068728 restraints weight = 31373.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 2.49
r_work: 0.2910 rms_B_bonded: 3.91 restraints_weight: 0.5000
r_work (final): 0.2910
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8513
moved from start:          0.2155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  12742  Z= 0.225
  Angle     :  0.623   9.056  17828  Z= 0.331
  Chirality :  0.040   0.204   2061
  Planarity :  0.004   0.041   1745
  Dihedral  : 20.780 176.262   3192
  Min Nonbonded Distance : 2.242

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  8.65 %
    Favored  : 90.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.24), residues: 1110
  helix:  0.07 (0.22), residues: 535
  sheet: -0.97 (0.52), residues: 107
  loop : -1.66 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 476 
 HIS   0.009   0.002   HIS A 167 
 PHE   0.020   0.002   PHE A  97 
 TYR   0.019   0.002   TYR A 325 
 ARG   0.006   0.001   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06605 (  430)
  hydrogen bonds       : angle       4.67992 ( 1211)
  covalent geometry    : bond        0.00523 (12742)
  covalent geometry    : angle       0.62310 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 42
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8663 (mmt) cc_final: 0.8292 (mmm)
  outliers start: 4
  outliers final: 4
  residues processed: 45
  average time/residue: 0.2953
  time to fit residues: 19.3660
Evaluate side-chains
  37 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  651 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 23 optimal weight:    8.9990
   chunk 62 optimal weight:    1.9990
   chunk 105 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 11 optimal weight:    1.9990
   chunk 87 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 29 optimal weight:    7.9990
   chunk 103 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   overall best weight:    1.2384

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.097571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.067797 restraints weight = 31321.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3114 rms_B_bonded: 2.53
r_work: 0.2851 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.2851
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8547
moved from start:          0.2555

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030  12742  Z= 0.181
  Angle     :  0.544   7.847  17828  Z= 0.292
  Chirality :  0.038   0.206   2061
  Planarity :  0.003   0.044   1745
  Dihedral  : 20.749 176.062   3192
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.80 %
    Allowed  : 11.23 %
    Favored  : 87.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.24), residues: 1110
  helix:  0.38 (0.23), residues: 536
  sheet: -1.08 (0.51), residues: 108
  loop : -1.66 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 476 
 HIS   0.007   0.001   HIS A 167 
 PHE   0.022   0.001   PHE A 643 
 TYR   0.016   0.001   TYR A 325 
 ARG   0.004   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05742 (  430)
  hydrogen bonds       : angle       4.39180 ( 1211)
  covalent geometry    : bond        0.00411 (12742)
  covalent geometry    : angle       0.54396 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  45 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 37
  time to evaluate  : 1.107 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8651 (mmt) cc_final: 0.8270 (mmm)
REVERT: A 1261 GLN cc_start: 0.8124 (tm-30) cc_final: 0.7921 (tm-30)
REVERT: A 1307 GLU cc_start: 0.8725 (tp30) cc_final: 0.8387 (tp30)
  outliers start: 8
  outliers final: 4
  residues processed: 42
  average time/residue: 0.2311
  time to fit residues: 15.4532
Evaluate side-chains
  37 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 117 optimal weight:    3.9990
   chunk 120 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 115 optimal weight:    6.9990
   chunk 87 optimal weight:    3.9990
   chunk 6 optimal weight:    0.9980
   chunk 57 optimal weight:    9.9990
   chunk 15 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 70 optimal weight:    7.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
A  46 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.096258 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.066572 restraints weight = 30971.625|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.37
r_work: 0.2831 rms_B_bonded: 3.84 restraints_weight: 0.5000
r_work (final): 0.2831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.3072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036  12742  Z= 0.219
  Angle     :  0.585   8.025  17828  Z= 0.313
  Chirality :  0.039   0.208   2061
  Planarity :  0.004   0.046   1745
  Dihedral  : 20.907 176.339   3192
  Min Nonbonded Distance : 2.247

Molprobity Statistics.
  All-atom Clashscore : 3.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.50 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.32 %
    Favored  : 84.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.24), residues: 1110
  helix:  0.32 (0.23), residues: 542
  sheet: -0.95 (0.49), residues: 117
  loop : -1.80 (0.25), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 476 
 HIS   0.008   0.001   HIS A 167 
 PHE   0.014   0.001   PHE A 105 
 TYR   0.018   0.002   TYR A 325 
 ARG   0.004   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06487 (  430)
  hydrogen bonds       : angle       4.44571 ( 1211)
  covalent geometry    : bond        0.00506 (12742)
  covalent geometry    : angle       0.58537 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 34
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  321 MET cc_start: 0.8687 (mmt) cc_final: 0.8293 (mmm)
REVERT: A 1307 GLU cc_start: 0.8693 (tp30) cc_final: 0.8425 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 48
  average time/residue: 0.2766
  time to fit residues: 19.9117
Evaluate side-chains
  42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 32
  time to evaluate  : 1.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 ARG
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  305 ILE
Chi-restraints excluded: chain A residue  647 VAL
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  998 ILE
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 40 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 80 optimal weight:    1.9990
   chunk 118 optimal weight:    3.9990
   chunk 103 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 89 optimal weight:    1.9990
   chunk 49 optimal weight:    0.0030
   overall best weight:    0.7996

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

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.097989 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.068323 restraints weight = 31002.507|
|-----------------------------------------------------------------------------|
r_work (start): 0.3126 rms_B_bonded: 2.44
r_work: 0.2881 rms_B_bonded: 3.87 restraints_weight: 0.5000
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8506
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12742  Z= 0.133
  Angle     :  0.505   8.163  17828  Z= 0.269
  Chirality :  0.036   0.198   2061
  Planarity :  0.003   0.043   1745
  Dihedral  : 20.826 176.506   3192
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 14.61 %
    Favored  : 84.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.25), residues: 1110
  helix:  0.62 (0.23), residues: 544
  sheet: -0.85 (0.49), residues: 117
  loop : -1.73 (0.26), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 167 
 PHE   0.009   0.001   PHE A  97 
 TYR   0.013   0.001   TYR A 325 
 ARG   0.003   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04732 (  430)
  hydrogen bonds       : angle       4.16112 ( 1211)
  covalent geometry    : bond        0.00293 (12742)
  covalent geometry    : angle       0.50531 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 1.134 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8498 (mp0)
REVERT: A  534 MET cc_start: 0.3455 (ppp) cc_final: 0.1236 (ppp)
REVERT: A 1307 GLU cc_start: 0.8625 (tp30) cc_final: 0.8369 (tp30)
  outliers start: 13
  outliers final: 7
  residues processed: 48
  average time/residue: 0.2194
  time to fit residues: 17.0895
Evaluate side-chains
  42 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 34
  time to evaluate  : 1.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1337 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 118 optimal weight:    3.9990
   chunk 2 optimal weight:    0.3980
   chunk 100 optimal weight:    0.0170
   chunk 59 optimal weight:    0.9990
   chunk 90 optimal weight:    0.3980
   chunk 99 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 28 optimal weight:    9.9990
   overall best weight:    0.5420

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

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.099181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.069526 restraints weight = 31325.730|
|-----------------------------------------------------------------------------|
r_work (start): 0.3156 rms_B_bonded: 2.45
r_work: 0.2915 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.2915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8455
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038  12742  Z= 0.110
  Angle     :  0.480   7.631  17828  Z= 0.256
  Chirality :  0.035   0.199   2061
  Planarity :  0.003   0.043   1745
  Dihedral  : 20.741 176.561   3192
  Min Nonbonded Distance : 2.304

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 15.21 %
    Favored  : 83.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.49 (0.25), residues: 1110
  helix:  0.92 (0.24), residues: 533
  sheet: -0.84 (0.49), residues: 118
  loop : -1.69 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 476 
 HIS   0.008   0.001   HIS A1262 
 PHE   0.008   0.001   PHE A1235 
 TYR   0.011   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A  70 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04083 (  430)
  hydrogen bonds       : angle       3.99343 ( 1211)
  covalent geometry    : bond        0.00238 (12742)
  covalent geometry    : angle       0.48026 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 38
  time to evaluate  : 2.043 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 GLU cc_start: 0.8780 (OUTLIER) cc_final: 0.8510 (mp0)
REVERT: A  698 HIS cc_start: 0.7725 (OUTLIER) cc_final: 0.7496 (m170)
REVERT: A 1307 GLU cc_start: 0.8711 (tp30) cc_final: 0.8455 (tp30)
  outliers start: 13
  outliers final: 7
  residues processed: 50
  average time/residue: 0.2883
  time to fit residues: 23.4780
Evaluate side-chains
  44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 35
  time to evaluate  : 1.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 15 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 8 optimal weight:    0.0470
   chunk 52 optimal weight:    7.9990
   chunk 53 optimal weight:    5.9990
   chunk 43 optimal weight:    0.9980
   chunk 69 optimal weight:    6.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.099757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.070637 restraints weight = 31085.929|
|-----------------------------------------------------------------------------|
r_work (start): 0.3186 rms_B_bonded: 2.28
r_work: 0.2966 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.3318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12742  Z= 0.119
  Angle     :  0.485  10.246  17828  Z= 0.257
  Chirality :  0.035   0.198   2061
  Planarity :  0.003   0.043   1745
  Dihedral  : 20.693 176.645   3192
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 3.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 15.51 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.25), residues: 1110
  helix:  0.97 (0.23), residues: 533
  sheet: -0.81 (0.49), residues: 118
  loop : -1.66 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A1262 
 PHE   0.011   0.001   PHE A 432 
 TYR   0.012   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04348 (  430)
  hydrogen bonds       : angle       3.97981 ( 1211)
  covalent geometry    : bond        0.00262 (12742)
  covalent geometry    : angle       0.48537 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 34
  time to evaluate  : 1.205 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8473 (mp0)
REVERT: A  534 MET cc_start: 0.3435 (ppp) cc_final: 0.3125 (tmm)
REVERT: A  698 HIS cc_start: 0.7756 (OUTLIER) cc_final: 0.7534 (m170)
  outliers start: 16
  outliers final: 12
  residues processed: 49
  average time/residue: 0.2264
  time to fit residues: 17.8971
Evaluate side-chains
  45 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 31
  time to evaluate  : 1.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  698 HIS
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1142 SER
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1177 ASN
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 86 optimal weight:    0.0670
   chunk 51 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 14 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   chunk 11 optimal weight:    0.0060
   chunk 6 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    1.9990
   overall best weight:    0.7536

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

Flipped N/Q/H residues before XYZ refinement:
** A1261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.099490 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.070209 restraints weight = 31186.091|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 2.35
r_work: 0.2951 rms_B_bonded: 3.78 restraints_weight: 0.5000
r_work (final): 0.2951
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8502
moved from start:          0.3386

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12742  Z= 0.126
  Angle     :  0.487   8.314  17828  Z= 0.258
  Chirality :  0.035   0.198   2061
  Planarity :  0.003   0.044   1745
  Dihedral  : 20.665 176.682   3192
  Min Nonbonded Distance : 2.282

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.30 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.39 (0.25), residues: 1110
  helix:  1.00 (0.23), residues: 533
  sheet: -0.79 (0.49), residues: 118
  loop : -1.63 (0.26), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.009   0.001   PHE A 491 
 TYR   0.012   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04437 (  430)
  hydrogen bonds       : angle       4.00041 ( 1211)
  covalent geometry    : bond        0.00281 (12742)
  covalent geometry    : angle       0.48656 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 32
  time to evaluate  : 1.163 
Fit side-chains
REVERT: A  441 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8503 (mp0)
REVERT: A  534 MET cc_start: 0.3228 (ppp) cc_final: 0.2854 (tmm)
  outliers start: 14
  outliers final: 11
  residues processed: 45
  average time/residue: 0.2158
  time to fit residues: 15.6875
Evaluate side-chains
  43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 31
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1142 SER
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1337 THR
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 107 optimal weight:    3.9990
   chunk 114 optimal weight:    2.9990
   chunk 120 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   chunk 2 optimal weight:    0.4980
   chunk 15 optimal weight:    0.5980
   chunk 52 optimal weight:    6.9990
   chunk 47 optimal weight:    0.9990
   chunk 60 optimal weight:    3.9990
   chunk 119 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN
** A1262 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.097499 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.068656 restraints weight = 31236.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3151 rms_B_bonded: 2.31
r_work: 0.2905 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2905
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8552
moved from start:          0.3496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  12742  Z= 0.174
  Angle     :  0.538  10.052  17828  Z= 0.284
  Chirality :  0.037   0.203   2061
  Planarity :  0.003   0.046   1745
  Dihedral  : 20.698 176.918   3192
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.50 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.50 (0.25), residues: 1110
  helix:  0.86 (0.23), residues: 529
  sheet: -0.90 (0.49), residues: 118
  loop : -1.57 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 476 
 HIS   0.006   0.001   HIS A 167 
 PHE   0.023   0.001   PHE A 432 
 TYR   0.016   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05546 (  430)
  hydrogen bonds       : angle       4.17706 ( 1211)
  covalent geometry    : bond        0.00399 (12742)
  covalent geometry    : angle       0.53764 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 30
  time to evaluate  : 1.147 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 GLU cc_start: 0.8728 (OUTLIER) cc_final: 0.8513 (mp0)
REVERT: A  534 MET cc_start: 0.3481 (ppp) cc_final: 0.2990 (tmm)
  outliers start: 14
  outliers final: 12
  residues processed: 44
  average time/residue: 0.2197
  time to fit residues: 15.6599
Evaluate side-chains
  43 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 30
  time to evaluate  : 1.132 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1142 SER
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1177 ASN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 80 optimal weight:    0.8980
   chunk 12 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 58 optimal weight:    0.9980
   chunk 116 optimal weight:    3.9990
   chunk 122 optimal weight:    2.9990
   chunk 62 optimal weight:    0.0970
   chunk 112 optimal weight:    9.9990
   chunk 120 optimal weight:    5.9990
   chunk 119 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.098602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.069998 restraints weight = 31074.454|
|-----------------------------------------------------------------------------|
r_work (start): 0.3178 rms_B_bonded: 2.32
r_work: 0.2933 rms_B_bonded: 3.80 restraints_weight: 0.5000
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8490
moved from start:          0.3518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12742  Z= 0.126
  Angle     :  0.499   8.137  17828  Z= 0.265
  Chirality :  0.036   0.198   2061
  Planarity :  0.003   0.044   1745
  Dihedral  : 20.655 176.894   3192
  Min Nonbonded Distance : 2.277

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  1.29 %
    Allowed  : 16.40 %
    Favored  : 82.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.41 (0.25), residues: 1110
  helix:  0.98 (0.23), residues: 528
  sheet: -0.88 (0.49), residues: 118
  loop : -1.58 (0.26), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 476 
 HIS   0.004   0.001   HIS A 167 
 PHE   0.008   0.001   PHE A 491 
 TYR   0.013   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04738 (  430)
  hydrogen bonds       : angle       4.08626 ( 1211)
  covalent geometry    : bond        0.00279 (12742)
  covalent geometry    : angle       0.49857 (17828)

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

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

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2220 Ramachandran restraints generated.
    1110 Oldfield, 0 Emsley, 1110 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 31
  time to evaluate  : 1.158 
Fit side-chains
   revert: symmetry clash
REVERT: A  441 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8492 (mp0)
REVERT: A  534 MET cc_start: 0.3303 (ppp) cc_final: 0.2808 (tmm)
  outliers start: 13
  outliers final: 12
  residues processed: 43
  average time/residue: 0.2340
  time to fit residues: 16.5058
Evaluate side-chains
  44 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 31
  time to evaluate  : 1.224 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  184 LEU
Chi-restraints excluded: chain A residue  296 LEU
Chi-restraints excluded: chain A residue  339 VAL
Chi-restraints excluded: chain A residue  441 GLU
Chi-restraints excluded: chain A residue  552 LEU
Chi-restraints excluded: chain A residue  651 LEU
Chi-restraints excluded: chain A residue  657 THR
Chi-restraints excluded: chain A residue  953 VAL
Chi-restraints excluded: chain A residue 1142 SER
Chi-restraints excluded: chain A residue 1146 VAL
Chi-restraints excluded: chain A residue 1177 ASN
Chi-restraints excluded: chain A residue 1352 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 13 optimal weight:    1.9990
   chunk 106 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 47 optimal weight:    0.0980
   chunk 27 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   chunk 44 optimal weight:    0.7980
   chunk 93 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A1177 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.098385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.069775 restraints weight = 31169.519|
|-----------------------------------------------------------------------------|
r_work (start): 0.3170 rms_B_bonded: 2.34
r_work: 0.2923 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.2923
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12742  Z= 0.145
  Angle     :  0.510  10.472  17828  Z= 0.269
  Chirality :  0.036   0.200   2061
  Planarity :  0.003   0.044   1745
  Dihedral  : 20.639 176.887   3192
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 3.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 16.30 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.25), residues: 1110
  helix:  0.97 (0.23), residues: 529
  sheet: -0.89 (0.49), residues: 118
  loop : -1.60 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 476 
 HIS   0.005   0.001   HIS A 167 
 PHE   0.010   0.001   PHE A 491 
 TYR   0.014   0.001   TYR A 325 
 ARG   0.002   0.000   ARG A 951 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04915 (  430)
  hydrogen bonds       : angle       4.09074 ( 1211)
  covalent geometry    : bond        0.00329 (12742)
  covalent geometry    : angle       0.50987 (17828)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5896.32 seconds
wall clock time: 103 minutes 8.92 seconds (6188.92 seconds total)