Starting phenix.real_space_refine
on Sat Aug 23 16:51:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yn9_33955/08_2025/7yn9_33955.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yn9_33955/08_2025/7yn9_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yn9_33955/08_2025/7yn9_33955.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yn9_33955/08_2025/7yn9_33955.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yn9_33955/08_2025/7yn9_33955.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yn9_33955/08_2025/7yn9_33955.cif"
  }
  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-2.0-5787/lib/python3.9/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: {'RNA': 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: 0.85
  Conformation dependent library (CDL) restraints added in 571.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 1.44
  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: 2.23

  Time building geometry restraints manager: 1.13 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: 17763
        2.08 -     4.16: 485
        4.16 -     6.24: 49
        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: 7952
       35.49 -    70.97: 226
       70.97 -   106.45: 23
      106.45 -   141.94: 0
      141.94 -   177.42: 1
  Dihedral angle restraints: 8202
    sinusoidal: 3835
      harmonic: 4367
  Sorted by residual:
  dihedral pdb=" CA  TRP A1512 "
           pdb=" C   TRP A1512 "
           pdb=" N   ARG A1513 "
           pdb=" CA  ARG A1513 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.44   33.56     0      5.00e+00 4.00e-02 4.51e+01
  dihedral pdb=" CA  ALA A 425 "
           pdb=" C   ALA A 425 "
           pdb=" N   LYS A 426 "
           pdb=" CA  LYS A 426 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.20  -26.80     0      5.00e+00 4.00e-02 2.87e+01
  dihedral pdb=" CA  PHE A 990 "
           pdb=" C   PHE A 990 "
           pdb=" N   LEU A 991 "
           pdb=" CA  LEU A 991 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.31   26.69     0      5.00e+00 4.00e-02 2.85e+01
  ... (remaining 8199 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.049: 1386
       0.049 -    0.099: 448
       0.099 -    0.148: 89
       0.148 -    0.198: 10
       0.198 -    0.247: 2
  Chirality restraints: 1935
  Sorted by residual:
  chirality pdb=" C3'   U B -14 "
            pdb=" C4'   U B -14 "
            pdb=" O3'   U B -14 "
            pdb=" C2'   U B -14 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.50   -0.25 2.00e-01 2.50e+01 1.53e+00
  chirality pdb=" CA  CYS A 123 "
            pdb=" N   CYS A 123 "
            pdb=" C   CYS A 123 "
            pdb=" CB  CYS A 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.32e+00
  chirality pdb=" C1'   A B  -2 "
            pdb=" O4'   A B  -2 "
            pdb=" C2'   A B  -2 "
            pdb=" N9    A B  -2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.25    0.19 2.00e-01 2.50e+01 9.07e-01
  ... (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:             5.930
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.270
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
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= 0.299
  Angle     :  0.830  10.399  18311  Z= 0.494
  Chirality :  0.050   0.247   1935
  Planarity :  0.006   0.105   2255
  Dihedral  : 16.329 177.424   5386
  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 aren 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
  covalent geometry    : bond        0.00657 (13455)
  covalent geometry    : angle       0.83015 (18311)
  hydrogen bonds       : bond        0.28207 (  232)
  hydrogen bonds       : angle       8.89630 (  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  : 0.331 
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: 0.1214
  time to fit residues: 18.7860
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  : 0.294 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
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: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.116575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.088061 restraints weight = 24568.525|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.089051 restraints weight = 18208.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.089662 restraints weight = 14620.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.090051 restraints weight = 11410.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.090095 restraints weight = 10834.658|
|-----------------------------------------------------------------------------|
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8384
moved from start:          0.1087

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  13455  Z= 0.167
  Angle     :  0.673  14.046  18311  Z= 0.352
  Chirality :  0.045   0.229   1935
  Planarity :  0.005   0.102   2255
  Dihedral  : 14.476 168.833   2231
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.98
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.50 %
    Favored  : 87.30 %
  Rotamer:
    Outliers :  0.98 %
    Allowed  : 13.29 %
    Favored  : 85.73 %
  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 aren not related in a simple way.
  whole: -4.49 (0.18), residues: 1504
  helix: -2.24 (0.28), residues: 287
  sheet: -2.30 (0.31), residues: 248
  loop : -3.64 (0.16), residues: 969

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 621 
 TYR   0.012   0.001   TYR A1126 
 PHE   0.020   0.001   PHE A 776 
 TRP   0.021   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 184 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (13455)
  covalent geometry    : angle       0.67322 (18311)
  hydrogen bonds       : bond        0.04655 (  232)
  hydrogen bonds       : angle       5.69490 (  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
  95 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 82
  time to evaluate  : 0.534 
Fit side-chains
REVERT: A   86 CYS cc_start: 0.7951 (OUTLIER) cc_final: 0.7648 (p)
REVERT: A  315 TRP cc_start: 0.6380 (m100) cc_final: 0.5961 (m100)
REVERT: A  601 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8180 (mttm)
REVERT: A 1211 MET cc_start: 0.8345 (tpt) cc_final: 0.7864 (tpt)
  outliers start: 13
  outliers final: 6
  residues processed: 93
  average time/residue: 0.1180
  time to fit residues: 16.7276
Evaluate side-chains
  79 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 72
  time to evaluate  : 0.491 
-------------------------------------------------------------------------------
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 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:    0.4980
   chunk 119 optimal weight:    7.9990
   chunk 12 optimal weight:    4.9990
   chunk 139 optimal weight:    2.9990
   chunk 84 optimal weight:    3.9990
   chunk 129 optimal weight:    0.9990
   chunk 106 optimal weight:    5.9990
   chunk 10 optimal weight:   10.0000
   chunk 130 optimal weight:    3.9990
   chunk 72 optimal weight:    0.9980
   chunk 145 optimal weight:    2.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 816 GLN
** A1056 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.116009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.087489 restraints weight = 24789.591|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.088890 restraints weight = 18296.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.089585 restraints weight = 13921.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.089837 restraints weight = 10874.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.089915 restraints weight = 10404.282|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8386
moved from start:          0.1311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035  13455  Z= 0.186
  Angle     :  0.656  12.526  18311  Z= 0.342
  Chirality :  0.046   0.230   1935
  Planarity :  0.005   0.101   2255
  Dihedral  : 14.316 168.035   2230
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 6.25
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 12.17 %
    Favored  : 87.63 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 15.11 %
    Favored  : 83.16 %
  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 aren not related in a simple way.
  whole: -4.18 (0.19), residues: 1504
  helix: -1.85 (0.29), residues: 302
  sheet: -1.99 (0.31), residues: 255
  loop : -3.54 (0.16), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 444 
 TYR   0.012   0.001   TYR A1126 
 PHE   0.021   0.002   PHE A 776 
 TRP   0.031   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A1473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00433 (13455)
  covalent geometry    : angle       0.65609 (18311)
  hydrogen bonds       : bond        0.04214 (  232)
  hydrogen bonds       : angle       5.16755 (  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
  101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.529 
Fit side-chains
REVERT: A  315 TRP cc_start: 0.6406 (m100) cc_final: 0.5978 (m100)
  outliers start: 23
  outliers final: 15
  residues processed: 96
  average time/residue: 0.1131
  time to fit residues: 16.6133
Evaluate side-chains
  87 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 72
  time to evaluate  : 0.522 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 THR
Chi-restraints excluded: chain A residue  234 VAL
Chi-restraints excluded: chain A residue  609 ARG
Chi-restraints excluded: chain A residue  654 ASP
Chi-restraints excluded: chain A residue  666 GLU
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 1148 LEU
Chi-restraints excluded: chain A residue 1156 VAL
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:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 86 optimal weight:    3.9990
   chunk 27 optimal weight:    9.9990
   chunk 148 optimal weight:    0.0770
   chunk 43 optimal weight:    3.9990
   chunk 127 optimal weight:    0.9980
   chunk 102 optimal weight:    0.0970
   overall best weight:    1.2340

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

Flipped N/Q/H residues before XYZ refinement:
** A 931 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1056 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.117360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.089298 restraints weight = 24562.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.090281 restraints weight = 17513.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.091253 restraints weight = 13654.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.091475 restraints weight = 10364.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.091524 restraints weight = 10196.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13455  Z= 0.146
  Angle     :  0.617  13.671  18311  Z= 0.321
  Chirality :  0.044   0.222   1935
  Planarity :  0.005   0.096   2255
  Dihedral  : 14.178 167.313   2229
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 5.86
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.90 %
    Favored  : 88.90 %
  Rotamer:
    Outliers :  1.74 %
    Allowed  : 16.62 %
    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 aren not related in a simple way.
  whole: -3.89 (0.19), residues: 1504
  helix: -1.51 (0.30), residues: 305
  sheet: -1.87 (0.30), residues: 257
  loop : -3.38 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 444 
 TYR   0.010   0.001   TYR A1126 
 PHE   0.018   0.001   PHE A 776 
 TRP   0.032   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (13455)
  covalent geometry    : angle       0.61739 (18311)
  hydrogen bonds       : bond        0.03494 (  232)
  hydrogen bonds       : angle       4.82416 (  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
  101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 78
  time to evaluate  : 0.528 
Fit side-chains
REVERT: A   25 ARG cc_start: 0.7454 (mtm180) cc_final: 0.7250 (mtm180)
REVERT: A  315 TRP cc_start: 0.6309 (m100) cc_final: 0.5882 (m100)
REVERT: A 1130 PHE cc_start: 0.7865 (m-80) cc_final: 0.7646 (m-80)
  outliers start: 23
  outliers final: 18
  residues processed: 95
  average time/residue: 0.1123
  time to fit residues: 16.4097
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  : 0.495 
-------------------------------------------------------------------------------
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  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  742 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 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:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 91 optimal weight:    3.9990
   chunk 126 optimal weight:    2.9990
   chunk 148 optimal weight:    0.0970
   chunk 81 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 33 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 140 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 931 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.118458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.090030 restraints weight = 24576.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.091005 restraints weight = 17755.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.091777 restraints weight = 13667.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.092087 restraints weight = 11003.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.092223 restraints weight = 10588.713|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8336
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  13455  Z= 0.121
  Angle     :  0.588  10.299  18311  Z= 0.305
  Chirality :  0.043   0.216   1935
  Planarity :  0.005   0.092   2255
  Dihedral  : 14.052 166.734   2229
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.70 %
    Favored  : 89.10 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.37 %
    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 aren not related in a simple way.
  whole: -3.64 (0.19), residues: 1504
  helix: -1.19 (0.31), residues: 299
  sheet: -1.70 (0.31), residues: 258
  loop : -3.24 (0.17), residues: 947

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 855 
 TYR   0.012   0.001   TYR A1082 
 PHE   0.015   0.001   PHE A 776 
 TRP   0.040   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 (13455)
  covalent geometry    : angle       0.58754 (18311)
  hydrogen bonds       : bond        0.03171 (  232)
  hydrogen bonds       : angle       4.59447 (  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
  103 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.552 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7892 (OUTLIER) cc_final: 0.7446 (pp)
REVERT: A 1037 MET cc_start: 0.6659 (mmm) cc_final: 0.6360 (mmm)
REVERT: A 1130 PHE cc_start: 0.7865 (m-80) cc_final: 0.7614 (m-80)
REVERT: A 1530 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8595 (mp)
  outliers start: 25
  outliers final: 18
  residues processed: 99
  average time/residue: 0.1060
  time to fit residues: 16.3817
Evaluate side-chains
  93 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 73
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
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  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  742 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 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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 40 optimal weight:    0.7980
   chunk 131 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 66 optimal weight:    0.2980
   chunk 108 optimal weight:    0.1980
   chunk 58 optimal weight:    4.9990
   chunk 68 optimal weight:    4.9990
   chunk 118 optimal weight:    2.9990
   chunk 67 optimal weight:    3.9990
   chunk 109 optimal weight:    5.9990
   chunk 26 optimal weight:    9.9990
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.117346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.088860 restraints weight = 24450.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.089987 restraints weight = 17667.831|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.090626 restraints weight = 13829.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.090992 restraints weight = 11052.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.091077 restraints weight = 10503.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3185
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.1750

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  13455  Z= 0.164
  Angle     :  0.616  12.492  18311  Z= 0.318
  Chirality :  0.044   0.224   1935
  Planarity :  0.005   0.094   2255
  Dihedral  : 14.023 167.000   2229
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.30 %
    Favored  : 88.50 %
  Rotamer:
    Outliers :  2.49 %
    Allowed  : 17.75 %
    Favored  : 79.76 %
  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 aren not related in a simple way.
  whole: -3.52 (0.20), residues: 1504
  helix: -1.06 (0.31), residues: 299
  sheet: -1.59 (0.32), residues: 263
  loop : -3.20 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 444 
 TYR   0.011   0.001   TYR A1126 
 PHE   0.019   0.001   PHE A 776 
 TRP   0.037   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 931 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (13455)
  covalent geometry    : angle       0.61559 (18311)
  hydrogen bonds       : bond        0.03393 (  232)
  hydrogen bonds       : angle       4.63134 (  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
  107 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 74
  time to evaluate  : 0.522 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7893 (OUTLIER) cc_final: 0.7436 (pp)
REVERT: A 1211 MET cc_start: 0.8308 (tpt) cc_final: 0.7336 (tpt)
REVERT: A 1530 LEU cc_start: 0.8913 (OUTLIER) cc_final: 0.8641 (mp)
  outliers start: 33
  outliers final: 24
  residues processed: 102
  average time/residue: 0.1096
  time to fit residues: 17.3111
Evaluate side-chains
  101 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 75
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
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  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  742 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  948 SER
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 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 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:    0.7980
   chunk 51 optimal weight:    5.9990
   chunk 141 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 131 optimal weight:    5.9990
   chunk 134 optimal weight:    4.9990
   chunk 104 optimal weight:    5.9990
   chunk 3 optimal weight:    6.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3617 r_free = 0.3617 target = 0.118729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3192 r_free = 0.3192 target = 0.090542 restraints weight = 24500.589|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.091785 restraints weight = 17538.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.092554 restraints weight = 13572.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.092787 restraints weight = 10666.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.092890 restraints weight = 10264.687|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  13455  Z= 0.133
  Angle     :  0.593  11.181  18311  Z= 0.306
  Chirality :  0.043   0.219   1935
  Planarity :  0.005   0.090   2255
  Dihedral  : 13.973 166.885   2229
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 5.90
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.77 %
    Favored  : 89.03 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 18.58 %
    Favored  : 79.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.37 (0.20), residues: 1504
  helix: -0.95 (0.31), residues: 305
  sheet: -1.51 (0.32), residues: 257
  loop : -3.08 (0.17), residues: 942

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 444 
 TYR   0.014   0.001   TYR A1082 
 PHE   0.016   0.001   PHE A 776 
 TRP   0.041   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (13455)
  covalent geometry    : angle       0.59290 (18311)
  hydrogen bonds       : bond        0.03135 (  232)
  hydrogen bonds       : angle       4.51479 (  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
  109 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 80
  time to evaluate  : 0.535 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7366 (pp)
REVERT: A 1037 MET cc_start: 0.6549 (mmm) cc_final: 0.6202 (mmm)
REVERT: A 1477 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7987 (mt)
REVERT: A 1530 LEU cc_start: 0.8872 (OUTLIER) cc_final: 0.8607 (mp)
  outliers start: 29
  outliers final: 22
  residues processed: 105
  average time/residue: 0.1134
  time to fit residues: 18.2399
Evaluate side-chains
  99 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 74
  time to evaluate  : 0.545 
-------------------------------------------------------------------------------
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  327 VAL
Chi-restraints excluded: chain A residue  410 LEU
Chi-restraints excluded: chain A residue  485 VAL
Chi-restraints excluded: chain A residue  609 ARG
Chi-restraints excluded: chain A residue  699 THR
Chi-restraints excluded: chain A residue  742 VAL
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 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 1530 LEU
Chi-restraints excluded: chain A residue 1539 ASP
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:    0.8980
   chunk 36 optimal weight:    0.8980
   chunk 34 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 120 optimal weight:    9.9990
   chunk 13 optimal weight:    0.6980
   chunk 54 optimal weight:    6.9990
   chunk 82 optimal weight:    0.3980
   chunk 145 optimal weight:    1.9990
   chunk 24 optimal weight:   10.0000
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A1516 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.119962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.091522 restraints weight = 24144.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.092975 restraints weight = 17313.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.093703 restraints weight = 12956.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.094020 restraints weight = 10200.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.094134 restraints weight = 9690.384|
|-----------------------------------------------------------------------------|
r_work (final): 0.3234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8304
moved from start:          0.2038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  13455  Z= 0.110
  Angle     :  0.577  13.496  18311  Z= 0.296
  Chirality :  0.042   0.213   1935
  Planarity :  0.005   0.089   2255
  Dihedral  : 13.887 166.491   2229
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  : 10.70 %
    Favored  : 89.16 %
  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 aren not related in a simple way.
  whole: -3.22 (0.20), residues: 1504
  helix: -0.68 (0.32), residues: 299
  sheet: -1.36 (0.32), residues: 257
  loop : -3.05 (0.17), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 924 
 TYR   0.009   0.001   TYR A1126 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.041   0.001   TRP A1097 
 HIS   0.003   0.001   HIS A 883 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (13455)
  covalent geometry    : angle       0.57683 (18311)
  hydrogen bonds       : bond        0.02896 (  232)
  hydrogen bonds       : angle       4.36192 (  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
  106 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 77
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7746 (OUTLIER) cc_final: 0.7257 (pp)
REVERT: A 1037 MET cc_start: 0.6484 (mmm) cc_final: 0.6161 (mmm)
REVERT: A 1247 ASN cc_start: 0.8118 (m-40) cc_final: 0.7248 (p0)
REVERT: A 1530 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8612 (mp)
  outliers start: 29
  outliers final: 21
  residues processed: 102
  average time/residue: 0.1132
  time to fit residues: 17.7389
Evaluate side-chains
  96 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
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  184 HIS
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  742 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  948 SER
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 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 1600 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 103 optimal weight:    0.7980
   chunk 136 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 73 optimal weight:    3.9990
   chunk 95 optimal weight:    8.9990
   chunk 65 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 97 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 66 optimal weight:    0.8980
   overall best weight:    1.5382

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

Flipped N/Q/H residues before XYZ refinement:
** A1056 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 = 0.3609 r_free = 0.3609 target = 0.118104 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.089512 restraints weight = 24453.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.090296 restraints weight = 17637.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.091633 restraints weight = 13093.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.091805 restraints weight = 10378.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3199 r_free = 0.3199 target = 0.091875 restraints weight = 10064.352|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8351
moved from start:          0.1962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  13455  Z= 0.170
  Angle     :  0.630  14.359  18311  Z= 0.323
  Chirality :  0.044   0.224   1935
  Planarity :  0.005   0.092   2255
  Dihedral  : 13.905 166.992   2229
  Min Nonbonded Distance : 2.303

Molprobity Statistics.
  All-atom Clashscore : 5.94
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 11.57 %
    Favored  : 88.23 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 18.35 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.25 (0.20), residues: 1504
  helix: -0.67 (0.32), residues: 298
  sheet: -1.55 (0.31), residues: 270
  loop : -3.04 (0.17), residues: 936

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 924 
 TYR   0.011   0.001   TYR A1126 
 PHE   0.019   0.001   PHE A 776 
 TRP   0.041   0.001   TRP A1097 
 HIS   0.004   0.001   HIS A1095 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 (13455)
  covalent geometry    : angle       0.63017 (18311)
  hydrogen bonds       : bond        0.03344 (  232)
  hydrogen bonds       : angle       4.51832 (  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
  106 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 75
  time to evaluate  : 0.595 
Fit side-chains
REVERT: A  410 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7360 (pp)
REVERT: A 1082 TYR cc_start: 0.6728 (t80) cc_final: 0.6443 (t80)
REVERT: A 1211 MET cc_start: 0.8357 (tpt) cc_final: 0.7469 (tpt)
REVERT: A 1477 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.8006 (mt)
REVERT: A 1530 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.8655 (mp)
  outliers start: 31
  outliers final: 23
  residues processed: 102
  average time/residue: 0.1087
  time to fit residues: 17.4537
Evaluate side-chains
  98 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
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  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  742 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  948 SER
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 1244 VAL
Chi-restraints excluded: chain A residue 1477 LEU
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 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:    0.0870
   chunk 28 optimal weight:    0.0000
   chunk 115 optimal weight:    0.9980
   chunk 96 optimal weight:    0.5980
   chunk 81 optimal weight:    0.0270
   chunk 104 optimal weight:    3.9990
   chunk 27 optimal weight:    7.9990
   chunk 94 optimal weight:    3.9990
   chunk 26 optimal weight:    7.9990
   chunk 16 optimal weight:    0.9990
   chunk 23 optimal weight:    4.9990
   overall best weight:    0.3420

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 194 HIS
A1056 GLN
A1516 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.122179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.093789 restraints weight = 24221.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.095168 restraints weight = 17049.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.095878 restraints weight = 13016.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.096423 restraints weight = 10267.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.096504 restraints weight = 9648.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.2314

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  13455  Z= 0.098
  Angle     :  0.572  11.641  18311  Z= 0.294
  Chirality :  0.042   0.205   1935
  Planarity :  0.004   0.084   2255
  Dihedral  : 13.809 166.194   2229
  Min Nonbonded Distance : 2.388

Molprobity Statistics.
  All-atom Clashscore : 5.47
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  9.51 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  1.51 %
    Allowed  : 19.18 %
    Favored  : 79.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.98 (0.20), residues: 1504
  helix: -0.37 (0.32), residues: 299
  sheet: -1.17 (0.33), residues: 257
  loop : -2.95 (0.18), residues: 948

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 924 
 TYR   0.008   0.001   TYR A1561 
 PHE   0.009   0.001   PHE A 776 
 TRP   0.042   0.001   TRP A1097 
 HIS   0.004   0.001   HIS A1095 

Details of bonding type rmsd
  covalent geometry    : bond        0.00213 (13455)
  covalent geometry    : angle       0.57150 (18311)
  hydrogen bonds       : bond        0.02725 (  232)
  hydrogen bonds       : angle       4.25930 (  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
  98 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.546 
Fit side-chains
REVERT: A 1037 MET cc_start: 0.6264 (mmm) cc_final: 0.5889 (mmm)
REVERT: A 1247 ASN cc_start: 0.8075 (m-40) cc_final: 0.7231 (p0)
REVERT: A 1530 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8574 (mp)
  outliers start: 20
  outliers final: 15
  residues processed: 97
  average time/residue: 0.1111
  time to fit residues: 16.8700
Evaluate side-chains
  86 residues out of total 1324 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  485 VAL
Chi-restraints excluded: chain A residue  742 VAL
Chi-restraints excluded: chain A residue  861 VAL
Chi-restraints excluded: chain A residue  948 SER
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 1244 VAL
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:    4.9990
   chunk 61 optimal weight:    0.7980
   chunk 153 optimal weight:    4.9990
   chunk 136 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 7 optimal weight:    6.9990
   chunk 29 optimal weight:    8.9990
   chunk 148 optimal weight:    0.0370
   chunk 143 optimal weight:    0.0980
   chunk 116 optimal weight:    4.9990
   chunk 135 optimal weight:    3.9990
   overall best weight:    0.7860

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3647 r_free = 0.3647 target = 0.120896 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3223 r_free = 0.3223 target = 0.092418 restraints weight = 24052.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.093393 restraints weight = 16758.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.094793 restraints weight = 12068.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.094956 restraints weight = 9583.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.095092 restraints weight = 9517.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8282
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  13455  Z= 0.114
  Angle     :  0.584  13.018  18311  Z= 0.297
  Chirality :  0.042   0.211   1935
  Planarity :  0.005   0.091   2255
  Dihedral  : 13.723 166.013   2229
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 5.51
  Ramachandran Plot:
    Outliers :  0.20 %
    Allowed  : 10.44 %
    Favored  : 89.36 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 19.71 %
    Favored  : 78.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.90 (0.20), residues: 1504
  helix: -0.40 (0.31), residues: 311
  sheet: -1.01 (0.32), residues: 265
  loop : -2.94 (0.18), residues: 928

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 924 
 TYR   0.016   0.001   TYR A1082 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.036   0.001   TRP A1097 
 HIS   0.004   0.001   HIS A1095 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (13455)
  covalent geometry    : angle       0.58413 (18311)
  hydrogen bonds       : bond        0.02880 (  232)
  hydrogen bonds       : angle       4.28582 (  675)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1988.87 seconds
wall clock time: 35 minutes 29.15 seconds (2129.15 seconds total)