Starting phenix.real_space_refine
on Sat Sep 12 03:30:21 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yn9_33955/09_2026/7yn9_33955.map"
  }
  resolution = 3.53
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      38      5.49       5
     S      56      5.16       5
     C    8114      2.51       5
     N    2329      2.21       5
     O    2531      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13068
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 12258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1514, 12258
          Classifications: {'peptide': 1514}
          Link IDs: {'PTRANS': 83, 'TRANS': 1430}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 38, 810
          Classifications: {'RNAv2': 38}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 6, 'rna3p_pur': 7, 'rna3p_pyr': 11}
          Link IDs: {'rna2p': 20, 'rna3p': 17}
  Time building chain proxies: 2.49, per 1000 atoms: 0.19
  Number of scatterers: 13068
  At special positions: 0
  Unit cell: (106.24, 171.81, 128.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      56     16.00
     P      38     15.00
     O    2531      8.00
     N    2329      7.00
     C    8114      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.00
  Conformation dependent library (CDL) restraints added in 509.5 milliseconds
  

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2816

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 20 sheets defined
      20.9% alpha, 15.9% beta
      0 base pairs and 14 stacking pairs defined.
    Time for finding SS restraints: 1.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 58 through 74
      removed outlier: 3.891A  pdb=" N   THR A  74 " --> pdb=" O   GLU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 130
    Processing helix  chain 'A' and resid 213 through 225
    Processing helix  chain 'A' and resid 261 through 275
      removed outlier: 3.610A  pdb=" N   ALA A 266 " --> pdb=" O   ALA A 262 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   GLU A 267 " --> pdb=" O   GLU A 263 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   GLN A 268 " --> pdb=" O   LYS A 264 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ILE A 270 " --> pdb=" O   ALA A 266 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   SER A 271 " --> pdb=" O   GLU A 267 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   ILE A 272 " --> pdb=" O   GLN A 268 " (cutoff:3.500A)
      removed outlier: 4.111A  pdb=" N   LEU A 273 " --> pdb=" O   ILE A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
      removed outlier: 3.745A  pdb=" N   ILE A 289 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 290 through 293
      removed outlier: 3.693A  pdb=" N   ARG A 293 " --> pdb=" O   ARG A 290 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 290 through 293'
    Processing helix  chain 'A' and resid 295 through 299
      removed outlier: 3.534A  pdb=" N   LEU A 298 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 333
    Processing helix  chain 'A' and resid 344 through 357
      removed outlier: 4.437A  pdb=" N   GLU A 350 " --> pdb=" O   GLY A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 362
      removed outlier: 4.223A  pdb=" N   LEU A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LYS A 362 " --> pdb=" O   ALA A 358 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 357 through 362'
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 3.797A  pdb=" N   VAL A 447 " --> pdb=" O   PRO A 443 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   TYR A 458 " --> pdb=" O   ASP A 454 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 555
      removed outlier: 3.903A  pdb=" N   THR A 547 " --> pdb=" O   ASP A 543 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   VAL A 548 " --> pdb=" O   ALA A 544 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU A 549 " --> pdb=" O   LEU A 545 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 562 through 566
    Processing helix  chain 'A' and resid 585 through 594
      removed outlier: 3.990A  pdb=" N   ASN A 589 " --> pdb=" O   GLU A 585 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   ASP A 590 " --> pdb=" O   ASN A 586 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   ASN A 594 " --> pdb=" O   ASP A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 607
      removed outlier: 3.595A  pdb=" N   GLU A 604 " --> pdb=" O   GLU A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 644 through 649
      removed outlier: 3.643A  pdb=" N   VAL A 648 " --> pdb=" O   ILE A 644 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 675 through 691
      removed outlier: 3.507A  pdb=" N   PHE A 679 " --> pdb=" O   LYS A 675 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   ILE A 690 " --> pdb=" O   ALA A 686 " (cutoff:3.500A)
      removed outlier: 3.852A  pdb=" N   HIS A 691 " --> pdb=" O   VAL A 687 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 714
      removed outlier: 3.831A  pdb=" N   ILE A 713 " --> pdb=" O   LEU A 709 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 751 through 755
      removed outlier: 4.148A  pdb=" N   LYS A 755 " --> pdb=" O   ALA A 752 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 784
    Processing helix  chain 'A' and resid 787 through 802
      removed outlier: 3.515A  pdb=" N   ALA A 791 " --> pdb=" O   GLU A 787 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   ALA A 795 " --> pdb=" O   ALA A 791 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   VAL A 799 " --> pdb=" O   ALA A 795 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 809 through 813
      removed outlier: 3.654A  pdb=" N   ILE A 812 " --> pdb=" O   LYS A 809 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 962
      removed outlier: 3.882A  pdb=" N   LEU A 950 " --> pdb=" O   PRO A 946 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   VAL A 954 " --> pdb=" O   LEU A 950 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   SER A 956 " --> pdb=" O   GLY A 952 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   VAL A 957 " --> pdb=" O   MET A 953 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   THR A 960 " --> pdb=" O   SER A 956 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   THR A 962 " --> pdb=" O   TYR A 958 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1165 through 1169
    Processing helix  chain 'A' and resid 1232 through 1247
      removed outlier: 3.859A  pdb=" N   LYS A1237 " --> pdb=" O   LYS A1233 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   TYR A1238 " --> pdb=" O   ALA A1234 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   LEU A1242 " --> pdb=" O   TYR A1238 " (cutoff:3.500A)
      removed outlier: 4.142A  pdb=" N   ARG A1243 " --> pdb=" O   LYS A1239 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   VAL A1244 " --> pdb=" O   GLU A1240 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR A1245 " --> pdb=" O   LEU A1241 " (cutoff:3.500A)
      removed outlier: 3.921A  pdb=" N   ASN A1246 " --> pdb=" O   LEU A1242 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1264
    Processing helix  chain 'A' and resid 1300 through 1305
      removed outlier: 3.837A  pdb=" N   MET A1305 " --> pdb=" O   GLY A1302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1342 through 1347
      removed outlier: 3.517A  pdb=" N   ARG A1346 " --> pdb=" O   CYS A1342 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU A1347 " --> pdb=" O   PRO A1343 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1342 through 1347'
    Processing helix  chain 'A' and resid 1420 through 1425
      removed outlier: 3.550A  pdb=" N   ILE A1424 " --> pdb=" O   ALA A1420 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1464 through 1476
      removed outlier: 3.607A  pdb=" N   GLY A1469 " --> pdb=" O   GLU A1465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1517
      No H-bonds generated for 'chain 'A' and resid 1515 through 1517'
    Processing helix  chain 'A' and resid 1518 through 1526
      removed outlier: 3.904A  pdb=" N   GLY A1524 " --> pdb=" O   PRO A1520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1529 through 1534
      removed outlier: 3.926A  pdb=" N   PHE A1534 " --> pdb=" O   LEU A1530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1537 through 1539
      No H-bonds generated for 'chain 'A' and resid 1537 through 1539'
    Processing helix  chain 'A' and resid 1540 through 1545
    Processing helix  chain 'A' and resid 1575 through 1579
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3
      removed outlier: 5.876A  pdb=" N   GLU A 201 " --> pdb=" O   LEU A 153 " (cutoff:3.500A)
      removed outlier: 4.181A  pdb=" N   LEU A 153 " --> pdb=" O   GLU A 201 " (cutoff:3.500A)
      removed outlier: 4.813A  pdb=" N   GLU A 203 " --> pdb=" O   GLY A 151 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2 through 3
      removed outlier: 3.573A  pdb=" N   GLY A 202 " --> pdb=" O   ILE A   7 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A   7 " --> pdb=" O   GLY A 202 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   GLU A  10 " --> pdb=" O   VAL A 234 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173
      removed outlier: 3.871A  pdb=" N   ARG A 171 " --> pdb=" O   ALA A 189 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 483 through 485
      removed outlier: 3.649A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 530 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 483 through 485
      removed outlier: 3.649A  pdb=" N   GLY A 408 " --> pdb=" O   PHE A 530 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 497 through 498
      removed outlier: 3.544A  pdb=" N   GLU A 497 " --> pdb=" O   VAL A 521 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 501 through 504
      removed outlier: 9.986A  pdb=" N   ARG A 501 " --> pdb=" O   GLY A 514 " (cutoff:3.500A)
      removed outlier: 10.328A  pdb=" N   GLY A 514 " --> pdb=" O   ARG A 501 " (cutoff:3.500A)
      removed outlier: 7.111A  pdb=" N   ARG A 503 " --> pdb=" O   ALA A 512 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 576 through 577
      removed outlier: 3.702A  pdb=" N   TYR A 577 " --> pdb=" O   ASN A 611 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   ASN A 611 " --> pdb=" O   TYR A 577 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 723 through 725
      removed outlier: 3.728A  pdb=" N   VAL A 630 " --> pdb=" O   GLY A 774 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   LYS A 823 " --> pdb=" O   ASN A 629 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 659 through 663
    Processing sheet with id=AB2, first strand: chain 'A' and resid 861 through 862
    Processing sheet with id=AB3, first strand: chain 'A' and resid 944 through 945
    Processing sheet with id=AB4, first strand: chain 'A' and resid 944 through 945
      removed outlier: 3.841A  pdb=" N   PHE A1456 " --> pdb=" O   CYS A 897 " (cutoff:3.500A)
      removed outlier: 5.087A  pdb=" N   LEU A 891 " --> pdb=" O   ASN A1462 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   THR A 892 " --> pdb=" O   LEU A1505 " (cutoff:3.500A)
      removed outlier: 4.923A  pdb=" N   LEU A1505 " --> pdb=" O   THR A 892 " (cutoff:3.500A)
      removed outlier: 6.892A  pdb=" N   LYS A 894 " --> pdb=" O   VAL A1503 " (cutoff:3.500A)
      removed outlier: 4.897A  pdb=" N   VAL A1503 " --> pdb=" O   LYS A 894 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ARG A 896 " --> pdb=" O   GLU A1501 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1227 through 1229
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1007 through 1012
      removed outlier: 4.122A  pdb=" N   GLU A1007 " --> pdb=" O   PHE A1220 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE A1220 " --> pdb=" O   GLU A1007 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'A' and resid 1120 through 1130
      removed outlier: 3.727A  pdb=" N   TYR A1126 " --> pdb=" O   ARG A1041 " (cutoff:3.500A)
      removed outlier: 4.307A  pdb=" N   ARG A1041 " --> pdb=" O   TYR A1126 " (cutoff:3.500A)
      removed outlier: 7.175A  pdb=" N   LYS A1128 " --> pdb=" O   VAL A1039 " (cutoff:3.500A)
      removed outlier: 4.919A  pdb=" N   VAL A1039 " --> pdb=" O   LYS A1128 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   PHE A1130 " --> pdb=" O   MET A1037 " (cutoff:3.500A)
      removed outlier: 5.103A  pdb=" N   MET A1037 " --> pdb=" O   PHE A1130 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   GLY A1146 " --> pdb=" O   VAL A1035 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'A' and resid 1081 through 1086
    Processing sheet with id=AB9, first strand: chain 'A' and resid 1187 through 1188
      removed outlier: 4.098A  pdb=" N   ASP A1187 " --> pdb=" O   VAL A1198 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'A' and resid 1200 through 1202
      removed outlier: 3.672A  pdb=" N   CYS A1201 " --> pdb=" O   TYR A1209 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'A' and resid 1278 through 1280
      removed outlier: 6.625A  pdb=" N   LYS A1278 " --> pdb=" O   GLU A1285 " (cutoff:3.500A)

    249 hydrogen bonds defined for protein.
    675 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      14 stacking parallelities
  Total time for adding SS restraints: 2.61

  Time building geometry restraints manager: 1.33 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3891
        1.33 -     1.45: 2336
        1.45 -     1.57: 7073
        1.57 -     1.69: 75
        1.69 -     1.81: 80
  Bond restraints: 13455
  Sorted by residual:
  bond pdb=" N   CYS A 965 "
       pdb=" CA  CYS A 965 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.22e-02 6.72e+03 6.57e+00
  bond pdb=" N   CYS A1312 "
       pdb=" CA  CYS A1312 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.031 1.22e-02 6.72e+03 6.31e+00
  bond pdb=" N   CYS A 711 "
       pdb=" CA  CYS A 711 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.35e-02 5.49e+03 5.61e+00
  bond pdb=" N   CYS A1345 "
       pdb=" CA  CYS A1345 "
    ideal  model  delta    sigma   weight residual
    1.455  1.485 -0.030 1.29e-02 6.01e+03 5.32e+00
  bond pdb=" N   CYS A  86 "
       pdb=" CA  CYS A  86 "
    ideal  model  delta    sigma   weight residual
    1.453  1.487 -0.035 1.51e-02 4.39e+03 5.25e+00
  ... (remaining 13450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 17606
        2.08 -     4.16: 601
        4.16 -     6.24: 90
        6.24 -     8.32: 10
        8.32 -    10.40: 4
  Bond angle restraints: 18311
  Sorted by residual:
  angle pdb=" C   ARG A 924 "
        pdb=" N   LYS A 925 "
        pdb=" CA  LYS A 925 "
      ideal   model   delta    sigma   weight residual
     122.44  115.51    6.93 1.19e+00 7.06e-01 3.39e+01
  angle pdb=" N   CYS A1345 "
        pdb=" CA  CYS A1345 "
        pdb=" C   CYS A1345 "
      ideal   model   delta    sigma   weight residual
     113.97  107.03    6.94 1.28e+00 6.10e-01 2.94e+01
  angle pdb=" N   VAL A 782 "
        pdb=" CA  VAL A 782 "
        pdb=" C   VAL A 782 "
      ideal   model   delta    sigma   weight residual
     111.81  107.41    4.40 8.60e-01 1.35e+00 2.61e+01
  angle pdb=" N   ILE A 479 "
        pdb=" CA  ILE A 479 "
        pdb=" C   ILE A 479 "
      ideal   model   delta    sigma   weight residual
     112.96  108.10    4.86 1.00e+00 1.00e+00 2.36e+01
  angle pdb=" N   VAL A1151 "
        pdb=" CA  VAL A1151 "
        pdb=" C   VAL A1151 "
      ideal   model   delta    sigma   weight residual
     112.17  108.14    4.03 9.50e-01 1.11e+00 1.80e+01
  ... (remaining 18306 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.49: 7804
       35.49 -    70.97: 260
       70.97 -   106.45: 21
      106.45 -   141.94: 0
      141.94 -   177.42: 1
  Dihedral angle restraints: 8086
    sinusoidal: 3719
      harmonic: 4367
  Sorted by residual:
  dihedral pdb=" C4'   A B  -2 "
           pdb=" C3'   A B  -2 "
           pdb=" C2'   A B  -2 "
           pdb=" C1'   A B  -2 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.37   74.71     1      3.10e+00 1.04e-01 7.36e+02
  dihedral pdb=" C4'   A B  10 "
           pdb=" C3'   A B  10 "
           pdb=" C2'   A B  10 "
           pdb=" C1'   A B  10 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.59   73.93     1      3.10e+00 1.04e-01 7.22e+02
  dihedral pdb=" C4'   C B  15 "
           pdb=" C3'   C B  15 "
           pdb=" C2'   C B  15 "
           pdb=" C1'   C B  15 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.35  -36.92   73.26     1      3.10e+00 1.04e-01 7.11e+02
  ... (remaining 8083 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.066: 1551
       0.066 -    0.131: 278
       0.131 -    0.197: 33
       0.197 -    0.262: 51
       0.262 -    0.328: 22
  Chirality restraints: 1935
  Sorted by residual:
  chirality pdb=" C3'   A B  -2 "
            pdb=" C4'   A B  -2 "
            pdb=" O3'   A B  -2 "
            pdb=" C2'   A B  -2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.50   -2.83    0.33 2.00e-01 2.50e+01 2.69e+00
  chirality pdb=" C2'   U B -14 "
            pdb=" C3'   U B -14 "
            pdb=" O2'   U B -14 "
            pdb=" C1'   U B -14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.47   -0.32 2.00e-01 2.50e+01 2.61e+00
  chirality pdb=" C2'   G B   3 "
            pdb=" C3'   G B   3 "
            pdb=" O2'   G B   3 "
            pdb=" C1'   G B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.79   -2.48   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1932 not shown)

  Planarity restraints: 2255
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR A 863 "    0.069 5.00e-02 4.00e+02   1.05e-01 1.76e+01
        pdb=" N   PRO A 864 "   -0.181 5.00e-02 4.00e+02
        pdb=" CA  PRO A 864 "    0.057 5.00e-02 4.00e+02
        pdb=" CD  PRO A 864 "    0.056 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A 768 "    0.046 5.00e-02 4.00e+02   7.01e-02 7.87e+00
        pdb=" N   PRO A 769 "   -0.121 5.00e-02 4.00e+02
        pdb=" CA  PRO A 769 "    0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO A 769 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 765 "   -0.045 5.00e-02 4.00e+02   6.74e-02 7.28e+00
        pdb=" N   PRO A 766 "    0.117 5.00e-02 4.00e+02
        pdb=" CA  PRO A 766 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 766 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 2252 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 643
        2.70 -     3.25: 12390
        3.25 -     3.80: 18833
        3.80 -     4.35: 24617
        4.35 -     4.90: 41635
  Nonbonded interactions: 98118
  Sorted by model distance:
  nonbonded pdb=" NE2 HIS A 865 "
            pdb=" OH  TYR A1561 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" O   SER A 211 "
            pdb=" NH1 ARG A 215 "
     model   vdw
     2.171 3.120
  nonbonded pdb=" OH  TYR A1014 "
            pdb=" OE2 GLU A1216 "
     model   vdw
     2.174 3.040
  nonbonded pdb=" OD1 ASN A1088 "
            pdb=" OG1 THR A1092 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" NZ  LYS A1004 "
            pdb=" O   PHE A1005 "
     model   vdw
     2.218 3.120
  ... (remaining 98113 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.400
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8615
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   0.062  13455  Z= 0.301
  Angle     :  0.897  10.399  18311  Z= 0.509
  Chirality :  0.069   0.328   1935
  Planarity :  0.006   0.105   2255
  Dihedral  : 17.094 177.424   5270
  Min Nonbonded Distance : 2.151

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 15.36 %
    Favored  : 84.44 %
  Rotamer:
    Outliers :  0.38 %
    Allowed  :  8.16 %
    Favored  : 91.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -5.33 (0.16), residues: 1504
  helix: -3.34 (0.23), residues: 274
  sheet: -2.82 (0.30), residues: 250
  loop : -4.07 (0.15), residues: 980

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 444 
 TYR   0.017   0.002   TYR A1245 
 PHE   0.023   0.002   PHE A 776 
 TRP   0.016   0.002   TRP A1466 
 HIS   0.005   0.001   HIS A1313 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00664 /  0.30 (13455)
  covalent geometry    : angle       0.89666 /  0.51 (18311)
  hydrogen bonds       : bond        0.28207 / 18.71 (  232)
  hydrogen bonds       : angle       8.89630 /  6.28 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.483 
Fit side-chains
REVERT: A   86 CYS cc_start: 0.6986 (OUTLIER) cc_final: 0.6771 (p)
REVERT: A  315 TRP cc_start: 0.6436 (m100) cc_final: 0.6109 (m100)
REVERT: A  711 CYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7830 (t)
  outliers start: 5
  outliers final: 1
  residues processed: 111
  average time/residue: 0.1479
  time to fit residues: 22.6278
Evaluate side-chains
  74 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 71
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  711 CYS
Chi-restraints excluded: chain A residue 1133 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    2.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:   10.0000
   chunk 122 optimal weight:    0.7980
   chunk 91 optimal weight:    1.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  43 HIS
A  71 ASN
A 518 ASN
A 531 GLN
A 963 ASN
** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1098 HIS
A1168 ASN
A1247 ASN
A1382 HIS
A1417 HIS
A1418 HIS
A1428 ASN
A1452 ASN
A1516 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.117754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.090297 restraints weight = 24574.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.091191 restraints weight = 17489.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.092152 restraints weight = 13592.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.092379 restraints weight = 10284.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.092419 restraints weight = 10210.470|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8544
moved from start:          0.1258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.099  13455  Z= 0.206
  Angle     :  1.019  16.607  18311  Z= 0.463
  Chirality :  0.100   1.471   1935
  Planarity :  0.006   0.103   2255
  Dihedral  : 14.190 175.974   2115
  Min Nonbonded Distance : 2.361

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.57 %
    Favored  : 87.23 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  : 12.99 %
    Favored  : 85.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -4.53 (0.18), residues: 1504
  helix: -2.30 (0.28), residues: 286
  sheet: -2.29 (0.30), residues: 250
  loop : -3.67 (0.16), residues: 968

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 621 
 TYR   0.012   0.001   TYR A1126 
 PHE   0.022   0.001   PHE A 776 
 TRP   0.024   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 931 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.21 (13455)
  covalent geometry    : angle       1.01915 /  0.46 (18311)
  hydrogen bonds       : bond        0.05151 /  3.33 (  232)
  hydrogen bonds       : angle       5.77786 /  4.10 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 0.548 
Fit side-chains
REVERT: A   86 CYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7599 (p)
REVERT: A  315 TRP cc_start: 0.6429 (m100) cc_final: 0.6034 (m100)
REVERT: A 1211 MET cc_start: 0.8385 (tpt) cc_final: 0.7865 (tpt)
  outliers start: 14
  outliers final: 7
  residues processed: 94
  average time/residue: 0.1030
  time to fit residues: 14.9613
Evaluate side-chains
  79 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.490 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   86 CYS
Chi-restraints excluded: chain A residue  654 ASP
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 119 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 129 optimal weight:    0.6980
   chunk 106 optimal weight:    4.9990
   chunk 10 optimal weight:    0.0770
   chunk 130 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 145 optimal weight:    2.9990
   overall best weight:    0.8740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.121264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.093922 restraints weight = 24591.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.094499 restraints weight = 17468.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.095483 restraints weight = 13877.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.095964 restraints weight = 10946.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.096062 restraints weight = 10392.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8473
moved from start:          0.1823

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  13455  Z= 0.139
  Angle     :  0.778  12.244  18311  Z= 0.368
  Chirality :  0.066   0.605   1935
  Planarity :  0.005   0.091   2255
  Dihedral  : 14.149 173.830   2114
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.70 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 14.73 %
    Favored  : 83.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.11 (0.19), residues: 1504
  helix: -1.85 (0.29), residues: 306
  sheet: -1.99 (0.30), residues: 258
  loop : -3.46 (0.16), residues: 940

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 621 
 TYR   0.009   0.001   TYR A1126 
 PHE   0.016   0.001   PHE A 776 
 TRP   0.039   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 883 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.14 (13455)
  covalent geometry    : angle       0.77844 /  0.37 (18311)
  hydrogen bonds       : bond        0.03638 /  2.34 (  232)
  hydrogen bonds       : angle       4.90911 /  3.45 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.505 
Fit side-chains
REVERT: A  127 GLU cc_start: 0.7461 (mp0) cc_final: 0.7256 (mp0)
REVERT: A  315 TRP cc_start: 0.6404 (m100) cc_final: 0.5988 (m100)
REVERT: A 1082 TYR cc_start: 0.6815 (t80) cc_final: 0.6561 (t80)
REVERT: A 1130 PHE cc_start: 0.7877 (m-80) cc_final: 0.7585 (m-80)
REVERT: A 1211 MET cc_start: 0.8425 (tpt) cc_final: 0.8121 (tpt)
REVERT: A 1247 ASN cc_start: 0.8136 (m-40) cc_final: 0.7269 (p0)
  outliers start: 17
  outliers final: 8
  residues processed: 97
  average time/residue: 0.1111
  time to fit residues: 16.5781
Evaluate side-chains
  83 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 75
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 58 optimal weight:    3.9990
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0470
   chunk 24 optimal weight:    8.9990
   chunk 59 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 27 optimal weight:   10.0000
   chunk 148 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 127 optimal weight:    0.8980
   chunk 102 optimal weight:    9.9990
   overall best weight:    2.1884

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 816 GLN
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1056 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.117155 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.089617 restraints weight = 24702.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3178 r_free = 0.3178 target = 0.090387 restraints weight = 17588.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.091182 restraints weight = 13942.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.091820 restraints weight = 11181.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.091868 restraints weight = 10525.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1736

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.041  13455  Z= 0.236
  Angle     :  0.846  10.882  18311  Z= 0.405
  Chirality :  0.074   0.721   1935
  Planarity :  0.005   0.103   2255
  Dihedral  : 14.440 179.343   2113
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.97 %
    Favored  : 86.84 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.54 %
    Favored  : 81.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.91 (0.19), residues: 1504
  helix: -1.55 (0.30), residues: 297
  sheet: -1.81 (0.31), residues: 263
  loop : -3.40 (0.17), residues: 944

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.014   0.001   TYR A1276 
 PHE   0.024   0.002   PHE A 776 
 TRP   0.033   0.002   TRP A1097 
 HIS   0.004   0.001   HIS A1095 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00556 /  0.24 (13455)
  covalent geometry    : angle       0.84572 /  0.40 (18311)
  hydrogen bonds       : bond        0.04166 /  2.68 (  232)
  hydrogen bonds       : angle       4.98902 /  3.52 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.604 
Fit side-chains
REVERT: A  127 GLU cc_start: 0.7584 (mp0) cc_final: 0.7259 (mp0)
REVERT: A  315 TRP cc_start: 0.6402 (m100) cc_final: 0.5965 (m100)
REVERT: A 1097 TRP cc_start: 0.7403 (m-10) cc_final: 0.7017 (m100)
REVERT: A 1130 PHE cc_start: 0.7881 (m-80) cc_final: 0.7665 (m-80)
  outliers start: 24
  outliers final: 18
  residues processed: 93
  average time/residue: 0.1077
  time to fit residues: 15.5880
Evaluate side-chains
  90 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  654 ASP
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1148 LEU
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 74 optimal weight:    0.5980
   chunk 91 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 148 optimal weight:    0.6980
   chunk 81 optimal weight:    4.9990
   chunk 10 optimal weight:    8.9990
   chunk 33 optimal weight:    7.9990
   chunk 40 optimal weight:    2.9990
   chunk 140 optimal weight:    0.9980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 931 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3665 r_free = 0.3665 target = 0.122069 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.094417 restraints weight = 24545.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.095399 restraints weight = 16558.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.096669 restraints weight = 12483.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.096809 restraints weight = 9654.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.096969 restraints weight = 9267.532|
|-----------------------------------------------------------------------------|
r_work (final): 0.3288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  13455  Z= 0.131
  Angle     :  0.726  12.172  18311  Z= 0.345
  Chirality :  0.062   0.528   1935
  Planarity :  0.005   0.087   2255
  Dihedral  : 14.307 176.682   2113
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.44 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 17.52 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.63 (0.19), residues: 1504
  helix: -1.21 (0.30), residues: 300
  sheet: -1.68 (0.31), residues: 262
  loop : -3.24 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 448 
 TYR   0.008   0.001   TYR A1126 
 PHE   0.015   0.001   PHE A 776 
 TRP   0.020   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1095 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.13 (13455)
  covalent geometry    : angle       0.72576 /  0.34 (18311)
  hydrogen bonds       : bond        0.03070 /  1.96 (  232)
  hydrogen bonds       : angle       4.57732 /  3.22 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.486 
Fit side-chains
REVERT: A  127 GLU cc_start: 0.7691 (mp0) cc_final: 0.7308 (mp0)
REVERT: A  410 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7445 (pp)
REVERT: A 1211 MET cc_start: 0.8438 (tpt) cc_final: 0.7848 (tpt)
REVERT: A 1247 ASN cc_start: 0.8109 (m-40) cc_final: 0.7282 (p0)
REVERT: A 1530 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8606 (mp)
  outliers start: 23
  outliers final: 14
  residues processed: 96
  average time/residue: 0.1082
  time to fit residues: 16.0171
Evaluate side-chains
  88 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 72
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 ASP
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1530 LEU
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 131 optimal weight:    5.9990
   chunk 35 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0570
   chunk 108 optimal weight:    5.9990
   chunk 58 optimal weight:    0.6980
   chunk 68 optimal weight:    5.9990
   chunk 118 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   overall best weight:    1.5504

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1095 HIS
A1516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.119300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.092063 restraints weight = 24459.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.092434 restraints weight = 17072.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.093353 restraints weight = 14035.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.093840 restraints weight = 11057.540|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.093899 restraints weight = 10584.698|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8512
moved from start:          0.2072

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  13455  Z= 0.179
  Angle     :  0.754   9.913  18311  Z= 0.360
  Chirality :  0.065   0.594   1935
  Planarity :  0.005   0.097   2255
  Dihedral  : 14.239 177.593   2113
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.37 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.60 %
    Favored  : 80.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.52 (0.20), residues: 1504
  helix: -1.06 (0.31), residues: 299
  sheet: -1.58 (0.31), residues: 267
  loop : -3.21 (0.17), residues: 938

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 448 
 TYR   0.011   0.001   TYR A1082 
 PHE   0.019   0.001   PHE A 776 
 TRP   0.028   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 883 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00414 /  0.18 (13455)
  covalent geometry    : angle       0.75435 /  0.36 (18311)
  hydrogen bonds       : bond        0.03422 /  2.19 (  232)
  hydrogen bonds       : angle       4.61978 /  3.25 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 71
  time to evaluate  : 0.488 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7490 (pp)
REVERT: A 1037 MET cc_start: 0.6541 (mmm) cc_final: 0.6197 (mmm)
REVERT: A 1082 TYR cc_start: 0.6743 (t80) cc_final: 0.6407 (t80)
REVERT: A 1097 TRP cc_start: 0.7285 (m-10) cc_final: 0.7047 (m-90)
REVERT: A 1211 MET cc_start: 0.8533 (tpt) cc_final: 0.7930 (tpt)
REVERT: A 1530 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8664 (mp)
  outliers start: 30
  outliers final: 21
  residues processed: 95
  average time/residue: 0.0973
  time to fit residues: 14.7502
Evaluate side-chains
  99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  185 ASP
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  654 ASP
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1530 LEU
Chi-restraints excluded: chain A residue 1539 ASP
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 120 optimal weight:    0.9980
   chunk 51 optimal weight:    6.9990
   chunk 141 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 131 optimal weight:    5.9990
   chunk 134 optimal weight:    3.9990
   chunk 104 optimal weight:    7.9990
   chunk 3 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   overall best weight:    1.1582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.121193 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.093216 restraints weight = 24573.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.094097 restraints weight = 16751.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.095515 restraints weight = 12308.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.095646 restraints weight = 9699.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.095819 restraints weight = 9793.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8487
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  13455  Z= 0.146
  Angle     :  0.725  13.002  18311  Z= 0.344
  Chirality :  0.062   0.537   1935
  Planarity :  0.005   0.088   2255
  Dihedral  : 14.216 176.980   2113
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 6.33
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.64 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  2.11 %
    Allowed  : 18.73 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.20), residues: 1504
  helix: -0.86 (0.31), residues: 300
  sheet: -1.48 (0.32), residues: 262
  loop : -3.16 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 448 
 TYR   0.010   0.001   TYR A1126 
 PHE   0.016   0.001   PHE A 776 
 TRP   0.020   0.001   TRP A1097 
 HIS   0.004   0.001   HIS A1095 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00333 /  0.15 (13455)
  covalent geometry    : angle       0.72546 /  0.34 (18311)
  hydrogen bonds       : bond        0.03113 /  1.98 (  232)
  hydrogen bonds       : angle       4.49308 /  3.17 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 79
  time to evaluate  : 0.596 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7897 (OUTLIER) cc_final: 0.7417 (pp)
REVERT: A 1037 MET cc_start: 0.6652 (mmm) cc_final: 0.6322 (mmm)
REVERT: A 1097 TRP cc_start: 0.7334 (m-10) cc_final: 0.6853 (m100)
REVERT: A 1211 MET cc_start: 0.8595 (OUTLIER) cc_final: 0.8049 (tpt)
REVERT: A 1247 ASN cc_start: 0.8159 (m-40) cc_final: 0.7288 (p0)
REVERT: A 1530 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8625 (mp)
  outliers start: 28
  outliers final: 19
  residues processed: 101
  average time/residue: 0.0999
  time to fit residues: 15.8265
Evaluate side-chains
  94 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  185 ASP
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  229 CYS
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1530 LEU
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 36 optimal weight:    0.0970
   chunk 34 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 120 optimal weight:   10.0000
   chunk 13 optimal weight:    0.4980
   chunk 54 optimal weight:    3.9990
   chunk 82 optimal weight:    0.8980
   chunk 145 optimal weight:    0.1980
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    0.7980
   overall best weight:    0.4978

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.124326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.096677 restraints weight = 24063.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.097803 restraints weight = 16030.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.099090 restraints weight = 11754.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.099334 restraints weight = 9348.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.099497 restraints weight = 9425.544|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8412
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13455  Z= 0.113
  Angle     :  0.683   9.757  18311  Z= 0.327
  Chirality :  0.057   0.402   1935
  Planarity :  0.005   0.086   2255
  Dihedral  : 14.099 176.561   2113
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.51 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.66 %
    Favored  : 79.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.20 (0.20), residues: 1504
  helix: -0.83 (0.31), residues: 318
  sheet: -1.28 (0.33), residues: 258
  loop : -3.03 (0.18), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 924 
 TYR   0.010   0.001   TYR A 930 
 PHE   0.010   0.001   PHE A 776 
 TRP   0.022   0.001   TRP A1097 
 HIS   0.006   0.001   HIS A1095 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00244 /  0.11 (13455)
  covalent geometry    : angle       0.68309 /  0.33 (18311)
  hydrogen bonds       : bond        0.02694 /  1.71 (  232)
  hydrogen bonds       : angle       4.21816 /  2.96 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.476 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7241 (pp)
REVERT: A 1097 TRP cc_start: 0.7337 (m-10) cc_final: 0.6761 (m100)
REVERT: A 1211 MET cc_start: 0.8567 (OUTLIER) cc_final: 0.8174 (tpt)
REVERT: A 1247 ASN cc_start: 0.8118 (m-40) cc_final: 0.7255 (p0)
REVERT: A 1530 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8580 (mp)
  outliers start: 29
  outliers final: 18
  residues processed: 104
  average time/residue: 0.0932
  time to fit residues: 15.3437
Evaluate side-chains
  92 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 71
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1073 PHE
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1530 LEU
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 32 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9990
   chunk 136 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 95 optimal weight:   10.0000
   chunk 65 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 97 optimal weight:    6.9990
   chunk 98 optimal weight:   20.0000
   chunk 66 optimal weight:    0.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.118961 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.091042 restraints weight = 24586.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.092127 restraints weight = 17122.169|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.093367 restraints weight = 12302.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3231 r_free = 0.3231 target = 0.093599 restraints weight = 9616.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.093703 restraints weight = 9851.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8524
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034  13455  Z= 0.228
  Angle     :  0.798  13.301  18311  Z= 0.381
  Chirality :  0.067   0.617   1935
  Planarity :  0.005   0.096   2255
  Dihedral  : 14.202 177.363   2113
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 6.84
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.90 %
    Favored  : 87.90 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 19.03 %
    Favored  : 78.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.07 %

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: -3.29 (0.20), residues: 1504
  helix: -0.76 (0.31), residues: 304
  sheet: -1.38 (0.32), residues: 267
  loop : -3.13 (0.17), residues: 933

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 924 
 TYR   0.013   0.001   TYR A1276 
 PHE   0.022   0.002   PHE A 776 
 TRP   0.019   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1473 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00535 /  0.23 (13455)
  covalent geometry    : angle       0.79846 /  0.38 (18311)
  hydrogen bonds       : bond        0.03620 /  2.31 (  232)
  hydrogen bonds       : angle       4.60135 /  3.25 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 73
  time to evaluate  : 0.323 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7433 (pp)
REVERT: A 1037 MET cc_start: 0.6562 (mmm) cc_final: 0.6193 (mmm)
REVERT: A 1097 TRP cc_start: 0.7389 (m-10) cc_final: 0.6901 (m100)
REVERT: A 1211 MET cc_start: 0.8597 (OUTLIER) cc_final: 0.8175 (tpt)
REVERT: A 1477 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.8025 (mt)
REVERT: A 1530 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8716 (mp)
  outliers start: 29
  outliers final: 22
  residues processed: 96
  average time/residue: 0.0923
  time to fit residues: 14.0123
Evaluate side-chains
  96 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    9 ILE
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  654 ASP
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1039 VAL
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1165 VAL
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1185 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1477 LEU
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1500 VAL
Chi-restraints excluded: chain A residue 1516 ASN
Chi-restraints excluded: chain A residue 1530 LEU
Chi-restraints excluded: chain A residue 1539 ASP
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0670
   chunk 115 optimal weight:    5.9990
   chunk 96 optimal weight:    0.6980
   chunk 81 optimal weight:    0.0770
   chunk 104 optimal weight:    7.9990
   chunk 27 optimal weight:    6.9990
   chunk 94 optimal weight:    0.6980
   chunk 26 optimal weight:    5.9990
   chunk 16 optimal weight:    0.2980
   chunk 23 optimal weight:    5.9990
   overall best weight:    0.3676

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 100 GLN
A1056 GLN
A1516 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.124608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.097311 restraints weight = 24252.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.098779 restraints weight = 15844.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.099819 restraints weight = 11712.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.100027 restraints weight = 9151.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.100231 restraints weight = 8667.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8395
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  13455  Z= 0.112
  Angle     :  0.706  15.289  18311  Z= 0.336
  Chirality :  0.057   0.406   1935
  Planarity :  0.005   0.081   2255
  Dihedral  : 14.117 175.624   2113
  Min Nonbonded Distance : 2.332

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.18 %
    Favored  : 90.69 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 19.71 %
    Favored  : 78.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -3.04 (0.20), residues: 1504
  helix: -0.67 (0.31), residues: 318
  sheet: -1.09 (0.33), residues: 263
  loop : -2.98 (0.18), residues: 923

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 924 
 TYR   0.017   0.001   TYR A1082 
 PHE   0.009   0.001   PHE A 776 
 TRP   0.021   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1095 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00236 /  0.11 (13455)
  covalent geometry    : angle       0.70622 /  0.34 (18311)
  hydrogen bonds       : bond        0.02646 /  1.67 (  232)
  hydrogen bonds       : angle       4.26557 /  3.00 (  675)

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

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

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3008 Ramachandran restraints generated.
    1504 Oldfield, 0 Emsley, 1504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 76
  time to evaluate  : 0.439 
Fit side-chains
REVERT: A  127 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7374 (mp0)
REVERT: A  410 LEU cc_start: 0.7793 (OUTLIER) cc_final: 0.7301 (pp)
REVERT: A 1037 MET cc_start: 0.6470 (mmm) cc_final: 0.6139 (mmm)
REVERT: A 1097 TRP cc_start: 0.7236 (m-10) cc_final: 0.6760 (m100)
REVERT: A 1211 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8187 (tpt)
REVERT: A 1247 ASN cc_start: 0.8122 (m-40) cc_final: 0.7292 (p0)
REVERT: A 1530 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8518 (mp)
  outliers start: 23
  outliers final: 15
  residues processed: 95
  average time/residue: 0.0995
  time to fit residues: 15.1392
Evaluate side-chains
  92 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 73
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 THR
Chi-restraints excluded: chain A residue  127 GLU
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  327 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  980 ASP
Chi-restraints excluded: chain A residue 1108 LEU
Chi-restraints excluded: chain A residue 1133 ILE
Chi-restraints excluded: chain A residue 1182 THR
Chi-restraints excluded: chain A residue 1211 MET
Chi-restraints excluded: chain A residue 1399 SER
Chi-restraints excluded: chain A residue 1485 LEU
Chi-restraints excluded: chain A residue 1491 MET
Chi-restraints excluded: chain A residue 1530 LEU
Chi-restraints excluded: chain A residue 1600 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 54 optimal weight:    0.0070
   chunk 61 optimal weight:    2.9990
   chunk 153 optimal weight:    3.9990
   chunk 136 optimal weight:    4.9990
   chunk 43 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 29 optimal weight:    9.9990
   chunk 148 optimal weight:    0.0770
   chunk 143 optimal weight:    0.0770
   chunk 116 optimal weight:    4.9990
   chunk 135 optimal weight:    0.9990
   overall best weight:    0.4316

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A1056 GLN
A1516 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.125343 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.098079 restraints weight = 23984.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.099393 restraints weight = 15376.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.100259 restraints weight = 12166.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.100556 restraints weight = 9430.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.100768 restraints weight = 8771.880|
|-----------------------------------------------------------------------------|
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8383
moved from start:          0.2771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  13455  Z= 0.110
  Angle     :  0.688  15.610  18311  Z= 0.325
  Chirality :  0.056   0.367   1935
  Planarity :  0.005   0.089   2255
  Dihedral  : 13.963 176.802   2113
  Min Nonbonded Distance : 2.347

Molprobity Statistics.
  All-atom Clashscore : 6.02
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.11 %
    Favored  : 89.76 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 19.86 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.87 (0.20), residues: 1504
  helix: -0.34 (0.31), residues: 312
  sheet: -0.97 (0.33), residues: 258
  loop : -2.93 (0.18), residues: 934

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 924 
 TYR   0.008   0.001   TYR A1126 
 PHE   0.011   0.001   PHE A 776 
 TRP   0.020   0.001   TRP A1097 
 HIS   0.005   0.001   HIS A1020 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.11 (13455)
  covalent geometry    : angle       0.68771 /  0.32 (18311)
  hydrogen bonds       : bond        0.02638 /  1.67 (  232)
  hydrogen bonds       : angle       4.10806 /  2.89 (  675)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1955.56 seconds
wall clock time: 34 minutes 50.68 seconds (2090.68 seconds total)