Starting phenix.real_space_refine
on Tue Feb  3 19:01:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9q9z_52968/02_2026/9q9z_52968.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9q9z_52968/02_2026/9q9z_52968.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9q9z_52968/02_2026/9q9z_52968.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9q9z_52968/02_2026/9q9z_52968.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9q9z_52968/02_2026/9q9z_52968.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9q9z_52968/02_2026/9q9z_52968.map"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.019
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     Zn      5      6.06       5
     S      45      5.16       5
     C    3901      2.51       5
     N    1082      2.21       5
     O    1114      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 45 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6147
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 757, 6142
          Classifications: {'peptide': 757}
          Link IDs: {'PCIS': 1, 'PTRANS': 35, 'TRANS': 720}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' ZN': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5501  SG  CYS A1264      33.711  57.712  13.272  1.00 96.09           S
  ATOM   5683  SG  CYS A1288      34.448  61.020  11.334  1.00 99.28           S
  ATOM   5815  SG  CYS A1306      32.118  61.063  14.313  1.00114.99           S
  ATOM   5710  SG  CYS A1292      27.985  66.499  15.114  1.00122.94           S
  ATOM   5786  SG  CYS A1302      28.370  69.447  17.588  1.00140.83           S
  ATOM   5759  SG  CYS A1298      21.187  75.927  17.403  1.00150.71           S
  ATOM   5918  SG  CYS A1318      24.527  77.560  18.479  1.00162.94           S
  ATOM   6064  SG  CYS A1337      21.180  79.524  18.577  1.00171.18           S
  ATOM   5948  SG  CYS A1322      19.316  83.818  20.173  1.00178.37           S
  ATOM   6036  SG  CYS A1333      19.674  87.294  22.480  1.00195.56           S
  ATOM   6099  SG  CYS A1341      16.670  84.807  22.291  1.00184.28           S
  ATOM   5987  SG  CYS A1327      14.270  95.203  19.420  1.00208.21           S
  ATOM   6121  SG  CYS A1344      17.532  95.595  21.846  1.00216.20           S
  ATOM   6136  SG  CYS A1363      14.216  98.665  21.301  1.00217.54           S

  Time building chain proxies: 1.66, per 1000 atoms: 0.27
  Number of scatterers: 6147
  At special positions: 0
  Unit cell: (90.44, 108.29, 101.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      5     29.99
     S      45     16.00
     O    1114      8.00
     N    1082      7.00
     C    3901      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.60
  Conformation dependent library (CDL) restraints added in 248.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1401 "
        pdb="ZN    ZN A1401 " - pdb=" ND1 HIS A1267 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A1306 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A1288 "
        pdb="ZN    ZN A1401 " - pdb=" SG  CYS A1264 "
      pdb="  ZN A1402 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A1313 "
        pdb="ZN    ZN A1402 " - pdb=" NE2 HIS A1307 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A1302 "
        pdb="ZN    ZN A1402 " - pdb=" SG  CYS A1292 "
      pdb="  ZN A1403 "
        pdb="ZN    ZN A1403 " - pdb=" ND1 HIS A1300 "
        pdb="ZN    ZN A1403 " - pdb=" SG  CYS A1337 "
        pdb="ZN    ZN A1403 " - pdb=" SG  CYS A1298 "
        pdb="ZN    ZN A1403 " - pdb=" SG  CYS A1318 "
      pdb="  ZN A1404 "
        pdb="ZN    ZN A1404 " - pdb=" SG  CYS A1322 "
        pdb="ZN    ZN A1404 " - pdb=" SG  CYS A1341 "
        pdb="ZN    ZN A1404 " - pdb=" SG  CYS A1333 "
      pdb="  ZN A1405 "
        pdb="ZN    ZN A1405 " - pdb=" SG  CYS A1363 "
        pdb="ZN    ZN A1405 " - pdb=" SG  CYS A1327 "
        pdb="ZN    ZN A1405 " - pdb=" ND1 HIS A1331 "
        pdb="ZN    ZN A1405 " - pdb=" SG  CYS A1344 "
      Number of angles added : 11


  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1444

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 6 sheets defined
      41.5% alpha, 14.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 341 through 347
    Processing helix  chain 'A' and resid 364 through 395
      Proline residue:  A 383  - end of helix
    Processing helix  chain 'A' and resid 473 through 479
      removed outlier: 3.541A  pdb=" N   ARG A 479 " --> pdb=" O   GLU A 475 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 487 through 495
      removed outlier: 3.882A  pdb=" N   GLN A 492 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   LEU A 493 " --> pdb=" O   GLN A 489 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   ALA A 495 " --> pdb=" O   GLN A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 525
      removed outlier: 4.012A  pdb=" N   TYR A 515 " --> pdb=" O   TYR A 511 " (cutoff:3.500A)
      removed outlier: 4.448A  pdb=" N   VAL A 518 " --> pdb=" O   ALA A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 532 through 537
    Processing helix  chain 'A' and resid 546 through 550
    Processing helix  chain 'A' and resid 557 through 563
    Processing helix  chain 'A' and resid 586 through 590
    Processing helix  chain 'A' and resid 599 through 612
    Processing helix  chain 'A' and resid 625 through 639
    Processing helix  chain 'A' and resid 639 through 644
      removed outlier: 4.084A  pdb=" N   TRP A 643 " --> pdb=" O   ASN A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 670
    Processing helix  chain 'A' and resid 689 through 692
    Processing helix  chain 'A' and resid 693 through 699
    Processing helix  chain 'A' and resid 700 through 707
    Processing helix  chain 'A' and resid 708 through 717
    Processing helix  chain 'A' and resid 969 through 977
      removed outlier: 4.026A  pdb=" N   HIS A 973 " --> pdb=" O   GLN A 969 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   ASP A 977 " --> pdb=" O   HIS A 973 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 991
    Processing helix  chain 'A' and resid 991 through 999
    Processing helix  chain 'A' and resid 1007 through 1011
    Processing helix  chain 'A' and resid 1012 through 1020
    Processing helix  chain 'A' and resid 1042 through 1049
    Processing helix  chain 'A' and resid 1054 through 1062
    Processing helix  chain 'A' and resid 1076 through 1084
      removed outlier: 4.113A  pdb=" N   LEU A1082 " --> pdb=" O   GLU A1078 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LEU A1083 " --> pdb=" O   ILE A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1094 through 1100
    Processing helix  chain 'A' and resid 1130 through 1146
    Processing helix  chain 'A' and resid 1150 through 1152
      No H-bonds generated for 'chain 'A' and resid 1150 through 1152'
    Processing helix  chain 'A' and resid 1160 through 1170
    Processing helix  chain 'A' and resid 1185 through 1188
      removed outlier: 3.941A  pdb=" N   GLN A1188 " --> pdb=" O   ASP A1185 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1185 through 1188'
    Processing helix  chain 'A' and resid 1213 through 1221
      removed outlier: 3.660A  pdb=" N   ILE A1217 " --> pdb=" O   ILE A1213 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1233 through 1238
      removed outlier: 3.567A  pdb=" N   LEU A1237 " --> pdb=" O   ASN A1233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1240 through 1253
    Processing helix  chain 'A' and resid 1276 through 1283
      removed outlier: 3.795A  pdb=" N   LYS A1282 " --> pdb=" O   ASP A1279 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 408 through 422
      removed outlier: 5.486A  pdb=" N   ILE A 416 " --> pdb=" O   GLN A 431 " (cutoff:3.500A)
      removed outlier: 6.701A  pdb=" N   GLN A 431 " --> pdb=" O   ILE A 416 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   THR A 418 " --> pdb=" O   LYS A 429 " (cutoff:3.500A)
      removed outlier: 6.968A  pdb=" N   ILE A 426 " --> pdb=" O   PHE A 486 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   PHE A 486 " --> pdb=" O   ILE A 426 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   GLN A 483 " --> pdb=" O   SER A 470 " (cutoff:3.500A)
      removed outlier: 6.059A  pdb=" N   LEU A 453 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   THR A 508 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   MET A 505 " --> pdb=" O   PHE A 412 " (cutoff:3.500A)
      removed outlier: 5.921A  pdb=" N   PHE A 412 " --> pdb=" O   MET A 505 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   GLU A 507 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 5.967A  pdb=" N   ILE A 410 " --> pdb=" O   GLU A 507 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 554 through 555
    Processing sheet with id=AA3, first strand: chain 'A' and resid 677 through 679
      removed outlier: 3.530A  pdb=" N   ILE A1030 " --> pdb=" O   VAL A1005 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   ALA A 615 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1180 through 1183
      removed outlier: 4.275A  pdb=" N   ARG A1180 " --> pdb=" O   ILE A1154 " (cutoff:3.500A)
      removed outlier: 7.345A  pdb=" N   ASP A1193 " --> pdb=" O   LYS A1225 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   PHE A1111 " --> pdb=" O   CYS A1230 " (cutoff:3.500A)
      removed outlier: 8.223A  pdb=" N   GLY A1257 " --> pdb=" O   LEU A1110 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   PHE A1112 " --> pdb=" O   GLY A1257 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 1120 through 1121
      removed outlier: 3.615A  pdb=" N   GLN A1129 " --> pdb=" O   GLN A1120 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1260 through 1263

    224 hydrogen bonds defined for protein.
    606 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: 1.05

  Time building geometry restraints manager: 0.77 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: 2041
        1.34 -     1.46: 1182
        1.46 -     1.58: 2987
        1.58 -     1.69: 0
        1.69 -     1.81: 61
  Bond restraints: 6271
  Sorted by residual:
  bond pdb=" N   THR A 418 "
       pdb=" CA  THR A 418 "
    ideal  model  delta    sigma   weight residual
    1.454  1.473 -0.019 1.30e-02 5.92e+03 2.12e+00
  bond pdb=" CG1 ILE A1002 "
       pdb=" CD1 ILE A1002 "
    ideal  model  delta    sigma   weight residual
    1.513  1.460  0.053 3.90e-02 6.57e+02 1.83e+00
  bond pdb=" C   ILE A 338 "
       pdb=" N   TYR A 339 "
    ideal  model  delta    sigma   weight residual
    1.331  1.315  0.016 1.48e-02 4.57e+03 1.19e+00
  bond pdb=" CA  VAL A1240 "
       pdb=" CB  VAL A1240 "
    ideal  model  delta    sigma   weight residual
    1.537  1.523  0.014 1.29e-02 6.01e+03 1.15e+00
  bond pdb=" CB  GLU A1101 "
       pdb=" CG  GLU A1101 "
    ideal  model  delta    sigma   weight residual
    1.520  1.552 -0.032 3.00e-02 1.11e+03 1.13e+00
  ... (remaining 6266 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.49: 8348
        2.49 -     4.97: 109
        4.97 -     7.46: 11
        7.46 -     9.95: 2
        9.95 -    12.43: 2
  Bond angle restraints: 8472
  Sorted by residual:
  angle pdb=" CB  MET A1228 "
        pdb=" CG  MET A1228 "
        pdb=" SD  MET A1228 "
      ideal   model   delta    sigma   weight residual
     112.70  123.50  -10.80 3.00e+00 1.11e-01 1.30e+01
  angle pdb=" N   ILE A 645 "
        pdb=" CA  ILE A 645 "
        pdb=" C   ILE A 645 "
      ideal   model   delta    sigma   weight residual
     111.90  109.00    2.90 8.10e-01 1.52e+00 1.28e+01
  angle pdb=" CA  LEU A 347 "
        pdb=" CB  LEU A 347 "
        pdb=" CG  LEU A 347 "
      ideal   model   delta    sigma   weight residual
     116.30  128.73  -12.43 3.50e+00 8.16e-02 1.26e+01
  angle pdb=" CA  MET A1171 "
        pdb=" CB  MET A1171 "
        pdb=" CG  MET A1171 "
      ideal   model   delta    sigma   weight residual
     114.10  120.95   -6.85 2.00e+00 2.50e-01 1.17e+01
  angle pdb=" N   LYS A 625 "
        pdb=" CA  LYS A 625 "
        pdb=" C   LYS A 625 "
      ideal   model   delta    sigma   weight residual
     114.04  109.90    4.14 1.24e+00 6.50e-01 1.12e+01
  ... (remaining 8467 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.72: 3339
       16.72 -    33.44: 384
       33.44 -    50.16: 84
       50.16 -    66.87: 22
       66.87 -    83.59: 5
  Dihedral angle restraints: 3834
    sinusoidal: 1610
      harmonic: 2224
  Sorted by residual:
  dihedral pdb=" CA  PHE A 512 "
           pdb=" C   PHE A 512 "
           pdb=" N   GLU A 513 "
           pdb=" CA  GLU A 513 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.03  -18.97     0      5.00e+00 4.00e-02 1.44e+01
  dihedral pdb=" CA  PHE A 461 "
           pdb=" C   PHE A 461 "
           pdb=" N   GLU A 462 "
           pdb=" CA  GLU A 462 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.14   17.86     0      5.00e+00 4.00e-02 1.28e+01
  dihedral pdb=" CA  ILE A 416 "
           pdb=" C   ILE A 416 "
           pdb=" N   ILE A 417 "
           pdb=" CA  ILE A 417 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.54  -16.46     0      5.00e+00 4.00e-02 1.08e+01
  ... (remaining 3831 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.043: 658
       0.043 -    0.086: 207
       0.086 -    0.129: 65
       0.129 -    0.172: 7
       0.172 -    0.215: 1
  Chirality restraints: 938
  Sorted by residual:
  chirality pdb=" CB  VAL A 381 "
            pdb=" CA  VAL A 381 "
            pdb=" CG1 VAL A 381 "
            pdb=" CG2 VAL A 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" CA  ILE A1002 "
            pdb=" N   ILE A1002 "
            pdb=" C   ILE A1002 "
            pdb=" CB  ILE A1002 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 6.95e-01
  chirality pdb=" CB  ILE A 652 "
            pdb=" CA  ILE A 652 "
            pdb=" CG1 ILE A 652 "
            pdb=" CG2 ILE A 652 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.16 2.00e-01 2.50e+01 6.65e-01
  ... (remaining 935 not shown)

  Planarity restraints: 1099
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 476 "    0.012 2.00e-02 2.50e+03   2.49e-02 6.21e+00
        pdb=" CG  ASP A 476 "   -0.043 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 476 "    0.016 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 476 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 532 "   -0.005 2.00e-02 2.50e+03   1.02e-02 1.81e+00
        pdb=" CG  PHE A 532 "    0.022 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 532 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 532 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 532 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 532 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 532 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1084 "   -0.022 5.00e-02 4.00e+02   3.30e-02 1.74e+00
        pdb=" N   PRO A1085 "    0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A1085 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A1085 "   -0.017 5.00e-02 4.00e+02
  ... (remaining 1096 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 2851
        2.97 -     3.45: 6391
        3.45 -     3.93: 9878
        3.93 -     4.42: 11099
        4.42 -     4.90: 17484
  Nonbonded interactions: 47703
  Sorted by model distance:
  nonbonded pdb=" O   TYR A 450 "
            pdb=" OE2 GLU A 513 "
     model   vdw
     2.482 3.040
  nonbonded pdb=" N   GLU A 496 "
            pdb=" OE1 GLU A 496 "
     model   vdw
     2.521 3.120
  nonbonded pdb=" OD1 ASP A 476 "
            pdb=" O   ILE A 481 "
     model   vdw
     2.541 3.040
  nonbonded pdb=" N   GLU A1101 "
            pdb=" OE1 GLU A1101 "
     model   vdw
     2.555 3.120
  nonbonded pdb=" N   VAL A1062 "
            pdb=" N   ASN A1063 "
     model   vdw
     2.593 2.560
  ... (remaining 47698 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.630
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.540
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.490
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7099
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      :  0.007   0.407   6290  Z= 0.258
  Angle     :  0.765  17.583   8483  Z= 0.400
  Chirality :  0.045   0.215    938
  Planarity :  0.004   0.033   1099
  Dihedral  : 15.111  83.594   2390
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.94 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.70 %
    Favored  : 79.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.10 (0.31), residues: 749
  helix: -0.22 (0.31), residues: 269
  sheet: -0.70 (0.48), residues: 120
  loop :  0.54 (0.34), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 534 
 TYR   0.018   0.002   TYR A 428 
 PHE   0.022   0.002   PHE A 532 
 TRP   0.013   0.002   TRP A1243 
 HIS   0.004   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00365 ( 6271)
  covalent geometry    : angle       0.73356 ( 8472)
  hydrogen bonds       : bond        0.23115 (  224)
  hydrogen bonds       : angle       7.84048 (  606)
  metal coordination   : bond        0.10711 (   19)
  metal coordination   : angle       6.04679 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 99
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 GLN cc_start: 0.7945 (tt0) cc_final: 0.7391 (pt0)
REVERT: A  420 MET cc_start: 0.6745 (mmm) cc_final: 0.6450 (mmm)
REVERT: A  493 LEU cc_start: 0.8482 (mp) cc_final: 0.8228 (mt)
REVERT: A 1229 TYR cc_start: 0.7745 (m-80) cc_final: 0.7462 (m-10)
  outliers start: 10
  outliers final: 6
  residues processed: 106
  average time/residue: 0.0763
  time to fit residues: 11.0148
Evaluate side-chains
  81 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  688 ILE
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue 1161 THR
Chi-restraints excluded: chain A residue 1256 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    4.9990
   chunk 45 optimal weight:    0.3980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 443 GLN
A 542 HIS
** A1015 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1041 ASN
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 GLN
A1182 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.138574 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.118434 restraints weight = 15516.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.120859 restraints weight = 10207.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.122595 restraints weight = 7469.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3865 r_free = 0.3865 target = 0.123836 restraints weight = 5948.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.124719 restraints weight = 5028.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7040
moved from start:          0.1541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6290  Z= 0.127
  Angle     :  0.599   8.526   8483  Z= 0.304
  Chirality :  0.043   0.171    938
  Planarity :  0.004   0.039   1099
  Dihedral  :  5.073  59.267    838
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.31
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.54 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.94 %
    Favored  : 80.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.32), residues: 749
  helix:  0.19 (0.32), residues: 259
  sheet: -0.40 (0.48), residues: 120
  loop :  0.78 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1168 
 TYR   0.013   0.001   TYR A 368 
 PHE   0.021   0.002   PHE A 380 
 TRP   0.007   0.001   TRP A 643 
 HIS   0.005   0.001   HIS A 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6271)
  covalent geometry    : angle       0.59537 ( 8472)
  hydrogen bonds       : bond        0.04260 (  224)
  hydrogen bonds       : angle       5.38277 (  606)
  metal coordination   : bond        0.00710 (   19)
  metal coordination   : angle       1.82997 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.246 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 GLN cc_start: 0.8017 (tt0) cc_final: 0.7503 (pt0)
REVERT: A  420 MET cc_start: 0.6842 (mmm) cc_final: 0.6529 (mmm)
REVERT: A 1052 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7508 (mp0)
  outliers start: 22
  outliers final: 10
  residues processed: 100
  average time/residue: 0.0815
  time to fit residues: 10.9322
Evaluate side-chains
  89 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1120 GLN
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1256 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 21 optimal weight:    0.0670
   chunk 27 optimal weight:    0.9990
   chunk 49 optimal weight:    0.6980
   chunk 55 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 35 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 542 HIS
A1015 HIS
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1072 GLN
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.138268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.117968 restraints weight = 15584.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.120448 restraints weight = 10314.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.122212 restraints weight = 7609.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.123454 restraints weight = 6067.163|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.124333 restraints weight = 5128.320|
|-----------------------------------------------------------------------------|
r_work (final): 0.3872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7050
moved from start:          0.1944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6290  Z= 0.110
  Angle     :  0.549   7.926   8483  Z= 0.280
  Chirality :  0.042   0.172    938
  Planarity :  0.004   0.037   1099
  Dihedral  :  4.827  58.001    834
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.80 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 16.52 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.56 (0.32), residues: 749
  helix:  0.38 (0.32), residues: 259
  sheet: -0.33 (0.48), residues: 120
  loop :  0.86 (0.35), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 713 
 TYR   0.013   0.001   TYR A 368 
 PHE   0.008   0.001   PHE A1056 
 TRP   0.006   0.001   TRP A 643 
 HIS   0.006   0.001   HIS A1182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 6271)
  covalent geometry    : angle       0.54647 ( 8472)
  hydrogen bonds       : bond        0.03892 (  224)
  hydrogen bonds       : angle       5.01426 (  606)
  metal coordination   : bond        0.00369 (   19)
  metal coordination   : angle       1.57053 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 MET cc_start: 0.8304 (mtt) cc_final: 0.8098 (mtm)
REVERT: A  393 GLN cc_start: 0.8078 (tt0) cc_final: 0.7547 (pt0)
REVERT: A  679 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8580 (tpt-90)
  outliers start: 17
  outliers final: 11
  residues processed: 104
  average time/residue: 0.0936
  time to fit residues: 12.6369
Evaluate side-chains
  87 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  679 ARG
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1108 SER
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1145 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 24 optimal weight:    5.9990
   chunk 2 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 60 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 12 optimal weight:    5.9990
   chunk 47 optimal weight:    4.9990
   chunk 31 optimal weight:    0.7980
   chunk 71 optimal weight:   20.0000
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 346 HIS
A 526 GLN
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1109 ASN
A1120 GLN
** A1323 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.133785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.113590 restraints weight = 15690.810|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.115849 restraints weight = 10665.888|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.117239 restraints weight = 8003.253|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.118564 restraints weight = 6563.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.119391 restraints weight = 5584.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.3013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   6290  Z= 0.189
  Angle     :  0.642   7.272   8483  Z= 0.331
  Chirality :  0.044   0.190    938
  Planarity :  0.004   0.041   1099
  Dihedral  :  5.309  58.176    832
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  3.07 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.64 %
    Allowed  : 15.80 %
    Favored  : 79.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.06 (0.31), residues: 749
  helix: -0.16 (0.31), residues: 276
  sheet: -0.37 (0.47), residues: 120
  loop :  0.43 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 612 
 TYR   0.016   0.002   TYR A 368 
 PHE   0.014   0.002   PHE A1056 
 TRP   0.008   0.001   TRP A 643 
 HIS   0.006   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 6271)
  covalent geometry    : angle       0.63414 ( 8472)
  hydrogen bonds       : bond        0.04406 (  224)
  hydrogen bonds       : angle       5.10520 (  606)
  metal coordination   : bond        0.00683 (   19)
  metal coordination   : angle       2.82003 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 78
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 MET cc_start: 0.8123 (mtt) cc_final: 0.7890 (mtm)
REVERT: A  393 GLN cc_start: 0.8174 (tt0) cc_final: 0.7813 (pt0)
REVERT: A  660 HIS cc_start: 0.7744 (OUTLIER) cc_final: 0.7145 (p90)
REVERT: A 1120 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7457 (mp10)
REVERT: A 1283 VAL cc_start: 0.5948 (OUTLIER) cc_final: 0.5563 (m)
REVERT: A 1285 GLU cc_start: 0.7773 (mp0) cc_final: 0.7467 (mt-10)
  outliers start: 32
  outliers final: 21
  residues processed: 101
  average time/residue: 0.0820
  time to fit residues: 10.8831
Evaluate side-chains
  94 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  660 HIS
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue  981 VAL
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1075 MET
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1120 GLN
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1176 PHE
Chi-restraints excluded: chain A residue 1230 CYS
Chi-restraints excluded: chain A residue 1244 SER
Chi-restraints excluded: chain A residue 1246 ILE
Chi-restraints excluded: chain A residue 1256 ILE
Chi-restraints excluded: chain A residue 1283 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 36 optimal weight:    5.9990
   chunk 51 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 2 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 4 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9980
   chunk 47 optimal weight:    0.7980
   chunk 42 optimal weight:    0.0770
   chunk 31 optimal weight:    0.5980
   overall best weight:    0.6538

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

Flipped N/Q/H residues before XYZ refinement:
A 526 GLN
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1192 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.136081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.116167 restraints weight = 16025.300|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.118657 restraints weight = 10600.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.120396 restraints weight = 7813.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.121627 restraints weight = 6238.887|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.122248 restraints weight = 5277.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7163
moved from start:          0.3224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6290  Z= 0.118
  Angle     :  0.582   9.197   8483  Z= 0.293
  Chirality :  0.042   0.177    938
  Planarity :  0.004   0.034   1099
  Dihedral  :  5.052  57.018    832
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  2.27 %
    Favored  : 97.46 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 16.23 %
    Favored  : 80.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.41 (0.32), residues: 749
  helix:  0.34 (0.33), residues: 259
  sheet: -0.28 (0.47), residues: 120
  loop :  0.64 (0.34), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 612 
 TYR   0.012   0.001   TYR A 368 
 PHE   0.010   0.001   PHE A1056 
 TRP   0.007   0.001   TRP A 643 
 HIS   0.004   0.001   HIS A1182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6271)
  covalent geometry    : angle       0.57828 ( 8472)
  hydrogen bonds       : bond        0.03766 (  224)
  hydrogen bonds       : angle       4.84792 (  606)
  metal coordination   : bond        0.00372 (   19)
  metal coordination   : angle       1.96167 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 MET cc_start: 0.8127 (mtt) cc_final: 0.7896 (mtm)
REVERT: A  393 GLN cc_start: 0.8164 (tt0) cc_final: 0.7712 (pt0)
REVERT: A  690 LYS cc_start: 0.8423 (tppt) cc_final: 0.8055 (tppt)
REVERT: A  995 LEU cc_start: 0.8698 (mt) cc_final: 0.7615 (tp)
REVERT: A 1120 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7687 (mp10)
REVERT: A 1283 VAL cc_start: 0.5819 (OUTLIER) cc_final: 0.5397 (m)
REVERT: A 1285 GLU cc_start: 0.7808 (mp0) cc_final: 0.7480 (mt-10)
  outliers start: 24
  outliers final: 16
  residues processed: 108
  average time/residue: 0.0812
  time to fit residues: 11.7755
Evaluate side-chains
  95 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 77
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1120 GLN
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1230 CYS
Chi-restraints excluded: chain A residue 1244 SER
Chi-restraints excluded: chain A residue 1256 ILE
Chi-restraints excluded: chain A residue 1283 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 0 optimal weight:    5.9990
   chunk 37 optimal weight:    0.0030
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 23 optimal weight:    0.5980
   chunk 16 optimal weight:    6.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1120 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.135995 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.116228 restraints weight = 15788.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.118661 restraints weight = 10466.332|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.120211 restraints weight = 7751.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.121572 restraints weight = 6254.594|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.122215 restraints weight = 5280.847|
|-----------------------------------------------------------------------------|
r_work (final): 0.3836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7164
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6290  Z= 0.117
  Angle     :  0.585   7.765   8483  Z= 0.295
  Chirality :  0.043   0.210    938
  Planarity :  0.004   0.036   1099
  Dihedral  :  5.028  56.797    832
  Min Nonbonded Distance : 2.416

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.20 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.81 %
    Favored  : 79.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.31), residues: 749
  helix:  0.37 (0.33), residues: 258
  sheet: -0.27 (0.47), residues: 120
  loop :  0.59 (0.34), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 612 
 TYR   0.017   0.001   TYR A1229 
 PHE   0.010   0.001   PHE A1056 
 TRP   0.006   0.001   TRP A 643 
 HIS   0.003   0.001   HIS A1182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 ( 6271)
  covalent geometry    : angle       0.58212 ( 8472)
  hydrogen bonds       : bond        0.03736 (  224)
  hydrogen bonds       : angle       4.80640 (  606)
  metal coordination   : bond        0.00430 (   19)
  metal coordination   : angle       1.81937 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.266 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  336 MET cc_start: 0.8060 (mtt) cc_final: 0.7839 (mtm)
REVERT: A  393 GLN cc_start: 0.8124 (tt0) cc_final: 0.7699 (pt0)
REVERT: A  446 LYS cc_start: 0.6742 (mttt) cc_final: 0.5618 (tttt)
REVERT: A  687 GLU cc_start: 0.8163 (tp30) cc_final: 0.7867 (tp30)
REVERT: A  995 LEU cc_start: 0.8600 (mt) cc_final: 0.7627 (tp)
REVERT: A 1283 VAL cc_start: 0.5859 (OUTLIER) cc_final: 0.5475 (m)
REVERT: A 1285 GLU cc_start: 0.7843 (mp0) cc_final: 0.7539 (mt-10)
  outliers start: 26
  outliers final: 22
  residues processed: 104
  average time/residue: 0.0839
  time to fit residues: 11.7992
Evaluate side-chains
  102 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 79
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1120 GLN
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1145 LEU
Chi-restraints excluded: chain A residue 1230 CYS
Chi-restraints excluded: chain A residue 1244 SER
Chi-restraints excluded: chain A residue 1256 ILE
Chi-restraints excluded: chain A residue 1283 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 56 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9990
   chunk 47 optimal weight:    0.7980
   chunk 23 optimal weight:    0.9980
   chunk 7 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 3 optimal weight:    0.0270
   chunk 2 optimal weight:    2.9990
   chunk 4 optimal weight:    0.6980
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
A 474 GLN
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1072 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.136697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.116958 restraints weight = 15844.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.119382 restraints weight = 10473.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.121124 restraints weight = 7739.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.122399 restraints weight = 6161.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.123288 restraints weight = 5189.606|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.3653

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6290  Z= 0.111
  Angle     :  0.584  10.425   8483  Z= 0.292
  Chirality :  0.043   0.171    938
  Planarity :  0.004   0.032   1099
  Dihedral  :  5.008  59.424    832
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 10.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 18.41 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.51 (0.31), residues: 749
  helix:  0.48 (0.33), residues: 258
  sheet: -0.05 (0.48), residues: 112
  loop :  0.56 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 612 
 TYR   0.012   0.001   TYR A 368 
 PHE   0.011   0.001   PHE A1056 
 TRP   0.005   0.001   TRP A 643 
 HIS   0.004   0.001   HIS A1128 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 ( 6271)
  covalent geometry    : angle       0.58160 ( 8472)
  hydrogen bonds       : bond        0.03571 (  224)
  hydrogen bonds       : angle       4.69465 (  606)
  metal coordination   : bond        0.00308 (   19)
  metal coordination   : angle       1.69491 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 GLN cc_start: 0.8093 (tt0) cc_final: 0.7599 (pt0)
REVERT: A  446 LYS cc_start: 0.6810 (mttt) cc_final: 0.5968 (mtpt)
REVERT: A  687 GLU cc_start: 0.8160 (tp30) cc_final: 0.7867 (tp30)
REVERT: A  995 LEU cc_start: 0.8588 (mt) cc_final: 0.7605 (tp)
REVERT: A 1283 VAL cc_start: 0.5821 (OUTLIER) cc_final: 0.5423 (m)
REVERT: A 1285 GLU cc_start: 0.7849 (mp0) cc_final: 0.7549 (mt-10)
REVERT: A 1304 ARG cc_start: 0.6540 (mtm180) cc_final: 0.6154 (mtm180)
  outliers start: 23
  outliers final: 20
  residues processed: 108
  average time/residue: 0.0749
  time to fit residues: 10.8867
Evaluate side-chains
  102 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 81
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1075 MET
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1230 CYS
Chi-restraints excluded: chain A residue 1244 SER
Chi-restraints excluded: chain A residue 1256 ILE
Chi-restraints excluded: chain A residue 1283 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0370
   chunk 5 optimal weight:    0.7980
   chunk 68 optimal weight:    3.9990
   chunk 73 optimal weight:    4.9990
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0870
   chunk 41 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.7638

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

Flipped N/Q/H residues before XYZ refinement:
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1072 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.136009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.116172 restraints weight = 15741.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.118601 restraints weight = 10461.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.120313 restraints weight = 7714.449|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.121528 restraints weight = 6161.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.122307 restraints weight = 5216.317|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6290  Z= 0.125
  Angle     :  0.624  13.528   8483  Z= 0.306
  Chirality :  0.044   0.228    938
  Planarity :  0.004   0.032   1099
  Dihedral  :  5.015  55.717    832
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 17.39 %
    Favored  : 78.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.42 (0.32), residues: 749
  helix:  0.39 (0.33), residues: 264
  sheet: -0.02 (0.49), residues: 112
  loop :  0.50 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 612 
 TYR   0.013   0.001   TYR A 368 
 PHE   0.012   0.001   PHE A1056 
 TRP   0.005   0.001   TRP A 643 
 HIS   0.003   0.001   HIS A 372 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 6271)
  covalent geometry    : angle       0.60345 ( 8472)
  hydrogen bonds       : bond        0.03689 (  224)
  hydrogen bonds       : angle       4.71801 (  606)
  metal coordination   : bond        0.00764 (   19)
  metal coordination   : angle       4.47907 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 80
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 GLN cc_start: 0.8105 (tt0) cc_final: 0.7699 (pt0)
REVERT: A  446 LYS cc_start: 0.6829 (mttt) cc_final: 0.5982 (mtpt)
REVERT: A  660 HIS cc_start: 0.7569 (OUTLIER) cc_final: 0.6799 (p90)
REVERT: A  687 GLU cc_start: 0.8182 (tp30) cc_final: 0.7903 (tp30)
REVERT: A  995 LEU cc_start: 0.8580 (mt) cc_final: 0.7608 (tp)
REVERT: A 1283 VAL cc_start: 0.5829 (OUTLIER) cc_final: 0.5435 (m)
REVERT: A 1285 GLU cc_start: 0.7901 (mp0) cc_final: 0.7579 (mt-10)
REVERT: A 1304 ARG cc_start: 0.6678 (mtm180) cc_final: 0.6283 (mtm180)
  outliers start: 30
  outliers final: 24
  residues processed: 101
  average time/residue: 0.0771
  time to fit residues: 10.5386
Evaluate side-chains
  104 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 78
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  630 LEU
Chi-restraints excluded: chain A residue  660 HIS
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1075 MET
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1106 VAL
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1145 LEU
Chi-restraints excluded: chain A residue 1161 THR
Chi-restraints excluded: chain A residue 1230 CYS
Chi-restraints excluded: chain A residue 1244 SER
Chi-restraints excluded: chain A residue 1256 ILE
Chi-restraints excluded: chain A residue 1283 VAL
Chi-restraints excluded: chain A residue 1298 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 24 optimal weight:    0.0970
   chunk 55 optimal weight:    0.6980
   chunk 5 optimal weight:    0.6980
   chunk 51 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 12 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 36 optimal weight:    0.2980
   chunk 38 optimal weight:    1.9990
   chunk 27 optimal weight:    2.9990
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1072 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.136803 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.116857 restraints weight = 15968.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.119321 restraints weight = 10636.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.121067 restraints weight = 7857.309|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.122322 restraints weight = 6269.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.123058 restraints weight = 5300.316|
|-----------------------------------------------------------------------------|
r_work (final): 0.3857
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.4071

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6290  Z= 0.112
  Angle     :  0.621  13.743   8483  Z= 0.306
  Chirality :  0.044   0.213    938
  Planarity :  0.004   0.031   1099
  Dihedral  :  4.886  55.042    832
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 12.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 18.12 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.48 (0.32), residues: 749
  helix:  0.45 (0.33), residues: 264
  sheet: -0.07 (0.48), residues: 112
  loop :  0.57 (0.34), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 612 
 TYR   0.011   0.001   TYR A 368 
 PHE   0.011   0.001   PHE A 512 
 TRP   0.006   0.001   TRP A 442 
 HIS   0.003   0.001   HIS A1182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6271)
  covalent geometry    : angle       0.61127 ( 8472)
  hydrogen bonds       : bond        0.03565 (  224)
  hydrogen bonds       : angle       4.62060 (  606)
  metal coordination   : bond        0.00463 (   19)
  metal coordination   : angle       3.05502 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 84
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 GLN cc_start: 0.8174 (tt0) cc_final: 0.7674 (pt0)
REVERT: A  446 LYS cc_start: 0.6841 (mttt) cc_final: 0.6007 (mtpt)
REVERT: A  660 HIS cc_start: 0.7547 (OUTLIER) cc_final: 0.6588 (p90)
REVERT: A  687 GLU cc_start: 0.8164 (tp30) cc_final: 0.7819 (tp30)
REVERT: A  995 LEU cc_start: 0.8556 (mt) cc_final: 0.7595 (tp)
REVERT: A 1052 GLU cc_start: 0.8093 (mp0) cc_final: 0.7820 (mp0)
REVERT: A 1283 VAL cc_start: 0.5760 (OUTLIER) cc_final: 0.5455 (m)
REVERT: A 1285 GLU cc_start: 0.7897 (mp0) cc_final: 0.7560 (mt-10)
REVERT: A 1304 ARG cc_start: 0.6651 (mtm180) cc_final: 0.6327 (mtm180)
  outliers start: 28
  outliers final: 20
  residues processed: 105
  average time/residue: 0.0767
  time to fit residues: 10.8923
Evaluate side-chains
  102 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 80
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  660 HIS
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1075 MET
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1145 LEU
Chi-restraints excluded: chain A residue 1161 THR
Chi-restraints excluded: chain A residue 1230 CYS
Chi-restraints excluded: chain A residue 1256 ILE
Chi-restraints excluded: chain A residue 1283 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 28 optimal weight:    4.9990
   chunk 29 optimal weight:    0.0980
   chunk 48 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 52 optimal weight:    4.9990
   chunk 40 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0870
   overall best weight:    0.4358

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

Flipped N/Q/H residues before XYZ refinement:
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1072 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.138152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.118363 restraints weight = 15897.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.120814 restraints weight = 10556.689|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.122557 restraints weight = 7799.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.123784 restraints weight = 6210.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3880 r_free = 0.3880 target = 0.124540 restraints weight = 5241.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.4222

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6290  Z= 0.113
  Angle     :  0.638  13.716   8483  Z= 0.312
  Chirality :  0.044   0.236    938
  Planarity :  0.004   0.032   1099
  Dihedral  :  4.822  54.337    832
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 11.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.70 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.32), residues: 749
  helix:  0.61 (0.33), residues: 258
  sheet:  0.04 (0.48), residues: 112
  loop :  0.62 (0.34), residues: 379

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 612 
 TYR   0.024   0.001   TYR A1100 
 PHE   0.016   0.001   PHE A 512 
 TRP   0.005   0.001   TRP A1243 
 HIS   0.003   0.001   HIS A1182 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6271)
  covalent geometry    : angle       0.63249 ( 8472)
  hydrogen bonds       : bond        0.03558 (  224)
  hydrogen bonds       : angle       4.61349 (  606)
  metal coordination   : bond        0.00349 (   19)
  metal coordination   : angle       2.49303 (   11)

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

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

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1498 Ramachandran restraints generated.
    749 Oldfield, 0 Emsley, 749 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 83
  time to evaluate  : 0.250 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  393 GLN cc_start: 0.8197 (tt0) cc_final: 0.7685 (pt0)
REVERT: A  446 LYS cc_start: 0.6827 (mttt) cc_final: 0.5950 (mtpt)
REVERT: A  513 GLU cc_start: 0.7876 (OUTLIER) cc_final: 0.7505 (mp0)
REVERT: A  687 GLU cc_start: 0.8125 (tp30) cc_final: 0.7784 (tp30)
REVERT: A  995 LEU cc_start: 0.8502 (mt) cc_final: 0.7560 (tp)
REVERT: A 1052 GLU cc_start: 0.8095 (mp0) cc_final: 0.7804 (mp0)
REVERT: A 1285 GLU cc_start: 0.7958 (mp0) cc_final: 0.7630 (mt-10)
REVERT: A 1304 ARG cc_start: 0.6470 (mtm180) cc_final: 0.6205 (mtm180)
  outliers start: 22
  outliers final: 19
  residues processed: 101
  average time/residue: 0.0813
  time to fit residues: 10.9392
Evaluate side-chains
  101 residues out of total 690 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  365 THR
Chi-restraints excluded: chain A residue  407 ASP
Chi-restraints excluded: chain A residue  414 THR
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  513 GLU
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  535 ASN
Chi-restraints excluded: chain A residue  584 VAL
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  968 LEU
Chi-restraints excluded: chain A residue  971 ASP
Chi-restraints excluded: chain A residue 1011 VAL
Chi-restraints excluded: chain A residue 1073 HIS
Chi-restraints excluded: chain A residue 1083 LEU
Chi-restraints excluded: chain A residue 1141 CYS
Chi-restraints excluded: chain A residue 1145 LEU
Chi-restraints excluded: chain A residue 1161 THR
Chi-restraints excluded: chain A residue 1230 CYS
Chi-restraints excluded: chain A residue 1256 ILE
Chi-restraints excluded: chain A residue 1283 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 61 optimal weight:    7.9990
   chunk 20 optimal weight:    2.9990
   chunk 5 optimal weight:    0.3980
   chunk 19 optimal weight:    2.9990
   chunk 41 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0050
   overall best weight:    0.6594

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

Flipped N/Q/H residues before XYZ refinement:
** A1026 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1072 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.137314 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.117548 restraints weight = 15651.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.119969 restraints weight = 10464.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3839 r_free = 0.3839 target = 0.121670 restraints weight = 7769.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3857 r_free = 0.3857 target = 0.122907 restraints weight = 6214.294|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3868 r_free = 0.3868 target = 0.123667 restraints weight = 5244.149|
|-----------------------------------------------------------------------------|
r_work (final): 0.3860
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7152
moved from start:          0.4352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6290  Z= 0.121
  Angle     :  0.636  13.507   8483  Z= 0.312
  Chirality :  0.044   0.230    938
  Planarity :  0.004   0.032   1099
  Dihedral  :  4.762  54.398    832
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 11.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 18.99 %
    Favored  : 77.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.78 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.32), residues: 749
  helix:  0.44 (0.33), residues: 265
  sheet:  0.08 (0.48), residues: 112
  loop :  0.54 (0.35), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 612 
 TYR   0.022   0.002   TYR A1100 
 PHE   0.012   0.001   PHE A1056 
 TRP   0.004   0.001   TRP A 643 
 HIS   0.003   0.001   HIS A1026 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6271)
  covalent geometry    : angle       0.63001 ( 8472)
  hydrogen bonds       : bond        0.03714 (  224)
  hydrogen bonds       : angle       4.58081 (  606)
  metal coordination   : bond        0.00372 (   19)
  metal coordination   : angle       2.44208 (   11)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1183.17 seconds
wall clock time: 21 minutes 8.00 seconds (1268.00 seconds total)