Starting phenix.real_space_refine
on Sun May 18 02:42:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ieo_35388/05_2025/8ieo_35388_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ieo_35388/05_2025/8ieo_35388.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.78
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ieo_35388/05_2025/8ieo_35388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ieo_35388/05_2025/8ieo_35388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ieo_35388/05_2025/8ieo_35388_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ieo_35388/05_2025/8ieo_35388_trim.cif"
  }
  resolution = 3.78
  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=   0.031
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: 8
    Type Number    sf(0)   Gaussians
     Al      1      5.89       5
     Mg      1      5.21       5
     S      53      5.16       5
     C    5156      2.51       5
     N    1377      2.21       5
     O    1408      1.98       5
     F       4      1.80       5
     H    8260      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 16260
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "P"
      Number of atoms: 16240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1031, 16240
          Classifications: {'peptide': 1031}
          Link IDs: {'CIS': 1, 'PTRANS': 68, 'TRANS': 961}
          Chain breaks: 7
    Chain: "P"
      Number of atoms: 20
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 20
          Unusual residues: {' MG': 1, 'ALF': 1, 'SPM': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 7.60, per 1000 atoms: 0.47
  Number of scatterers: 16260
  At special positions: 0
  Unit cell: (89.79, 119.355, 129.21, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      53     16.00
     Al      1     13.00
     Mg      1     11.99
     F       4      9.00
     O    1408      8.00
     N    1377      7.00
     C    5156      6.00
     H    8260      1.00
    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: 4.13
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1926

  Finding SS restraints...
    Secondary structure from input PDB file:
      34 helices and 5 sheets defined
      45.2% alpha, 7.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.28
  Creating SS restraints...
    Processing helix  chain 'P' and resid 49 through 58
      removed outlier: 3.830A  pdb=" N   VAL P  53 " --> pdb=" O   GLY P  49 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 59 through 67
      removed outlier: 4.093A  pdb=" N   LEU P  62 " --> pdb=" O   GLY P  59 " (cutoff:3.500A)
      removed outlier: 4.131A  pdb=" N   LEU P  63 " --> pdb=" O   ILE P  60 " (cutoff:3.500A)
      removed outlier: 3.828A  pdb=" N   LEU P  64 " --> pdb=" O   PRO P  61 " (cutoff:3.500A)
      removed outlier: 4.197A  pdb=" N   ARG P  66 " --> pdb=" O   LEU P  63 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 68 through 75
      removed outlier: 4.438A  pdb=" N   GLY P  72 " --> pdb=" O   LYS P  68 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 187 through 192
      removed outlier: 3.730A  pdb=" N   GLY P 191 " --> pdb=" O   LEU P 187 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 208 through 217
      removed outlier: 4.267A  pdb=" N   ARG P 212 " --> pdb=" O   ASP P 208 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 238 through 252
      removed outlier: 3.635A  pdb=" N   GLY P 242 " --> pdb=" O   ASN P 238 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   PHE P 243 " --> pdb=" O   PRO P 239 " (cutoff:3.500A)
      removed outlier: 5.181A  pdb=" N   GLN P 244 " --> pdb=" O   TYR P 240 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA P 245 " --> pdb=" O   TYR P 241 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU P 252 " --> pdb=" O   ILE P 248 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 256 through 289
      removed outlier: 3.811A  pdb=" N   ALA P 260 " --> pdb=" O   TYR P 256 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   CYS P 262 " --> pdb=" O   TRP P 258 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   VAL P 289 " --> pdb=" O   LEU P 285 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 398 through 401
      removed outlier: 4.082A  pdb=" N   CYS P 401 " --> pdb=" O   THR P 398 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'P' and resid 398 through 401'
    Processing helix  chain 'P' and resid 402 through 413
      removed outlier: 3.506A  pdb=" N   LEU P 407 " --> pdb=" O   ALA P 403 " (cutoff:3.500A)
      removed outlier: 4.122A  pdb=" N   ILE P 411 " --> pdb=" O   LEU P 407 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   LEU P 412 " --> pdb=" O   VAL P 408 " (cutoff:3.500A)
      removed outlier: 4.445A  pdb=" N   HIS P 413 " --> pdb=" O   SER P 409 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 422 through 445
      removed outlier: 3.511A  pdb=" N   GLY P 439 " --> pdb=" O   LEU P 435 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   ILE P 441 " --> pdb=" O   LEU P 437 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   TYR P 442 " --> pdb=" O   LEU P 438 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   ILE P 444 " --> pdb=" O   THR P 440 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 445 through 450
      removed outlier: 3.898A  pdb=" N   ARG P 449 " --> pdb=" O   PHE P 445 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 456 through 467
      removed outlier: 3.859A  pdb=" N   ARG P 460 " --> pdb=" O   GLU P 456 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 472 through 491
      removed outlier: 4.074A  pdb=" N   MET P 477 " --> pdb=" O   LEU P 473 " (cutoff:3.500A)
      removed outlier: 3.712A  pdb=" N   THR P 478 " --> pdb=" O   PRO P 474 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   VAL P 479 " --> pdb=" O   ALA P 475 " (cutoff:3.500A)
      removed outlier: 4.370A  pdb=" N   CYS P 480 " --> pdb=" O   ALA P 476 " (cutoff:3.500A)
      removed outlier: 4.040A  pdb=" N   GLN P 491 " --> pdb=" O   ARG P 487 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 549 through 558
      removed outlier: 4.385A  pdb=" N   ARG P 553 " --> pdb=" O   GLY P 549 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 572 through 581
      removed outlier: 3.584A  pdb=" N   THR P 581 " --> pdb=" O   MET P 577 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 656 through 664
    Processing helix  chain 'P' and resid 674 through 683
    Processing helix  chain 'P' and resid 696 through 707
    Processing helix  chain 'P' and resid 709 through 714
    Processing helix  chain 'P' and resid 731 through 742
      removed outlier: 3.612A  pdb=" N   VAL P 735 " --> pdb=" O   GLN P 731 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR P 742 " --> pdb=" O   ALA P 738 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 753 through 764
      removed outlier: 3.520A  pdb=" N   THR P 759 " --> pdb=" O   GLN P 755 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 826 through 836
      removed outlier: 3.616A  pdb=" N   VAL P 834 " --> pdb=" O   PHE P 830 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   LYS P 835 " --> pdb=" O   GLY P 831 " (cutoff:3.500A)
      removed outlier: 4.172A  pdb=" N   HIS P 836 " --> pdb=" O   ILE P 832 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 840 through 848
      removed outlier: 3.903A  pdb=" N   LEU P 845 " --> pdb=" O   LEU P 841 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   GLN P 847 " --> pdb=" O   LYS P 843 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 855 through 868
      removed outlier: 4.324A  pdb=" N   THR P 860 " --> pdb=" O   PRO P 856 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   GLU P 861 " --> pdb=" O   GLU P 857 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 882 through 889
    Processing helix  chain 'P' and resid 899 through 904
      removed outlier: 4.047A  pdb=" N   VAL P 903 " --> pdb=" O   GLU P 899 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 914 through 953
      removed outlier: 4.380A  pdb=" N   MET P 918 " --> pdb=" O   GLU P 914 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   THR P 953 " --> pdb=" O   LEU P 949 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 960 through 976
      removed outlier: 3.805A  pdb=" N   ILE P 970 " --> pdb=" O   ILE P 966 " (cutoff:3.500A)
      removed outlier: 3.553A  pdb=" N   THR P 971 " --> pdb=" O   ASP P 967 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 998 through 1026
      removed outlier: 3.607A  pdb=" N   LEU P1002 " --> pdb=" O   SER P 998 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1044 through 1063
      removed outlier: 3.575A  pdb=" N   THR P1048 " --> pdb=" O   ASN P1044 " (cutoff:3.500A)
      removed outlier: 3.519A  pdb=" N   VAL P1049 " --> pdb=" O   TYR P1045 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   VAL P1050 " --> pdb=" O   GLU P1046 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU P1053 " --> pdb=" O   VAL P1049 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   PHE P1056 " --> pdb=" O   SER P1052 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLN P1057 " --> pdb=" O   LEU P1053 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   TYR P1058 " --> pdb=" O   SER P1054 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   LEU P1059 " --> pdb=" O   SER P1055 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA P1063 " --> pdb=" O   LEU P1059 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1079 through 1096
      removed outlier: 4.013A  pdb=" N   VAL P1083 " --> pdb=" O   VAL P1079 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ALA P1084 " --> pdb=" O   PRO P1080 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1115 through 1140
      removed outlier: 3.785A  pdb=" N   GLN P1140 " --> pdb=" O   SER P1136 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1141 through 1148
      removed outlier: 4.122A  pdb=" N   CYS P1145 " --> pdb=" O   CYS P1141 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   LEU P1146 " --> pdb=" O   LEU P1142 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 1158 through 1166
      removed outlier: 3.503A  pdb=" N   ARG P1164 " --> pdb=" O   LYS P1160 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'P' and resid 165 through 167
      removed outlier: 4.374A  pdb=" N   ILE P 174 " --> pdb=" O   TYR P 183 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   TYR P 183 " --> pdb=" O   ILE P 174 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   ILE P 176 " --> pdb=" O   ALA P 181 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   ALA P 181 " --> pdb=" O   ILE P 176 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'P' and resid 304 through 308
      removed outlier: 4.455A  pdb=" N   GLU P 305 " --> pdb=" O   VAL P 297 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   VAL P 297 " --> pdb=" O   GLU P 305 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   CYS P 296 " --> pdb=" O   VAL P 319 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   CYS P 317 " --> pdb=" O   CYS P 298 " (cutoff:3.500A)
      removed outlier: 6.802A  pdb=" N   LEU P 392 " --> pdb=" O   VAL P 334 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   VAL P 334 " --> pdb=" O   LEU P 392 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   THR P 396 " --> pdb=" O   ASP P 330 " (cutoff:3.500A)
      removed outlier: 7.654A  pdb=" N   ASP P 330 " --> pdb=" O   THR P 396 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'P' and resid 352 through 354
      removed outlier: 3.748A  pdb=" N   VAL P 352 " --> pdb=" O   VAL P 340 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   VAL P 340 " --> pdb=" O   VAL P 352 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LYS P 354 " --> pdb=" O   CYS P 338 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLU P 337 " --> pdb=" O   ARG P 384 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'P' and resid 850 through 851
      removed outlier: 8.581A  pdb=" N   PHE P 851 " --> pdb=" O   ALA P 746 " (cutoff:3.500A)
      removed outlier: 6.297A  pdb=" N   MET P 748 " --> pdb=" O   PHE P 851 " (cutoff:3.500A)
      removed outlier: 5.915A  pdb=" N   VAL P 510 " --> pdb=" O   VAL P 747 " (cutoff:3.500A)
      removed outlier: 7.016A  pdb=" N   VAL P 749 " --> pdb=" O   VAL P 510 " (cutoff:3.500A)
      removed outlier: 5.289A  pdb=" N   PHE P 512 " --> pdb=" O   VAL P 749 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   PHE P 906 " --> pdb=" O   GLY P 892 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'P' and resid 524 through 528
      removed outlier: 3.848A  pdb=" N   ASP P 524 " --> pdb=" O   ARG P 725 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   MET P 526 " --> pdb=" O   VAL P 723 " (cutoff:3.500A)
      removed outlier: 8.426A  pdb=" N   VAL P 723 " --> pdb=" O   MET P 526 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   VAL P 528 " --> pdb=" O   LEU P 721 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   LEU P 721 " --> pdb=" O   VAL P 528 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   LEU P 690 " --> pdb=" O   LEU P 719 " (cutoff:3.500A)
      removed outlier: 4.942A  pdb=" N   LEU P 721 " --> pdb=" O   VAL P 688 " (cutoff:3.500A)
      removed outlier: 6.944A  pdb=" N   VAL P 688 " --> pdb=" O   LEU P 721 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   GLY P 655 " --> pdb=" O   ALA P 689 " (cutoff:3.500A)
      removed outlier: 4.664A  pdb=" N   GLU P 650 " --> pdb=" O   VAL P 641 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   VAL P 641 " --> pdb=" O   GLU P 650 " (cutoff:3.500A)
      removed outlier: 7.541A  pdb=" N   SER P 638 " --> pdb=" O   ARG P 627 " (cutoff:3.500A)
      removed outlier: 5.449A  pdb=" N   ARG P 627 " --> pdb=" O   SER P 638 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   VAL P 640 " --> pdb=" O   LEU P 625 " (cutoff:3.500A)

    302 hydrogen bonds defined for protein.
    891 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: 5.27

  Time building geometry restraints manager: 4.82 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 8233
        1.03 -     1.23: 28
        1.23 -     1.42: 3247
        1.42 -     1.62: 4839
        1.62 -     1.81: 83
  Bond restraints: 16430
  Sorted by residual:
  bond pdb=" F1  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.684  1.800 -0.116 2.00e-02 2.50e+03 3.37e+01
  bond pdb=" F2  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.685  1.800 -0.115 2.00e-02 2.50e+03 3.31e+01
  bond pdb=" F4  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.686  1.801 -0.115 2.00e-02 2.50e+03 3.29e+01
  bond pdb=" F3  ALF P1201 "
       pdb="AL   ALF P1201 "
    ideal  model  delta    sigma   weight residual
    1.685  1.799 -0.114 2.00e-02 2.50e+03 3.25e+01
  bond pdb=" N   TRP P 608 "
       pdb=" CA  TRP P 608 "
    ideal  model  delta    sigma   weight residual
    1.458  1.491 -0.033 1.90e-02 2.77e+03 3.06e+00
  ... (remaining 16425 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    14.26: 29832
       14.26 -    28.51: 4
       28.51 -    42.77: 0
       42.77 -    57.02: 0
       57.02 -    71.28: 2
  Bond angle restraints: 29838
  Sorted by residual:
  angle pdb=" F1  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F2  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     108.68  179.96  -71.28 3.00e+00 1.11e-01 5.64e+02
  angle pdb=" F3  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F4  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     109.63  179.98  -70.35 3.00e+00 1.11e-01 5.50e+02
  angle pdb=" N   PRO P 621 "
        pdb=" CD  PRO P 621 "
        pdb=" CG  PRO P 621 "
      ideal   model   delta    sigma   weight residual
     103.20   92.92   10.28 1.50e+00 4.44e-01 4.70e+01
  angle pdb=" F2  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F4  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     110.21   89.99   20.22 3.00e+00 1.11e-01 4.54e+01
  angle pdb=" F1  ALF P1201 "
        pdb="AL   ALF P1201 "
        pdb=" F3  ALF P1201 "
      ideal   model   delta    sigma   weight residual
     109.69   90.03   19.66 3.00e+00 1.11e-01 4.29e+01
  ... (remaining 29833 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.87: 6857
       17.87 -    35.74: 600
       35.74 -    53.61: 192
       53.61 -    71.48: 55
       71.48 -    89.35: 15
  Dihedral angle restraints: 7719
    sinusoidal: 4299
      harmonic: 3420
  Sorted by residual:
  dihedral pdb=" CB  GLU P 139 "
           pdb=" CG  GLU P 139 "
           pdb=" CD  GLU P 139 "
           pdb=" OE1 GLU P 139 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.16  -87.16     1      3.00e+01 1.11e-03 1.01e+01
  dihedral pdb=" N   PRO P 621 "
           pdb=" CG  PRO P 621 "
           pdb=" CD  PRO P 621 "
           pdb=" CB  PRO P 621 "
      ideal   model   delta sinusoidal    sigma   weight residual
      30.00   70.06  -40.06     1      1.50e+01 4.44e-03 1.00e+01
  dihedral pdb=" CG  ARG P 636 "
           pdb=" CD  ARG P 636 "
           pdb=" NE  ARG P 636 "
           pdb=" CZ  ARG P 636 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  131.96  -41.96     2      1.50e+01 4.44e-03 9.54e+00
  ... (remaining 7716 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 899
       0.029 -    0.058: 261
       0.058 -    0.087: 84
       0.087 -    0.116: 62
       0.116 -    0.145: 11
  Chirality restraints: 1317
  Sorted by residual:
  chirality pdb=" CA  VAL P 767 "
            pdb=" N   VAL P 767 "
            pdb=" C   VAL P 767 "
            pdb=" CB  VAL P 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.59   -0.14 2.00e-01 2.50e+01 5.24e-01
  chirality pdb=" CA  ILE P 350 "
            pdb=" N   ILE P 350 "
            pdb=" C   ILE P 350 "
            pdb=" CB  ILE P 350 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.43e-01
  chirality pdb=" CA  VAL P 620 "
            pdb=" N   VAL P 620 "
            pdb=" C   VAL P 620 "
            pdb=" CB  VAL P 620 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.02e-01
  ... (remaining 1314 not shown)

  Planarity restraints: 2353
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL P1079 "   -0.077 5.00e-02 4.00e+02   1.18e-01 2.21e+01
        pdb=" N   PRO P1080 "    0.203 5.00e-02 4.00e+02
        pdb=" CA  PRO P1080 "   -0.063 5.00e-02 4.00e+02
        pdb=" CD  PRO P1080 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG P1073 "    0.029 5.00e-02 4.00e+02   4.43e-02 3.14e+00
        pdb=" N   PRO P1074 "   -0.077 5.00e-02 4.00e+02
        pdb=" CA  PRO P1074 "    0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO P1074 "    0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN P1026 "   -0.028 5.00e-02 4.00e+02   4.17e-02 2.78e+00
        pdb=" N   PRO P1027 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO P1027 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO P1027 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2350 not shown)

  Histogram of nonbonded interaction distances:
        1.66 -     2.25: 1969
        2.25 -     2.83: 35361
        2.83 -     3.42: 38926
        3.42 -     4.01: 50199
        4.01 -     4.60: 76597
  Nonbonded interactions: 203052
  Sorted by model distance:
  nonbonded pdb="HH12 ARG P 745 "
            pdb=" O   GLY P 848 "
     model   vdw
     1.657 2.450
  nonbonded pdb=" HZ3 LYS P 514 "
            pdb=" OD2 ASP P 752 "
     model   vdw
     1.681 2.450
  nonbonded pdb=" O   LYS P 514 "
            pdb=" HG1 THR P 519 "
     model   vdw
     1.701 2.450
  nonbonded pdb=" O   MET P 477 "
            pdb=" HG1 THR P 481 "
     model   vdw
     1.709 2.450
  nonbonded pdb=" OE2 GLU P 337 "
            pdb=" HE  ARG P 384 "
     model   vdw
     1.711 2.450
  ... (remaining 203047 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:             1.540
  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:             0.270
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.110
  Set scattering table:                    0.140
  Process input model:                     33.680
  Find NCS groups from input model:        0.110
  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:2.500
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   38.980
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6394
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   0.116   8170  Z= 0.177
  Angle     :  1.197  71.275  11117  Z= 0.471
  Chirality :  0.037   0.145   1317
  Planarity :  0.004   0.118   1397
  Dihedral  : 15.040  89.347   3014
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 17.69 %
    Favored  : 82.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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 (0.28), residues: 1015
  helix:  3.04 (0.29), residues: 386
  sheet: -0.34 (0.71), residues: 51
  loop : -1.16 (0.25), residues: 578

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.000   TRP P 100 
 HIS   0.006   0.000   HIS P 413 
 PHE   0.009   0.000   PHE P1081 
 TYR   0.009   0.000   TYR P 183 
 ARG   0.004   0.000   ARG P 980 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.17570 (  302)
  hydrogen bonds       : angle       5.91963 (  891)
  covalent geometry    : bond        0.00368 ( 8170)
  covalent geometry    : angle       1.19665 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 1.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 1
  outliers final: 0
  residues processed: 104
  average time/residue: 0.3550
  time to fit residues: 53.5080
Evaluate side-chains
  101 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 86 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 41 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 60 optimal weight:   10.0000
   chunk 93 optimal weight:    0.2980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
P 944 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.223639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.189109 restraints weight = 34038.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.187631 restraints weight = 32787.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4184 r_free = 0.4184 target = 0.191080 restraints weight = 24742.602|
|-----------------------------------------------------------------------------|
r_work (final): 0.4182
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6714
moved from start:          0.1318

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8170  Z= 0.144
  Angle     :  0.852  31.263  11117  Z= 0.352
  Chirality :  0.039   0.142   1317
  Planarity :  0.005   0.090   1397
  Dihedral  :  3.306  41.848   1128
  Min Nonbonded Distance : 1.758

Molprobity Statistics.
  All-atom Clashscore : 2.33
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.53 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 16.67 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  0.20 (0.28), residues: 1015
  helix:  2.34 (0.28), residues: 410
  sheet: -1.11 (0.62), residues: 61
  loop : -1.56 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 251 
 HIS   0.005   0.001   HIS P 413 
 PHE   0.017   0.001   PHE P 906 
 TYR   0.011   0.001   TYR P 259 
 ARG   0.003   0.000   ARG P 821 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03693 (  302)
  hydrogen bonds       : angle       4.34349 (  891)
  covalent geometry    : bond        0.00331 ( 8170)
  covalent geometry    : angle       0.85151 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 113
  time to evaluate  : 1.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  239 PRO cc_start: 0.6043 (Cg_exo) cc_final: 0.5818 (Cg_endo)
REVERT: P  844 VAL cc_start: 0.6366 (OUTLIER) cc_final: 0.4591 (m)
  outliers start: 8
  outliers final: 5
  residues processed: 117
  average time/residue: 0.3824
  time to fit residues: 63.3728
Evaluate side-chains
  109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 103
  time to evaluate  : 1.109 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  211 VAL
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  725 ARG
Chi-restraints excluded: chain P residue  844 VAL
Chi-restraints excluded: chain P residue  849 THR
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 100 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0770
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0970
   chunk 16 optimal weight:    0.5980
   chunk 91 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   overall best weight:    0.4536

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

Flipped N/Q/H residues before XYZ refinement:
P 822 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4467 r_free = 0.4467 target = 0.220402 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.185158 restraints weight = 32796.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.184232 restraints weight = 25176.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.186551 restraints weight = 21281.049|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.1704

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8170  Z= 0.095
  Angle     :  0.797  29.786  11117  Z= 0.315
  Chirality :  0.037   0.142   1317
  Planarity :  0.004   0.070   1397
  Dihedral  :  3.085  41.504   1128
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 1.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.43 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  0.68 %
    Allowed  : 16.78 %
    Favored  : 82.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  0.34 (0.28), residues: 1015
  helix:  2.53 (0.29), residues: 411
  sheet: -0.94 (0.65), residues: 61
  loop : -1.58 (0.25), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP P 100 
 HIS   0.005   0.001   HIS P 413 
 PHE   0.009   0.001   PHE P 906 
 TYR   0.010   0.001   TYR P 871 
 ARG   0.002   0.000   ARG P 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03929 (  302)
  hydrogen bonds       : angle       4.06369 (  891)
  covalent geometry    : bond        0.00235 ( 8170)
  covalent geometry    : angle       0.79683 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 1.278 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  213 LYS cc_start: 0.7430 (tptp) cc_final: 0.6889 (mttp)
REVERT: P  238 ASN cc_start: 0.6195 (m110) cc_final: 0.5989 (m-40)
REVERT: P  239 PRO cc_start: 0.6110 (Cg_exo) cc_final: 0.5896 (Cg_endo)
REVERT: P  955 ASN cc_start: 0.5247 (p0) cc_final: 0.4871 (p0)
  outliers start: 6
  outliers final: 4
  residues processed: 112
  average time/residue: 0.3963
  time to fit residues: 62.5249
Evaluate side-chains
  102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  844 VAL
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 3 optimal weight:    0.6980
   chunk 74 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9980
   chunk 64 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 79 optimal weight:    0.9980
   chunk 91 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0060
   chunk 35 optimal weight:    4.9990
   chunk 97 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    0.6996

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

Flipped N/Q/H residues before XYZ refinement:
P 244 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.209479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.171906 restraints weight = 32679.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.170092 restraints weight = 33346.606|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.173334 restraints weight = 26144.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3999
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7038
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   8170  Z= 0.128
  Angle     :  0.829  30.691  11117  Z= 0.339
  Chirality :  0.039   0.137   1317
  Planarity :  0.004   0.068   1397
  Dihedral  :  3.732  52.198   1128
  Min Nonbonded Distance : 1.902

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 16.10 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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: -0.07 (0.27), residues: 1015
  helix:  2.18 (0.28), residues: 411
  sheet: -1.03 (0.60), residues: 67
  loop : -1.83 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP P 251 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.012   0.001   PHE P1081 
 TYR   0.022   0.001   TYR P 871 
 ARG   0.007   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03709 (  302)
  hydrogen bonds       : angle       3.94838 (  891)
  covalent geometry    : bond        0.00311 ( 8170)
  covalent geometry    : angle       0.82864 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 107
  time to evaluate  : 1.131 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  239 PRO cc_start: 0.6262 (Cg_exo) cc_final: 0.6061 (Cg_endo)
REVERT: P  240 TYR cc_start: 0.7911 (OUTLIER) cc_final: 0.6960 (t80)
REVERT: P  771 GLU cc_start: 0.8255 (OUTLIER) cc_final: 0.7226 (mm-30)
REVERT: P  844 VAL cc_start: 0.6922 (OUTLIER) cc_final: 0.6663 (t)
  outliers start: 13
  outliers final: 7
  residues processed: 117
  average time/residue: 0.4206
  time to fit residues: 67.6426
Evaluate side-chains
  106 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  211 VAL
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  467 VAL
Chi-restraints excluded: chain P residue  725 ARG
Chi-restraints excluded: chain P residue  771 GLU
Chi-restraints excluded: chain P residue  844 VAL
Chi-restraints excluded: chain P residue  849 THR
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 5 optimal weight:    3.9990
   chunk 75 optimal weight:    1.9990
   chunk 90 optimal weight:    0.4980
   chunk 76 optimal weight:    0.4980
   chunk 10 optimal weight:    0.0980
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 70 optimal weight:    0.0020
   overall best weight:    0.4188

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.209631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3966 r_free = 0.3966 target = 0.168916 restraints weight = 33069.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.168814 restraints weight = 24393.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.170298 restraints weight = 21291.673|
|-----------------------------------------------------------------------------|
r_work (final): 0.3960
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7101
moved from start:          0.2922

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   8170  Z= 0.091
  Angle     :  0.800  29.779  11117  Z= 0.317
  Chirality :  0.037   0.133   1317
  Planarity :  0.004   0.055   1397
  Dihedral  :  3.528  52.734   1128
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 2.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 17.80 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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:  0.13 (0.28), residues: 1015
  helix:  2.44 (0.28), residues: 405
  sheet: -0.93 (0.61), residues: 67
  loop : -1.75 (0.25), residues: 543

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP P 100 
 HIS   0.005   0.001   HIS P 413 
 PHE   0.009   0.001   PHE P1081 
 TYR   0.015   0.001   TYR P 871 
 ARG   0.006   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03417 (  302)
  hydrogen bonds       : angle       3.82560 (  891)
  covalent geometry    : bond        0.00225 ( 8170)
  covalent geometry    : angle       0.79970 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 100
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  240 TYR cc_start: 0.7898 (OUTLIER) cc_final: 0.6963 (t80)
REVERT: P  724 MET cc_start: 0.8149 (mmt) cc_final: 0.7793 (mmt)
REVERT: P  771 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7066 (mm-30)
  outliers start: 7
  outliers final: 4
  residues processed: 106
  average time/residue: 0.3910
  time to fit residues: 58.9309
Evaluate side-chains
  100 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 94
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  298 CYS
Chi-restraints excluded: chain P residue  771 GLU
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:    0.0070
   chunk 72 optimal weight:    0.9980
   chunk 102 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0070
   chunk 38 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.204560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.165863 restraints weight = 32598.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.165184 restraints weight = 34875.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3952 r_free = 0.3952 target = 0.168600 restraints weight = 25203.271|
|-----------------------------------------------------------------------------|
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7112
moved from start:          0.3444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8170  Z= 0.110
  Angle     :  0.815  29.977  11117  Z= 0.329
  Chirality :  0.038   0.135   1317
  Planarity :  0.004   0.064   1397
  Dihedral  :  3.776  56.536   1128
  Min Nonbonded Distance : 1.868

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.81 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 17.23 %
    Favored  : 81.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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: -0.00 (0.28), residues: 1015
  helix:  2.20 (0.28), residues: 413
  sheet: -0.74 (0.62), residues: 67
  loop : -1.82 (0.25), residues: 535

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP P  55 
 HIS   0.007   0.001   HIS P 413 
 PHE   0.012   0.001   PHE P1081 
 TYR   0.023   0.001   TYR P 871 
 ARG   0.007   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03539 (  302)
  hydrogen bonds       : angle       3.81538 (  891)
  covalent geometry    : bond        0.00267 ( 8170)
  covalent geometry    : angle       0.81480 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 1.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  240 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7095 (t80)
REVERT: P  724 MET cc_start: 0.8276 (mmt) cc_final: 0.7954 (mmt)
REVERT: P  771 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7562 (tt0)
REVERT: P  963 PHE cc_start: 0.8756 (OUTLIER) cc_final: 0.8172 (t80)
  outliers start: 12
  outliers final: 8
  residues processed: 101
  average time/residue: 0.4057
  time to fit residues: 57.4400
Evaluate side-chains
  96 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  211 VAL
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  467 VAL
Chi-restraints excluded: chain P residue  518 LEU
Chi-restraints excluded: chain P residue  725 ARG
Chi-restraints excluded: chain P residue  771 GLU
Chi-restraints excluded: chain P residue  860 THR
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  963 PHE
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 77 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   chunk 43 optimal weight:    1.9990
   chunk 88 optimal weight:    0.9980
   chunk 64 optimal weight:    0.7980
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 71 optimal weight:    0.8980
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.198670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.158504 restraints weight = 32241.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.158569 restraints weight = 36212.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3877 r_free = 0.3877 target = 0.161865 restraints weight = 24963.432|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.4136

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8170  Z= 0.132
  Angle     :  0.837  30.176  11117  Z= 0.345
  Chirality :  0.039   0.130   1317
  Planarity :  0.004   0.055   1397
  Dihedral  :  4.097  58.666   1128
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.71 %
    Favored  : 94.19 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 17.23 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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: -0.25 (0.28), residues: 1015
  helix:  1.91 (0.28), residues: 420
  sheet: -0.92 (0.60), residues: 77
  loop : -1.94 (0.26), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP P 100 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.015   0.001   PHE P 906 
 TYR   0.027   0.001   TYR P 871 
 ARG   0.005   0.000   ARG P 991 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04069 (  302)
  hydrogen bonds       : angle       3.87106 (  891)
  covalent geometry    : bond        0.00320 ( 8170)
  covalent geometry    : angle       0.83729 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 86
  time to evaluate  : 1.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  240 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.6778 (t80)
REVERT: P  771 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.7739 (tt0)
REVERT: P  822 HIS cc_start: 0.6276 (m170) cc_final: 0.6051 (m170)
REVERT: P  865 GLU cc_start: 0.8082 (tp30) cc_final: 0.7865 (mm-30)
REVERT: P  871 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.6078 (t80)
REVERT: P  963 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8345 (t80)
  outliers start: 18
  outliers final: 10
  residues processed: 98
  average time/residue: 0.4922
  time to fit residues: 67.7531
Evaluate side-chains
  96 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 82
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  211 VAL
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  355 THR
Chi-restraints excluded: chain P residue  467 VAL
Chi-restraints excluded: chain P residue  725 ARG
Chi-restraints excluded: chain P residue  771 GLU
Chi-restraints excluded: chain P residue  849 THR
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  955 ASN
Chi-restraints excluded: chain P residue  963 PHE
Chi-restraints excluded: chain P residue 1078 ASN
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 45 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 84 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
P 726 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.196061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.154461 restraints weight = 32053.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.152999 restraints weight = 37732.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.156017 restraints weight = 30005.053|
|-----------------------------------------------------------------------------|
r_work (final): 0.3813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7296
moved from start:          0.4506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   8170  Z= 0.127
  Angle     :  0.827  30.178  11117  Z= 0.338
  Chirality :  0.038   0.133   1317
  Planarity :  0.004   0.081   1397
  Dihedral  :  4.134  59.616   1128
  Min Nonbonded Distance : 1.844

Molprobity Statistics.
  All-atom Clashscore : 3.25
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.21 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 17.91 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    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: -0.28 (0.28), residues: 1015
  helix:  1.89 (0.27), residues: 422
  sheet: -0.84 (0.62), residues: 77
  loop : -2.00 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P  55 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.016   0.001   PHE P1081 
 TYR   0.026   0.001   TYR P 871 
 ARG   0.003   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03952 (  302)
  hydrogen bonds       : angle       3.91595 (  891)
  covalent geometry    : bond        0.00310 ( 8170)
  covalent geometry    : angle       0.82696 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  240 TYR cc_start: 0.7941 (OUTLIER) cc_final: 0.6836 (t80)
REVERT: P  771 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.7740 (tt0)
REVERT: P  822 HIS cc_start: 0.6514 (m170) cc_final: 0.6271 (m170)
REVERT: P  865 GLU cc_start: 0.8176 (tp30) cc_final: 0.7859 (mm-30)
REVERT: P  871 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.6032 (t80)
REVERT: P  963 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8306 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 97
  average time/residue: 0.4117
  time to fit residues: 55.9089
Evaluate side-chains
  94 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 82
  time to evaluate  : 1.127 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  346 THR
Chi-restraints excluded: chain P residue  467 VAL
Chi-restraints excluded: chain P residue  725 ARG
Chi-restraints excluded: chain P residue  726 ASN
Chi-restraints excluded: chain P residue  771 GLU
Chi-restraints excluded: chain P residue  849 THR
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  963 PHE
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 40 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0970
   chunk 91 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 72 optimal weight:    0.6980
   chunk 79 optimal weight:    0.9980
   chunk 89 optimal weight:    0.0070
   chunk 70 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9990
   chunk 50 optimal weight:    4.9990
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.196967 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.153685 restraints weight = 32231.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.152523 restraints weight = 34203.406|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.156429 restraints weight = 27269.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7306
moved from start:          0.4570

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   8170  Z= 0.098
  Angle     :  0.816  29.688  11117  Z= 0.328
  Chirality :  0.038   0.132   1317
  Planarity :  0.004   0.068   1397
  Dihedral  :  4.044  59.621   1128
  Min Nonbonded Distance : 1.916

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.52 %
    Favored  : 94.38 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.48 %
    Favored  : 80.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    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: -0.18 (0.28), residues: 1015
  helix:  2.01 (0.28), residues: 422
  sheet: -0.88 (0.61), residues: 77
  loop : -1.96 (0.26), residues: 516

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 251 
 HIS   0.007   0.001   HIS P 413 
 PHE   0.012   0.001   PHE P1081 
 TYR   0.020   0.001   TYR P 871 
 ARG   0.003   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03668 (  302)
  hydrogen bonds       : angle       3.81507 (  891)
  covalent geometry    : bond        0.00238 ( 8170)
  covalent geometry    : angle       0.81608 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.164 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P  240 TYR cc_start: 0.7917 (OUTLIER) cc_final: 0.6771 (t80)
REVERT: P  771 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.7711 (tt0)
REVERT: P  822 HIS cc_start: 0.6436 (m170) cc_final: 0.6211 (m170)
REVERT: P  865 GLU cc_start: 0.8131 (tp30) cc_final: 0.7835 (mm-30)
REVERT: P  871 TYR cc_start: 0.7962 (OUTLIER) cc_final: 0.6014 (t80)
REVERT: P  963 PHE cc_start: 0.8886 (OUTLIER) cc_final: 0.8335 (t80)
  outliers start: 11
  outliers final: 7
  residues processed: 93
  average time/residue: 0.4285
  time to fit residues: 54.9852
Evaluate side-chains
  96 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 1.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  333 LEU
Chi-restraints excluded: chain P residue  346 THR
Chi-restraints excluded: chain P residue  725 ARG
Chi-restraints excluded: chain P residue  771 GLU
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  955 ASN
Chi-restraints excluded: chain P residue  963 PHE
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9990
   chunk 83 optimal weight:    0.2980
   chunk 46 optimal weight:    4.9990
   chunk 57 optimal weight:    4.9990
   chunk 37 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 95 optimal weight:    0.5980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.7786

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

Flipped N/Q/H residues before XYZ refinement:
P 626 HIS
P 726 ASN
P 777 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.192473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.149867 restraints weight = 32085.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.149107 restraints weight = 37146.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.152520 restraints weight = 27918.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.5076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8170  Z= 0.126
  Angle     :  0.839  30.016  11117  Z= 0.348
  Chirality :  0.039   0.131   1317
  Planarity :  0.004   0.080   1397
  Dihedral  :  4.256  57.802   1128
  Min Nonbonded Distance : 1.859

Molprobity Statistics.
  All-atom Clashscore : 3.81
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.70 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 18.37 %
    Favored  : 80.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    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 (0.28), residues: 1015
  helix:  1.90 (0.27), residues: 424
  sheet: -0.66 (0.58), residues: 85
  loop : -2.08 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP P  55 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.014   0.001   PHE P1081 
 TYR   0.028   0.001   TYR P 871 
 ARG   0.004   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04050 (  302)
  hydrogen bonds       : angle       3.88043 (  891)
  covalent geometry    : bond        0.00311 ( 8170)
  covalent geometry    : angle       0.83941 (11117)

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

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

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2030 Ramachandran restraints generated.
    1015 Oldfield, 0 Emsley, 1015 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 1.098 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: P   57 MET cc_start: 0.6777 (tmm) cc_final: 0.6482 (tmm)
REVERT: P  240 TYR cc_start: 0.8020 (OUTLIER) cc_final: 0.6702 (t80)
REVERT: P  524 ASP cc_start: 0.8322 (t0) cc_final: 0.7981 (t0)
REVERT: P  771 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.7796 (tt0)
REVERT: P  865 GLU cc_start: 0.8256 (tp30) cc_final: 0.7880 (mm-30)
REVERT: P  963 PHE cc_start: 0.8914 (OUTLIER) cc_final: 0.8358 (t80)
  outliers start: 13
  outliers final: 9
  residues processed: 103
  average time/residue: 0.4510
  time to fit residues: 64.1252
Evaluate side-chains
  96 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  333 LEU
Chi-restraints excluded: chain P residue  346 THR
Chi-restraints excluded: chain P residue  467 VAL
Chi-restraints excluded: chain P residue  725 ARG
Chi-restraints excluded: chain P residue  726 ASN
Chi-restraints excluded: chain P residue  771 GLU
Chi-restraints excluded: chain P residue  871 TYR
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  963 PHE
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1126 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 19 optimal weight:    0.5980
   chunk 76 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 84 optimal weight:    0.3980
   chunk 5 optimal weight:    0.7980
   chunk 0 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 87 optimal weight:    0.4980
   chunk 50 optimal weight:    8.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.193003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.147495 restraints weight = 32236.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.146447 restraints weight = 33425.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.150373 restraints weight = 23027.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.5174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.266   8170  Z= 0.280
  Angle     :  1.097  59.192  11117  Z= 0.585
  Chirality :  0.039   0.155   1317
  Planarity :  0.005   0.082   1397
  Dihedral  :  4.261  57.821   1128
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.80 %
    Favored  : 93.10 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 18.71 %
    Favored  : 80.05 %
  Cbeta Deviations :  0.10 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.10 %
    Twisted Proline : 1.49 %
    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 (0.28), residues: 1015
  helix:  1.90 (0.27), residues: 424
  sheet: -0.67 (0.57), residues: 85
  loop : -2.09 (0.26), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 251 
 HIS   0.005   0.001   HIS P  51 
 PHE   0.014   0.001   PHE P1081 
 TYR   0.028   0.001   TYR P 871 
 ARG   0.005   0.000   ARG P 397 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04031 (  302)
  hydrogen bonds       : angle       3.87778 (  891)
  covalent geometry    : bond        0.00522 ( 8170)
  covalent geometry    : angle       1.09735 (11117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4586.34 seconds
wall clock time: 79 minutes 47.17 seconds (4787.17 seconds total)