Starting phenix.real_space_refine
on Tue Mar  3 22:25:52 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7op8_13014/03_2026/7op8_13014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7op8_13014/03_2026/7op8_13014.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7op8_13014/03_2026/7op8_13014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7op8_13014/03_2026/7op8_13014.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7op8_13014/03_2026/7op8_13014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7op8_13014/03_2026/7op8_13014.cif"
  }
  resolution = 3.5
  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=   0.071
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: 7
    Type Number    sf(0)   Gaussians
     Mg      1      5.21       5
     S      53      5.16       5
     Be      1      3.05       5
     C    5761      2.51       5
     N    1472      2.21       5
     O    1581      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8872
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8867
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1118, 8867
          Classifications: {'peptide': 1118}
          Link IDs: {'PTRANS': 56, 'TRANS': 1061}
          Chain breaks: 8
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 5
          Unusual residues: {' MG': 1, 'BEF': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 1.99, per 1000 atoms: 0.22
  Number of scatterers: 8872
  At special positions: 0
  Unit cell: (83.2, 97.344, 143.104, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      53     16.00
     Mg      1     11.99
     F       3      9.00
     O    1581      8.00
     N    1472      7.00
     C    5761      6.00
     Be      1      4.00
    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: 0.68
  Conformation dependent library (CDL) restraints added in 384.6 milliseconds
  

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2112

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 12 sheets defined
      44.0% alpha, 11.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 228 through 240
      removed outlier: 3.824A  pdb=" N   ILE A 232 " --> pdb=" O   ILE A 228 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   TYR A 233 " --> pdb=" O   GLY A 229 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   VAL A 235 " --> pdb=" O   ALA A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 250
      removed outlier: 3.550A  pdb=" N   LEU A 246 " --> pdb=" O   GLY A 242 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   TRP A 250 " --> pdb=" O   LEU A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 259
      removed outlier: 3.920A  pdb=" N   LYS A 257 " --> pdb=" O   LYS A 253 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 297
      removed outlier: 3.585A  pdb=" N   THR A 296 " --> pdb=" O   PRO A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 363 through 373
    Processing helix  chain 'A' and resid 388 through 393
      removed outlier: 3.659A  pdb=" N   ILE A 392 " --> pdb=" O   LEU A 388 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 408
      removed outlier: 3.997A  pdb=" N   PHE A 402 " --> pdb=" O   ALA A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 444
      removed outlier: 3.519A  pdb=" N   ALA A 416 " --> pdb=" O   TYR A 412 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   ALA A 417 " --> pdb=" O   TYR A 413 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 519
    Processing helix  chain 'A' and resid 529 through 535
      removed outlier: 3.821A  pdb=" N   HIS A 535 " --> pdb=" O   ASP A 531 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 568
    Processing helix  chain 'A' and resid 569 through 579
    Processing helix  chain 'A' and resid 587 through 591
      removed outlier: 3.515A  pdb=" N   GLU A 590 " --> pdb=" O   LYS A 587 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 593 through 614
      removed outlier: 3.873A  pdb=" N   GLY A 604 " --> pdb=" O   GLY A 600 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU A 605 " --> pdb=" O   CYS A 601 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   VAL A 612 " --> pdb=" O   ILE A 608 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ASN A 613 " --> pdb=" O   VAL A 609 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE A 614 " --> pdb=" O   SER A 610 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 619 through 630
      removed outlier: 3.659A  pdb=" N   LEU A 623 " --> pdb=" O   LEU A 619 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   ILE A 624 " --> pdb=" O   HIS A 620 " (cutoff:3.500A)
      removed outlier: 4.834A  pdb=" N   LEU A 625 " --> pdb=" O   TRP A 621 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   LEU A 626 " --> pdb=" O   THR A 622 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   ARG A 627 " --> pdb=" O   LEU A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 658
      removed outlier: 3.729A  pdb=" N   THR A 645 " --> pdb=" O   PRO A 641 " (cutoff:3.500A)
      removed outlier: 3.657A  pdb=" N   ILE A 646 " --> pdb=" O   ALA A 642 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   LYS A 658 " --> pdb=" O   ARG A 654 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 668
      removed outlier: 3.586A  pdb=" N   VAL A 668 " --> pdb=" O   PRO A 665 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 669 through 674
      removed outlier: 3.642A  pdb=" N   GLY A 672 " --> pdb=" O   ASN A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 748 through 760
    Processing helix  chain 'A' and resid 773 through 784
    Processing helix  chain 'A' and resid 880 through 891
      removed outlier: 3.567A  pdb=" N   ALA A 891 " --> pdb=" O   TYR A 887 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 915 through 919
      removed outlier: 3.530A  pdb=" N   GLU A 918 " --> pdb=" O   THR A 915 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 938 through 949
    Processing helix  chain 'A' and resid 960 through 971
    Processing helix  chain 'A' and resid 1042 through 1053
      removed outlier: 3.851A  pdb=" N   ASP A1051 " --> pdb=" O   ARG A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1054 through 1064
    Processing helix  chain 'A' and resid 1072 through 1086
      removed outlier: 3.851A  pdb=" N   ILE A1086 " --> pdb=" O   LYS A1082 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1100 through 1105
      removed outlier: 3.796A  pdb=" N   LYS A1104 " --> pdb=" O   CYS A1100 " (cutoff:3.500A)
      removed outlier: 4.002A  pdb=" N   ALA A1105 " --> pdb=" O   ALA A1101 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1100 through 1105'
    Processing helix  chain 'A' and resid 1131 through 1143
      removed outlier: 4.349A  pdb=" N   GLU A1135 " --> pdb=" O   ARG A1131 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   GLY A1140 " --> pdb=" O   VAL A1136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1144 through 1167
      removed outlier: 3.683A  pdb=" N   TYR A1153 " --> pdb=" O   SER A1149 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   SER A1155 " --> pdb=" O   PHE A1151 " (cutoff:3.500A)
      removed outlier: 3.981A  pdb=" N   LEU A1156 " --> pdb=" O   LYS A1152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1168 through 1170
      No H-bonds generated for 'chain 'A' and resid 1168 through 1170'
    Processing helix  chain 'A' and resid 1178 through 1187
      removed outlier: 3.514A  pdb=" N   LEU A1187 " --> pdb=" O   ILE A1183 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1188 through 1196
      removed outlier: 3.912A  pdb=" N   PHE A1194 " --> pdb=" O   PRO A1190 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER A1196 " --> pdb=" O   ALA A1192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1215 through 1243
      Proline residue:  A1221  - end of helix
      removed outlier: 3.508A  pdb=" N   ILE A1232 " --> pdb=" O   VAL A1228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1260 through 1282
      removed outlier: 3.733A  pdb=" N   ALA A1269 " --> pdb=" O   THR A1265 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   GLY A1278 " --> pdb=" O   TYR A1274 " (cutoff:3.500A)
      removed outlier: 4.799A  pdb=" N   VAL A1279 " --> pdb=" O   ILE A1275 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   VAL A1280 " --> pdb=" O   LEU A1276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1297 through 1313
    Processing helix  chain 'A' and resid 1316 through 1323
      removed outlier: 3.557A  pdb=" N   PHE A1320 " --> pdb=" O   PRO A1316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1329 through 1352
      removed outlier: 3.714A  pdb=" N   HIS A1352 " --> pdb=" O   TRP A1348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1354 through 1363
    Processing helix  chain 'A' and resid 1377 through 1392
      removed outlier: 3.605A  pdb=" N   TYR A1392 " --> pdb=" O   PHE A1388 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 209
    Processing sheet with id=AA2, first strand: chain 'A' and resid 207 through 209
    Processing sheet with id=AA3, first strand: chain 'A' and resid 322 through 325
    Processing sheet with id=AA4, first strand: chain 'A' and resid 451 through 455
    Processing sheet with id=AA5, first strand: chain 'A' and resid 472 through 473
    Processing sheet with id=AA6, first strand: chain 'A' and resid 508 through 510
      removed outlier: 6.156A  pdb=" N   ASN A 497 " --> pdb=" O   LEU A 543 " (cutoff:3.500A)
      removed outlier: 5.797A  pdb=" N   LEU A 543 " --> pdb=" O   ASN A 497 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 660 through 662
      removed outlier: 6.922A  pdb=" N   SER A1111 " --> pdb=" O   SER A1125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 955
      removed outlier: 7.047A  pdb=" N   LEU A 676 " --> pdb=" O   GLY A1091 " (cutoff:3.500A)
      removed outlier: 7.953A  pdb=" N   CYS A1093 " --> pdb=" O   LEU A 676 " (cutoff:3.500A)
      removed outlier: 7.348A  pdb=" N   CYS A 678 " --> pdb=" O   CYS A1093 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 704 through 705
      removed outlier: 3.654A  pdb=" N   ARG A 704 " --> pdb=" O   SER A 699 " (cutoff:3.500A)
      removed outlier: 5.187A  pdb=" N   VAL A 692 " --> pdb=" O   GLU A 932 " (cutoff:3.500A)
      removed outlier: 6.090A  pdb=" N   GLU A 932 " --> pdb=" O   VAL A 692 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLY A 694 " --> pdb=" O   ILE A 930 " (cutoff:3.500A)
      removed outlier: 5.890A  pdb=" N   VAL A 926 " --> pdb=" O   ALA A 698 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   PHE A 925 " --> pdb=" O   THR A 900 " (cutoff:3.500A)
      removed outlier: 6.062A  pdb=" N   THR A 900 " --> pdb=" O   PHE A 925 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   GLY A 927 " --> pdb=" O   CYS A 898 " (cutoff:3.500A)
      removed outlier: 7.201A  pdb=" N   SER A 846 " --> pdb=" O   ALA A 835 " (cutoff:3.500A)
      removed outlier: 4.972A  pdb=" N   ALA A 835 " --> pdb=" O   SER A 846 " (cutoff:3.500A)
      removed outlier: 6.789A  pdb=" N   ILE A 848 " --> pdb=" O   LEU A 833 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 764 through 765
      removed outlier: 3.712A  pdb=" N   ARG A 764 " --> pdb=" O   VAL A 771 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   VAL A 771 " --> pdb=" O   ARG A 764 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'A' and resid 981 through 986
      removed outlier: 4.143A  pdb=" N   LYS A 996 " --> pdb=" O   ILE A 986 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1039 through 1041
      removed outlier: 7.147A  pdb=" N   ILE A1039 " --> pdb=" O   LYS A1066 " (cutoff:3.500A)
      removed outlier: 5.769A  pdb=" N   TYR A1068 " --> pdb=" O   ILE A1039 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   VAL A1041 " --> pdb=" O   TYR A1068 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    363 hydrogen bonds defined for protein.
    1029 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.47

  Time building geometry restraints manager: 0.92 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2528
        1.34 -     1.46: 1707
        1.46 -     1.58: 4778
        1.58 -     1.69: 0
        1.69 -     1.81: 77
  Bond restraints: 9090
  Sorted by residual:
  bond pdb=" F2  BEF A1401 "
       pdb="BE   BEF A1401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.560 -0.084 2.00e-02 2.50e+03 1.75e+01
  bond pdb=" F3  BEF A1401 "
       pdb="BE   BEF A1401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.544 -0.068 2.00e-02 2.50e+03 1.16e+01
  bond pdb=" F1  BEF A1401 "
       pdb="BE   BEF A1401 "
    ideal  model  delta    sigma   weight residual
    1.476  1.531 -0.055 2.00e-02 2.50e+03 7.67e+00
  bond pdb=" C   ASP A1010 "
       pdb=" N   PRO A1011 "
    ideal  model  delta    sigma   weight residual
    1.334  1.374 -0.040 2.34e-02 1.83e+03 2.93e+00
  bond pdb=" C   ARG A1285 "
       pdb=" N   PRO A1286 "
    ideal  model  delta    sigma   weight residual
    1.334  1.373 -0.039 2.34e-02 1.83e+03 2.85e+00
  ... (remaining 9085 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.50: 12060
        2.50 -     5.00: 233
        5.00 -     7.50: 47
        7.50 -    10.01: 6
       10.01 -    12.51: 3
  Bond angle restraints: 12349
  Sorted by residual:
  angle pdb=" F2  BEF A1401 "
        pdb="BE   BEF A1401 "
        pdb=" F3  BEF A1401 "
      ideal   model   delta    sigma   weight residual
     119.96  107.45   12.51 3.00e+00 1.11e-01 1.74e+01
  angle pdb=" CA  LYS A1383 "
        pdb=" CB  LYS A1383 "
        pdb=" CG  LYS A1383 "
      ideal   model   delta    sigma   weight residual
     114.10  121.43   -7.33 2.00e+00 2.50e-01 1.34e+01
  angle pdb=" C   VAL A1251 "
        pdb=" N   ASP A1252 "
        pdb=" CA  ASP A1252 "
      ideal   model   delta    sigma   weight residual
     121.70  128.21   -6.51 1.80e+00 3.09e-01 1.31e+01
  angle pdb=" C   GLU A 975 "
        pdb=" CA  GLU A 975 "
        pdb=" CB  GLU A 975 "
      ideal   model   delta    sigma   weight residual
     109.54  116.11   -6.57 1.84e+00 2.95e-01 1.28e+01
  angle pdb=" CB  GLU A1078 "
        pdb=" CG  GLU A1078 "
        pdb=" CD  GLU A1078 "
      ideal   model   delta    sigma   weight residual
     112.60  118.49   -5.89 1.70e+00 3.46e-01 1.20e+01
  ... (remaining 12344 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.90: 4763
       16.90 -    33.80: 509
       33.80 -    50.70: 89
       50.70 -    67.61: 10
       67.61 -    84.51: 11
  Dihedral angle restraints: 5382
    sinusoidal: 2120
      harmonic: 3262
  Sorted by residual:
  dihedral pdb=" CA  TRP A 345 "
           pdb=" C   TRP A 345 "
           pdb=" N   LYS A 346 "
           pdb=" CA  LYS A 346 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.48  -19.52     0      5.00e+00 4.00e-02 1.52e+01
  dihedral pdb=" CA  GLU A 866 "
           pdb=" C   GLU A 866 "
           pdb=" N   CYS A 867 "
           pdb=" CA  CYS A 867 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.27   18.73     0      5.00e+00 4.00e-02 1.40e+01
  dihedral pdb=" CA  PRO A 252 "
           pdb=" C   PRO A 252 "
           pdb=" N   LYS A 253 "
           pdb=" CA  LYS A 253 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.58  -18.42     0      5.00e+00 4.00e-02 1.36e+01
  ... (remaining 5379 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.068: 1159
       0.068 -    0.135: 222
       0.135 -    0.203: 20
       0.203 -    0.271: 5
       0.271 -    0.339: 2
  Chirality restraints: 1408
  Sorted by residual:
  chirality pdb=" CB  VAL A 468 "
            pdb=" CA  VAL A 468 "
            pdb=" CG1 VAL A 468 "
            pdb=" CG2 VAL A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.29   -0.34 2.00e-01 2.50e+01 2.87e+00
  chirality pdb=" CB  THR A 429 "
            pdb=" CA  THR A 429 "
            pdb=" OG1 THR A 429 "
            pdb=" CG2 THR A 429 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.27    0.29 2.00e-01 2.50e+01 2.03e+00
  chirality pdb=" CB  VAL A 472 "
            pdb=" CA  VAL A 472 "
            pdb=" CG1 VAL A 472 "
            pdb=" CG2 VAL A 472 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.47e+00
  ... (remaining 1405 not shown)

  Planarity restraints: 1546
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 624 "   -0.016 2.00e-02 2.50e+03   3.16e-02 9.96e+00
        pdb=" C   ILE A 624 "    0.055 2.00e-02 2.50e+03
        pdb=" O   ILE A 624 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   LEU A 625 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A1339 "    0.016 2.00e-02 2.50e+03   2.29e-02 9.21e+00
        pdb=" CG  PHE A1339 "   -0.052 2.00e-02 2.50e+03
        pdb=" CD1 PHE A1339 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 PHE A1339 "    0.019 2.00e-02 2.50e+03
        pdb=" CE1 PHE A1339 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 PHE A1339 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE A1339 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A1004 "   -0.046 5.00e-02 4.00e+02   7.09e-02 8.05e+00
        pdb=" N   PRO A1005 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO A1005 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A1005 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1543 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 68
        2.54 -     3.13: 6591
        3.13 -     3.72: 13856
        3.72 -     4.31: 18444
        4.31 -     4.90: 30770
  Nonbonded interactions: 69729
  Sorted by model distance:
  nonbonded pdb="BE   BEF A1401 "
            pdb="MG    MG A1402 "
     model   vdw
     1.950 1.550
  nonbonded pdb=" F3  BEF A1401 "
            pdb="MG    MG A1402 "
     model   vdw
     2.002 2.120
  nonbonded pdb=" F1  BEF A1401 "
            pdb="MG    MG A1402 "
     model   vdw
     2.023 2.120
  nonbonded pdb=" F2  BEF A1401 "
            pdb="MG    MG A1402 "
     model   vdw
     2.139 2.120
  nonbonded pdb=" O   THR A 682 "
            pdb="MG    MG A1402 "
     model   vdw
     2.181 2.170
  ... (remaining 69724 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.490
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     9.570
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.350
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.700
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7474
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      :  0.004   0.084   9090  Z= 0.195
  Angle     :  0.861  12.507  12349  Z= 0.432
  Chirality :  0.054   0.339   1408
  Planarity :  0.006   0.071   1546
  Dihedral  : 14.437  84.507   3270
  Min Nonbonded Distance : 1.950

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.73 (0.23), residues: 1100
  helix: -0.34 (0.23), residues: 419
  sheet: -1.50 (0.46), residues: 119
  loop : -1.69 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 227 
 TYR   0.045   0.002   TYR A1088 
 PHE   0.052   0.002   PHE A1339 
 TRP   0.026   0.001   TRP A1245 
 HIS   0.009   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00436 ( 9090)
  covalent geometry    : angle       0.86093 (12349)
  hydrogen bonds       : bond        0.18019 (  359)
  hydrogen bonds       : angle       6.84051 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 0.271 
Fit side-chains
REVERT: A  221 SER cc_start: 0.6503 (t) cc_final: 0.6000 (t)
REVERT: A 1129 ASP cc_start: 0.7067 (p0) cc_final: 0.6577 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0670
  time to fit residues: 16.1090
Evaluate side-chains
  121 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 65 optimal weight:    7.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    0.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
A 333 HIS
A1225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4448 r_free = 0.4448 target = 0.197278 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.157756 restraints weight = 13210.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.159892 restraints weight = 7896.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.160977 restraints weight = 7950.007|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.161733 restraints weight = 5718.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.162251 restraints weight = 5226.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
moved from start:          0.1537

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072   9090  Z= 0.192
  Angle     :  0.642   8.057  12349  Z= 0.330
  Chirality :  0.046   0.241   1408
  Planarity :  0.005   0.048   1546
  Dihedral  :  4.936  21.904   1213
  Min Nonbonded Distance : 1.291

Molprobity Statistics.
  All-atom Clashscore : 8.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  1.85 %
    Allowed  : 11.19 %
    Favored  : 86.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.29 (0.24), residues: 1100
  helix:  0.31 (0.24), residues: 430
  sheet: -1.44 (0.45), residues: 130
  loop : -1.67 (0.26), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1138 
 TYR   0.029   0.002   TYR A1088 
 PHE   0.038   0.002   PHE A1339 
 TRP   0.010   0.001   TRP A1245 
 HIS   0.002   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00462 ( 9090)
  covalent geometry    : angle       0.64246 (12349)
  hydrogen bonds       : bond        0.03834 (  359)
  hydrogen bonds       : angle       4.94187 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 138
  time to evaluate  : 0.347 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7295 (t) cc_final: 0.6954 (t)
REVERT: A  223 PHE cc_start: 0.7117 (m-80) cc_final: 0.6690 (m-80)
REVERT: A  530 HIS cc_start: 0.6949 (OUTLIER) cc_final: 0.6453 (t-90)
REVERT: A  975 GLU cc_start: 0.7286 (tm-30) cc_final: 0.6860 (tm-30)
REVERT: A 1129 ASP cc_start: 0.7511 (p0) cc_final: 0.6962 (p0)
REVERT: A 1231 MET cc_start: 0.7216 (mmm) cc_final: 0.6821 (mmm)
  outliers start: 18
  outliers final: 13
  residues processed: 149
  average time/residue: 0.0594
  time to fit residues: 13.7232
Evaluate side-chains
  132 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 118
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  985 PHE
Chi-restraints excluded: chain A residue 1098 ASN
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1305 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 42 optimal weight:   20.0000
   chunk 90 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 47 optimal weight:    0.9980
   chunk 18 optimal weight:    8.9990
   chunk 40 optimal weight:    9.9990
   chunk 43 optimal weight:    0.0060
   chunk 10 optimal weight:    2.9990
   chunk 32 optimal weight:    0.7980
   chunk 102 optimal weight:    3.9990
   chunk 106 optimal weight:    0.9990
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
A1225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4430 r_free = 0.4430 target = 0.195372 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.156589 restraints weight = 13308.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.156037 restraints weight = 8892.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4037 r_free = 0.4037 target = 0.158136 restraints weight = 7792.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.158850 restraints weight = 5876.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.159061 restraints weight = 5685.387|
|-----------------------------------------------------------------------------|
r_work (final): 0.4084
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.1659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9090  Z= 0.130
  Angle     :  0.580   8.096  12349  Z= 0.294
  Chirality :  0.044   0.199   1408
  Planarity :  0.004   0.046   1546
  Dihedral  :  4.674  21.175   1213
  Min Nonbonded Distance : 1.393

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 14.37 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.98 (0.25), residues: 1100
  helix:  0.63 (0.25), residues: 436
  sheet: -1.34 (0.45), residues: 130
  loop : -1.56 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 440 
 TYR   0.024   0.001   TYR A1088 
 PHE   0.027   0.001   PHE A1339 
 TRP   0.009   0.001   TRP A 270 
 HIS   0.014   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9090)
  covalent geometry    : angle       0.57981 (12349)
  hydrogen bonds       : bond        0.03340 (  359)
  hydrogen bonds       : angle       4.69406 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7282 (t) cc_final: 0.6882 (t)
REVERT: A  223 PHE cc_start: 0.7106 (m-80) cc_final: 0.6663 (m-80)
REVERT: A  530 HIS cc_start: 0.6894 (OUTLIER) cc_final: 0.6392 (t-90)
REVERT: A  975 GLU cc_start: 0.7380 (tm-30) cc_final: 0.6980 (tm-30)
REVERT: A 1129 ASP cc_start: 0.7512 (p0) cc_final: 0.6955 (p0)
REVERT: A 1225 HIS cc_start: 0.8086 (OUTLIER) cc_final: 0.7264 (t70)
REVERT: A 1231 MET cc_start: 0.7163 (mmm) cc_final: 0.6754 (mmm)
  outliers start: 22
  outliers final: 15
  residues processed: 141
  average time/residue: 0.0633
  time to fit residues: 14.3391
Evaluate side-chains
  135 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 118
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  691 ASP
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue 1095 ASP
Chi-restraints excluded: chain A residue 1098 ASN
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1305 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:    0.7980
   chunk 14 optimal weight:    6.9990
   chunk 48 optimal weight:    0.5980
   chunk 37 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 15 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 22 optimal weight:    0.8980
   chunk 40 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 613 ASN
A1225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4409 r_free = 0.4409 target = 0.193433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.154577 restraints weight = 13485.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.154122 restraints weight = 8896.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.156154 restraints weight = 7830.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.156967 restraints weight = 5929.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.157155 restraints weight = 5654.109|
|-----------------------------------------------------------------------------|
r_work (final): 0.4063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7667
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9090  Z= 0.142
  Angle     :  0.575   7.799  12349  Z= 0.291
  Chirality :  0.043   0.199   1408
  Planarity :  0.004   0.041   1546
  Dihedral  :  4.567  21.621   1213
  Min Nonbonded Distance : 1.351

Molprobity Statistics.
  All-atom Clashscore : 8.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 15.71 %
    Favored  : 81.31 %
  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 are not related in a simple way.
  whole: -0.92 (0.25), residues: 1100
  helix:  0.77 (0.25), residues: 433
  sheet: -1.41 (0.44), residues: 132
  loop : -1.57 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1241 
 TYR   0.024   0.001   TYR A1088 
 PHE   0.020   0.001   PHE A1339 
 TRP   0.006   0.001   TRP A 270 
 HIS   0.014   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 9090)
  covalent geometry    : angle       0.57533 (12349)
  hydrogen bonds       : bond        0.03153 (  359)
  hydrogen bonds       : angle       4.54965 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.251 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7306 (t) cc_final: 0.6885 (t)
REVERT: A  223 PHE cc_start: 0.7136 (m-80) cc_final: 0.6717 (m-80)
REVERT: A  530 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.6410 (t-90)
REVERT: A  975 GLU cc_start: 0.7436 (tm-30) cc_final: 0.7186 (tm-30)
REVERT: A 1129 ASP cc_start: 0.7579 (p0) cc_final: 0.7027 (p0)
REVERT: A 1135 GLU cc_start: 0.6119 (OUTLIER) cc_final: 0.5652 (mp0)
REVERT: A 1225 HIS cc_start: 0.8077 (OUTLIER) cc_final: 0.7337 (t70)
REVERT: A 1231 MET cc_start: 0.7242 (mmm) cc_final: 0.6811 (mmm)
  outliers start: 29
  outliers final: 20
  residues processed: 143
  average time/residue: 0.0603
  time to fit residues: 13.6421
Evaluate side-chains
  138 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 115
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 TRP
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  691 ASP
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1095 ASP
Chi-restraints excluded: chain A residue 1098 ASN
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1305 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 73 optimal weight:    1.9990
   chunk 16 optimal weight:    6.9990
   chunk 104 optimal weight:    4.9990
   chunk 95 optimal weight:    1.9990
   chunk 83 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 23 optimal weight:    5.9990
   chunk 110 optimal weight:    2.9990
   chunk 6 optimal weight:    0.0570
   chunk 107 optimal weight:    4.9990
   overall best weight:    1.8106

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS
A1225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.187528 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.148121 restraints weight = 13456.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.150277 restraints weight = 8206.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.151717 restraints weight = 7745.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.152096 restraints weight = 5762.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.152687 restraints weight = 5443.921|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075   9090  Z= 0.240
  Angle     :  0.651   8.785  12349  Z= 0.332
  Chirality :  0.046   0.223   1408
  Planarity :  0.004   0.053   1546
  Dihedral  :  4.897  23.872   1213
  Min Nonbonded Distance : 1.278

Molprobity Statistics.
  All-atom Clashscore : 9.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.09 %
    Favored  : 92.91 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 17.76 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.14 (0.25), residues: 1100
  helix:  0.58 (0.25), residues: 435
  sheet: -1.57 (0.46), residues: 126
  loop : -1.69 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1288 
 TYR   0.047   0.002   TYR A1088 
 PHE   0.018   0.002   PHE A1092 
 TRP   0.009   0.001   TRP A 350 
 HIS   0.023   0.002   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00573 ( 9090)
  covalent geometry    : angle       0.65100 (12349)
  hydrogen bonds       : bond        0.03470 (  359)
  hydrogen bonds       : angle       4.63443 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 119
  time to evaluate  : 0.218 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7510 (t) cc_final: 0.7100 (t)
REVERT: A  223 PHE cc_start: 0.7248 (m-80) cc_final: 0.6807 (m-80)
REVERT: A  975 GLU cc_start: 0.7496 (tm-30) cc_final: 0.7249 (tm-30)
REVERT: A 1135 GLU cc_start: 0.6226 (OUTLIER) cc_final: 0.5651 (mp0)
REVERT: A 1231 MET cc_start: 0.7384 (mmm) cc_final: 0.6963 (mmm)
  outliers start: 31
  outliers final: 26
  residues processed: 138
  average time/residue: 0.0705
  time to fit residues: 14.7357
Evaluate side-chains
  139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 112
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  691 ASP
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1071 MET
Chi-restraints excluded: chain A residue 1095 ASP
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1219 LEU
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 73 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 13 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 3 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 21 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 41 optimal weight:    8.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** A 367 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.186610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.146995 restraints weight = 13424.015|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.150488 restraints weight = 8553.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.151377 restraints weight = 7045.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.151774 restraints weight = 5823.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.151830 restraints weight = 5677.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   9090  Z= 0.207
  Angle     :  0.627   8.748  12349  Z= 0.320
  Chirality :  0.045   0.224   1408
  Planarity :  0.004   0.038   1546
  Dihedral  :  4.888  24.003   1213
  Min Nonbonded Distance : 1.288

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.40 %
    Favored  : 77.31 %
  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 are not related in a simple way.
  whole: -1.16 (0.25), residues: 1100
  helix:  0.54 (0.24), residues: 435
  sheet: -1.64 (0.45), residues: 126
  loop : -1.66 (0.26), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1288 
 TYR   0.038   0.002   TYR A1088 
 PHE   0.020   0.001   PHE A1393 
 TRP   0.009   0.001   TRP A1012 
 HIS   0.020   0.002   HIS A 367 

Details of bonding type rmsd
  covalent geometry    : bond        0.00501 ( 9090)
  covalent geometry    : angle       0.62683 (12349)
  hydrogen bonds       : bond        0.03411 (  359)
  hydrogen bonds       : angle       4.63535 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7500 (t) cc_final: 0.7073 (t)
REVERT: A  223 PHE cc_start: 0.7213 (m-80) cc_final: 0.6755 (m-80)
REVERT: A  530 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.6462 (t-90)
REVERT: A  975 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7356 (tm-30)
REVERT: A 1088 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.6922 (t80)
REVERT: A 1135 GLU cc_start: 0.6185 (OUTLIER) cc_final: 0.5626 (mp0)
REVERT: A 1225 HIS cc_start: 0.8021 (OUTLIER) cc_final: 0.7348 (t70)
REVERT: A 1231 MET cc_start: 0.7407 (mmm) cc_final: 0.7001 (mmm)
REVERT: A 1311 MET cc_start: 0.6962 (OUTLIER) cc_final: 0.6311 (tpp)
  outliers start: 32
  outliers final: 26
  residues processed: 142
  average time/residue: 0.0729
  time to fit residues: 15.8345
Evaluate side-chains
  147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 116
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 TRP
Chi-restraints excluded: chain A residue  296 THR
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  691 ASP
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1049 ILE
Chi-restraints excluded: chain A residue 1071 MET
Chi-restraints excluded: chain A residue 1088 TYR
Chi-restraints excluded: chain A residue 1095 ASP
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1145 VAL
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1193 VAL
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1219 LEU
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1311 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 40 optimal weight:    9.9990
   chunk 20 optimal weight:    2.9990
   chunk 99 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 46 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 43 optimal weight:    0.2980
   chunk 66 optimal weight:    8.9990
   chunk 8 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A 367 HIS
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.191930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.153557 restraints weight = 13395.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.153388 restraints weight = 8342.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.155570 restraints weight = 8383.970|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.156101 restraints weight = 5875.119|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.156695 restraints weight = 5457.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.4054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.2632

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9090  Z= 0.129
  Angle     :  0.582  10.204  12349  Z= 0.294
  Chirality :  0.043   0.193   1408
  Planarity :  0.004   0.037   1546
  Dihedral  :  4.663  22.711   1213
  Min Nonbonded Distance : 1.374

Molprobity Statistics.
  All-atom Clashscore : 8.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 19.71 %
    Favored  : 77.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.25), residues: 1100
  helix:  0.78 (0.25), residues: 435
  sheet: -1.59 (0.46), residues: 127
  loop : -1.54 (0.26), residues: 538

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 627 
 TYR   0.037   0.002   TYR A1392 
 PHE   0.022   0.001   PHE A1393 
 TRP   0.008   0.001   TRP A1245 
 HIS   0.013   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 9090)
  covalent geometry    : angle       0.58228 (12349)
  hydrogen bonds       : bond        0.03061 (  359)
  hydrogen bonds       : angle       4.48628 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 133
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7420 (t) cc_final: 0.6990 (t)
REVERT: A  223 PHE cc_start: 0.7183 (m-80) cc_final: 0.6731 (m-80)
REVERT: A  530 HIS cc_start: 0.6881 (OUTLIER) cc_final: 0.6421 (t-90)
REVERT: A 1088 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.6677 (t80)
REVERT: A 1135 GLU cc_start: 0.6094 (OUTLIER) cc_final: 0.5584 (mp0)
REVERT: A 1225 HIS cc_start: 0.8004 (OUTLIER) cc_final: 0.7352 (t70)
REVERT: A 1231 MET cc_start: 0.7447 (mmm) cc_final: 0.7031 (mmm)
REVERT: A 1311 MET cc_start: 0.6946 (OUTLIER) cc_final: 0.6242 (tpp)
  outliers start: 32
  outliers final: 23
  residues processed: 154
  average time/residue: 0.0645
  time to fit residues: 15.4740
Evaluate side-chains
  151 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 123
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 TRP
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  514 THR
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  691 ASP
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1071 MET
Chi-restraints excluded: chain A residue 1088 TYR
Chi-restraints excluded: chain A residue 1095 ASP
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1219 LEU
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1311 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 23 optimal weight:    6.9990
   chunk 81 optimal weight:    1.9990
   chunk 52 optimal weight:    0.5980
   chunk 60 optimal weight:   10.0000
   chunk 98 optimal weight:    0.9990
   chunk 7 optimal weight:    0.2980
   chunk 12 optimal weight:    3.9990
   chunk 73 optimal weight:    0.5980
   chunk 15 optimal weight:    0.6980
   chunk 6 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4386 r_free = 0.4386 target = 0.191129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.153276 restraints weight = 13350.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3982 r_free = 0.3982 target = 0.152918 restraints weight = 8824.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.154664 restraints weight = 7714.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.155547 restraints weight = 6019.576|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.155692 restraints weight = 5679.783|
|-----------------------------------------------------------------------------|
r_work (final): 0.4048
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7696
moved from start:          0.2614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9090  Z= 0.128
  Angle     :  0.594   8.239  12349  Z= 0.296
  Chirality :  0.043   0.192   1408
  Planarity :  0.004   0.036   1546
  Dihedral  :  4.570  22.541   1213
  Min Nonbonded Distance : 1.399

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.33 %
    Favored  : 76.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.25), residues: 1100
  helix:  0.81 (0.25), residues: 436
  sheet: -1.58 (0.45), residues: 133
  loop : -1.48 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 627 
 TYR   0.031   0.002   TYR A 397 
 PHE   0.029   0.001   PHE A1339 
 TRP   0.008   0.001   TRP A1245 
 HIS   0.010   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9090)
  covalent geometry    : angle       0.59366 (12349)
  hydrogen bonds       : bond        0.03004 (  359)
  hydrogen bonds       : angle       4.39921 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 128
  time to evaluate  : 0.334 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7474 (t) cc_final: 0.7035 (t)
REVERT: A  223 PHE cc_start: 0.7154 (m-80) cc_final: 0.6699 (m-80)
REVERT: A  530 HIS cc_start: 0.6866 (OUTLIER) cc_final: 0.6407 (t-90)
REVERT: A 1088 TYR cc_start: 0.8545 (OUTLIER) cc_final: 0.6647 (t80)
REVERT: A 1135 GLU cc_start: 0.6107 (OUTLIER) cc_final: 0.5611 (mp0)
REVERT: A 1225 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7426 (t70)
REVERT: A 1231 MET cc_start: 0.7333 (mmm) cc_final: 0.6945 (mmm)
REVERT: A 1311 MET cc_start: 0.6965 (OUTLIER) cc_final: 0.6279 (tpp)
  outliers start: 34
  outliers final: 25
  residues processed: 151
  average time/residue: 0.0703
  time to fit residues: 16.2748
Evaluate side-chains
  154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 124
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 TRP
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  691 ASP
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  926 VAL
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1055 THR
Chi-restraints excluded: chain A residue 1071 MET
Chi-restraints excluded: chain A residue 1088 TYR
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1219 LEU
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1311 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 59 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 11 optimal weight:    0.7980
   chunk 10 optimal weight:    5.9990
   chunk 49 optimal weight:    3.9990
   chunk 0 optimal weight:    2.9990
   chunk 62 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 96 optimal weight:    6.9990
   chunk 3 optimal weight:    0.9980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.189929 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.150946 restraints weight = 13326.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.153043 restraints weight = 8129.442|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.153953 restraints weight = 7601.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.154857 restraints weight = 5973.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.155310 restraints weight = 5470.377|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.2734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   9090  Z= 0.165
  Angle     :  0.622  12.482  12349  Z= 0.310
  Chirality :  0.044   0.210   1408
  Planarity :  0.004   0.036   1546
  Dihedral  :  4.638  23.208   1213
  Min Nonbonded Distance : 1.360

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.73 %
    Favored  : 93.27 %
  Rotamer:
    Outliers :  3.49 %
    Allowed  : 20.53 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.93 (0.25), residues: 1100
  helix:  0.74 (0.25), residues: 436
  sheet: -1.64 (0.44), residues: 133
  loop : -1.51 (0.27), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 627 
 TYR   0.031   0.002   TYR A1088 
 PHE   0.036   0.001   PHE A1339 
 TRP   0.008   0.001   TRP A1245 
 HIS   0.007   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00398 ( 9090)
  covalent geometry    : angle       0.62196 (12349)
  hydrogen bonds       : bond        0.03134 (  359)
  hydrogen bonds       : angle       4.44301 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.328 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 SER cc_start: 0.7427 (t) cc_final: 0.7012 (t)
REVERT: A  223 PHE cc_start: 0.7166 (m-80) cc_final: 0.6719 (m-80)
REVERT: A  530 HIS cc_start: 0.6874 (OUTLIER) cc_final: 0.6420 (t-90)
REVERT: A 1088 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.6935 (t80)
REVERT: A 1135 GLU cc_start: 0.6121 (OUTLIER) cc_final: 0.5626 (mp0)
REVERT: A 1225 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7283 (t70)
REVERT: A 1231 MET cc_start: 0.7398 (mmm) cc_final: 0.7012 (mmm)
REVERT: A 1311 MET cc_start: 0.6989 (OUTLIER) cc_final: 0.6346 (tpp)
  outliers start: 34
  outliers final: 28
  residues processed: 149
  average time/residue: 0.0697
  time to fit residues: 16.0879
Evaluate side-chains
  155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 122
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 TRP
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  385 LEU
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  487 SER
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  926 VAL
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue  985 PHE
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1055 THR
Chi-restraints excluded: chain A residue 1071 MET
Chi-restraints excluded: chain A residue 1088 TYR
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1219 LEU
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1311 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 14 optimal weight:    0.0470
   chunk 46 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 60 optimal weight:    9.9990
   chunk 79 optimal weight:    0.9980
   chunk 15 optimal weight:    0.8980
   chunk 76 optimal weight:    0.9990
   chunk 109 optimal weight:    0.0980
   chunk 16 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 32 optimal weight:    0.4980
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1225 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4418 r_free = 0.4418 target = 0.196248 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.154207 restraints weight = 13598.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.159003 restraints weight = 7662.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.162042 restraints weight = 5377.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.163624 restraints weight = 4367.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4120 r_free = 0.4120 target = 0.164861 restraints weight = 3897.196|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7632
moved from start:          0.2716

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9090  Z= 0.121
  Angle     :  0.601  11.871  12349  Z= 0.298
  Chirality :  0.043   0.188   1408
  Planarity :  0.004   0.037   1546
  Dihedral  :  4.543  22.414   1213
  Min Nonbonded Distance : 1.433

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.15 %
    Favored  : 75.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.86 (0.25), residues: 1100
  helix:  0.81 (0.25), residues: 437
  sheet: -1.60 (0.44), residues: 133
  loop : -1.48 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 627 
 TYR   0.023   0.001   TYR A1088 
 PHE   0.030   0.001   PHE A1339 
 TRP   0.008   0.001   TRP A1245 
 HIS   0.010   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 9090)
  covalent geometry    : angle       0.60071 (12349)
  hydrogen bonds       : bond        0.02948 (  359)
  hydrogen bonds       : angle       4.35573 ( 1029)

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

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

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2200 Ramachandran restraints generated.
    1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.336 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 SER cc_start: 0.7520 (t) cc_final: 0.6982 (t)
REVERT: A  223 PHE cc_start: 0.7257 (m-80) cc_final: 0.6741 (m-10)
REVERT: A  530 HIS cc_start: 0.6850 (OUTLIER) cc_final: 0.6387 (t-90)
REVERT: A  594 ARG cc_start: 0.7174 (ttt180) cc_final: 0.6950 (ttt180)
REVERT: A 1088 TYR cc_start: 0.8476 (OUTLIER) cc_final: 0.6656 (t80)
REVERT: A 1135 GLU cc_start: 0.6002 (OUTLIER) cc_final: 0.5510 (mp0)
REVERT: A 1225 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7369 (t70)
REVERT: A 1231 MET cc_start: 0.7220 (mmm) cc_final: 0.6840 (mmm)
REVERT: A 1311 MET cc_start: 0.7069 (OUTLIER) cc_final: 0.6402 (tpp)
  outliers start: 31
  outliers final: 24
  residues processed: 148
  average time/residue: 0.0682
  time to fit residues: 15.4031
Evaluate side-chains
  154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  263 THR
Chi-restraints excluded: chain A residue  270 TRP
Chi-restraints excluded: chain A residue  347 ASP
Chi-restraints excluded: chain A residue  414 TYR
Chi-restraints excluded: chain A residue  419 ILE
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  527 THR
Chi-restraints excluded: chain A residue  530 HIS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  895 VAL
Chi-restraints excluded: chain A residue  926 VAL
Chi-restraints excluded: chain A residue  943 ILE
Chi-restraints excluded: chain A residue  971 CYS
Chi-restraints excluded: chain A residue  980 CYS
Chi-restraints excluded: chain A residue  985 PHE
Chi-restraints excluded: chain A residue 1013 THR
Chi-restraints excluded: chain A residue 1055 THR
Chi-restraints excluded: chain A residue 1071 MET
Chi-restraints excluded: chain A residue 1088 TYR
Chi-restraints excluded: chain A residue 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1219 LEU
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1276 LEU
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1311 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 110 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 97 optimal weight:    5.9990
   chunk 96 optimal weight:    0.9980
   chunk 85 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   chunk 90 optimal weight:    6.9990
   chunk 67 optimal weight:    0.6980
   chunk 94 optimal weight:    2.9990
   chunk 93 optimal weight:    0.6980
   chunk 68 optimal weight:    0.1980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 950 ASN
A1225 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.193035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.154958 restraints weight = 13294.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.154280 restraints weight = 8305.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.156577 restraints weight = 8466.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4021 r_free = 0.4021 target = 0.157245 restraints weight = 5929.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.157802 restraints weight = 5479.440|
|-----------------------------------------------------------------------------|
r_work (final): 0.4070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.2795

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9090  Z= 0.125
  Angle     :  0.608  11.264  12349  Z= 0.303
  Chirality :  0.043   0.191   1408
  Planarity :  0.004   0.036   1546
  Dihedral  :  4.495  22.436   1213
  Min Nonbonded Distance : 1.430

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 21.77 %
    Favored  : 75.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.82 (0.25), residues: 1100
  helix:  0.88 (0.25), residues: 435
  sheet: -1.55 (0.45), residues: 133
  loop : -1.48 (0.27), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 627 
 TYR   0.061   0.002   TYR A1392 
 PHE   0.044   0.001   PHE A1339 
 TRP   0.008   0.001   TRP A1245 
 HIS   0.008   0.001   HIS A1225 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 9090)
  covalent geometry    : angle       0.60828 (12349)
  hydrogen bonds       : bond        0.02963 (  359)
  hydrogen bonds       : angle       4.35341 ( 1029)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1429.71 seconds
wall clock time: 25 minutes 24.30 seconds (1524.30 seconds total)