Starting phenix.real_space_refine
on Thu May 15 00:59:33 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8p1k_17352/05_2025/8p1k_17352.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8p1k_17352/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8p1k_17352/05_2025/8p1k_17352.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8p1k_17352/05_2025/8p1k_17352.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8p1k_17352/05_2025/8p1k_17352.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8p1k_17352/05_2025/8p1k_17352.cif"
  }
  resolution = 3.24
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.038
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 12.98, per 1000 atoms: 1.06
  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: 3.15
  Conformation dependent library (CDL) restraints added in 3.1 seconds
  

  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: 1.83
  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: 5.49

  Time building geometry restraints manager: 3.68 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:             2.000
  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:          0.500
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     40.120
  Find NCS groups from input model:        0.160
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.950
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.65 (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
 TRP   0.012   0.001   TRP A1056 
 HIS   0.005   0.001   HIS A 489 
 PHE   0.010   0.001   PHE A1341 
 TYR   0.015   0.001   TYR A 713 
 ARG   0.008   0.000   ARG A 346 

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

*********************** 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  : 1.287 
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: 0.2777
  time to fit residues: 94.3787
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  : 1.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 127 optimal weight:    8.9990
   chunk 114 optimal weight:    3.9990
   chunk 63 optimal weight:    0.7980
   chunk 39 optimal weight:    6.9990
   chunk 77 optimal weight:    4.9990
   chunk 61 optimal weight:    0.5980
   chunk 118 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 71 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 137 optimal weight:    3.9990
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 323 ASN
A 457 ASN
A 489 HIS
A1096 HIS
A1298 HIS
A1378 ASN
** A1501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1575 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.167395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.115607 restraints weight = 17893.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.3295 rms_B_bonded: 3.05
r_work: 0.3091 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3093 r_free = 0.3093    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3092 r_free = 0.3092    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3092
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.1468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  12535  Z= 0.137
  Angle     :  0.531   7.379  16938  Z= 0.273
  Chirality :  0.041   0.165   1883
  Planarity :  0.004   0.062   2138
  Dihedral  :  3.565  19.306   1650
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  5.41 %
    Favored  : 93.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.62 (0.22), residues: 1509
  helix:  1.83 (0.18), residues: 859
  sheet:  1.25 (0.50), residues: 112
  loop : -0.15 (0.27), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1056 
 HIS   0.004   0.001   HIS A 278 
 PHE   0.027   0.001   PHE A1132 
 TYR   0.020   0.001   TYR A1026 
 ARG   0.005   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03824 (  695)
  hydrogen bonds       : angle       4.42009 ( 2038)
  covalent geometry    : bond        0.00327 (12535)
  covalent geometry    : angle       0.53133 (16938)

*********************** 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
  170 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 157
  time to evaluate  : 1.284 
Fit side-chains
   revert: symmetry clash
REVERT: A  239 ASN cc_start: 0.8607 (t0) cc_final: 0.8286 (t0)
REVERT: A  245 ASP cc_start: 0.7991 (m-30) cc_final: 0.7651 (t0)
REVERT: A  325 ILE cc_start: 0.8809 (mt) cc_final: 0.8527 (tp)
REVERT: A  363 GLN cc_start: 0.7526 (pm20) cc_final: 0.7298 (mt0)
REVERT: A  457 ASN cc_start: 0.8235 (m110) cc_final: 0.7675 (t0)
REVERT: A  607 ASN cc_start: 0.8200 (m-40) cc_final: 0.7703 (m110)
REVERT: A  728 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7780 (mm-30)
REVERT: A  819 GLU cc_start: 0.8357 (pp20) cc_final: 0.8126 (pp20)
REVERT: A  867 LYS cc_start: 0.8312 (tptm) cc_final: 0.7941 (tptt)
REVERT: A  892 ARG cc_start: 0.6681 (tpt170) cc_final: 0.6380 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7681 (tttp) cc_final: 0.7291 (ttpt)
REVERT: A  967 MET cc_start: 0.8325 (ttm) cc_final: 0.8065 (tpp)
REVERT: A 1030 MET cc_start: 0.6954 (ptt) cc_final: 0.5322 (mmm)
REVERT: A 1128 HIS cc_start: 0.7473 (m170) cc_final: 0.7195 (m170)
REVERT: A 1366 VAL cc_start: 0.8044 (t) cc_final: 0.7843 (p)
REVERT: A 1445 GLN cc_start: 0.8300 (mp10) cc_final: 0.7715 (mt0)
REVERT: A 1483 ARG cc_start: 0.5460 (mmt180) cc_final: 0.5037 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7324 (tt0) cc_final: 0.6635 (mt0)
  outliers start: 13
  outliers final: 9
  residues processed: 164
  average time/residue: 0.2473
  time to fit residues: 58.3503
Evaluate side-chains
  147 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 138
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
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  297 SER
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 1425 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 144 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 71 optimal weight:    0.4980
   chunk 46 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0370
   chunk 109 optimal weight:    1.9990
   chunk 14 optimal weight:   10.0000
   chunk 99 optimal weight:    0.2980
   chunk 149 optimal weight:    9.9990
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.9662

-------------------------------------------------------------------------------
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 = 0.3903 r_free = 0.3903 target = 0.166946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.116303 restraints weight = 22167.275|
|-----------------------------------------------------------------------------|
r_work (start): 0.3308 rms_B_bonded: 3.27
r_work: 0.3033 rms_B_bonded: 3.96 restraints_weight: 0.5000
r_work (final): 0.3033
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3040
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3040 r_free = 0.3040    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3040
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1780

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= 0.124
  Angle     :  0.501  12.876  16938  Z= 0.256
  Chirality :  0.040   0.158   1883
  Planarity :  0.003   0.049   2138
  Dihedral  :  3.525  19.215   1650
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.52 %
    Favored  : 92.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.66 (0.22), residues: 1509
  helix:  1.91 (0.18), residues: 853
  sheet:  1.11 (0.49), residues: 112
  loop : -0.17 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1056 
 HIS   0.003   0.001   HIS A1365 
 PHE   0.016   0.001   PHE A 585 
 TYR   0.016   0.001   TYR A1026 
 ARG   0.007   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03530 (  695)
  hydrogen bonds       : angle       4.21642 ( 2038)
  covalent geometry    : bond        0.00297 (12535)
  covalent geometry    : angle       0.50116 (16938)

*********************** 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
  156 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 143
  time to evaluate  : 1.611 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4138 (mpp) cc_final: 0.3106 (ttt)
REVERT: A  239 ASN cc_start: 0.8654 (t0) cc_final: 0.8333 (t0)
REVERT: A  245 ASP cc_start: 0.8099 (m-30) cc_final: 0.7751 (t0)
REVERT: A  325 ILE cc_start: 0.8813 (mt) cc_final: 0.8538 (tp)
REVERT: A  363 GLN cc_start: 0.7558 (pm20) cc_final: 0.7321 (mt0)
REVERT: A  457 ASN cc_start: 0.8187 (m110) cc_final: 0.7728 (t0)
REVERT: A  728 GLU cc_start: 0.8097 (mm-30) cc_final: 0.7809 (mm-30)
REVERT: A  819 GLU cc_start: 0.8447 (pp20) cc_final: 0.8185 (pp20)
REVERT: A  867 LYS cc_start: 0.8348 (tptm) cc_final: 0.8069 (tptt)
REVERT: A  892 ARG cc_start: 0.6781 (tpt170) cc_final: 0.6467 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7740 (tttp) cc_final: 0.7322 (ttpt)
REVERT: A 1030 MET cc_start: 0.7021 (ptt) cc_final: 0.5457 (mmm)
REVERT: A 1128 HIS cc_start: 0.7575 (m170) cc_final: 0.7243 (m170)
REVERT: A 1445 GLN cc_start: 0.8303 (mp10) cc_final: 0.7726 (mt0)
REVERT: A 1483 ARG cc_start: 0.5697 (mmt180) cc_final: 0.5205 (tpp80)
  outliers start: 13
  outliers final: 8
  residues processed: 151
  average time/residue: 0.2454
  time to fit residues: 54.3203
Evaluate side-chains
  144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 136
  time to evaluate  : 1.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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 1321 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 137 optimal weight:    5.9990
   chunk 83 optimal weight:    8.9990
   chunk 87 optimal weight:    0.0060
   chunk 120 optimal weight:    7.9990
   chunk 136 optimal weight:    1.9990
   chunk 84 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 73 optimal weight:    0.6980
   chunk 23 optimal weight:    3.9990
   chunk 112 optimal weight:    6.9990
   overall best weight:    1.4800

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.164717 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113146 restraints weight = 18601.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3265 rms_B_bonded: 2.85
r_work: 0.3047 rms_B_bonded: 3.35 restraints_weight: 0.5000
r_work (final): 0.3047
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.28   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7752
moved from start:          0.2098

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  12535  Z= 0.158
  Angle     :  0.515  10.859  16938  Z= 0.266
  Chirality :  0.041   0.164   1883
  Planarity :  0.003   0.046   2138
  Dihedral  :  3.592  19.018   1650
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.92 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  :  7.86 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.58 (0.22), residues: 1509
  helix:  1.86 (0.18), residues: 853
  sheet:  1.02 (0.49), residues: 112
  loop : -0.20 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A1131 
 HIS   0.005   0.001   HIS A  36 
 PHE   0.018   0.001   PHE A 585 
 TYR   0.015   0.001   TYR A1026 
 ARG   0.012   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03729 (  695)
  hydrogen bonds       : angle       4.20963 ( 2038)
  covalent geometry    : bond        0.00387 (12535)
  covalent geometry    : angle       0.51474 (16938)

*********************** 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
  151 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 136
  time to evaluate  : 1.340 
Fit side-chains
REVERT: A   94 MET cc_start: 0.4190 (mpp) cc_final: 0.3173 (ttt)
REVERT: A  239 ASN cc_start: 0.8653 (t0) cc_final: 0.8323 (t0)
REVERT: A  245 ASP cc_start: 0.8133 (m-30) cc_final: 0.7844 (t0)
REVERT: A  325 ILE cc_start: 0.8865 (mt) cc_final: 0.8624 (tp)
REVERT: A  363 GLN cc_start: 0.7528 (pm20) cc_final: 0.7298 (mt0)
REVERT: A  457 ASN cc_start: 0.8258 (m110) cc_final: 0.7764 (t0)
REVERT: A  819 GLU cc_start: 0.8455 (pp20) cc_final: 0.8173 (pp20)
REVERT: A  867 LYS cc_start: 0.8442 (tptm) cc_final: 0.8107 (tptt)
REVERT: A  892 ARG cc_start: 0.6785 (tpt170) cc_final: 0.6405 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7784 (tttp) cc_final: 0.7350 (ttpt)
REVERT: A 1030 MET cc_start: 0.7006 (ptt) cc_final: 0.5623 (mmm)
REVERT: A 1128 HIS cc_start: 0.7629 (m170) cc_final: 0.7416 (m170)
REVERT: A 1172 LEU cc_start: 0.6488 (mm) cc_final: 0.6207 (mm)
REVERT: A 1445 GLN cc_start: 0.8272 (mp10) cc_final: 0.7693 (mt0)
REVERT: A 1483 ARG cc_start: 0.5736 (mmt180) cc_final: 0.5212 (tpp80)
REVERT: A 1572 VAL cc_start: 0.8024 (p) cc_final: 0.7811 (t)
  outliers start: 15
  outliers final: 11
  residues processed: 148
  average time/residue: 0.2464
  time to fit residues: 53.3474
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  : 1.331 
-------------------------------------------------------------------------------
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  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 1321 THR
Chi-restraints excluded: chain A residue 1351 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 74 optimal weight:    3.9990
   chunk 139 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 84 optimal weight:    0.7980
   chunk 109 optimal weight:    0.9990
   chunk 73 optimal weight:    0.7980
   chunk 98 optimal weight:    0.7980
   overall best weight:    0.8580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.167909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.117418 restraints weight = 16074.369|
|-----------------------------------------------------------------------------|
r_work (start): 0.3302 rms_B_bonded: 2.76
r_work: 0.3140 rms_B_bonded: 3.08 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3146
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3146 r_free = 0.3146    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3146
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2162

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= 0.113
  Angle     :  0.482  10.886  16938  Z= 0.249
  Chirality :  0.039   0.179   1883
  Planarity :  0.003   0.042   2138
  Dihedral  :  3.509  19.280   1650
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 5.33
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.79 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  :  8.82 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.68 (0.22), residues: 1509
  helix:  1.96 (0.18), residues: 854
  sheet:  1.02 (0.49), residues: 112
  loop : -0.17 (0.27), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1056 
 HIS   0.003   0.001   HIS A 608 
 PHE   0.015   0.001   PHE A 585 
 TYR   0.013   0.001   TYR A1026 
 ARG   0.007   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03356 (  695)
  hydrogen bonds       : angle       4.08428 ( 2038)
  covalent geometry    : bond        0.00270 (12535)
  covalent geometry    : angle       0.48197 (16938)

*********************** 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
  140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 130
  time to evaluate  : 1.410 
Fit side-chains
REVERT: A   94 MET cc_start: 0.4161 (mpp) cc_final: 0.3131 (ttt)
REVERT: A  184 MET cc_start: 0.7700 (ptp) cc_final: 0.7488 (ptm)
REVERT: A  239 ASN cc_start: 0.8572 (t0) cc_final: 0.8347 (t0)
REVERT: A  457 ASN cc_start: 0.8333 (m110) cc_final: 0.7988 (t0)
REVERT: A  867 LYS cc_start: 0.8732 (tptm) cc_final: 0.8475 (tptt)
REVERT: A  892 ARG cc_start: 0.6736 (tpt170) cc_final: 0.6383 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7958 (tttp) cc_final: 0.7641 (ttpt)
REVERT: A 1030 MET cc_start: 0.6789 (ptt) cc_final: 0.5738 (mmm)
REVERT: A 1172 LEU cc_start: 0.6194 (mm) cc_final: 0.5962 (mm)
REVERT: A 1204 ASP cc_start: 0.8075 (m-30) cc_final: 0.7597 (m-30)
REVERT: A 1445 GLN cc_start: 0.8249 (mp10) cc_final: 0.7746 (mt0)
REVERT: A 1483 ARG cc_start: 0.5569 (mmt180) cc_final: 0.5304 (tpp80)
REVERT: A 1575 GLN cc_start: 0.7505 (tt0) cc_final: 0.6906 (mt0)
  outliers start: 10
  outliers final: 8
  residues processed: 136
  average time/residue: 0.2538
  time to fit residues: 50.3890
Evaluate side-chains
  133 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 125
  time to evaluate  : 1.463 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 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 88 optimal weight:    0.9980
   chunk 77 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 134 optimal weight:    0.6980
   chunk 1 optimal weight:    8.9990
   chunk 99 optimal weight:    5.9990
   chunk 120 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 97 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   chunk 31 optimal weight:    7.9990
   overall best weight:    1.2782

-------------------------------------------------------------------------------
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 = 0.3880 r_free = 0.3880 target = 0.165096 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.115531 restraints weight = 25670.407|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 3.61
r_work: 0.3001 rms_B_bonded: 3.89 restraints_weight: 0.5000
r_work (final): 0.3001
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2996
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2996 r_free = 0.2996    target_work(ls_wunit_k1) = 0.092         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2996
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2341

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= 0.138
  Angle     :  0.494   9.619  16938  Z= 0.256
  Chirality :  0.040   0.177   1883
  Planarity :  0.003   0.042   2138
  Dihedral  :  3.524  18.579   1650
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.01
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.05 %
    Favored  : 96.88 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  :  9.41 %
    Favored  : 89.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.22), residues: 1509
  helix:  1.97 (0.18), residues: 848
  sheet:  0.95 (0.49), residues: 112
  loop : -0.19 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A1056 
 HIS   0.003   0.001   HIS A 608 
 PHE   0.017   0.001   PHE A 585 
 TYR   0.012   0.001   TYR A1382 
 ARG   0.007   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03496 (  695)
  hydrogen bonds       : angle       4.10710 ( 2038)
  covalent geometry    : bond        0.00338 (12535)
  covalent geometry    : angle       0.49370 (16938)

*********************** 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
  141 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 127
  time to evaluate  : 1.435 
Fit side-chains
REVERT: A   94 MET cc_start: 0.4447 (mpp) cc_final: 0.3486 (ttt)
REVERT: A  239 ASN cc_start: 0.8654 (t0) cc_final: 0.8345 (t0)
REVERT: A  318 CYS cc_start: 0.8172 (m) cc_final: 0.7952 (m)
REVERT: A  457 ASN cc_start: 0.8250 (m110) cc_final: 0.7829 (t0)
REVERT: A  541 ASP cc_start: 0.8190 (m-30) cc_final: 0.7619 (t0)
REVERT: A  867 LYS cc_start: 0.8468 (tptm) cc_final: 0.8105 (tptt)
REVERT: A  892 ARG cc_start: 0.6839 (tpt170) cc_final: 0.6399 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7718 (tttp) cc_final: 0.7351 (ttpt)
REVERT: A 1030 MET cc_start: 0.7147 (ptt) cc_final: 0.5817 (mmm)
REVERT: A 1172 LEU cc_start: 0.6380 (mm) cc_final: 0.6108 (mm)
REVERT: A 1204 ASP cc_start: 0.8078 (m-30) cc_final: 0.7563 (m-30)
REVERT: A 1445 GLN cc_start: 0.8305 (mp10) cc_final: 0.7722 (mt0)
REVERT: A 1483 ARG cc_start: 0.5695 (mmt180) cc_final: 0.5212 (tpp80)
REVERT: A 1572 VAL cc_start: 0.8069 (p) cc_final: 0.7851 (t)
REVERT: A 1575 GLN cc_start: 0.7424 (tt0) cc_final: 0.6757 (mt0)
  outliers start: 14
  outliers final: 12
  residues processed: 137
  average time/residue: 0.2519
  time to fit residues: 50.8528
Evaluate side-chains
  137 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 125
  time to evaluate  : 1.299 
-------------------------------------------------------------------------------
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 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 97 optimal weight:    8.9990
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    9.9990
   chunk 48 optimal weight:    0.9980
   chunk 61 optimal weight:    0.0980
   chunk 84 optimal weight:    0.8980
   chunk 98 optimal weight:    0.7980
   chunk 115 optimal weight:    0.9990
   chunk 126 optimal weight:    0.9980
   chunk 128 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3919 r_free = 0.3919 target = 0.168193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112020 restraints weight = 22679.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3250 rms_B_bonded: 2.81
r_work: 0.3111 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3094
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3094 r_free = 0.3094    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3094
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.2382

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= 0.104
  Angle     :  0.460   8.880  16938  Z= 0.239
  Chirality :  0.039   0.139   1883
  Planarity :  0.003   0.040   2138
  Dihedral  :  3.421  18.138   1650
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 5.41
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.66 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  9.86 %
    Favored  : 89.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.22), residues: 1509
  helix:  2.10 (0.18), residues: 848
  sheet:  0.94 (0.49), residues: 112
  loop : -0.20 (0.26), residues: 549

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 473 
 HIS   0.004   0.001   HIS A1128 
 PHE   0.021   0.001   PHE A1330 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.006   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03147 (  695)
  hydrogen bonds       : angle       4.00140 ( 2038)
  covalent geometry    : bond        0.00246 (12535)
  covalent geometry    : angle       0.46040 (16938)

*********************** 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
  145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 1.387 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4372 (mpp) cc_final: 0.3404 (ttt)
REVERT: A  239 ASN cc_start: 0.8632 (t0) cc_final: 0.8380 (t0)
REVERT: A  457 ASN cc_start: 0.8327 (m110) cc_final: 0.7952 (t0)
REVERT: A  867 LYS cc_start: 0.8742 (tptm) cc_final: 0.8442 (tptt)
REVERT: A  892 ARG cc_start: 0.6827 (tpt170) cc_final: 0.6475 (mtt-85)
REVERT: A  963 LYS cc_start: 0.8017 (tttp) cc_final: 0.7705 (ttpt)
REVERT: A 1030 MET cc_start: 0.7094 (ptt) cc_final: 0.5882 (mmm)
REVERT: A 1172 LEU cc_start: 0.6244 (mm) cc_final: 0.6022 (mm)
REVERT: A 1204 ASP cc_start: 0.8109 (m-30) cc_final: 0.7624 (m-30)
REVERT: A 1341 PHE cc_start: 0.7851 (t80) cc_final: 0.7648 (t80)
REVERT: A 1445 GLN cc_start: 0.8283 (mp10) cc_final: 0.7762 (mt0)
REVERT: A 1483 ARG cc_start: 0.5655 (mmt180) cc_final: 0.5420 (tpp80)
REVERT: A 1572 VAL cc_start: 0.8162 (p) cc_final: 0.7927 (t)
REVERT: A 1575 GLN cc_start: 0.7493 (tt0) cc_final: 0.7242 (tt0)
  outliers start: 11
  outliers final: 9
  residues processed: 141
  average time/residue: 0.2729
  time to fit residues: 56.7356
Evaluate side-chains
  140 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 131
  time to evaluate  : 1.336 
-------------------------------------------------------------------------------
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 1271 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 142 optimal weight:    0.8980
   chunk 113 optimal weight:    1.9990
   chunk 126 optimal weight:    1.9990
   chunk 96 optimal weight:    0.8980
   chunk 57 optimal weight:    2.9990
   chunk 115 optimal weight:    0.7980
   chunk 137 optimal weight:    1.9990
   chunk 7 optimal weight:    9.9990
   chunk 100 optimal weight:    0.0570
   chunk 99 optimal weight:    0.9990
   chunk 121 optimal weight:    6.9990
   overall best weight:    0.7300

-------------------------------------------------------------------------------
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 = 0.3898 r_free = 0.3898 target = 0.166738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.118093 restraints weight = 26766.104|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.92
r_work: 0.3026 rms_B_bonded: 4.07 restraints_weight: 0.5000
r_work (final): 0.3026
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3031
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3031 r_free = 0.3031    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3031
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7753
moved from start:          0.2459

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= 0.104
  Angle     :  0.458   8.187  16938  Z= 0.237
  Chirality :  0.038   0.139   1883
  Planarity :  0.003   0.044   2138
  Dihedral  :  3.385  17.931   1650
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  3.12 %
    Favored  : 96.81 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.23 %
    Favored  : 88.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.85 (0.22), residues: 1509
  helix:  2.15 (0.18), residues: 850
  sheet:  0.96 (0.49), residues: 112
  loop : -0.16 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1056 
 HIS   0.003   0.001   HIS A1128 
 PHE   0.021   0.001   PHE A1330 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.006   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03111 (  695)
  hydrogen bonds       : angle       3.96691 ( 2038)
  covalent geometry    : bond        0.00245 (12535)
  covalent geometry    : angle       0.45762 (16938)

*********************** 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
  145 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 133
  time to evaluate  : 1.498 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4373 (mpp) cc_final: 0.3406 (ttt)
REVERT: A  239 ASN cc_start: 0.8651 (t0) cc_final: 0.8346 (t0)
REVERT: A  457 ASN cc_start: 0.8225 (m110) cc_final: 0.7818 (t0)
REVERT: A  541 ASP cc_start: 0.8168 (m-30) cc_final: 0.7611 (t0)
REVERT: A  867 LYS cc_start: 0.8537 (tptm) cc_final: 0.8157 (tptt)
REVERT: A  892 ARG cc_start: 0.6805 (tpt170) cc_final: 0.6373 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7917 (tttp) cc_final: 0.7540 (ttpt)
REVERT: A 1030 MET cc_start: 0.7076 (ptt) cc_final: 0.5811 (mmm)
REVERT: A 1172 LEU cc_start: 0.6458 (mm) cc_final: 0.6221 (mm)
REVERT: A 1204 ASP cc_start: 0.8075 (m-30) cc_final: 0.7545 (m-30)
REVERT: A 1341 PHE cc_start: 0.7919 (t80) cc_final: 0.7704 (t80)
REVERT: A 1445 GLN cc_start: 0.8283 (mp10) cc_final: 0.7713 (mt0)
REVERT: A 1483 ARG cc_start: 0.5744 (mmt180) cc_final: 0.5349 (tpp80)
REVERT: A 1572 VAL cc_start: 0.8038 (p) cc_final: 0.7803 (t)
REVERT: A 1575 GLN cc_start: 0.7394 (tt0) cc_final: 0.7125 (tt0)
  outliers start: 12
  outliers final: 11
  residues processed: 140
  average time/residue: 0.2435
  time to fit residues: 50.1177
Evaluate side-chains
  139 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 128
  time to evaluate  : 1.515 
-------------------------------------------------------------------------------
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  299 ILE
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 1351 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 120 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 11 optimal weight:   20.0000
   chunk 114 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 61 optimal weight:    0.7980
   chunk 91 optimal weight:    5.9990
   chunk 85 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9990
   chunk 130 optimal weight:    0.9980
   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
A1412 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.166454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.113013 restraints weight = 34241.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3268 rms_B_bonded: 3.49
r_work: 0.3034 rms_B_bonded: 3.85 restraints_weight: 0.5000
r_work (final): 0.3034
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3042
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3042 r_free = 0.3042    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3042
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2547

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= 0.111
  Angle     :  0.460   7.847  16938  Z= 0.239
  Chirality :  0.039   0.140   1883
  Planarity :  0.003   0.050   2138
  Dihedral  :  3.378  17.640   1650
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 4.88
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.66 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  1.04 %
    Allowed  : 10.45 %
    Favored  : 88.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.86 (0.22), residues: 1509
  helix:  2.16 (0.18), residues: 850
  sheet:  0.94 (0.49), residues: 112
  loop : -0.16 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A1056 
 HIS   0.003   0.001   HIS A1128 
 PHE   0.021   0.001   PHE A1330 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.005   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03167 (  695)
  hydrogen bonds       : angle       3.95754 ( 2038)
  covalent geometry    : bond        0.00267 (12535)
  covalent geometry    : angle       0.46050 (16938)

*********************** 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
  142 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 1.287 
Fit side-chains
REVERT: A   94 MET cc_start: 0.4453 (mpp) cc_final: 0.3557 (ttt)
REVERT: A  239 ASN cc_start: 0.8625 (t0) cc_final: 0.8294 (t0)
REVERT: A  457 ASN cc_start: 0.8194 (m110) cc_final: 0.7772 (t0)
REVERT: A  541 ASP cc_start: 0.8187 (m-30) cc_final: 0.7655 (t0)
REVERT: A  867 LYS cc_start: 0.8424 (tptm) cc_final: 0.8047 (tptt)
REVERT: A  892 ARG cc_start: 0.6777 (tpt170) cc_final: 0.6359 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7805 (tttp) cc_final: 0.7464 (ttpt)
REVERT: A 1030 MET cc_start: 0.7044 (ptt) cc_final: 0.5795 (mmm)
REVERT: A 1172 LEU cc_start: 0.6440 (mm) cc_final: 0.6196 (mm)
REVERT: A 1204 ASP cc_start: 0.8021 (m-30) cc_final: 0.7488 (m-30)
REVERT: A 1445 GLN cc_start: 0.8271 (mp10) cc_final: 0.7705 (mt0)
REVERT: A 1483 ARG cc_start: 0.5773 (mmt180) cc_final: 0.5349 (tpp80)
REVERT: A 1572 VAL cc_start: 0.8020 (p) cc_final: 0.7793 (t)
REVERT: A 1575 GLN cc_start: 0.7367 (tt0) cc_final: 0.7096 (tt0)
  outliers start: 14
  outliers final: 12
  residues processed: 137
  average time/residue: 0.2390
  time to fit residues: 48.3122
Evaluate side-chains
  138 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 126
  time to evaluate  : 1.303 
-------------------------------------------------------------------------------
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  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 1351 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 115 optimal weight:    0.9990
   chunk 83 optimal weight:    9.9990
   chunk 148 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   chunk 146 optimal weight:    0.9990
   chunk 139 optimal weight:    0.8980
   chunk 128 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 147 optimal weight:    5.9990
   chunk 119 optimal weight:    0.8980
   chunk 97 optimal weight:    0.0020
   overall best weight:    0.7188

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS
A1412 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.167435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.119234 restraints weight = 27080.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3336 rms_B_bonded: 4.15
r_work: 0.3045 rms_B_bonded: 3.86 restraints_weight: 0.5000
r_work (final): 0.3045
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3048
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3048 r_free = 0.3048    target_work(ls_wunit_k1) = 0.095         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3048
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2597

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= 0.102
  Angle     :  0.453   7.705  16938  Z= 0.235
  Chirality :  0.038   0.137   1883
  Planarity :  0.003   0.052   2138
  Dihedral  :  3.333  17.423   1650
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 5.09
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.79 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 10.75 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.92 (0.22), residues: 1509
  helix:  2.22 (0.18), residues: 849
  sheet:  0.93 (0.49), residues: 112
  loop : -0.15 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 473 
 HIS   0.004   0.001   HIS A1128 
 PHE   0.020   0.001   PHE A1330 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.005   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03043 (  695)
  hydrogen bonds       : angle       3.92203 ( 2038)
  covalent geometry    : bond        0.00240 (12535)
  covalent geometry    : angle       0.45280 (16938)

********************** 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
  144 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 1.383 
Fit side-chains
   revert: symmetry clash
REVERT: A   94 MET cc_start: 0.4404 (mpp) cc_final: 0.3496 (ttt)
REVERT: A  184 MET cc_start: 0.7744 (ptp) cc_final: 0.7011 (mmp)
REVERT: A  239 ASN cc_start: 0.8612 (t0) cc_final: 0.8280 (t0)
REVERT: A  457 ASN cc_start: 0.8162 (m110) cc_final: 0.7752 (t0)
REVERT: A  541 ASP cc_start: 0.8188 (m-30) cc_final: 0.7654 (t0)
REVERT: A  867 LYS cc_start: 0.8403 (tptm) cc_final: 0.8020 (tptt)
REVERT: A  892 ARG cc_start: 0.6789 (tpt170) cc_final: 0.6365 (mtt-85)
REVERT: A  963 LYS cc_start: 0.7818 (tttp) cc_final: 0.7499 (ttpt)
REVERT: A 1030 MET cc_start: 0.7025 (ptt) cc_final: 0.5797 (mmm)
REVERT: A 1172 LEU cc_start: 0.6346 (mm) cc_final: 0.6114 (mm)
REVERT: A 1204 ASP cc_start: 0.7952 (m-30) cc_final: 0.7414 (m-30)
REVERT: A 1445 GLN cc_start: 0.8267 (mp10) cc_final: 0.7714 (mt0)
REVERT: A 1483 ARG cc_start: 0.5846 (mmt180) cc_final: 0.5394 (tpp80)
REVERT: A 1572 VAL cc_start: 0.7988 (p) cc_final: 0.7758 (t)
REVERT: A 1575 GLN cc_start: 0.7296 (tt0) cc_final: 0.7076 (tt0)
  outliers start: 12
  outliers final: 10
  residues processed: 140
  average time/residue: 0.2420
  time to fit residues: 50.1673
Evaluate side-chains
  139 residues out of total 1347 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 1.382 
-------------------------------------------------------------------------------
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  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 1271 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 151
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 73 optimal weight:    0.9990
   chunk 70 optimal weight:    0.9990
   chunk 144 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 102 optimal weight:    0.5980
   chunk 90 optimal weight:    0.0980
   chunk 146 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.6584

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

Flipped N/Q/H residues before XYZ refinement:
A1128 HIS
A1412 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3908 r_free = 0.3908 target = 0.167784 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.118130 restraints weight = 24969.868|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 3.49
r_work: 0.3050 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3050
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3058
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3058 r_free = 0.3058    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.31   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3058
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2631

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= 0.099
  Angle     :  0.456   9.855  16938  Z= 0.234
  Chirality :  0.038   0.137   1883
  Planarity :  0.003   0.053   2138
  Dihedral  :  3.310  17.242   1650
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 4.80
  Ramachandran Plot:
    Outliers :  0.07 %
    Allowed  :  2.52 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 10.75 %
    Favored  : 88.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.22), residues: 1509
  helix:  2.28 (0.18), residues: 847
  sheet:  0.94 (0.49), residues: 112
  loop : -0.14 (0.26), residues: 550

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 473 
 HIS   0.003   0.001   HIS A1128 
 PHE   0.020   0.001   PHE A1330 
 TYR   0.012   0.001   TYR A 713 
 ARG   0.005   0.000   ARG A  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02993 (  695)
  hydrogen bonds       : angle       3.89847 ( 2038)
  covalent geometry    : bond        0.00232 (12535)
  covalent geometry    : angle       0.45600 (16938)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6590.14 seconds
wall clock time: 115 minutes 4.59 seconds (6904.59 seconds total)