Starting phenix.real_space_refine
on Sat Jun 14 18:32:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ieo_35388/06_2025/8ieo_35388_trim.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ieo_35388/06_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_35388/06_2025/8ieo_35388.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ieo_35388/06_2025/8ieo_35388.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ieo_35388/06_2025/8ieo_35388_trim.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ieo_35388/06_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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 7.76, per 1000 atoms: 0.48
  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: 3.90
  Conformation dependent library (CDL) restraints added in 1.4 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: 1.20
  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: 5.31

  Time building geometry restraints manager: 4.83 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:             1.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.260
  Extract box with map and model:          0.560
  Check model and map are aligned:         0.110
  Set scattering table:                    0.130
  Process input model:                     34.760
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.510
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.840
-------------------------------------------------------------------------------
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  : 1.266 
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: 0.3802
  time to fit residues: 57.4159
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  : 1.133 
-------------------------------------------------------------------------------
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 = 50)----------------|
| r_work = 0.4179 r_free = 0.4179 target = 0.189167 restraints weight = 34038.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.187820 restraints weight = 32176.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.191074 restraints weight = 24625.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
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  41.847   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       4.34348 (  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  : 1.196 
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: 0.6040 (Cg_exo) cc_final: 0.5815 (Cg_endo)
REVERT: P  844 VAL cc_start: 0.6366 (OUTLIER) cc_final: 0.4590 (m)
  outliers start: 8
  outliers final: 5
  residues processed: 117
  average time/residue: 0.3968
  time to fit residues: 65.9703
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  : 1.182 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 66 optimal weight:    0.0040
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    7.9990
   chunk 81 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 16 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5592

-------------------------------------------------------------------------------
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 = 0.4448 r_free = 0.4448 target = 0.218364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.179428 restraints weight = 32776.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.178967 restraints weight = 27189.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.181269 restraints weight = 20836.931|
|-----------------------------------------------------------------------------|
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6905
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8170  Z= 0.107
  Angle     :  0.803  29.980  11117  Z= 0.320
  Chirality :  0.038   0.144   1317
  Planarity :  0.004   0.069   1397
  Dihedral  :  3.177  43.680   1128
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 1.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.63 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  0.79 %
    Allowed  : 16.55 %
    Favored  : 82.65 %
  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:  0.28 (0.28), residues: 1015
  helix:  2.47 (0.28), residues: 412
  sheet: -0.80 (0.62), residues: 66
  loop : -1.64 (0.25), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP P 100 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.013   0.001   PHE P 906 
 TYR   0.014   0.001   TYR P 871 
 ARG   0.002   0.000   ARG P 384 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04229 (  302)
  hydrogen bonds       : angle       4.08736 (  891)
  covalent geometry    : bond        0.00263 ( 8170)
  covalent geometry    : angle       0.80314 (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
  115 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 108
  time to evaluate  : 1.118 
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: 0.7438 (tptp) cc_final: 0.6826 (mptt)
REVERT: P  239 PRO cc_start: 0.6207 (Cg_exo) cc_final: 0.5980 (Cg_endo)
REVERT: P  724 MET cc_start: 0.7970 (mmt) cc_final: 0.7604 (mmt)
REVERT: P  771 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7264 (tt0)
REVERT: P  822 HIS cc_start: 0.3898 (m170) cc_final: 0.3596 (m170)
REVERT: P  875 MET cc_start: 0.7996 (tpt) cc_final: 0.7436 (tpt)
REVERT: P  955 ASN cc_start: 0.5374 (p0) cc_final: 0.4982 (p0)
  outliers start: 7
  outliers final: 4
  residues processed: 114
  average time/residue: 0.4092
  time to fit residues: 66.5305
Evaluate side-chains
  104 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 99
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  771 GLU
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:    0.7980
   chunk 74 optimal weight:    1.9990
   chunk 94 optimal weight:    0.9990
   chunk 64 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 97 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
P 207 GLN
P 244 GLN
P 780 HIS
P 822 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.201361 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.160506 restraints weight = 32528.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3845 r_free = 0.3845 target = 0.158739 restraints weight = 38193.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.162141 restraints weight = 27930.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7218
moved from start:          0.3408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   8170  Z= 0.184
  Angle     :  0.893  30.473  11117  Z= 0.385
  Chirality :  0.041   0.138   1317
  Planarity :  0.005   0.069   1397
  Dihedral  :  4.519  56.867   1128
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.90 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 16.89 %
    Favored  : 81.07 %
  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: -0.67 (0.27), residues: 1015
  helix:  1.53 (0.27), residues: 418
  sheet: -1.16 (0.57), residues: 77
  loop : -2.13 (0.25), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP P 251 
 HIS   0.007   0.001   HIS P 772 
 PHE   0.019   0.002   PHE P1081 
 TYR   0.035   0.002   TYR P 871 
 ARG   0.004   0.000   ARG P1109 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04759 (  302)
  hydrogen bonds       : angle       4.27244 (  891)
  covalent geometry    : bond        0.00443 ( 8170)
  covalent geometry    : angle       0.89298 (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
  124 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 106
  time to evaluate  : 1.187 
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: 0.8000 (OUTLIER) cc_final: 0.6670 (t80)
REVERT: P  288 MET cc_start: 0.5452 (ttt) cc_final: 0.5246 (ttt)
REVERT: P  771 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.7946 (tt0)
REVERT: P  875 MET cc_start: 0.8454 (tpt) cc_final: 0.7964 (tpt)
REVERT: P  963 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8127 (t80)
REVERT: P  991 ARG cc_start: 0.8093 (mtm-85) cc_final: 0.7765 (mtm110)
  outliers start: 18
  outliers final: 11
  residues processed: 116
  average time/residue: 0.4761
  time to fit residues: 74.9167
Evaluate side-chains
  109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 95
  time to evaluate  : 1.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  207 GLN
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  517 THR
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  940 TYR
Chi-restraints excluded: chain P residue  963 PHE
Chi-restraints excluded: chain P residue 1095 LEU
Chi-restraints excluded: chain P residue 1096 VAL
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:    1.9990
   chunk 5 optimal weight:    0.0770
   chunk 75 optimal weight:    1.9990
   chunk 90 optimal weight:    0.1980
   chunk 76 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 36 optimal weight:    3.9990
   chunk 7 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9990
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8542

-------------------------------------------------------------------------------
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 = 0.4273 r_free = 0.4273 target = 0.200356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.158404 restraints weight = 32408.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.158069 restraints weight = 34820.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.161209 restraints weight = 24779.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7223
moved from start:          0.3798

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   8170  Z= 0.130
  Angle     :  0.833  30.195  11117  Z= 0.344
  Chirality :  0.039   0.135   1317
  Planarity :  0.004   0.056   1397
  Dihedral  :  4.141  58.670   1128
  Min Nonbonded Distance : 1.855

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.12 %
    Favored  : 94.78 %
  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: -0.56 (0.27), residues: 1015
  helix:  1.66 (0.27), residues: 420
  sheet: -1.16 (0.58), residues: 77
  loop : -2.10 (0.25), residues: 518

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P  55 
 HIS   0.005   0.001   HIS P 413 
 PHE   0.014   0.001   PHE P1081 
 TYR   0.026   0.001   TYR P 871 
 ARG   0.004   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04266 (  302)
  hydrogen bonds       : angle       4.07843 (  891)
  covalent geometry    : bond        0.00317 ( 8170)
  covalent geometry    : angle       0.83262 (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
  109 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 1.312 
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: 0.7874 (OUTLIER) cc_final: 0.6744 (t80)
REVERT: P  288 MET cc_start: 0.5520 (ttt) cc_final: 0.5274 (ttt)
REVERT: P  771 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7831 (tt0)
REVERT: P  871 TYR cc_start: 0.7824 (OUTLIER) cc_final: 0.6037 (t80)
REVERT: P  875 MET cc_start: 0.8537 (tpt) cc_final: 0.8044 (tpt)
REVERT: P  963 PHE cc_start: 0.8790 (OUTLIER) cc_final: 0.8190 (t80)
REVERT: P  981 THR cc_start: 0.8159 (OUTLIER) cc_final: 0.7924 (m)
REVERT: P  991 ARG cc_start: 0.8002 (mtm-85) cc_final: 0.7707 (mtm110)
  outliers start: 18
  outliers final: 10
  residues processed: 104
  average time/residue: 0.4404
  time to fit residues: 63.8672
Evaluate side-chains
  100 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 85
  time to evaluate  : 1.128 
-------------------------------------------------------------------------------
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  346 THR
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  963 PHE
Chi-restraints excluded: chain P residue  981 THR
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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 89 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9990
   chunk 102 optimal weight:    0.9980
   chunk 42 optimal weight:    0.0060
   chunk 38 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9980
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 15 optimal weight:    0.3980
   chunk 62 optimal weight:    0.9990
   overall best weight:    0.6796

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

Flipped N/Q/H residues before XYZ refinement:
** P 207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4257 r_free = 0.4257 target = 0.198600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.155527 restraints weight = 32239.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.154903 restraints weight = 33103.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.158204 restraints weight = 23934.290|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7287
moved from start:          0.4158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8170  Z= 0.114
  Angle     :  0.812  29.838  11117  Z= 0.329
  Chirality :  0.038   0.130   1317
  Planarity :  0.004   0.074   1397
  Dihedral  :  4.057  59.741   1128
  Min Nonbonded Distance : 1.890

Molprobity Statistics.
  All-atom Clashscore : 2.64
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.90 %
    Favored  : 93.00 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.01 %
    Favored  : 80.73 %
  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: -0.40 (0.27), residues: 1015
  helix:  1.79 (0.28), residues: 423
  sheet: -1.05 (0.59), residues: 77
  loop : -2.04 (0.25), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 251 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.014   0.001   PHE P1081 
 TYR   0.021   0.001   TYR P 871 
 ARG   0.009   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03857 (  302)
  hydrogen bonds       : angle       3.94019 (  891)
  covalent geometry    : bond        0.00280 ( 8170)
  covalent geometry    : angle       0.81241 (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
  108 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.091 
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  240 TYR cc_start: 0.7944 (OUTLIER) cc_final: 0.6746 (t80)
REVERT: P  288 MET cc_start: 0.5678 (ttt) cc_final: 0.5397 (ttt)
REVERT: P  771 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.7804 (tt0)
REVERT: P  875 MET cc_start: 0.8533 (tpt) cc_final: 0.7999 (tpt)
REVERT: P  963 PHE cc_start: 0.8856 (OUTLIER) cc_final: 0.8256 (t80)
REVERT: P  967 ASP cc_start: 0.7406 (m-30) cc_final: 0.7118 (m-30)
REVERT: P  991 ARG cc_start: 0.8025 (mtm-85) cc_final: 0.7760 (mtm-85)
  outliers start: 20
  outliers final: 11
  residues processed: 103
  average time/residue: 0.4072
  time to fit residues: 58.5713
Evaluate side-chains
  97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 1.634 
-------------------------------------------------------------------------------
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  355 THR
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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0980
   chunk 39 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9990
   chunk 12 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 71 optimal weight:    0.9990
   chunk 73 optimal weight:    0.5980
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.4245 r_free = 0.4245 target = 0.197331 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.154504 restraints weight = 32172.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.154509 restraints weight = 34804.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.158165 restraints weight = 23208.555|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7273
moved from start:          0.4423

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= 0.107
  Angle     :  0.814  29.830  11117  Z= 0.329
  Chirality :  0.038   0.133   1317
  Planarity :  0.004   0.061   1397
  Dihedral  :  3.982  59.388   1128
  Min Nonbonded Distance : 1.897

Molprobity Statistics.
  All-atom Clashscore : 2.89
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.32 %
    Favored  : 94.58 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 18.03 %
    Favored  : 80.16 %
  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: -0.29 (0.28), residues: 1015
  helix:  1.86 (0.28), residues: 423
  sheet: -0.91 (0.60), residues: 77
  loop : -1.98 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP P  55 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.010   0.001   PHE P1081 
 TYR   0.019   0.001   TYR P 871 
 ARG   0.006   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03778 (  302)
  hydrogen bonds       : angle       3.88720 (  891)
  covalent geometry    : bond        0.00263 ( 8170)
  covalent geometry    : angle       0.81423 (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: 16
    poor density    : 88
  time to evaluate  : 1.521 
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: 0.7950 (OUTLIER) cc_final: 0.6815 (t80)
REVERT: P  771 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.7734 (tt0)
REVERT: P  871 TYR cc_start: 0.7960 (OUTLIER) cc_final: 0.6191 (t80)
REVERT: P  875 MET cc_start: 0.8570 (tpt) cc_final: 0.8118 (tpt)
REVERT: P  963 PHE cc_start: 0.8850 (OUTLIER) cc_final: 0.8296 (t80)
REVERT: P  991 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7805 (mtm-85)
  outliers start: 16
  outliers final: 9
  residues processed: 99
  average time/residue: 0.5342
  time to fit residues: 74.9070
Evaluate side-chains
  97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 84
  time to evaluate  : 1.617 
-------------------------------------------------------------------------------
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  355 THR
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 45 optimal weight:    0.3980
   chunk 6 optimal weight:    0.6980
   chunk 84 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 82 optimal weight:    0.5980
   chunk 42 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 79 optimal weight:    0.9990
   chunk 91 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.7182

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4231 r_free = 0.4231 target = 0.195688 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.154283 restraints weight = 32067.789|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.153934 restraints weight = 36525.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.156723 restraints weight = 25717.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7300
moved from start:          0.4638

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8170  Z= 0.116
  Angle     :  0.814  29.805  11117  Z= 0.329
  Chirality :  0.038   0.131   1317
  Planarity :  0.004   0.078   1397
  Dihedral  :  4.078  58.989   1128
  Min Nonbonded Distance : 1.873

Molprobity Statistics.
  All-atom Clashscore : 3.01
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.50 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 18.03 %
    Favored  : 80.27 %
  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: 423
  sheet: -0.87 (0.61), residues: 77
  loop : -1.99 (0.26), residues: 515

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP P 251 
 HIS   0.006   0.001   HIS P 413 
 PHE   0.013   0.001   PHE P 400 
 TYR   0.021   0.001   TYR P 871 
 ARG   0.006   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  302)
  hydrogen bonds       : angle       3.86605 (  891)
  covalent geometry    : bond        0.00286 ( 8170)
  covalent geometry    : angle       0.81444 (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: 15
    poor density    : 84
  time to evaluate  : 1.275 
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  771 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.7741 (tt0)
REVERT: P  875 MET cc_start: 0.8555 (tpt) cc_final: 0.8045 (tpt)
REVERT: P  963 PHE cc_start: 0.8898 (OUTLIER) cc_final: 0.8347 (t80)
REVERT: P  981 THR cc_start: 0.8250 (OUTLIER) cc_final: 0.8027 (m)
  outliers start: 15
  outliers final: 11
  residues processed: 96
  average time/residue: 0.5657
  time to fit residues: 75.7814
Evaluate side-chains
  97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 1.690 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  107 VAL
Chi-restraints excluded: chain P residue  346 THR
Chi-restraints excluded: chain P residue  355 THR
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  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  981 THR
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:    1.9990
   chunk 91 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9990
   chunk 88 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9980
   chunk 79 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0870
   chunk 70 optimal weight:    0.3980
   chunk 3 optimal weight:    0.1980
   chunk 50 optimal weight:    2.9990
   overall best weight:    0.5158

-------------------------------------------------------------------------------
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 = 0.4235 r_free = 0.4235 target = 0.196622 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.152867 restraints weight = 32413.483|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.151651 restraints weight = 37087.144|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.155321 restraints weight = 26363.557|
|-----------------------------------------------------------------------------|
r_work (final): 0.3800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.4839

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     :  0.809  30.075  11117  Z= 0.325
  Chirality :  0.038   0.132   1317
  Planarity :  0.004   0.072   1397
  Dihedral  :  3.974  59.042   1128
  Min Nonbonded Distance : 1.942

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  5.22 %
    Favored  : 94.68 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 18.59 %
    Favored  : 79.82 %
  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: -0.16 (0.28), residues: 1015
  helix:  2.06 (0.28), residues: 423
  sheet: -0.82 (0.60), residues: 79
  loop : -1.99 (0.26), residues: 513

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   0.009   0.001   PHE P1081 
 TYR   0.018   0.001   TYR P 871 
 ARG   0.007   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03508 (  302)
  hydrogen bonds       : angle       3.77641 (  891)
  covalent geometry    : bond        0.00243 ( 8170)
  covalent geometry    : angle       0.80893 (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
  97 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 1.132 
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: symmetry clash
REVERT: P  240 TYR cc_start: 0.7989 (OUTLIER) cc_final: 0.6728 (t80)
REVERT: P  771 GLU cc_start: 0.8511 (OUTLIER) cc_final: 0.7729 (tt0)
REVERT: P  875 MET cc_start: 0.8517 (tpt) cc_final: 0.8061 (tpt)
REVERT: P  963 PHE cc_start: 0.8864 (OUTLIER) cc_final: 0.8293 (t80)
  outliers start: 14
  outliers final: 11
  residues processed: 93
  average time/residue: 0.4496
  time to fit residues: 59.3703
Evaluate side-chains
  94 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 1.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  107 VAL
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  241 TYR
Chi-restraints excluded: chain P residue  355 THR
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 103
   random chunks:
   chunk 99 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    0.9990
   chunk 83 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 57 optimal weight:    0.0980
   chunk 37 optimal weight:    2.9990
   chunk 9 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9980
   chunk 80 optimal weight:    1.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4200 r_free = 0.4200 target = 0.192406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.150311 restraints weight = 32025.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.149146 restraints weight = 39017.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.152364 restraints weight = 27682.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.5148

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8170  Z= 0.119
  Angle     :  0.821  29.850  11117  Z= 0.335
  Chirality :  0.038   0.131   1317
  Planarity :  0.004   0.079   1397
  Dihedral  :  4.180  58.108   1128
  Min Nonbonded Distance : 1.882

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.70 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 18.48 %
    Favored  : 79.82 %
  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: -0.19 (0.28), residues: 1015
  helix:  1.96 (0.27), residues: 423
  sheet: -0.67 (0.55), residues: 90
  loop : -2.00 (0.26), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP P 251 
 HIS   0.007   0.001   HIS P 413 
 PHE   0.014   0.001   PHE P1081 
 TYR   0.024   0.001   TYR P 871 
 ARG   0.005   0.000   ARG P 286 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03864 (  302)
  hydrogen bonds       : angle       3.84705 (  891)
  covalent geometry    : bond        0.00294 ( 8170)
  covalent geometry    : angle       0.82110 (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
  102 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 1.114 
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: symmetry clash
REVERT: P  240 TYR cc_start: 0.8037 (OUTLIER) cc_final: 0.6677 (t80)
REVERT: P  771 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.7717 (tt0)
REVERT: P  875 MET cc_start: 0.8528 (tpt) cc_final: 0.8056 (tpt)
REVERT: P  963 PHE cc_start: 0.8878 (OUTLIER) cc_final: 0.8317 (t80)
REVERT: P  981 THR cc_start: 0.8356 (OUTLIER) cc_final: 0.8147 (m)
  outliers start: 15
  outliers final: 10
  residues processed: 99
  average time/residue: 0.4334
  time to fit residues: 58.9875
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  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain P residue  107 VAL
Chi-restraints excluded: chain P residue  233 VAL
Chi-restraints excluded: chain P residue  240 TYR
Chi-restraints excluded: chain P residue  241 TYR
Chi-restraints excluded: chain P residue  346 THR
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  871 TYR
Chi-restraints excluded: chain P residue  940 TYR
Chi-restraints excluded: chain P residue  963 PHE
Chi-restraints excluded: chain P residue  981 THR
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:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 90 optimal weight:    0.2980
   chunk 84 optimal weight:    0.7980
   chunk 5 optimal weight:    0.9980
   chunk 0 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   chunk 87 optimal weight:    0.6980
   chunk 50 optimal weight:   10.0000
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.4218 r_free = 0.4218 target = 0.194642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.150617 restraints weight = 32155.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.148918 restraints weight = 35249.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.152682 restraints weight = 25067.344|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7459
moved from start:          0.5359

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   8170  Z= 0.114
  Angle     :  0.819  29.959  11117  Z= 0.333
  Chirality :  0.038   0.130   1317
  Planarity :  0.005   0.073   1397
  Dihedral  :  4.180  58.181   1128
  Min Nonbonded Distance : 1.891

Molprobity Statistics.
  All-atom Clashscore : 3.93
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  6.50 %
    Favored  : 93.40 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 18.71 %
    Favored  : 79.59 %
  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: -0.19 (0.28), residues: 1015
  helix:  1.94 (0.27), residues: 426
  sheet: -0.65 (0.58), residues: 85
  loop : -1.99 (0.26), residues: 504

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   0.010   0.001   PHE P1081 
 TYR   0.023   0.001   TYR P 871 
 ARG   0.010   0.000   ARG P 397 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03805 (  302)
  hydrogen bonds       : angle       3.83384 (  891)
  covalent geometry    : bond        0.00280 ( 8170)
  covalent geometry    : angle       0.81946 (11117)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5273.82 seconds
wall clock time: 93 minutes 13.62 seconds (5593.62 seconds total)