Starting phenix.real_space_refine
on Tue May 13 17:26:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ci5_16670/05_2025/8ci5_16670.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ci5_16670/05_2025/8ci5_16670.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ci5_16670/05_2025/8ci5_16670.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ci5_16670/05_2025/8ci5_16670.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ci5_16670/05_2025/8ci5_16670.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ci5_16670/05_2025/8ci5_16670.cif"
  }
  resolution = 3.2
  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=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     S      49      5.16       5
     C    6629      2.51       5
     N    1738      2.21       5
     O    1938      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 10365
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 10128
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 1258, 10124
          Classifications: {'peptide': 1258}
          Link IDs: {'PTRANS': 41, 'TRANS': 1216}
          Chain breaks: 15
      Conformer: "B"
        Number of residues, atoms: 1258, 10124
          Classifications: {'peptide': 1258}
          Link IDs: {'PTRANS': 41, 'TRANS': 1216}
          Chain breaks: 15
          bond proxies already assigned to first conformer: 10337
    Chain: "C"
      Number of atoms: 237
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 237
          Classifications: {'RNA': 11}
          Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 5, 'rna3p_pyr': 4}
          Link IDs: {'rna2p': 2, 'rna3p': 8}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AGLY A1047 " occ=0.50
      ... (6 atoms not shown)
      pdb=" O  BGLY A1047 " occ=0.50
  Time building chain proxies: 10.90, per 1000 atoms: 1.05
  Number of scatterers: 10365
  At special positions: 0
  Unit cell: (101.15, 88.4, 125.8, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      49     16.00
     P      11     15.00
     O    1938      8.00
     N    1738      7.00
     C    6629      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.61
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2388

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 12 sheets defined
      57.1% alpha, 8.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 239 through 252
      removed outlier: 3.760A  pdb=" N   LEU A 243 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   THR A 252 " --> pdb=" O   LYS A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 277
      removed outlier: 3.961A  pdb=" N   VAL A 277 " --> pdb=" O   ASN A 273 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 278 through 282
    Processing helix  chain 'A' and resid 306 through 322
    Processing helix  chain 'A' and resid 328 through 343
    Processing helix  chain 'A' and resid 345 through 353
      removed outlier: 3.821A  pdb=" N   ILE A 350 " --> pdb=" O   ARG A 346 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ASN A 351 " --> pdb=" O   ASP A 347 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   TYR A 353 " --> pdb=" O   ILE A 349 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 378
      removed outlier: 4.031A  pdb=" N   LEU A 378 " --> pdb=" O   LEU A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
      removed outlier: 3.694A  pdb=" N   LYS A 383 " --> pdb=" O   ASN A 379 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   SER A 384 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 410 through 426
    Processing helix  chain 'A' and resid 451 through 464
    Processing helix  chain 'A' and resid 464 through 469
    Processing helix  chain 'A' and resid 471 through 491
      removed outlier: 3.690A  pdb=" N   HIS A 475 " --> pdb=" O   THR A 471 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ASP A 482 " --> pdb=" O   HIS A 478 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 573
    Processing helix  chain 'A' and resid 573 through 594
    Processing helix  chain 'A' and resid 598 through 616
      removed outlier: 3.681A  pdb=" N   GLN A 616 " --> pdb=" O   LEU A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 617 through 635
      removed outlier: 3.587A  pdb=" N   CYS A 621 " --> pdb=" O   LYS A 617 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   ILE A 623 " --> pdb=" O   LYS A 619 " (cutoff:3.500A)
      removed outlier: 4.173A  pdb=" N   TYR A 629 " --> pdb=" O   ASP A 625 " (cutoff:3.500A)
      Proline residue:  A 632  - end of helix
      removed outlier: 3.611A  pdb=" N   THR A 635 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 640 through 649
      removed outlier: 3.667A  pdb=" N   PHE A 649 " --> pdb=" O   ILE A 645 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 675
      removed outlier: 3.754A  pdb=" N   VAL A 659 " --> pdb=" O   SER A 655 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASN A 675 " --> pdb=" O   SER A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 713 through 727
      removed outlier: 4.347A  pdb=" N   LEU A 717 " --> pdb=" O   HIS A 713 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 721 " --> pdb=" O   LEU A 717 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU A 727 " --> pdb=" O   THR A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 734 through 739
    Processing helix  chain 'A' and resid 742 through 761
      removed outlier: 4.583A  pdb=" N   THR A 746 " --> pdb=" O   ILE A 742 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 768
      removed outlier: 3.523A  pdb=" N   MET A 765 " --> pdb=" O   GLY A 761 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 770 through 777
    Processing helix  chain 'A' and resid 787 through 803
    Processing helix  chain 'A' and resid 805 through 815
      removed outlier: 3.579A  pdb=" N   MET A 814 " --> pdb=" O   SER A 810 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASN A 815 " --> pdb=" O   SER A 811 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 826 through 830
      removed outlier: 3.923A  pdb=" N   SER A 830 " --> pdb=" O   ARG A 827 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 848 through 861
      removed outlier: 3.567A  pdb=" N   ASN A 858 " --> pdb=" O   ILE A 854 " (cutoff:3.500A)
      removed outlier: 4.326A  pdb=" N   ARG A 859 " --> pdb=" O   ARG A 855 " (cutoff:3.500A)
      removed outlier: 4.494A  pdb=" N   GLN A 861 " --> pdb=" O   LEU A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 873
    Processing helix  chain 'A' and resid 899 through 918
    Processing helix  chain 'A' and resid 932 through 947
      removed outlier: 3.661A  pdb=" N   ALA A 947 " --> pdb=" O   ALA A 943 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 984 through 992
      removed outlier: 4.451A  pdb=" N   ARG A 988 " --> pdb=" O   ALA A 984 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   ALA A 992 " --> pdb=" O   ARG A 988 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1002 through 1011
    Processing helix  chain 'A' and resid 1021 through 1030
      removed outlier: 3.515A  pdb=" N   ASP A1029 " --> pdb=" O   HIS A1025 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1036 through 1045
      removed outlier: 3.611A  pdb=" N   ASP A1040 " --> pdb=" O   GLU A1036 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   PHE A1041 " --> pdb=" O   ALA A1037 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   PHE A1045 " --> pdb=" O   PHE A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1062 through 1083
    Processing helix  chain 'A' and resid 1115 through 1127
      removed outlier: 3.668A  pdb=" N   ALA A1127 " --> pdb=" O   GLN A1123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1135
      removed outlier: 3.642A  pdb=" N   ALA A1134 " --> pdb=" O   HIS A1131 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   VAL A1135 " --> pdb=" O   TRP A1132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1139 through 1154
    Processing helix  chain 'A' and resid 1186 through 1192
      removed outlier: 3.521A  pdb=" N   LEU A1190 " --> pdb=" O   PHE A1186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1201 through 1219
      removed outlier: 3.654A  pdb=" N   ASP A1205 " --> pdb=" O   GLY A1201 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   CYS A1213 " --> pdb=" O   ALA A1209 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LEU A1219 " --> pdb=" O   LYS A1215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1222 through 1242
    Processing helix  chain 'A' and resid 1250 through 1254
    Processing helix  chain 'A' and resid 1283 through 1301
      removed outlier: 3.905A  pdb=" N   LYS A1287 " --> pdb=" O   GLY A1283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1303 through 1318
      removed outlier: 3.617A  pdb=" N   LEU A1318 " --> pdb=" O   PHE A1314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1355 through 1366
    Processing helix  chain 'A' and resid 1367 through 1371
      removed outlier: 3.707A  pdb=" N   ASP A1370 " --> pdb=" O   PRO A1367 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1376 through 1390
      removed outlier: 3.534A  pdb=" N   LEU A1380 " --> pdb=" O   GLY A1376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1390 through 1398
    Processing helix  chain 'A' and resid 1401 through 1408
      removed outlier: 4.240A  pdb=" N   LEU A1405 " --> pdb=" O   SER A1401 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   ARG A1406 " --> pdb=" O   PRO A1402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1427 through 1440
    Processing helix  chain 'A' and resid 1449 through 1456
    Processing helix  chain 'A' and resid 1504 through 1513
      removed outlier: 4.239A  pdb=" N   TYR A1512 " --> pdb=" O   ILE A1508 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1515 through 1525
    Processing helix  chain 'A' and resid 1531 through 1547
      removed outlier: 4.108A  pdb=" N   GLN A1537 " --> pdb=" O   SER A1533 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   GLU A1546 " --> pdb=" O   GLY A1542 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1553 through 1558
      removed outlier: 4.200A  pdb=" N   LEU A1557 " --> pdb=" O   LEU A1553 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   LYS A1558 " --> pdb=" O   PRO A1554 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1553 through 1558'
    Processing helix  chain 'A' and resid 1560 through 1567
      removed outlier: 3.534A  pdb=" N   LEU A1564 " --> pdb=" O   ILE A1560 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ALA A1567 " --> pdb=" O   LEU A1563 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1582 through 1593
      removed outlier: 3.774A  pdb=" N   SER A1588 " --> pdb=" O   GLU A1584 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   TYR A1589 " --> pdb=" O   SER A1585 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 260 through 261
      removed outlier: 3.700A  pdb=" N   THR A1164 " --> pdb=" O   SER A 971 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   TYR A1105 " --> pdb=" O   MET A 968 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   ALA A1101 " --> pdb=" O   ALA A 972 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY A1106 " --> pdb=" O   PHE A1091 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 283 through 284
      removed outlier: 5.830A  pdb=" N   LYS A 283 " --> pdb=" O   SER A 405 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 296 through 298
      removed outlier: 4.158A  pdb=" N   ILE A 536 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 500 through 504
      removed outlier: 5.174A  pdb=" N   THR A 530 " --> pdb=" O   SER A 558 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   VAL A 553 " --> pdb=" O   ILE A 550 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 500 through 504
      removed outlier: 3.570A  pdb=" N   ILE A 563 " --> pdb=" O   ILE A 526 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 703
    Processing sheet with id=AA7, first strand: chain 'A' and resid 896 through 898
      removed outlier: 7.082A  pdb=" N   ALA A 880 " --> pdb=" O   PHE A1019 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 952 through 954
    Processing sheet with id=AA9, first strand: chain 'A' and resid 964 through 965
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1170 through 1172
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1418 through 1420
    Processing sheet with id=AB3, first strand: chain 'A' and resid 1486 through 1491

    508 hydrogen bonds defined for protein.
    1443 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: 4.09

  Time building geometry restraints manager: 2.80 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 2288
        1.33 -     1.45: 2508
        1.45 -     1.57: 5715
        1.57 -     1.69: 22
        1.69 -     1.81: 79
  Bond restraints: 10612
  Sorted by residual:
  bond pdb=" CA  SER A1193 "
       pdb=" C   SER A1193 "
    ideal  model  delta    sigma   weight residual
    1.522  1.462  0.061 1.34e-02 5.57e+03 2.04e+01
  bond pdb=" C   ILE A1264 "
       pdb=" N   PRO A1265 "
    ideal  model  delta    sigma   weight residual
    1.337  1.366 -0.030 9.80e-03 1.04e+04 9.14e+00
  bond pdb=" N   GLN A1059 "
       pdb=" CA  GLN A1059 "
    ideal  model  delta    sigma   weight residual
    1.457  1.496 -0.039 1.29e-02 6.01e+03 9.03e+00
  bond pdb=" C   ALA A 845 "
       pdb=" N   ALA A 846 "
    ideal  model  delta    sigma   weight residual
    1.334  1.294  0.040 1.52e-02 4.33e+03 6.89e+00
  bond pdb=" CA  LEU A 464 "
       pdb=" C   LEU A 464 "
    ideal  model  delta    sigma   weight residual
    1.524  1.506  0.018 7.00e-03 2.04e+04 6.89e+00
  ... (remaining 10607 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.56: 13734
        2.56 -     5.13: 572
        5.13 -     7.69: 66
        7.69 -    10.26: 9
       10.26 -    12.82: 5
  Bond angle restraints: 14386
  Sorted by residual:
  angle pdb=" CA  PRO A1391 "
        pdb=" N   PRO A1391 "
        pdb=" CD  PRO A1391 "
      ideal   model   delta    sigma   weight residual
     112.00  100.12   11.88 1.40e+00 5.10e-01 7.20e+01
  angle pdb=" N   VAL A1049 "
        pdb=" CA  VAL A1049 "
        pdb=" C   VAL A1049 "
      ideal   model   delta    sigma   weight residual
     113.47  106.24    7.23 1.01e+00 9.80e-01 5.13e+01
  angle pdb=" N   VAL A 277 "
        pdb=" CA  VAL A 277 "
        pdb=" C   VAL A 277 "
      ideal   model   delta    sigma   weight residual
     111.77  105.89    5.88 1.04e+00 9.25e-01 3.19e+01
  angle pdb=" C   SER A1531 "
        pdb=" N   LEU A1532 "
        pdb=" CA  LEU A1532 "
      ideal   model   delta    sigma   weight residual
     120.44  126.63   -6.19 1.30e+00 5.92e-01 2.27e+01
  angle pdb=" N   VAL A1252 "
        pdb=" CA  VAL A1252 "
        pdb=" C   VAL A1252 "
      ideal   model   delta    sigma   weight residual
     113.07  106.88    6.19 1.37e+00 5.33e-01 2.04e+01
  ... (remaining 14381 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.94: 6034
       26.94 -    53.87: 266
       53.87 -    80.81: 41
       80.81 -   107.75: 6
      107.75 -   134.68: 1
  Dihedral angle restraints: 6348
    sinusoidal: 2658
      harmonic: 3690
  Sorted by residual:
  dihedral pdb=" O4'   U C   7 "
           pdb=" C1'   U C   7 "
           pdb=" N1    U C   7 "
           pdb=" C2    U C   7 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   65.32  134.68     1      1.50e+01 4.44e-03 7.27e+01
  dihedral pdb=" CA  SER A 926 "
           pdb=" C   SER A 926 "
           pdb=" N   TYR A 927 "
           pdb=" CA  TYR A 927 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.12  -29.88     0      5.00e+00 4.00e-02 3.57e+01
  dihedral pdb=" CA  ARG A 893 "
           pdb=" C   ARG A 893 "
           pdb=" N   GLY A 894 "
           pdb=" CA  GLY A 894 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.88  -26.12     0      5.00e+00 4.00e-02 2.73e+01
  ... (remaining 6345 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1262
       0.078 -    0.157: 312
       0.157 -    0.235: 33
       0.235 -    0.314: 2
       0.314 -    0.392: 2
  Chirality restraints: 1611
  Sorted by residual:
  chirality pdb=" CB  VAL A1135 "
            pdb=" CA  VAL A1135 "
            pdb=" CG1 VAL A1135 "
            pdb=" CG2 VAL A1135 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.24   -0.39 2.00e-01 2.50e+01 3.84e+00
  chirality pdb=" CA  PRO A1391 "
            pdb=" N   PRO A1391 "
            pdb=" C   PRO A1391 "
            pdb=" CB  PRO A1391 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.36    0.36 2.00e-01 2.50e+01 3.19e+00
  chirality pdb=" CB  VAL A1394 "
            pdb=" CA  VAL A1394 "
            pdb=" CG1 VAL A1394 "
            pdb=" CG2 VAL A1394 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.36   -0.27 2.00e-01 2.50e+01 1.77e+00
  ... (remaining 1608 not shown)

  Planarity restraints: 1772
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A1292 "    0.016 2.00e-02 2.50e+03   3.17e-02 1.00e+01
        pdb=" C   GLN A1292 "   -0.055 2.00e-02 2.50e+03
        pdb=" O   GLN A1292 "    0.021 2.00e-02 2.50e+03
        pdb=" N   ALA A1293 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP A1390 "   -0.053 5.00e-02 4.00e+02   7.30e-02 8.53e+00
        pdb=" N   PRO A1391 "    0.126 5.00e-02 4.00e+02
        pdb=" CA  PRO A1391 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A1391 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A1297 "   -0.014 2.00e-02 2.50e+03   2.87e-02 8.22e+00
        pdb=" C   TYR A1297 "    0.050 2.00e-02 2.50e+03
        pdb=" O   TYR A1297 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   LYS A1298 "   -0.017 2.00e-02 2.50e+03
  ... (remaining 1769 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1227
        2.73 -     3.27: 9735
        3.27 -     3.82: 16550
        3.82 -     4.36: 20800
        4.36 -     4.90: 35442
  Nonbonded interactions: 83754
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 408 "
            pdb=" NE2 GLN A 414 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" OE2 GLU A 739 "
            pdb=" OG  SER A1021 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" O   GLU A1580 "
            pdb=" OG  SER A1585 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR A 913 "
            pdb=" OG1 THR A 990 "
     model   vdw
     2.233 3.040
  nonbonded pdb=" O   LEU A1119 "
            pdb=" OG  SER A1122 "
     model   vdw
     2.242 3.040
  ... (remaining 83749 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
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:             3.180
  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:          0.410
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     32.850
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.060
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8361
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      :  0.014   0.116  10612  Z= 0.586
  Angle     :  1.190  12.820  14386  Z= 0.665
  Chirality :  0.067   0.392   1611
  Planarity :  0.008   0.073   1772
  Dihedral  : 15.440 134.683   3960
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.57 %
    Allowed  :  8.32 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.45 %
    Favored  : 99.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.88 (0.20), residues: 1229
  helix: -2.14 (0.16), residues: 658
  sheet: -2.93 (0.44), residues: 105
  loop : -2.94 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.004   TRP A1424 
 HIS   0.011   0.003   HIS A 733 
 PHE   0.048   0.005   PHE A1437 
 TYR   0.039   0.004   TYR A 504 
 ARG   0.029   0.002   ARG A1239 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17699 (  498)
  hydrogen bonds       : angle       6.88475 ( 1443)
  covalent geometry    : bond        0.01401 (10612)
  covalent geometry    : angle       1.18965 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 1.170 
Fit side-chains
REVERT: A  345 ASN cc_start: 0.7830 (t0) cc_final: 0.7598 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.2686
  time to fit residues: 44.2971
Evaluate side-chains
  101 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.059 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 106 optimal weight:    0.0970
   chunk 95 optimal weight:    0.9980
   chunk 52 optimal weight:    0.6980
   chunk 32 optimal weight:    0.6980
   chunk 64 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 98 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 73 optimal weight:    0.5980
   chunk 114 optimal weight:    2.9990
   overall best weight:    0.5378

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

Flipped N/Q/H residues before XYZ refinement:
A 331 GLN
A 478 HIS
A 626 ASN
** A 935 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1059 GLN
A1126 GLN
A1379 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.124571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.099960 restraints weight = 15997.072|
|-----------------------------------------------------------------------------|
r_work (start): 0.3213 rms_B_bonded: 1.74
r_work: 0.3099 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2979 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.2979
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2983 r_free = 0.2983    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8479
moved from start:          0.1471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10612  Z= 0.130
  Angle     :  0.569   7.940  14386  Z= 0.305
  Chirality :  0.041   0.164   1611
  Planarity :  0.005   0.057   1772
  Dihedral  :  9.119 133.466   1522
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.57 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  3.78 %
    Favored  : 96.04 %
  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: -1.82 (0.22), residues: 1229
  helix: -0.29 (0.19), residues: 658
  sheet: -1.99 (0.48), residues: 105
  loop : -2.29 (0.25), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 474 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.025   0.002   PHE A1186 
 TYR   0.016   0.001   TYR A 504 
 ARG   0.003   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05073 (  498)
  hydrogen bonds       : angle       4.79914 ( 1443)
  covalent geometry    : bond        0.00282 (10612)
  covalent geometry    : angle       0.56873 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 125
  time to evaluate  : 1.212 
Fit side-chains
REVERT: A  561 MET cc_start: 0.8370 (mmt) cc_final: 0.8142 (mmm)
REVERT: A  893 ARG cc_start: 0.6694 (ttt-90) cc_final: 0.6286 (tpp80)
REVERT: A 1120 TYR cc_start: 0.7822 (t80) cc_final: 0.7451 (t80)
REVERT: A 1239 ARG cc_start: 0.7843 (ptp-110) cc_final: 0.7630 (ttp80)
  outliers start: 2
  outliers final: 1
  residues processed: 125
  average time/residue: 0.2863
  time to fit residues: 48.9494
Evaluate side-chains
  109 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 108
  time to evaluate  : 1.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1133 HIS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 9 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0970
   chunk 4 optimal weight:    0.6980
   chunk 104 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 125 optimal weight:    4.9990
   chunk 115 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 95 optimal weight:    0.7980
   overall best weight:    0.6778

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.124226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.099484 restraints weight = 16348.901|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.76
r_work: 0.3085 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2963 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2963
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2972
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2972 r_free = 0.2972    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2972
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8483
moved from start:          0.1756

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10612  Z= 0.129
  Angle     :  0.525   7.641  14386  Z= 0.277
  Chirality :  0.040   0.169   1611
  Planarity :  0.004   0.059   1772
  Dihedral  :  8.698 133.533   1522
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.89 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  6.29 %
    Favored  : 93.53 %
  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: -0.89 (0.23), residues: 1229
  helix:  0.53 (0.20), residues: 661
  sheet: -1.55 (0.49), residues: 105
  loop : -1.99 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 946 
 HIS   0.003   0.001   HIS A 733 
 PHE   0.021   0.002   PHE A1186 
 TYR   0.012   0.001   TYR A1383 
 ARG   0.002   0.000   ARG A 281 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04744 (  498)
  hydrogen bonds       : angle       4.45909 ( 1443)
  covalent geometry    : bond        0.00288 (10612)
  covalent geometry    : angle       0.52452 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 115
  time to evaluate  : 1.133 
Fit side-chains
REVERT: A 1120 TYR cc_start: 0.7853 (t80) cc_final: 0.7483 (t80)
REVERT: A 1489 ARG cc_start: 0.8039 (mmt-90) cc_final: 0.7831 (mmm160)
  outliers start: 2
  outliers final: 2
  residues processed: 116
  average time/residue: 0.2876
  time to fit residues: 45.7639
Evaluate side-chains
  108 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 1.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue 1133 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 107 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 85 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   overall best weight:    0.9182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3540 r_free = 0.3540 target = 0.123599 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.098710 restraints weight = 16142.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3189 rms_B_bonded: 1.76
r_work: 0.3070 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2949 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2949
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2958
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2958 r_free = 0.2958    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8494
moved from start:          0.1804

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10612  Z= 0.146
  Angle     :  0.532   7.268  14386  Z= 0.280
  Chirality :  0.041   0.193   1611
  Planarity :  0.004   0.062   1772
  Dihedral  :  8.612 131.708   1522
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 4.27
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.32 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  7.46 %
    Favored  : 91.91 %
  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: -0.53 (0.23), residues: 1229
  helix:  0.85 (0.20), residues: 661
  sheet: -1.37 (0.50), residues: 105
  loop : -1.86 (0.26), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 474 
 HIS   0.004   0.001   HIS A 733 
 PHE   0.021   0.002   PHE A1186 
 TYR   0.013   0.001   TYR A 504 
 ARG   0.004   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04853 (  498)
  hydrogen bonds       : angle       4.40541 ( 1443)
  covalent geometry    : bond        0.00337 (10612)
  covalent geometry    : angle       0.53239 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 117
  time to evaluate  : 1.198 
Fit side-chains
REVERT: A 1120 TYR cc_start: 0.7849 (t80) cc_final: 0.7528 (t80)
REVERT: A 1173 LEU cc_start: 0.6021 (OUTLIER) cc_final: 0.5583 (pp)
REVERT: A 1451 PHE cc_start: 0.7315 (m-10) cc_final: 0.7109 (m-10)
  outliers start: 7
  outliers final: 3
  residues processed: 121
  average time/residue: 0.2923
  time to fit residues: 47.8923
Evaluate side-chains
  116 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 112
  time to evaluate  : 1.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1539 MET
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 7 optimal weight:    0.4980
   chunk 5 optimal weight:    2.9990
   chunk 20 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 109 optimal weight:    0.9990
   chunk 45 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 112 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   overall best weight:    0.7780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.124346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.099496 restraints weight = 16089.609|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.75
r_work: 0.3086 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.29 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2971
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2971 r_free = 0.2971    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2971
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8481
moved from start:          0.1972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10612  Z= 0.130
  Angle     :  0.515   7.537  14386  Z= 0.269
  Chirality :  0.040   0.177   1611
  Planarity :  0.004   0.061   1772
  Dihedral  :  8.535 130.585   1522
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.13
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.49 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  8.45 %
    Favored  : 90.56 %
  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: -0.21 (0.24), residues: 1229
  helix:  1.07 (0.20), residues: 662
  sheet: -1.19 (0.50), residues: 105
  loop : -1.67 (0.26), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.020   0.002   PHE A1186 
 TYR   0.019   0.001   TYR A 927 
 ARG   0.003   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04519 (  498)
  hydrogen bonds       : angle       4.29307 ( 1443)
  covalent geometry    : bond        0.00297 (10612)
  covalent geometry    : angle       0.51517 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 121
  time to evaluate  : 1.222 
Fit side-chains
REVERT: A 1120 TYR cc_start: 0.7862 (t80) cc_final: 0.7466 (t80)
REVERT: A 1173 LEU cc_start: 0.6013 (OUTLIER) cc_final: 0.5580 (pp)
REVERT: A 1489 ARG cc_start: 0.7964 (mmt-90) cc_final: 0.7484 (mmt180)
  outliers start: 11
  outliers final: 6
  residues processed: 128
  average time/residue: 0.2827
  time to fit residues: 49.1651
Evaluate side-chains
  120 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 113
  time to evaluate  : 1.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1539 MET
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 14 optimal weight:    1.9990
   chunk 55 optimal weight:    0.3980
   chunk 94 optimal weight:    0.9990
   chunk 89 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 100 optimal weight:    4.9990
   chunk 58 optimal weight:    0.0270
   chunk 37 optimal weight:    0.7980
   overall best weight:    0.6038

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.125220 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.100359 restraints weight = 16145.049|
|-----------------------------------------------------------------------------|
r_work (start): 0.3222 rms_B_bonded: 1.76
r_work: 0.3106 rms_B_bonded: 2.56 restraints_weight: 0.5000
r_work: 0.2987 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.2987
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2988
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2988 r_free = 0.2988    target_work(ls_wunit_k1) = 0.085         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2988
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.2112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10612  Z= 0.115
  Angle     :  0.500   8.246  14386  Z= 0.260
  Chirality :  0.040   0.172   1611
  Planarity :  0.004   0.061   1772
  Dihedral  :  8.468 130.194   1522
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 4.42
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.08 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.17 %
    Favored  : 89.84 %
  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:  0.06 (0.24), residues: 1229
  helix:  1.26 (0.20), residues: 662
  sheet: -0.97 (0.50), residues: 99
  loop : -1.53 (0.26), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.020   0.001   PHE A1186 
 TYR   0.016   0.001   TYR A 927 
 ARG   0.004   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04195 (  498)
  hydrogen bonds       : angle       4.17712 ( 1443)
  covalent geometry    : bond        0.00255 (10612)
  covalent geometry    : angle       0.50026 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 117
  time to evaluate  : 1.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  893 ARG cc_start: 0.6477 (ttt-90) cc_final: 0.6242 (ttt-90)
REVERT: A 1120 TYR cc_start: 0.7865 (t80) cc_final: 0.7466 (t80)
REVERT: A 1173 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5593 (pp)
REVERT: A 1489 ARG cc_start: 0.7965 (mmt-90) cc_final: 0.7720 (mmt-90)
  outliers start: 11
  outliers final: 7
  residues processed: 124
  average time/residue: 0.2759
  time to fit residues: 46.5569
Evaluate side-chains
  124 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 116
  time to evaluate  : 1.083 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 43 optimal weight:    0.0670
   chunk 6 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 66 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 1 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 32 optimal weight:    0.4980
   chunk 2 optimal weight:    0.7980
   chunk 92 optimal weight:    0.6980
   chunk 99 optimal weight:    0.0270
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1404 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.126949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.102218 restraints weight = 16373.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.78
r_work: 0.3131 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3011 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.3011
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3012
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3012 r_free = 0.3012    target_work(ls_wunit_k1) = 0.087         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3012
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8434
moved from start:          0.2377

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  10612  Z= 0.097
  Angle     :  0.488  10.640  14386  Z= 0.250
  Chirality :  0.039   0.167   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.398 130.587   1522
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.08
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.26 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  :  9.26 %
    Favored  : 90.20 %
  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:  0.29 (0.24), residues: 1229
  helix:  1.44 (0.20), residues: 665
  sheet: -0.82 (0.50), residues: 99
  loop : -1.43 (0.27), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 946 
 HIS   0.003   0.000   HIS A 743 
 PHE   0.018   0.001   PHE A1186 
 TYR   0.012   0.001   TYR A 913 
 ARG   0.004   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03672 (  498)
  hydrogen bonds       : angle       4.04158 ( 1443)
  covalent geometry    : bond        0.00208 (10612)
  covalent geometry    : angle       0.48820 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 124
  time to evaluate  : 1.110 
Fit side-chains
   revert: symmetry clash
REVERT: A  893 ARG cc_start: 0.6370 (ttt-90) cc_final: 0.6148 (ttt-90)
REVERT: A 1173 LEU cc_start: 0.6016 (OUTLIER) cc_final: 0.5634 (pp)
REVERT: A 1508 ILE cc_start: 0.8297 (mt) cc_final: 0.8071 (mm)
REVERT: A 1555 GLU cc_start: 0.7720 (mp0) cc_final: 0.6626 (tt0)
  outliers start: 6
  outliers final: 5
  residues processed: 128
  average time/residue: 0.2687
  time to fit residues: 46.8791
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 117
  time to evaluate  : 1.055 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 26 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 93 optimal weight:    0.0020
   chunk 16 optimal weight:    3.9990
   chunk 79 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 108 optimal weight:    0.7980
   chunk 94 optimal weight:    0.5980
   chunk 86 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 7 optimal weight:    0.1980
   overall best weight:    0.4788

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

Flipped N/Q/H residues before XYZ refinement:
** A 828 ASN ** 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 = 0.3580 r_free = 0.3580 target = 0.126516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.101678 restraints weight = 16095.826|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 1.77
r_work: 0.3128 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3007 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.3007
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3004
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3004 r_free = 0.3004    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3004
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8442
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  10612  Z= 0.106
  Angle     :  0.504  11.038  14386  Z= 0.258
  Chirality :  0.039   0.176   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.371 130.009   1522
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 4.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.92 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  9.71 %
    Favored  : 89.48 %
  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:  0.42 (0.24), residues: 1229
  helix:  1.54 (0.20), residues: 666
  sheet: -0.79 (0.52), residues: 94
  loop : -1.36 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 946 
 HIS   0.003   0.001   HIS A 733 
 PHE   0.019   0.001   PHE A1186 
 TYR   0.010   0.001   TYR A1383 
 ARG   0.003   0.000   ARG A1301 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03870 (  498)
  hydrogen bonds       : angle       4.05407 ( 1443)
  covalent geometry    : bond        0.00234 (10612)
  covalent geometry    : angle       0.50404 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 118
  time to evaluate  : 1.277 
Fit side-chains
   revert: symmetry clash
REVERT: A  346 ARG cc_start: 0.7947 (tpt-90) cc_final: 0.7730 (tpt-90)
REVERT: A  893 ARG cc_start: 0.6447 (ttt-90) cc_final: 0.6241 (ttt-90)
REVERT: A 1043 ASP cc_start: 0.7642 (m-30) cc_final: 0.7325 (m-30)
REVERT: A 1094 PHE cc_start: 0.7858 (p90) cc_final: 0.7632 (p90)
REVERT: A 1120 TYR cc_start: 0.7904 (t80) cc_final: 0.7616 (t80)
REVERT: A 1173 LEU cc_start: 0.5983 (OUTLIER) cc_final: 0.5597 (pp)
REVERT: A 1399 MET cc_start: 0.6089 (OUTLIER) cc_final: 0.5426 (ttt)
REVERT: A 1508 ILE cc_start: 0.8235 (mt) cc_final: 0.7960 (mm)
REVERT: A 1555 GLU cc_start: 0.7679 (mp0) cc_final: 0.6575 (tt0)
REVERT: A 1572 VAL cc_start: 0.8181 (t) cc_final: 0.7826 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 124
  average time/residue: 0.2707
  time to fit residues: 46.2566
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 115
  time to evaluate  : 1.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  362 THR
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1215 LYS
Chi-restraints excluded: chain A residue 1399 MET
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 92 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 99 optimal weight:    0.8980
   chunk 59 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 56 optimal weight:    4.9990
   chunk 125 optimal weight:    4.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
** A 828 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 935 ASN
A1059 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.122621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.097626 restraints weight = 16306.213|
|-----------------------------------------------------------------------------|
r_work (start): 0.3173 rms_B_bonded: 1.76
r_work: 0.3054 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2931 rms_B_bonded: 4.31 restraints_weight: 0.2500
r_work (final): 0.2931
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2935
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2935 r_free = 0.2935    target_work(ls_wunit_k1) = 0.082         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2935
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.2032

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10612  Z= 0.191
  Angle     :  0.597  10.037  14386  Z= 0.308
  Chirality :  0.042   0.182   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.509 125.790   1522
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.73 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  :  9.26 %
    Favored  : 89.84 %
  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:  0.14 (0.24), residues: 1229
  helix:  1.27 (0.20), residues: 666
  sheet: -0.91 (0.52), residues: 94
  loop : -1.40 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 474 
 HIS   0.005   0.001   HIS A 733 
 PHE   0.023   0.002   PHE A1186 
 TYR   0.018   0.002   TYR A 927 
 ARG   0.003   0.000   ARG A 469 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05299 (  498)
  hydrogen bonds       : angle       4.38388 ( 1443)
  covalent geometry    : bond        0.00453 (10612)
  covalent geometry    : angle       0.59709 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 113
  time to evaluate  : 1.096 
Fit side-chains
   revert: symmetry clash
REVERT: A 1043 ASP cc_start: 0.7718 (m-30) cc_final: 0.7396 (m-30)
REVERT: A 1120 TYR cc_start: 0.7913 (t80) cc_final: 0.7682 (t80)
REVERT: A 1173 LEU cc_start: 0.6007 (OUTLIER) cc_final: 0.5561 (pp)
REVERT: A 1399 MET cc_start: 0.6264 (OUTLIER) cc_final: 0.5550 (ttt)
REVERT: A 1508 ILE cc_start: 0.8323 (mt) cc_final: 0.7987 (mm)
  outliers start: 10
  outliers final: 6
  residues processed: 118
  average time/residue: 0.2822
  time to fit residues: 44.9545
Evaluate side-chains
  117 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 109
  time to evaluate  : 1.173 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue  522 VAL
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1133 HIS
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1399 MET
Chi-restraints excluded: chain A residue 1570 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 105 optimal weight:    0.0050
   chunk 5 optimal weight:    1.9990
   chunk 97 optimal weight:    0.7980
   chunk 117 optimal weight:    0.4980
   chunk 107 optimal weight:    0.5980
   chunk 116 optimal weight:    2.9990
   chunk 35 optimal weight:    0.7980
   chunk 96 optimal weight:    0.7980
   chunk 51 optimal weight:    0.5980
   chunk 43 optimal weight:    0.0000
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.3398

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.125478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.100298 restraints weight = 16310.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.3209 rms_B_bonded: 1.87
r_work: 0.3088 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.2964 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2964
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2967
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2967 r_free = 0.2967    target_work(ls_wunit_k1) = 0.084         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2967
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.2434

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10612  Z= 0.101
  Angle     :  0.515  10.931  14386  Z= 0.263
  Chirality :  0.039   0.167   1611
  Planarity :  0.004   0.060   1772
  Dihedral  :  8.367 126.869   1522
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 4.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.85 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  9.53 %
    Favored  : 89.84 %
  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:  0.43 (0.24), residues: 1229
  helix:  1.51 (0.20), residues: 666
  sheet: -0.78 (0.50), residues: 99
  loop : -1.30 (0.27), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.020   0.001   PHE A1437 
 TYR   0.010   0.001   TYR A 913 
 ARG   0.003   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  498)
  hydrogen bonds       : angle       4.06508 ( 1443)
  covalent geometry    : bond        0.00213 (10612)
  covalent geometry    : angle       0.51541 (14386)

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

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

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2458 Ramachandran restraints generated.
    1229 Oldfield, 0 Emsley, 1229 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 116
  time to evaluate  : 1.193 
Fit side-chains
   revert: symmetry clash
REVERT: A  859 ARG cc_start: 0.6732 (ptt90) cc_final: 0.6508 (ptt-90)
REVERT: A  893 ARG cc_start: 0.6747 (ttt-90) cc_final: 0.6349 (tpp80)
REVERT: A 1039 GLN cc_start: 0.8453 (tp40) cc_final: 0.8215 (tp-100)
REVERT: A 1043 ASP cc_start: 0.7748 (m-30) cc_final: 0.7461 (m-30)
REVERT: A 1120 TYR cc_start: 0.7879 (t80) cc_final: 0.7589 (t80)
REVERT: A 1173 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5618 (pp)
REVERT: A 1399 MET cc_start: 0.6124 (OUTLIER) cc_final: 0.5426 (ttt)
REVERT: A 1508 ILE cc_start: 0.8175 (mt) cc_final: 0.7918 (mm)
  outliers start: 7
  outliers final: 3
  residues processed: 120
  average time/residue: 0.2735
  time to fit residues: 44.9342
Evaluate side-chains
  118 residues out of total 1112 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 113
  time to evaluate  : 1.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 ILE
Chi-restraints excluded: chain A residue 1126 GLN
Chi-restraints excluded: chain A residue 1173 LEU
Chi-restraints excluded: chain A residue 1197 LEU
Chi-restraints excluded: chain A residue 1399 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 112 optimal weight:    0.0770
   chunk 106 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 24 optimal weight:    0.0970
   chunk 66 optimal weight:    5.9990
   chunk 47 optimal weight:    1.9990
   chunk 118 optimal weight:    0.9990
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 95 optimal weight:    0.7980
   chunk 122 optimal weight:    4.9990
   overall best weight:    0.5940

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

Flipped N/Q/H residues before XYZ refinement:
** A 828 ASN ** 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 = 0.3547 r_free = 0.3547 target = 0.124396 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.099020 restraints weight = 16095.069|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 1.89
r_work: 0.3068 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.2941 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2941
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2945
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2945 r_free = 0.2945    target_work(ls_wunit_k1) = 0.083         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2945
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8458
moved from start:          0.2391

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10612  Z= 0.116
  Angle     :  0.530  10.375  14386  Z= 0.271
  Chirality :  0.039   0.174   1611
  Planarity :  0.004   0.059   1772
  Dihedral  :  8.360 126.118   1522
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.45 %
    Allowed  : 10.16 %
    Favored  : 89.39 %
  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:  0.49 (0.24), residues: 1229
  helix:  1.54 (0.20), residues: 670
  sheet: -0.79 (0.52), residues: 94
  loop : -1.24 (0.28), residues: 465

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 474 
 HIS   0.003   0.001   HIS A 743 
 PHE   0.019   0.001   PHE A1186 
 TYR   0.011   0.001   TYR A1383 
 ARG   0.004   0.000   ARG A 918 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  498)
  hydrogen bonds       : angle       4.10128 ( 1443)
  covalent geometry    : bond        0.00261 (10612)
  covalent geometry    : angle       0.52979 (14386)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5787.30 seconds
wall clock time: 101 minutes 1.85 seconds (6061.85 seconds total)