Starting phenix.real_space_refine
on Sat Aug 23 13:52:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p1k_17352/08_2025/8p1k_17352.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p1k_17352/08_2025/8p1k_17352.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p1k_17352/08_2025/8p1k_17352.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p1k_17352/08_2025/8p1k_17352.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p1k_17352/08_2025/8p1k_17352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p1k_17352/08_2025/8p1k_17352.map"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    7885      2.51       5
     N    2062      2.21       5
     O    2252      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 12261
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 12261
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1518, 12249
          Classifications: {'peptide': 1518}
          Link IDs: {'PTRANS': 51, 'TRANS': 1466}
          Chain breaks: 5
      Conformer: "B"
        Number of residues, atoms: 1518, 12249
          Classifications: {'peptide': 1518}
          Link IDs: {'PTRANS': 51, 'TRANS': 1466}
          Chain breaks: 5
          bond proxies already assigned to first conformer: 12507
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 662 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR A 662 " occ=0.50
  Time building chain proxies: 4.31, per 1000 atoms: 0.35
  Number of scatterers: 12261
  At special positions: 0
  Unit cell: (86.676, 125.82, 126.752, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      62     16.00
     O    2252      8.00
     N    2062      7.00
     C    7885      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.90
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2900

  Finding SS restraints...
    Secondary structure from input PDB file:
      71 helices and 12 sheets defined
      61.2% alpha, 10.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 1 through 13
      removed outlier: 4.021A  pdb=" N   GLU A  13 " --> pdb=" O   ASN A   9 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 20 through 47
      removed outlier: 3.863A  pdb=" N   VAL A  39 " --> pdb=" O   ARG A  35 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 56 through 65
    Processing helix  chain 'A' and resid 67 through 75
    Processing helix  chain 'A' and resid 87 through 94
      removed outlier: 3.653A  pdb=" N   LYS A  93 " --> pdb=" O   LYS A  89 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   MET A  94 " --> pdb=" O   ALA A  90 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 145
      removed outlier: 5.123A  pdb=" N   ALA A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   GLY A 131 " --> pdb=" O   LYS A 127 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 167 through 172
    Processing helix  chain 'A' and resid 176 through 198
      removed outlier: 3.690A  pdb=" N   VAL A 180 " --> pdb=" O   ARG A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 200 through 214
      removed outlier: 4.359A  pdb=" N   ALA A 205 " --> pdb=" O   THR A 201 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   ALA A 206 " --> pdb=" O   GLU A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 252
      removed outlier: 3.797A  pdb=" N   LEU A 243 " --> pdb=" O   ASN A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 281
      removed outlier: 3.561A  pdb=" N   GLN A 280 " --> pdb=" O   ALA A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 306 through 323
      removed outlier: 3.683A  pdb=" N   ILE A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
      removed outlier: 3.795A  pdb=" N   ASN A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 343
    Processing helix  chain 'A' and resid 345 through 354
      removed outlier: 3.625A  pdb=" N   TYR A 353 " --> pdb=" O   MET A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 391
    Processing helix  chain 'A' and resid 409 through 429
    Processing helix  chain 'A' and resid 449 through 463
      removed outlier: 3.594A  pdb=" N   LYS A 453 " --> pdb=" O   THR A 449 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   PHE A 454 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
      removed outlier: 4.565A  pdb=" N   GLN A 460 " --> pdb=" O   GLN A 456 " (cutoff:3.500A)
      removed outlier: 4.659A  pdb=" N   LYS A 461 " --> pdb=" O   ASN A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 463 through 468
    Processing helix  chain 'A' and resid 470 through 490
      removed outlier: 3.923A  pdb=" N   HIS A 474 " --> pdb=" O   THR A 470 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 572
    Processing helix  chain 'A' and resid 572 through 593
    Processing helix  chain 'A' and resid 597 through 614
    Processing helix  chain 'A' and resid 616 through 634
      removed outlier: 3.975A  pdb=" N   TYR A 628 " --> pdb=" O   ASP A 624 " (cutoff:3.500A)
      Proline residue:  A 631  - end of helix
    Processing helix  chain 'A' and resid 639 through 647
      removed outlier: 3.614A  pdb=" N   LEU A 643 " --> pdb=" O   GLY A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 674
      removed outlier: 3.583A  pdb=" N   VAL A 658 " --> pdb=" O   SER A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 726
      removed outlier: 3.819A  pdb=" N   LEU A 716 " --> pdb=" O   HIS A 712 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   VAL A 720 " --> pdb=" O   LEU A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 727 through 732
      removed outlier: 6.300A  pdb=" N   GLY A 730 " --> pdb=" O   PHE A 727 " (cutoff:3.500A)
      removed outlier: 3.987A  pdb=" N   LEU A 731 " --> pdb=" O   GLU A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 760
      removed outlier: 3.546A  pdb=" N   LYS A 740 " --> pdb=" O   ASN A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 767
    Processing helix  chain 'A' and resid 769 through 777
    Processing helix  chain 'A' and resid 786 through 802
      removed outlier: 3.893A  pdb=" N   VAL A 800 " --> pdb=" O   GLU A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 814
    Processing helix  chain 'A' and resid 820 through 824
      removed outlier: 3.639A  pdb=" N   SER A 823 " --> pdb=" O   PRO A 820 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN A 824 " --> pdb=" O   TYR A 821 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 820 through 824'
    Processing helix  chain 'A' and resid 848 through 859
      removed outlier: 3.515A  pdb=" N   ASN A 858 " --> pdb=" O   ARG A 854 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 864 through 872
    Processing helix  chain 'A' and resid 883 through 887
      removed outlier: 3.842A  pdb=" N   ARG A 887 " --> pdb=" O   LYS A 884 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 898 through 917
    Processing helix  chain 'A' and resid 918 through 920
      No H-bonds generated for 'chain 'A' and resid 918 through 920'
    Processing helix  chain 'A' and resid 927 through 931
      removed outlier: 3.618A  pdb=" N   LYS A 930 " --> pdb=" O   GLY A 927 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 932 through 947
    Processing helix  chain 'A' and resid 983 through 992
      removed outlier: 4.009A  pdb=" N   ARG A 987 " --> pdb=" O   ALA A 983 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   PHE A 988 " --> pdb=" O   LYS A 984 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 999 through 1012
    Processing helix  chain 'A' and resid 1020 through 1030
      removed outlier: 3.577A  pdb=" N   MET A1030 " --> pdb=" O   TYR A1026 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1044
      removed outlier: 3.780A  pdb=" N   PHE A1044 " --> pdb=" O   PHE A1040 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1061 through 1084
    Processing helix  chain 'A' and resid 1114 through 1126
    Processing helix  chain 'A' and resid 1128 through 1133
      removed outlier: 3.732A  pdb=" N   SER A1133 " --> pdb=" O   HIS A1130 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1137 through 1153
      removed outlier: 3.583A  pdb=" N   SER A1141 " --> pdb=" O   GLU A1137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1175
      removed outlier: 3.612A  pdb=" N   THR A1174 " --> pdb=" O   GLU A1170 " (cutoff:3.500A)
      removed outlier: 3.631A  pdb=" N   PHE A1175 " --> pdb=" O   PHE A1171 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1170 through 1175'
    Processing helix  chain 'A' and resid 1184 through 1192
      removed outlier: 4.133A  pdb=" N   ILE A1188 " --> pdb=" O   PRO A1184 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1200 through 1218
    Processing helix  chain 'A' and resid 1221 through 1241
    Processing helix  chain 'A' and resid 1249 through 1253
    Processing helix  chain 'A' and resid 1257 through 1261
      removed outlier: 3.688A  pdb=" N   THR A1261 " --> pdb=" O   HIS A1258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1262 through 1266
    Processing helix  chain 'A' and resid 1272 through 1279
    Processing helix  chain 'A' and resid 1282 through 1300
      removed outlier: 3.738A  pdb=" N   LYS A1286 " --> pdb=" O   GLY A1282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1301 through 1318
    Processing helix  chain 'A' and resid 1354 through 1365
    Processing helix  chain 'A' and resid 1366 through 1370
    Processing helix  chain 'A' and resid 1375 through 1388
    Processing helix  chain 'A' and resid 1389 through 1397
    Processing helix  chain 'A' and resid 1400 through 1409
    Processing helix  chain 'A' and resid 1410 through 1414
      removed outlier: 4.198A  pdb=" N   HIS A1413 " --> pdb=" O   ALA A1410 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET A1414 " --> pdb=" O   LYS A1411 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1410 through 1414'
    Processing helix  chain 'A' and resid 1425 through 1439
    Processing helix  chain 'A' and resid 1443 through 1454
    Processing helix  chain 'A' and resid 1502 through 1512
    Processing helix  chain 'A' and resid 1514 through 1525
    Processing helix  chain 'A' and resid 1531 through 1546
    Processing helix  chain 'A' and resid 1554 through 1568
      Proline residue:  A1561  - end of helix
    Processing helix  chain 'A' and resid 1581 through 1592
    Processing sheet with id=AA1, first strand: chain 'A' and resid 98 through 102
    Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261
    Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261
      removed outlier: 7.692A  pdb=" N   LYS A 958 " --> pdb=" O   LEU A 954 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LEU A 954 " --> pdb=" O   LYS A 958 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 296 through 297
    Processing sheet with id=AA5, first strand: chain 'A' and resid 499 through 503
    Processing sheet with id=AA6, first strand: chain 'A' and resid 499 through 503
    Processing sheet with id=AA7, first strand: chain 'A' and resid 701 through 702
    Processing sheet with id=AA8, first strand: chain 'A' and resid 832 through 837
      removed outlier: 5.626A  pdb=" N   SER A 844 " --> pdb=" O   GLY A 835 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 895 through 897
      removed outlier: 4.165A  pdb=" N   ALA A 877 " --> pdb=" O   LYS A1014 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ILE A 881 " --> pdb=" O   PHE A1018 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1417 through 1419
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1485 through 1486
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1489 through 1491

    713 hydrogen bonds defined for protein.
    2038 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.24

  Time building geometry restraints manager: 1.25 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 3903
        1.34 -     1.46: 2364
        1.46 -     1.58: 6162
        1.58 -     1.70: 0
        1.70 -     1.81: 106
  Bond restraints: 12535
  Sorted by residual:
  bond pdb=" C   GLN A 223 "
       pdb=" N   PRO A 224 "
    ideal  model  delta    sigma   weight residual
    1.331  1.343 -0.012 7.90e-03 1.60e+04 2.17e+00
  bond pdb=" CB  GLN A 413 "
       pdb=" CG  GLN A 413 "
    ideal  model  delta    sigma   weight residual
    1.520  1.486  0.034 3.00e-02 1.11e+03 1.26e+00
  bond pdb=" CA  THR A1454 "
       pdb=" CB  THR A1454 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.50e-02 4.44e+03 1.26e+00
  bond pdb=" CB  MET A 735 "
       pdb=" CG  MET A 735 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.18e+00
  bond pdb=" CG  GLN A 413 "
       pdb=" CD  GLN A 413 "
    ideal  model  delta    sigma   weight residual
    1.516  1.490  0.026 2.50e-02 1.60e+03 1.11e+00
  ... (remaining 12530 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.81: 16862
        2.81 -     5.62: 67
        5.62 -     8.43: 5
        8.43 -    11.24: 3
       11.24 -    14.06: 1
  Bond angle restraints: 16938
  Sorted by residual:
  angle pdb=" CB  MET A 735 "
        pdb=" CG  MET A 735 "
        pdb=" SD  MET A 735 "
      ideal   model   delta    sigma   weight residual
     112.70  126.76  -14.06 3.00e+00 1.11e-01 2.19e+01
  angle pdb=" CB  MET A 349 "
        pdb=" CG  MET A 349 "
        pdb=" SD  MET A 349 "
      ideal   model   delta    sigma   weight residual
     112.70  122.38   -9.68 3.00e+00 1.11e-01 1.04e+01
  angle pdb=" CB  MET A1447 "
        pdb=" CG  MET A1447 "
        pdb=" SD  MET A1447 "
      ideal   model   delta    sigma   weight residual
     112.70  121.75   -9.05 3.00e+00 1.11e-01 9.11e+00
  angle pdb=" CA  ARG A  30 "
        pdb=" CB  ARG A  30 "
        pdb=" CG  ARG A  30 "
      ideal   model   delta    sigma   weight residual
     114.10  120.06   -5.96 2.00e+00 2.50e-01 8.89e+00
  angle pdb=" CG1 ILE A1333 "
        pdb=" CB  ILE A1333 "
        pdb=" CG2 ILE A1333 "
      ideal   model   delta    sigma   weight residual
     110.70  102.01    8.69 3.00e+00 1.11e-01 8.38e+00
  ... (remaining 16933 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.32: 6918
       17.32 -    34.63: 528
       34.63 -    51.95: 85
       51.95 -    69.26: 10
       69.26 -    86.58: 7
  Dihedral angle restraints: 7548
    sinusoidal: 3068
      harmonic: 4480
  Sorted by residual:
  dihedral pdb=" CA  TYR A 128 "
           pdb=" C   TYR A 128 "
           pdb=" N   GLU A 129 "
           pdb=" CA  GLU A 129 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.48  -18.52     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  MET A1246 "
           pdb=" C   MET A1246 "
           pdb=" N   VAL A1247 "
           pdb=" CA  VAL A1247 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -163.48  -16.52     0      5.00e+00 4.00e-02 1.09e+01
  dihedral pdb=" CA  LYS A  10 "
           pdb=" C   LYS A  10 "
           pdb=" N   LEU A  11 "
           pdb=" CA  LEU A  11 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.90   16.10     0      5.00e+00 4.00e-02 1.04e+01
  ... (remaining 7545 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 1479
       0.045 -    0.090: 320
       0.090 -    0.135: 78
       0.135 -    0.180: 5
       0.180 -    0.225: 1
  Chirality restraints: 1883
  Sorted by residual:
  chirality pdb=" CB  ILE A1333 "
            pdb=" CA  ILE A1333 "
            pdb=" CG1 ILE A1333 "
            pdb=" CG2 ILE A1333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  GLN A 223 "
            pdb=" N   GLN A 223 "
            pdb=" C   GLN A 223 "
            pdb=" CB  GLN A 223 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.89e-01
  chirality pdb=" CB  ILE A 482 "
            pdb=" CA  ILE A 482 "
            pdb=" CG1 ILE A 482 "
            pdb=" CG2 ILE A 482 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.78e-01
  ... (remaining 1880 not shown)

  Planarity restraints: 2138
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB BTYR A 662 "   -0.016 2.00e-02 2.50e+03   1.67e-02 5.58e+00
        pdb=" CG BTYR A 662 "    0.040 2.00e-02 2.50e+03
        pdb=" CD1BTYR A 662 "   -0.014 2.00e-02 2.50e+03
        pdb=" CD2BTYR A 662 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1BTYR A 662 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2BTYR A 662 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ BTYR A 662 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH BTYR A 662 "    0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 513 "   -0.027 5.00e-02 4.00e+02   4.12e-02 2.71e+00
        pdb=" N   PRO A 514 "    0.071 5.00e-02 4.00e+02
        pdb=" CA  PRO A 514 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 514 "   -0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A1221 "   -0.023 5.00e-02 4.00e+02   3.53e-02 1.99e+00
        pdb=" N   PRO A1222 "    0.061 5.00e-02 4.00e+02
        pdb=" CA  PRO A1222 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1222 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 2135 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.70: 225
        2.70 -     3.25: 12165
        3.25 -     3.80: 19870
        3.80 -     4.35: 24923
        4.35 -     4.90: 42709
  Nonbonded interactions: 99892
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 855 "
            pdb=" OE1 GLU A 871 "
     model   vdw
     2.156 3.040
  nonbonded pdb=" OG  SER A  48 "
            pdb=" OD1 ASN A  50 "
     model   vdw
     2.181 3.040
  nonbonded pdb=" OG  SER A 515 "
            pdb=" O   PHE A 524 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OH  TYR A 869 "
            pdb=" OD2 ASP A1007 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG1 THR A 459 "
            pdb=" OE1 GLN A1223 "
     model   vdw
     2.222 3.040
  ... (remaining 99887 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.560
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.560
  Find NCS groups from input model:        0.060
  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:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.680
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6775
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   0.053  12535  Z= 0.120
  Angle     :  0.533  14.055  16938  Z= 0.284
  Chirality :  0.039   0.225   1883
  Planarity :  0.003   0.041   2138
  Dihedral  : 12.481  86.578   4648
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.99 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.65 (0.22), residues: 1509
  helix:  1.89 (0.18), residues: 851
  sheet:  1.29 (0.50), residues: 112
  loop : -0.18 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 346 
 TYR   0.015   0.001   TYR A 713 
 PHE   0.010   0.001   PHE A1341 
 TRP   0.012   0.001   TRP A1056 
 HIS   0.005   0.001   HIS A 489 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (12535)
  covalent geometry    : angle       0.53321 (16938)
  hydrogen bonds       : bond        0.13370 (  695)
  hydrogen bonds       : angle       5.32532 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.0844 (ptt) cc_final: 0.0090 (mpp)
REVERT: A  239 ASN cc_start: 0.8289 (t0) cc_final: 0.7906 (t0)
REVERT: A  245 ASP cc_start: 0.7464 (m-30) cc_final: 0.7142 (t0)
REVERT: A  289 ARG cc_start: 0.7250 (mtp180) cc_final: 0.6900 (mmm-85)
REVERT: A  325 ILE cc_start: 0.8706 (mt) cc_final: 0.8448 (tp)
REVERT: A  359 PHE cc_start: 0.8154 (t80) cc_final: 0.7901 (t80)
REVERT: A  363 GLN cc_start: 0.7505 (pm20) cc_final: 0.7152 (mt0)
REVERT: A  457 ASN cc_start: 0.7565 (m-40) cc_final: 0.7307 (t0)
REVERT: A  597 LEU cc_start: 0.8068 (mt) cc_final: 0.7808 (mt)
REVERT: A  607 ASN cc_start: 0.7276 (m-40) cc_final: 0.6681 (m110)
REVERT: A  628 TYR cc_start: 0.7857 (m-10) cc_final: 0.7629 (m-10)
REVERT: A  728 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7467 (mm-30)
REVERT: A  819 GLU cc_start: 0.7962 (pp20) cc_final: 0.7692 (pp20)
REVERT: A  867 LYS cc_start: 0.7288 (tptm) cc_final: 0.6967 (tptt)
REVERT: A  892 ARG cc_start: 0.6385 (tpt170) cc_final: 0.5897 (mtp85)
REVERT: A  917 LYS cc_start: 0.7825 (ttpp) cc_final: 0.7599 (tttm)
REVERT: A  963 LYS cc_start: 0.7112 (tttp) cc_final: 0.6835 (ttpt)
REVERT: A 1147 GLU cc_start: 0.7483 (tt0) cc_final: 0.7238 (tt0)
REVERT: A 1335 LYS cc_start: 0.7344 (ttpt) cc_final: 0.7132 (ttmm)
REVERT: A 1366 VAL cc_start: 0.7750 (t) cc_final: 0.7533 (p)
REVERT: A 1445 GLN cc_start: 0.8262 (mp10) cc_final: 0.7626 (mt0)
REVERT: A 1483 ARG cc_start: 0.5344 (mmt180) cc_final: 0.4865 (tpp80)
REVERT: A 1519 SER cc_start: 0.7060 (m) cc_final: 0.6846 (t)
REVERT: A 1523 ASP cc_start: 0.7971 (m-30) cc_final: 0.7461 (m-30)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1338
  time to fit residues: 45.6118
Evaluate side-chains
  150 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.496 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 98 optimal weight:    0.7980
   chunk 107 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.8980
   chunk 124 optimal weight:    5.9990
   chunk 103 optimal weight:    0.5980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:   10.0000
   overall best weight:    2.4584

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

Flipped N/Q/H residues before XYZ refinement:
A 323 ASN
A 489 HIS
A1298 HIS
A1378 ASN
** A1413 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1575 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.162631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.111736 restraints weight = 24278.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3245 rms_B_bonded: 3.59
r_work: 0.2950 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2950
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2933
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2933 r_free = 0.2933    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2932 r_free = 0.2932    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2932
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7807
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  12535  Z= 0.240
  Angle     :  0.602   7.135  16938  Z= 0.313
  Chirality :  0.044   0.184   1883
  Planarity :  0.004   0.063   2138
  Dihedral  :  3.801  19.506   1650
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 6.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.32 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  :  5.56 %
    Favored  : 92.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.21), residues: 1509
  helix:  1.57 (0.17), residues: 853
  sheet:  1.13 (0.49), residues: 112
  loop : -0.21 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A  35 
 TYR   0.017   0.002   TYR A1026 
 PHE   0.028   0.002   PHE A1132 
 TRP   0.024   0.002   TRP A1056 
 HIS   0.006   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00591 (12535)
  covalent geometry    : angle       0.60246 (16938)
  hydrogen bonds       : bond        0.04631 (  695)
  hydrogen bonds       : angle       4.61184 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 152
  time to evaluate  : 0.766 
Fit side-chains
REVERT: A  239 ASN cc_start: 0.8690 (t0) cc_final: 0.8362 (t0)
REVERT: A  245 ASP cc_start: 0.8145 (m-30) cc_final: 0.7819 (t0)
REVERT: A  325 ILE cc_start: 0.8863 (mt) cc_final: 0.8629 (tp)
REVERT: A  359 PHE cc_start: 0.8728 (t80) cc_final: 0.8477 (t80)
REVERT: A  363 GLN cc_start: 0.7605 (pm20) cc_final: 0.7334 (mt0)
REVERT: A  457 ASN cc_start: 0.8410 (m-40) cc_final: 0.7746 (t0)
REVERT: A  819 GLU cc_start: 0.8496 (pp20) cc_final: 0.8240 (pp20)
REVERT: A  867 LYS cc_start: 0.8420 (tptm) cc_final: 0.8022 (tptt)
REVERT: A  892 ARG cc_start: 0.6847 (tpt170) cc_final: 0.6477 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7709 (tttp) cc_final: 0.7298 (ttpt)
REVERT: A 1030 MET cc_start: 0.6965 (ptt) cc_final: 0.5333 (mmm)
REVERT: A 1128 HIS cc_start: 0.7597 (m170) cc_final: 0.7342 (m170)
REVERT: A 1172 LEU cc_start: 0.6599 (mm) cc_final: 0.6282 (mm)
REVERT: A 1335 LYS cc_start: 0.8179 (ttpt) cc_final: 0.7967 (ttmm)
REVERT: A 1445 GLN cc_start: 0.8333 (mp10) cc_final: 0.7752 (mt0)
REVERT: A 1483 ARG cc_start: 0.5523 (mmt180) cc_final: 0.5026 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7537 (tt0) cc_final: 0.6695 (mt0)
  outliers start: 20
  outliers final: 15
  residues processed: 166
  average time/residue: 0.1227
  time to fit residues: 29.4630
Evaluate side-chains
  147 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 ASP
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue 1261 THR
Chi-restraints excluded: chain A residue 1321 THR
Chi-restraints excluded: chain A residue 1351 ASP
Chi-restraints excluded: chain A residue 1393 VAL
Chi-restraints excluded: chain A residue 1425 THR
Chi-restraints excluded: chain A residue 1489 THR
Chi-restraints excluded: chain A residue 1517 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 32 optimal weight:    0.0040
   chunk 81 optimal weight:    2.9990
   chunk 57 optimal weight:    0.9990
   chunk 150 optimal weight:    4.9990
   chunk 12 optimal weight:    9.9990
   chunk 134 optimal weight:    1.9990
   chunk 139 optimal weight:    2.9990
   chunk 125 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 148 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.7996

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

Flipped N/Q/H residues before XYZ refinement:
A 457 ASN
** A1501 ASN ** 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 = 0.3894 r_free = 0.3894 target = 0.166274 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.115915 restraints weight = 24368.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.3296 rms_B_bonded: 3.64
r_work: 0.3004 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3004
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3008
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3008 r_free = 0.3008    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3008
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7774
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12535  Z= 0.119
  Angle     :  0.502  14.274  16938  Z= 0.257
  Chirality :  0.040   0.151   1883
  Planarity :  0.003   0.047   2138
  Dihedral  :  3.638  19.186   1650
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.66 %
    Favored  : 97.34 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  7.04 %
    Favored  : 91.92 %
  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 aren not related in a simple way.
  whole:  1.54 (0.22), residues: 1509
  helix:  1.83 (0.18), residues: 851
  sheet:  1.05 (0.50), residues: 112
  loop : -0.23 (0.26), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A  35 
 TYR   0.014   0.001   TYR A1026 
 PHE   0.032   0.001   PHE A1341 
 TRP   0.016   0.001   TRP A1056 
 HIS   0.003   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (12535)
  covalent geometry    : angle       0.50184 (16938)
  hydrogen bonds       : bond        0.03548 (  695)
  hydrogen bonds       : angle       4.26407 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 144
  time to evaluate  : 0.527 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4263 (mpp) cc_final: 0.3240 (ttt)
REVERT: A  239 ASN cc_start: 0.8642 (t0) cc_final: 0.8336 (t0)
REVERT: A  245 ASP cc_start: 0.8131 (m-30) cc_final: 0.7796 (t0)
REVERT: A  325 ILE cc_start: 0.8840 (mt) cc_final: 0.8610 (tp)
REVERT: A  359 PHE cc_start: 0.8723 (t80) cc_final: 0.8460 (t80)
REVERT: A  363 GLN cc_start: 0.7574 (pm20) cc_final: 0.7341 (mt0)
REVERT: A  819 GLU cc_start: 0.8498 (pp20) cc_final: 0.8224 (pp20)
REVERT: A  867 LYS cc_start: 0.8328 (tptm) cc_final: 0.7978 (tptt)
REVERT: A  892 ARG cc_start: 0.6792 (tpt170) cc_final: 0.6403 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7707 (tttp) cc_final: 0.7277 (ttpt)
REVERT: A 1030 MET cc_start: 0.6979 (ptt) cc_final: 0.5432 (mmm)
REVERT: A 1128 HIS cc_start: 0.7564 (m170) cc_final: 0.7318 (m170)
REVERT: A 1172 LEU cc_start: 0.6477 (mm) cc_final: 0.6172 (mm)
REVERT: A 1335 LYS cc_start: 0.8151 (ttpt) cc_final: 0.7940 (ttmm)
REVERT: A 1445 GLN cc_start: 0.8327 (mp10) cc_final: 0.7697 (mt0)
REVERT: A 1483 ARG cc_start: 0.5621 (mmt180) cc_final: 0.5099 (tpp80)
  outliers start: 14
  outliers final: 9
  residues processed: 153
  average time/residue: 0.1202
  time to fit residues: 26.6559
Evaluate side-chains
  145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 136
  time to evaluate  : 0.514 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue 1351 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 50 optimal weight:    1.9990
   chunk 77 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 58 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 44 optimal weight:    0.6980
   chunk 65 optimal weight:    5.9990
   chunk 123 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 62 optimal weight:    0.0980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A1501 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.168565 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.117001 restraints weight = 18514.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 2.78
r_work: 0.3134 rms_B_bonded: 3.33 restraints_weight: 0.5000
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3145
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3145 r_free = 0.3145    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3145
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7986
moved from start:          0.2029

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  12535  Z= 0.103
  Angle     :  0.480  13.437  16938  Z= 0.247
  Chirality :  0.039   0.142   1883
  Planarity :  0.003   0.045   2138
  Dihedral  :  3.518  18.905   1650
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.92 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  :  8.45 %
    Favored  : 91.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.22), residues: 1509
  helix:  1.95 (0.18), residues: 855
  sheet:  0.98 (0.50), residues: 112
  loop : -0.18 (0.26), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  30 
 TYR   0.014   0.001   TYR A1026 
 PHE   0.014   0.001   PHE A1330 
 TRP   0.017   0.001   TRP A1131 
 HIS   0.002   0.001   HIS A 608 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (12535)
  covalent geometry    : angle       0.48034 (16938)
  hydrogen bonds       : bond        0.03266 (  695)
  hydrogen bonds       : angle       4.12465 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4160 (mpp) cc_final: 0.3098 (ttt)
REVERT: A  239 ASN cc_start: 0.8585 (t0) cc_final: 0.8359 (t0)
REVERT: A  359 PHE cc_start: 0.8921 (t80) cc_final: 0.8678 (t80)
REVERT: A  457 ASN cc_start: 0.8339 (m110) cc_final: 0.7901 (t0)
REVERT: A  892 ARG cc_start: 0.6720 (tpt170) cc_final: 0.6378 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7969 (tttp) cc_final: 0.7617 (ttpt)
REVERT: A 1030 MET cc_start: 0.6944 (ptt) cc_final: 0.5688 (mmm)
REVERT: A 1172 LEU cc_start: 0.6207 (mm) cc_final: 0.5960 (mm)
REVERT: A 1445 GLN cc_start: 0.8237 (mp10) cc_final: 0.7741 (mt0)
REVERT: A 1483 ARG cc_start: 0.5627 (mmt180) cc_final: 0.5256 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7423 (tt0) cc_final: 0.7001 (mt0)
  outliers start: 7
  outliers final: 5
  residues processed: 140
  average time/residue: 0.1209
  time to fit residues: 24.7524
Evaluate side-chains
  129 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 124
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  496 LYS
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 129 optimal weight:    3.9990
   chunk 29 optimal weight:    4.9990
   chunk 68 optimal weight:    6.9990
   chunk 75 optimal weight:    0.9990
   chunk 62 optimal weight:    3.9990
   chunk 32 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 20 optimal weight:    1.9990
   chunk 145 optimal weight:    5.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.166460 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.116706 restraints weight = 26097.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3311 rms_B_bonded: 3.45
r_work: 0.3031 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3031
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3038
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.29   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3038 r_free = 0.3038    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3038
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7749
moved from start:          0.2214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  12535  Z= 0.116
  Angle     :  0.479  10.341  16938  Z= 0.248
  Chirality :  0.039   0.181   1883
  Planarity :  0.003   0.041   2138
  Dihedral  :  3.479  18.718   1650
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 5.37
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.99 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.27 %
    Favored  : 89.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.22), residues: 1509
  helix:  1.96 (0.18), residues: 855
  sheet:  0.96 (0.49), residues: 112
  loop : -0.16 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A  35 
 TYR   0.012   0.001   TYR A 713 
 PHE   0.031   0.001   PHE A1132 
 TRP   0.013   0.001   TRP A1056 
 HIS   0.003   0.001   HIS A1128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (12535)
  covalent geometry    : angle       0.47853 (16938)
  hydrogen bonds       : bond        0.03279 (  695)
  hydrogen bonds       : angle       4.08267 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 127
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4316 (mpp) cc_final: 0.3299 (ttt)
REVERT: A  239 ASN cc_start: 0.8647 (t0) cc_final: 0.8342 (t0)
REVERT: A  359 PHE cc_start: 0.8752 (t80) cc_final: 0.8467 (t80)
REVERT: A  457 ASN cc_start: 0.8207 (m110) cc_final: 0.7801 (t0)
REVERT: A  892 ARG cc_start: 0.6739 (tpt170) cc_final: 0.6410 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7726 (tttp) cc_final: 0.7322 (ttpt)
REVERT: A 1030 MET cc_start: 0.6877 (ptt) cc_final: 0.5658 (mmm)
REVERT: A 1172 LEU cc_start: 0.6309 (mm) cc_final: 0.6039 (mm)
REVERT: A 1445 GLN cc_start: 0.8276 (mp10) cc_final: 0.7697 (mt0)
REVERT: A 1483 ARG cc_start: 0.5617 (mmt180) cc_final: 0.5173 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7322 (tt0) cc_final: 0.6801 (mt0)
  outliers start: 15
  outliers final: 12
  residues processed: 137
  average time/residue: 0.1205
  time to fit residues: 24.0104
Evaluate side-chains
  135 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 123
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue  834 SER
Chi-restraints excluded: chain A residue 1271 MET
Chi-restraints excluded: chain A residue 1351 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 35 optimal weight:    3.9990
   chunk 2 optimal weight:    5.9990
   chunk 60 optimal weight:    0.4980
   chunk 106 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 148 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 49 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 80 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 223 GLN
A1128 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.165095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.114372 restraints weight = 18855.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3283 rms_B_bonded: 2.70
r_work: 0.3075 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.3075
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3082
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3082 r_free = 0.3082    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3082
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7977
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  12535  Z= 0.167
  Angle     :  0.506   8.678  16938  Z= 0.263
  Chirality :  0.041   0.152   1883
  Planarity :  0.003   0.041   2138
  Dihedral  :  3.595  18.518   1650
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 5.45
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.19 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  9.41 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.22), residues: 1509
  helix:  1.82 (0.18), residues: 862
  sheet:  0.89 (0.50), residues: 112
  loop : -0.21 (0.27), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A  35 
 TYR   0.012   0.001   TYR A1382 
 PHE   0.019   0.001   PHE A 585 
 TRP   0.018   0.001   TRP A1056 
 HIS   0.004   0.001   HIS A1365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (12535)
  covalent geometry    : angle       0.50566 (16938)
  hydrogen bonds       : bond        0.03719 (  695)
  hydrogen bonds       : angle       4.19672 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4217 (mpp) cc_final: 0.3214 (ttt)
REVERT: A  239 ASN cc_start: 0.8676 (t0) cc_final: 0.8416 (t0)
REVERT: A  359 PHE cc_start: 0.8858 (t80) cc_final: 0.8603 (t80)
REVERT: A  457 ASN cc_start: 0.8335 (m110) cc_final: 0.7950 (t0)
REVERT: A  541 ASP cc_start: 0.8094 (m-30) cc_final: 0.7675 (t0)
REVERT: A  892 ARG cc_start: 0.6837 (tpt170) cc_final: 0.6406 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7944 (tttp) cc_final: 0.7574 (ttpt)
REVERT: A 1030 MET cc_start: 0.7083 (ptt) cc_final: 0.5807 (mmm)
REVERT: A 1204 ASP cc_start: 0.8131 (m-30) cc_final: 0.7695 (m-30)
REVERT: A 1445 GLN cc_start: 0.8283 (mp10) cc_final: 0.7766 (mt0)
REVERT: A 1483 ARG cc_start: 0.5673 (mmt180) cc_final: 0.5321 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7545 (tt0) cc_final: 0.6980 (mt0)
  outliers start: 15
  outliers final: 12
  residues processed: 134
  average time/residue: 0.1152
  time to fit residues: 22.6863
Evaluate side-chains
  133 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 121
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue 1271 MET
Chi-restraints excluded: chain A residue 1351 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 139 optimal weight:    4.9990
   chunk 5 optimal weight:    3.9990
   chunk 145 optimal weight:    4.9990
   chunk 45 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 81 optimal weight:    2.9990
   chunk 17 optimal weight:    3.9990
   chunk 78 optimal weight:    0.9990
   chunk 19 optimal weight:    9.9990
   chunk 135 optimal weight:    5.9990
   chunk 107 optimal weight:    0.0970
   overall best weight:    1.5984

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.163340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.114962 restraints weight = 25586.913|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 3.66
r_work: 0.2984 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.2984
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2984
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2984 r_free = 0.2984    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2984
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7806
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12535  Z= 0.162
  Angle     :  0.505   7.563  16938  Z= 0.262
  Chirality :  0.041   0.186   1883
  Planarity :  0.003   0.039   2138
  Dihedral  :  3.601  18.324   1650
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 5.66
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.19 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  :  9.79 %
    Favored  : 89.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.48 (0.22), residues: 1509
  helix:  1.80 (0.17), residues: 860
  sheet:  0.79 (0.49), residues: 112
  loop : -0.26 (0.27), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  35 
 TYR   0.012   0.001   TYR A1382 
 PHE   0.020   0.001   PHE A1330 
 TRP   0.017   0.001   TRP A1056 
 HIS   0.004   0.001   HIS A1365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 (12535)
  covalent geometry    : angle       0.50494 (16938)
  hydrogen bonds       : bond        0.03660 (  695)
  hydrogen bonds       : angle       4.17972 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 120
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A   94 MET cc_start: 0.4390 (mpp) cc_final: 0.3411 (ttt)
REVERT: A  239 ASN cc_start: 0.8663 (t0) cc_final: 0.8362 (t0)
REVERT: A  325 ILE cc_start: 0.8819 (tp) cc_final: 0.8616 (tp)
REVERT: A  359 PHE cc_start: 0.8691 (t80) cc_final: 0.8410 (t80)
REVERT: A  457 ASN cc_start: 0.8258 (m110) cc_final: 0.7835 (t0)
REVERT: A  541 ASP cc_start: 0.8222 (m-30) cc_final: 0.7655 (t0)
REVERT: A  892 ARG cc_start: 0.6796 (tpt170) cc_final: 0.6354 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7757 (tttp) cc_final: 0.7402 (ttpt)
REVERT: A 1030 MET cc_start: 0.7158 (ptt) cc_final: 0.5845 (mmm)
REVERT: A 1445 GLN cc_start: 0.8301 (mp10) cc_final: 0.7722 (mt0)
REVERT: A 1483 ARG cc_start: 0.5799 (mmt180) cc_final: 0.5268 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7467 (tt0) cc_final: 0.6893 (mt0)
  outliers start: 16
  outliers final: 14
  residues processed: 130
  average time/residue: 0.1147
  time to fit residues: 22.0299
Evaluate side-chains
  132 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  279 CYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  299 ILE
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue 1271 MET
Chi-restraints excluded: chain A residue 1333 ILE
Chi-restraints excluded: chain A residue 1351 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 33 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 110 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0670
   chunk 141 optimal weight:    2.9990
   chunk 149 optimal weight:    1.9990
   chunk 145 optimal weight:    0.5980
   chunk 84 optimal weight:    0.4980
   chunk 43 optimal weight:    0.6980
   chunk 92 optimal weight:    0.5980
   overall best weight:    0.4918

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3903 r_free = 0.3903 target = 0.167340 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.115436 restraints weight = 30252.222|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 3.62
r_work: 0.3028 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3028
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3034
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3034 r_free = 0.3034    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3034
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  12535  Z= 0.098
  Angle     :  0.460   9.009  16938  Z= 0.239
  Chirality :  0.038   0.152   1883
  Planarity :  0.003   0.036   2138
  Dihedral  :  3.413  17.912   1650
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.74
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.72 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.23 %
    Favored  : 88.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.22), residues: 1509
  helix:  2.05 (0.18), residues: 855
  sheet:  0.80 (0.49), residues: 112
  loop : -0.18 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  35 
 TYR   0.014   0.001   TYR A1026 
 PHE   0.021   0.001   PHE A1330 
 TRP   0.015   0.001   TRP A 473 
 HIS   0.004   0.001   HIS A1128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (12535)
  covalent geometry    : angle       0.45982 (16938)
  hydrogen bonds       : bond        0.03034 (  695)
  hydrogen bonds       : angle       3.98325 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 135
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4417 (mpp) cc_final: 0.3460 (ttt)
REVERT: A  239 ASN cc_start: 0.8623 (t0) cc_final: 0.8318 (t0)
REVERT: A  359 PHE cc_start: 0.8615 (t80) cc_final: 0.8378 (t80)
REVERT: A  410 HIS cc_start: 0.7705 (m90) cc_final: 0.7427 (m90)
REVERT: A  457 ASN cc_start: 0.8180 (m110) cc_final: 0.7776 (t0)
REVERT: A  541 ASP cc_start: 0.8202 (m-30) cc_final: 0.7600 (t0)
REVERT: A  564 LEU cc_start: 0.8453 (mt) cc_final: 0.8217 (mt)
REVERT: A  607 ASN cc_start: 0.8314 (m110) cc_final: 0.7916 (m110)
REVERT: A  735 MET cc_start: 0.8328 (tmm) cc_final: 0.8123 (tmm)
REVERT: A  892 ARG cc_start: 0.6800 (tpt170) cc_final: 0.6414 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7695 (tttp) cc_final: 0.7375 (ttpt)
REVERT: A 1030 MET cc_start: 0.7075 (ptt) cc_final: 0.5818 (mmm)
REVERT: A 1445 GLN cc_start: 0.8288 (mp10) cc_final: 0.7731 (mt0)
REVERT: A 1483 ARG cc_start: 0.5872 (mmt180) cc_final: 0.5319 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7394 (tt0) cc_final: 0.6834 (mt0)
REVERT: A 1593 MET cc_start: 0.8929 (tpp) cc_final: 0.8586 (tpp)
  outliers start: 13
  outliers final: 10
  residues processed: 141
  average time/residue: 0.1162
  time to fit residues: 24.2676
Evaluate side-chains
  136 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 126
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue 1271 MET
Chi-restraints excluded: chain A residue 1333 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 3 optimal weight:    9.9990
   chunk 54 optimal weight:    0.7980
   chunk 26 optimal weight:    0.8980
   chunk 11 optimal weight:    8.9990
   chunk 85 optimal weight:    0.7980
   chunk 75 optimal weight:    0.9980
   chunk 122 optimal weight:    6.9990
   chunk 101 optimal weight:    3.9990
   chunk 88 optimal weight:    0.8980
   chunk 137 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.166059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.118466 restraints weight = 26913.193|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 3.96
r_work: 0.3026 rms_B_bonded: 3.90 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3029
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3029 r_free = 0.3029    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3029
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2575

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12535  Z= 0.114
  Angle     :  0.469   9.145  16938  Z= 0.243
  Chirality :  0.039   0.157   1883
  Planarity :  0.003   0.039   2138
  Dihedral  :  3.409  17.820   1650
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.86 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.82 %
    Favored  : 88.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.22), residues: 1509
  helix:  2.03 (0.18), residues: 861
  sheet:  0.84 (0.49), residues: 112
  loop : -0.17 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  35 
 TYR   0.012   0.001   TYR A1026 
 PHE   0.022   0.001   PHE A1330 
 TRP   0.020   0.001   TRP A1131 
 HIS   0.003   0.001   HIS A1128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (12535)
  covalent geometry    : angle       0.46889 (16938)
  hydrogen bonds       : bond        0.03200 (  695)
  hydrogen bonds       : angle       4.00118 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 132
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A   94 MET cc_start: 0.4345 (mpp) cc_final: 0.3379 (ttt)
REVERT: A  239 ASN cc_start: 0.8642 (t0) cc_final: 0.8322 (t0)
REVERT: A  359 PHE cc_start: 0.8672 (t80) cc_final: 0.8446 (t80)
REVERT: A  410 HIS cc_start: 0.7729 (m90) cc_final: 0.7453 (m90)
REVERT: A  457 ASN cc_start: 0.8214 (m110) cc_final: 0.7810 (t0)
REVERT: A  541 ASP cc_start: 0.8194 (m-30) cc_final: 0.7645 (t0)
REVERT: A  735 MET cc_start: 0.8370 (tmm) cc_final: 0.8110 (tmm)
REVERT: A  892 ARG cc_start: 0.6805 (tpt170) cc_final: 0.6407 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7843 (tttp) cc_final: 0.7508 (ttpt)
REVERT: A 1030 MET cc_start: 0.7060 (ptt) cc_final: 0.5825 (mmm)
REVERT: A 1445 GLN cc_start: 0.8271 (mp10) cc_final: 0.7733 (mt0)
REVERT: A 1483 ARG cc_start: 0.5847 (mmt180) cc_final: 0.5321 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7446 (tt0) cc_final: 0.6812 (mt0)
  outliers start: 11
  outliers final: 10
  residues processed: 137
  average time/residue: 0.1170
  time to fit residues: 23.6029
Evaluate side-chains
  141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 131
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue 1271 MET
Chi-restraints excluded: chain A residue 1333 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 46 optimal weight:    3.9990
   chunk 74 optimal weight:    2.9990
   chunk 117 optimal weight:    1.9990
   chunk 134 optimal weight:    0.0170
   chunk 2 optimal weight:    3.9990
   chunk 144 optimal weight:    6.9990
   chunk 61 optimal weight:    1.9990
   chunk 22 optimal weight:    1.9990
   chunk 139 optimal weight:    3.9990
   chunk 148 optimal weight:    5.9990
   chunk 131 optimal weight:    0.5980
   overall best weight:    1.3224

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.164293 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.115622 restraints weight = 26264.496|
|-----------------------------------------------------------------------------|
r_work (start): 0.3299 rms_B_bonded: 3.64
r_work: 0.2996 rms_B_bonded: 3.93 restraints_weight: 0.5000
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2998
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2998 r_free = 0.2998    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2998
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7799
moved from start:          0.2677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  12535  Z= 0.143
  Angle     :  0.491   8.855  16938  Z= 0.255
  Chirality :  0.040   0.178   1883
  Planarity :  0.003   0.041   2138
  Dihedral  :  3.496  17.682   1650
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.25 %
    Favored  : 96.68 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  : 10.97 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.22), residues: 1509
  helix:  1.97 (0.18), residues: 861
  sheet:  0.80 (0.49), residues: 112
  loop : -0.19 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1407 
 TYR   0.013   0.001   TYR A1026 
 PHE   0.022   0.001   PHE A1330 
 TRP   0.017   0.001   TRP A1056 
 HIS   0.004   0.001   HIS A1365 

Details of bonding type rmsd
  covalent geometry    : bond        0.00349 (12535)
  covalent geometry    : angle       0.49068 (16938)
  hydrogen bonds       : bond        0.03486 (  695)
  hydrogen bonds       : angle       4.07618 ( 2038)

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

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

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3018 Ramachandran restraints generated.
    1509 Oldfield, 0 Emsley, 1509 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 128
  time to evaluate  : 0.509 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4431 (mpp) cc_final: 0.3520 (ttt)
REVERT: A  239 ASN cc_start: 0.8665 (t0) cc_final: 0.8350 (t0)
REVERT: A  318 CYS cc_start: 0.8113 (m) cc_final: 0.7867 (m)
REVERT: A  359 PHE cc_start: 0.8664 (t80) cc_final: 0.8392 (t80)
REVERT: A  410 HIS cc_start: 0.7725 (m90) cc_final: 0.7457 (m90)
REVERT: A  457 ASN cc_start: 0.8270 (m110) cc_final: 0.7831 (t0)
REVERT: A  541 ASP cc_start: 0.8195 (m-30) cc_final: 0.7737 (t0)
REVERT: A  892 ARG cc_start: 0.6840 (tpt170) cc_final: 0.6429 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7917 (tttp) cc_final: 0.7568 (ttpt)
REVERT: A 1030 MET cc_start: 0.7060 (ptt) cc_final: 0.5839 (mmm)
REVERT: A 1445 GLN cc_start: 0.8269 (mp10) cc_final: 0.7723 (mt0)
REVERT: A 1483 ARG cc_start: 0.5691 (mmt180) cc_final: 0.5292 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7416 (tt0) cc_final: 0.6781 (mt0)
  outliers start: 13
  outliers final: 11
  residues processed: 134
  average time/residue: 0.1181
  time to fit residues: 23.4164
Evaluate side-chains
  138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 127
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  252 SER
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  432 THR
Chi-restraints excluded: chain A residue  515 SER
Chi-restraints excluded: chain A residue  525 ILE
Chi-restraints excluded: chain A residue  559 VAL
Chi-restraints excluded: chain A residue  613 ILE
Chi-restraints excluded: chain A residue  700 VAL
Chi-restraints excluded: chain A residue 1271 MET
Chi-restraints excluded: chain A residue 1333 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 102 optimal weight:    0.8980
   chunk 134 optimal weight:    5.9990
   chunk 130 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 71 optimal weight:    0.9980
   chunk 36 optimal weight:    0.5980
   chunk 136 optimal weight:    0.3980
   chunk 42 optimal weight:    0.0170
   chunk 80 optimal weight:    3.9990
   chunk 17 optimal weight:    4.9990
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3906 r_free = 0.3906 target = 0.167474 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.113510 restraints weight = 29437.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 3.99
r_work: 0.3027 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3027
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3027 r_free = 0.3027    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3027
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  12535  Z= 0.098
  Angle     :  0.461   9.751  16938  Z= 0.239
  Chirality :  0.038   0.162   1883
  Planarity :  0.003   0.038   2138
  Dihedral  :  3.375  17.397   1650
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.72 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.90 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.81 (0.22), residues: 1509
  helix:  2.10 (0.18), residues: 861
  sheet:  0.82 (0.49), residues: 112
  loop : -0.15 (0.27), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  35 
 TYR   0.013   0.001   TYR A1026 
 PHE   0.023   0.001   PHE A1330 
 TRP   0.017   0.001   TRP A1131 
 HIS   0.005   0.001   HIS A1128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 (12535)
  covalent geometry    : angle       0.46094 (16938)
  hydrogen bonds       : bond        0.03026 (  695)
  hydrogen bonds       : angle       3.94373 ( 2038)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3362.19 seconds
wall clock time: 58 minutes 34.39 seconds (3514.39 seconds total)