Starting phenix.real_space_refine
on Thu Mar 13 15:47:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7op8_13014/03_2025/7op8_13014.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7op8_13014/03_2025/7op8_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_2025/7op8_13014.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7op8_13014/03_2025/7op8_13014.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7op8_13014/03_2025/7op8_13014.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7op8_13014/03_2025/7op8_13014.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.071
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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 6.17, per 1000 atoms: 0.70
  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: 2.31
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 1.15
  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: 3.33

  Time building geometry restraints manager: 2.74 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:             3.450
  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:          0.340
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     25.560
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.840
-------------------------------------------------------------------------------
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= 0.272
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (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
 TRP   0.026   0.001   TRP A1245 
 HIS   0.009   0.001   HIS A1225 
 PHE   0.052   0.002   PHE A1339 
 TYR   0.045   0.002   TYR A1088 
 ARG   0.006   0.000   ARG A 227 

*********************** 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  : 0.935 
Fit side-chains
REVERT: A  221 SER cc_start: 0.6503 (t) cc_final: 0.6000 (t)
REVERT: A 1129 ASP cc_start: 0.7068 (p0) cc_final: 0.6577 (p0)
  outliers start: 0
  outliers final: 0
  residues processed: 157
  average time/residue: 0.1547
  time to fit residues: 36.8326
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  : 0.879 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    3.9990
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    0.0770
   chunk 44 optimal weight:    2.9990
   chunk 87 optimal weight:    0.6980
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 64 optimal weight:    2.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    0.8940

-------------------------------------------------------------------------------
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 = 0.4479 r_free = 0.4479 target = 0.200235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.161979 restraints weight = 13149.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.161732 restraints weight = 8502.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.164011 restraints weight = 8478.160|
|-----------------------------------------------------------------------------|
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   9090  Z= 0.227
  Angle     :  0.613   8.025  12349  Z= 0.313
  Chirality :  0.045   0.221   1408
  Planarity :  0.005   0.047   1546
  Dihedral  :  4.817  22.141   1213
  Min Nonbonded Distance : 1.223

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.55 %
    Favored  : 94.45 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 10.57 %
    Favored  : 87.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.24), residues: 1100
  helix:  0.32 (0.24), residues: 435
  sheet: -1.36 (0.45), residues: 129
  loop : -1.65 (0.26), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1245 
 HIS   0.002   0.001   HIS A 367 
 PHE   0.039   0.001   PHE A1339 
 TYR   0.023   0.002   TYR A1088 
 ARG   0.003   0.000   ARG A 594 

*********************** 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
  155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 138
  time to evaluate  : 1.419 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7212 (t) cc_final: 0.6864 (t)
REVERT: A  223 PHE cc_start: 0.7035 (m-80) cc_final: 0.6596 (m-80)
REVERT: A  530 HIS cc_start: 0.6954 (OUTLIER) cc_final: 0.6448 (t-90)
REVERT: A  975 GLU cc_start: 0.7198 (tm-30) cc_final: 0.6781 (tm-30)
REVERT: A 1129 ASP cc_start: 0.7397 (p0) cc_final: 0.6859 (p0)
REVERT: A 1231 MET cc_start: 0.7171 (mmm) cc_final: 0.6786 (mmm)
  outliers start: 17
  outliers final: 12
  residues processed: 149
  average time/residue: 0.2132
  time to fit residues: 49.9719
Evaluate side-chains
  134 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 121
  time to evaluate  : 0.807 
-------------------------------------------------------------------------------
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 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 57 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 70 optimal weight:    0.1980
   chunk 28 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 91 optimal weight:    8.9990
   chunk 41 optimal weight:    0.5980
   chunk 109 optimal weight:    9.9990
   chunk 12 optimal weight:    4.9990
   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 367 HIS
A 613 ASN
A1225 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.192043 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.152656 restraints weight = 13459.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.152109 restraints weight = 9123.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.153893 restraints weight = 7883.546|
|-----------------------------------------------------------------------------|
r_work (final): 0.4020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.1841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   9090  Z= 0.283
  Angle     :  0.609   7.552  12349  Z= 0.312
  Chirality :  0.045   0.218   1408
  Planarity :  0.004   0.046   1546
  Dihedral  :  4.807  22.355   1213
  Min Nonbonded Distance : 1.325

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.27 %
    Favored  : 93.73 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 13.76 %
    Favored  : 83.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.05 (0.25), residues: 1100
  helix:  0.61 (0.25), residues: 434
  sheet: -1.45 (0.45), residues: 132
  loop : -1.60 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 270 
 HIS   0.031   0.002   HIS A1225 
 PHE   0.026   0.001   PHE A1339 
 TYR   0.034   0.002   TYR A1088 
 ARG   0.003   0.000   ARG A 440 

*********************** 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
  156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 131
  time to evaluate  : 0.960 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7369 (t) cc_final: 0.6974 (t)
REVERT: A  223 PHE cc_start: 0.7213 (m-80) cc_final: 0.6779 (m-80)
REVERT: A  530 HIS cc_start: 0.6907 (OUTLIER) cc_final: 0.6418 (t-90)
REVERT: A  975 GLU cc_start: 0.7398 (tm-30) cc_final: 0.7149 (tm-30)
REVERT: A 1231 MET cc_start: 0.7253 (mmm) cc_final: 0.6840 (mmm)
REVERT: A 1344 PHE cc_start: 0.8566 (t80) cc_final: 0.8268 (t80)
  outliers start: 25
  outliers final: 20
  residues processed: 147
  average time/residue: 0.1483
  time to fit residues: 33.7481
Evaluate side-chains
  144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 123
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  676 LEU
Chi-restraints excluded: chain A residue  691 ASP
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 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 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 81 optimal weight:    0.8980
   chunk 103 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 82 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9980
   chunk 4 optimal weight:    0.1980
   chunk 104 optimal weight:    2.9990
   chunk 87 optimal weight:    0.5980
   chunk 92 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.4422 r_free = 0.4422 target = 0.194643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.155559 restraints weight = 13252.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.157624 restraints weight = 7901.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.158979 restraints weight = 7660.774|
|-----------------------------------------------------------------------------|
r_work (final): 0.4083
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9090  Z= 0.186
  Angle     :  0.570   7.876  12349  Z= 0.289
  Chirality :  0.043   0.188   1408
  Planarity :  0.004   0.043   1546
  Dihedral  :  4.605  21.248   1213
  Min Nonbonded Distance : 1.371

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  2.36 %
    Allowed  : 17.15 %
    Favored  : 80.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.25), residues: 1100
  helix:  0.77 (0.25), residues: 433
  sheet: -1.35 (0.45), residues: 130
  loop : -1.53 (0.26), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.017   0.001   HIS A 367 
 PHE   0.021   0.001   PHE A1339 
 TYR   0.024   0.001   TYR A1088 
 ARG   0.002   0.000   ARG A1288 

*********************** 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
  158 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 135
  time to evaluate  : 1.336 
Fit side-chains
   revert: symmetry clash
REVERT: A  221 SER cc_start: 0.7253 (t) cc_final: 0.6840 (t)
REVERT: A  223 PHE cc_start: 0.7039 (m-80) cc_final: 0.6630 (m-80)
REVERT: A  975 GLU cc_start: 0.7407 (tm-30) cc_final: 0.7168 (tm-30)
REVERT: A 1135 GLU cc_start: 0.6123 (OUTLIER) cc_final: 0.5672 (mp0)
REVERT: A 1231 MET cc_start: 0.7267 (mmm) cc_final: 0.6875 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 150
  average time/residue: 0.2338
  time to fit residues: 54.5684
Evaluate side-chains
  139 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 120
  time to evaluate  : 0.994 
-------------------------------------------------------------------------------
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  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 1135 GLU
Chi-restraints excluded: chain A residue 1187 LEU
Chi-restraints excluded: chain A residue 1195 MET
Chi-restraints excluded: chain A residue 1225 HIS
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 90 optimal weight:    1.9990
   chunk 101 optimal weight:    2.9990
   chunk 86 optimal weight:    3.9990
   chunk 41 optimal weight:    5.9990
   chunk 54 optimal weight:    5.9990
   chunk 97 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0470
   chunk 85 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9990
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.9282

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

Flipped N/Q/H residues before XYZ refinement:
** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.192430 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4032 r_free = 0.4032 target = 0.153103 restraints weight = 13304.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.156157 restraints weight = 7993.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.157158 restraints weight = 7276.553|
|-----------------------------------------------------------------------------|
r_work (final): 0.4073
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7662
moved from start:          0.2122

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9090  Z= 0.224
  Angle     :  0.586   8.564  12349  Z= 0.295
  Chirality :  0.043   0.176   1408
  Planarity :  0.004   0.038   1546
  Dihedral  :  4.577  22.080   1213
  Min Nonbonded Distance : 1.323

Molprobity Statistics.
  All-atom Clashscore : 8.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 17.86 %
    Favored  : 79.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.25), residues: 1100
  helix:  0.78 (0.25), residues: 433
  sheet: -1.49 (0.44), residues: 132
  loop : -1.53 (0.26), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 270 
 HIS   0.010   0.001   HIS A1225 
 PHE   0.026   0.001   PHE A1344 
 TYR   0.026   0.001   TYR A1088 
 ARG   0.013   0.000   ARG A 292 

*********************** 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
  154 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.894 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7275 (t) cc_final: 0.6862 (t)
REVERT: A  223 PHE cc_start: 0.7097 (m-80) cc_final: 0.6717 (m-80)
REVERT: A  530 HIS cc_start: 0.6857 (OUTLIER) cc_final: 0.6378 (t-90)
REVERT: A  975 GLU cc_start: 0.7422 (tm-30) cc_final: 0.7181 (tm-30)
REVERT: A 1135 GLU cc_start: 0.6145 (OUTLIER) cc_final: 0.5673 (mp0)
REVERT: A 1242 GLN cc_start: 0.8190 (pp30) cc_final: 0.7935 (mp10)
  outliers start: 29
  outliers final: 22
  residues processed: 143
  average time/residue: 0.1826
  time to fit residues: 39.5222
Evaluate side-chains
  144 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 120
  time to evaluate  : 0.893 
-------------------------------------------------------------------------------
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 1071 MET
Chi-restraints excluded: chain A residue 1095 ASP
Chi-restraints excluded: chain A residue 1098 ASN
Chi-restraints excluded: chain A residue 1135 GLU
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 1303 VAL
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 5 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 1 optimal weight:    0.3980
   chunk 13 optimal weight:    0.6980
   chunk 63 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 99 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9980
   overall best weight:    0.7180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.192780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.153705 restraints weight = 13268.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.156203 restraints weight = 7967.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.157091 restraints weight = 7300.077|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7651
moved from start:          0.2225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9090  Z= 0.195
  Angle     :  0.571   7.338  12349  Z= 0.287
  Chirality :  0.043   0.177   1408
  Planarity :  0.004   0.038   1546
  Dihedral  :  4.514  21.685   1213
  Min Nonbonded Distance : 1.358

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.82 %
    Favored  : 94.18 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.58 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.81 (0.25), residues: 1100
  helix:  0.90 (0.25), residues: 435
  sheet: -1.49 (0.44), residues: 132
  loop : -1.51 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 270 
 HIS   0.005   0.001   HIS A1225 
 PHE   0.015   0.001   PHE A1339 
 TYR   0.026   0.001   TYR A1088 
 ARG   0.002   0.000   ARG A1288 

*********************** 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
  165 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 140
  time to evaluate  : 1.721 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  221 SER cc_start: 0.7344 (t) cc_final: 0.6929 (t)
REVERT: A  223 PHE cc_start: 0.7086 (m-80) cc_final: 0.6666 (m-80)
REVERT: A  530 HIS cc_start: 0.6848 (OUTLIER) cc_final: 0.6370 (t-90)
REVERT: A  594 ARG cc_start: 0.7253 (ttt180) cc_final: 0.7027 (ttt180)
REVERT: A  903 ILE cc_start: 0.7809 (mm) cc_final: 0.7569 (mm)
REVERT: A  975 GLU cc_start: 0.7506 (tm-30) cc_final: 0.7243 (tm-30)
REVERT: A 1135 GLU cc_start: 0.6090 (OUTLIER) cc_final: 0.5651 (mp0)
  outliers start: 25
  outliers final: 21
  residues processed: 156
  average time/residue: 0.1794
  time to fit residues: 41.4592
Evaluate side-chains
  147 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 124
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
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  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 1098 ASN
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 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0570
   chunk 98 optimal weight:    6.9990
   chunk 53 optimal weight:    4.9990
   chunk 7 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 101 optimal weight:    4.9990
   chunk 58 optimal weight:    6.9990
   chunk 12 optimal weight:    4.9990
   chunk 50 optimal weight:    0.8980
   chunk 91 optimal weight:    6.9990
   overall best weight:    1.6902

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

Flipped N/Q/H residues before XYZ refinement:
A1225 HIS
** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4358 r_free = 0.4358 target = 0.188085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.148206 restraints weight = 13378.388|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.150372 restraints weight = 8417.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.151181 restraints weight = 7640.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7759
moved from start:          0.2560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071   9090  Z= 0.339
  Angle     :  0.653   8.818  12349  Z= 0.332
  Chirality :  0.045   0.193   1408
  Planarity :  0.004   0.036   1546
  Dihedral  :  4.790  23.857   1213
  Min Nonbonded Distance : 1.311

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 19.51 %
    Favored  : 77.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.07 (0.25), residues: 1100
  helix:  0.66 (0.25), residues: 434
  sheet: -1.64 (0.44), residues: 132
  loop : -1.63 (0.26), residues: 534

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A1245 
 HIS   0.016   0.001   HIS A1225 
 PHE   0.032   0.002   PHE A1339 
 TYR   0.041   0.002   TYR A1088 
 ARG   0.003   0.000   ARG A 292 

*********************** 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
  156 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 126
  time to evaluate  : 1.100 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7502 (t) cc_final: 0.7089 (t)
REVERT: A  223 PHE cc_start: 0.7219 (m-80) cc_final: 0.6753 (m-80)
REVERT: A  530 HIS cc_start: 0.6925 (OUTLIER) cc_final: 0.6461 (t-90)
REVERT: A 1088 TYR cc_start: 0.8822 (OUTLIER) cc_final: 0.7083 (t80)
REVERT: A 1135 GLU cc_start: 0.6183 (OUTLIER) cc_final: 0.5660 (mp0)
  outliers start: 30
  outliers final: 21
  residues processed: 146
  average time/residue: 0.2032
  time to fit residues: 45.2652
Evaluate side-chains
  140 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 116
  time to evaluate  : 1.397 
-------------------------------------------------------------------------------
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 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 1303 VAL
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 10 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9980
   chunk 45 optimal weight:    3.9990
   chunk 107 optimal weight:    0.8980
   chunk 49 optimal weight:    1.9990
   chunk 51 optimal weight:    3.9990
   chunk 89 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
A1225 HIS
** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4373 r_free = 0.4373 target = 0.189971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3998 r_free = 0.3998 target = 0.150591 restraints weight = 13508.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.152611 restraints weight = 8208.836|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.153799 restraints weight = 7752.628|
|-----------------------------------------------------------------------------|
r_work (final): 0.4027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7709
moved from start:          0.2599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9090  Z= 0.227
  Angle     :  0.624  14.309  12349  Z= 0.313
  Chirality :  0.044   0.183   1408
  Planarity :  0.004   0.037   1546
  Dihedral  :  4.673  22.948   1213
  Min Nonbonded Distance : 1.373

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.64 %
    Favored  : 93.36 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 20.02 %
    Favored  : 76.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.02 (0.25), residues: 1100
  helix:  0.71 (0.25), residues: 435
  sheet: -1.64 (0.44), residues: 132
  loop : -1.62 (0.26), residues: 533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A1245 
 HIS   0.006   0.001   HIS A 367 
 PHE   0.036   0.001   PHE A1339 
 TYR   0.030   0.002   TYR A1088 
 ARG   0.004   0.000   ARG A 292 

*********************** 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
  155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 123
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7432 (t) cc_final: 0.7013 (t)
REVERT: A  223 PHE cc_start: 0.7169 (m-80) cc_final: 0.6697 (m-80)
REVERT: A  530 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6441 (t-90)
REVERT: A  594 ARG cc_start: 0.7264 (ttt180) cc_final: 0.7063 (ttt180)
REVERT: A 1088 TYR cc_start: 0.8646 (OUTLIER) cc_final: 0.6718 (t80)
REVERT: A 1135 GLU cc_start: 0.6122 (OUTLIER) cc_final: 0.5610 (mp0)
REVERT: A 1242 GLN cc_start: 0.8131 (pp30) cc_final: 0.7788 (mp10)
  outliers start: 32
  outliers final: 26
  residues processed: 146
  average time/residue: 0.1718
  time to fit residues: 38.4208
Evaluate side-chains
  148 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 119
  time to evaluate  : 1.042 
-------------------------------------------------------------------------------
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  587 LYS
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  926 VAL
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 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 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 1303 VAL
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 9 optimal weight:    0.5980
   chunk 41 optimal weight:    5.9990
   chunk 79 optimal weight:    0.5980
   chunk 4 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 72 optimal weight:    0.9990
   chunk 32 optimal weight:    6.9990
   chunk 31 optimal weight:    4.9990
   chunk 39 optimal weight:    4.9990
   chunk 35 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A1225 HIS
A1394 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4348 r_free = 0.4348 target = 0.187405 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.148357 restraints weight = 13322.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.150664 restraints weight = 8107.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.151436 restraints weight = 7714.489|
|-----------------------------------------------------------------------------|
r_work (final): 0.4004
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7698
moved from start:          0.2664

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9090  Z= 0.211
  Angle     :  0.632  15.836  12349  Z= 0.313
  Chirality :  0.044   0.183   1408
  Planarity :  0.005   0.084   1546
  Dihedral  :  4.627  22.923   1213
  Min Nonbonded Distance : 1.406

Molprobity Statistics.
  All-atom Clashscore : 9.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 20.33 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.25), residues: 1100
  helix:  0.73 (0.25), residues: 436
  sheet: -1.63 (0.45), residues: 132
  loop : -1.57 (0.26), residues: 532

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A1245 
 HIS   0.014   0.001   HIS A 367 
 PHE   0.030   0.001   PHE A1339 
 TYR   0.026   0.001   TYR A1088 
 ARG   0.003   0.000   ARG A 455 

*********************** 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
  162 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 126
  time to evaluate  : 0.916 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7394 (t) cc_final: 0.6978 (t)
REVERT: A  223 PHE cc_start: 0.7101 (m-80) cc_final: 0.6639 (m-80)
REVERT: A  530 HIS cc_start: 0.6889 (OUTLIER) cc_final: 0.6431 (t-90)
REVERT: A 1088 TYR cc_start: 0.8556 (OUTLIER) cc_final: 0.6655 (t80)
REVERT: A 1135 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5607 (mp0)
REVERT: A 1242 GLN cc_start: 0.8087 (pp30) cc_final: 0.7755 (mp10)
  outliers start: 36
  outliers final: 29
  residues processed: 151
  average time/residue: 0.1575
  time to fit residues: 36.6516
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  : 0.890 
-------------------------------------------------------------------------------
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  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  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  923 LEU
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 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 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1155 SER
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 1303 VAL
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 74 optimal weight:    6.9990
   chunk 40 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 68 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 6 optimal weight:    0.0670
   chunk 34 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 39 optimal weight:    2.9990
   chunk 29 optimal weight:    0.4980
   chunk 9 optimal weight:    0.8980
   overall best weight:    0.8922

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

Flipped N/Q/H residues before XYZ refinement:
A1225 HIS
A1394 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4344 r_free = 0.4344 target = 0.186899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.147820 restraints weight = 13406.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.150842 restraints weight = 8261.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.151467 restraints weight = 7425.765|
|-----------------------------------------------------------------------------|
r_work (final): 0.4005
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.2724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   9090  Z= 0.228
  Angle     :  0.637  16.326  12349  Z= 0.315
  Chirality :  0.044   0.185   1408
  Planarity :  0.005   0.078   1546
  Dihedral  :  4.644  23.196   1213
  Min Nonbonded Distance : 1.391

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  3.59 %
    Allowed  : 20.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.25), residues: 1100
  helix:  0.71 (0.25), residues: 436
  sheet: -1.67 (0.44), residues: 133
  loop : -1.58 (0.26), residues: 531

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1245 
 HIS   0.011   0.001   HIS A 367 
 PHE   0.042   0.001   PHE A1339 
 TYR   0.029   0.001   TYR A1088 
 ARG   0.006   0.000   ARG A 594 

********************** 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
  155 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 120
  time to evaluate  : 1.007 
Fit side-chains
REVERT: A  221 SER cc_start: 0.7391 (t) cc_final: 0.6935 (t)
REVERT: A  223 PHE cc_start: 0.7106 (m-80) cc_final: 0.6612 (m-10)
REVERT: A  530 HIS cc_start: 0.6899 (OUTLIER) cc_final: 0.6444 (t-90)
REVERT: A 1088 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.6711 (t80)
REVERT: A 1135 GLU cc_start: 0.6089 (OUTLIER) cc_final: 0.5605 (mp0)
REVERT: A 1242 GLN cc_start: 0.8066 (pp30) cc_final: 0.7751 (mp10)
  outliers start: 35
  outliers final: 31
  residues processed: 144
  average time/residue: 0.1558
  time to fit residues: 34.7993
Evaluate side-chains
  153 residues out of total 974 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 1.035 
-------------------------------------------------------------------------------
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  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  587 LYS
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  923 LEU
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  985 PHE
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 1133 VAL
Chi-restraints excluded: chain A residue 1135 GLU
Chi-restraints excluded: chain A residue 1155 SER
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 1303 VAL
Chi-restraints excluded: chain A residue 1305 LEU
Chi-restraints excluded: chain A residue 1384 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0170
   chunk 7 optimal weight:    0.2980
   chunk 40 optimal weight:    7.9990
   chunk 109 optimal weight:    9.9990
   chunk 47 optimal weight:    0.9980
   chunk 69 optimal weight:    0.5980
   chunk 52 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
A1394 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4374 r_free = 0.4374 target = 0.189563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.150821 restraints weight = 13235.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.154271 restraints weight = 7889.238|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.154674 restraints weight = 7458.164|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.2727

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9090  Z= 0.174
  Angle     :  0.618  14.388  12349  Z= 0.305
  Chirality :  0.043   0.178   1408
  Planarity :  0.004   0.069   1546
  Dihedral  :  4.515  22.399   1213
  Min Nonbonded Distance : 1.483

Molprobity Statistics.
  All-atom Clashscore : 9.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.45 %
    Favored  : 93.55 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.87 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.25), residues: 1100
  helix:  0.81 (0.25), residues: 437
  sheet: -1.58 (0.45), residues: 133
  loop : -1.50 (0.27), residues: 530

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A1245 
 HIS   0.011   0.001   HIS A1225 
 PHE   0.037   0.001   PHE A1339 
 TYR   0.020   0.001   TYR A1088 
 ARG   0.004   0.000   ARG A 292 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2807.06 seconds
wall clock time: 51 minutes 22.84 seconds (3082.84 seconds total)