Starting phenix.real_space_refine
on Fri Jul 25 16:57:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbr_61323/07_2025/9jbr_61323.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbr_61323/07_2025/9jbr_61323.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbr_61323/07_2025/9jbr_61323.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbr_61323/07_2025/9jbr_61323.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbr_61323/07_2025/9jbr_61323.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbr_61323/07_2025/9jbr_61323.cif"
  }
  resolution = 3.4
  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=   0.003 sd=   0.037
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: 4
    Type Number    sf(0)   Gaussians
     S      47      5.16       5
     C    5101      2.51       5
     N    1326      2.21       5
     O    1425      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 7899
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1009, 7899
          Classifications: {'peptide': 1009}
          Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 955}
          Chain breaks: 1
  Time building chain proxies: 5.01, per 1000 atoms: 0.63
  Number of scatterers: 7899
  At special positions: 0
  Unit cell: (74.048, 93.184, 144.768, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      47     16.00
     O    1425      8.00
     N    1326      7.00
     C    5101      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.20
  Conformation dependent library (CDL) restraints added in 984.2 milliseconds
  

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1908

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 7 sheets defined
      50.9% alpha, 12.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.95
  Creating SS restraints...
    Processing helix  chain 'A' and resid 118 through 120
      No H-bonds generated for 'chain 'A' and resid 118 through 120'
    Processing helix  chain 'A' and resid 121 through 130
      removed outlier: 4.494A  pdb=" N   HIS A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   CYS A 126 " --> pdb=" O   VAL A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 198
      removed outlier: 3.892A  pdb=" N   GLY A 197 " --> pdb=" O   PHE A 194 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 206
      removed outlier: 4.264A  pdb=" N   TYR A 203 " --> pdb=" O   ALA A 199 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   GLN A 204 " --> pdb=" O   PHE A 200 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   SER A 205 " --> pdb=" O   SER A 201 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 223
      removed outlier: 3.548A  pdb=" N   GLY A 223 " --> pdb=" O   GLU A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 243
      removed outlier: 3.754A  pdb=" N   THR A 243 " --> pdb=" O   LYS A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 260
    Processing helix  chain 'A' and resid 262 through 286
    Processing helix  chain 'A' and resid 286 through 294
      removed outlier: 4.289A  pdb=" N   GLU A 290 " --> pdb=" O   ARG A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 374 through 382
      removed outlier: 6.425A  pdb=" N   ARG A 380 " --> pdb=" O   GLN A 376 " (cutoff:3.500A)
      removed outlier: 6.206A  pdb=" N   LEU A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   HIS A 382 " --> pdb=" O   ASP A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 420
    Processing helix  chain 'A' and resid 421 through 432
    Processing helix  chain 'A' and resid 441 through 468
      removed outlier: 3.860A  pdb=" N   PHE A 454 " --> pdb=" O   PHE A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 489
      removed outlier: 3.646A  pdb=" N   LEU A 477 " --> pdb=" O   ASN A 473 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   VAL A 489 " --> pdb=" O   LEU A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 511
      removed outlier: 3.761A  pdb=" N   GLU A 496 " --> pdb=" O   GLU A 492 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   LEU A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   SER A 498 " --> pdb=" O   PRO A 494 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   LYS A 510 " --> pdb=" O   ILE A 506 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   LEU A 511 " --> pdb=" O   ALA A 507 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 517 through 519
      No H-bonds generated for 'chain 'A' and resid 517 through 519'
    Processing helix  chain 'A' and resid 520 through 525
      removed outlier: 3.766A  pdb=" N   GLY A 525 " --> pdb=" O   ILE A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 574
    Processing helix  chain 'A' and resid 588 through 599
      removed outlier: 3.687A  pdb=" N   MET A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 656 through 661
    Processing helix  chain 'A' and resid 670 through 681
      removed outlier: 4.032A  pdb=" N   GLU A 681 " --> pdb=" O   GLU A 677 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 698 through 704
      removed outlier: 3.715A  pdb=" N   ARG A 702 " --> pdb=" O   HIS A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 705 through 709
    Processing helix  chain 'A' and resid 727 through 738
      removed outlier: 4.212A  pdb=" N   ALA A 731 " --> pdb=" O   ALA A 727 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 750 through 761
    Processing helix  chain 'A' and resid 800 through 807
    Processing helix  chain 'A' and resid 813 through 823
    Processing helix  chain 'A' and resid 823 through 831
      removed outlier: 3.857A  pdb=" N   LEU A 827 " --> pdb=" O   ASP A 823 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 832 through 834
      No H-bonds generated for 'chain 'A' and resid 832 through 834'
    Processing helix  chain 'A' and resid 841 through 855
      removed outlier: 3.527A  pdb=" N   LEU A 855 " --> pdb=" O   SER A 851 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 865 through 873
      removed outlier: 4.397A  pdb=" N   GLY A 870 " --> pdb=" O   THR A 866 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   ALA A 871 " --> pdb=" O   ASN A 867 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS A 873 " --> pdb=" O   VAL A 869 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 968 through 1008
    Processing helix  chain 'A' and resid 1013 through 1033
      removed outlier: 3.692A  pdb=" N   ARG A1033 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1051 through 1079
      removed outlier: 3.755A  pdb=" N   ILE A1055 " --> pdb=" O   ASN A1051 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   SER A1068 " --> pdb=" O   VAL A1064 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1097 through 1118
    Processing helix  chain 'A' and resid 1127 through 1130
    Processing helix  chain 'A' and resid 1131 through 1151
    Processing helix  chain 'A' and resid 1153 through 1161
      removed outlier: 3.564A  pdb=" N   ASN A1157 " --> pdb=" O   SER A1153 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1166 through 1195
      removed outlier: 3.867A  pdb=" N   VAL A1172 " --> pdb=" O   GLU A1168 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 142 through 143
      removed outlier: 3.677A  pdb=" N   VAL A 142 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   VAL A 156 " --> pdb=" O   VAL A 142 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161
      removed outlier: 4.361A  pdb=" N   SER A 171 " --> pdb=" O   HIS A 159 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ASN A 161 " --> pdb=" O   VAL A 169 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   VAL A 169 " --> pdb=" O   ASN A 161 " (cutoff:3.500A)
      removed outlier: 4.748A  pdb=" N   LEU A 170 " --> pdb=" O   TYR A 181 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 308 through 313
      removed outlier: 5.509A  pdb=" N   GLN A 302 " --> pdb=" O   SER A 324 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ILE A 322 " --> pdb=" O   TYR A 304 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 359 through 361
      removed outlier: 3.525A  pdb=" N   GLN A 392 " --> pdb=" O   ILE A 346 " (cutoff:3.500A)
      removed outlier: 6.899A  pdb=" N   ASP A 348 " --> pdb=" O   VAL A 390 " (cutoff:3.500A)
      removed outlier: 5.625A  pdb=" N   VAL A 390 " --> pdb=" O   ASP A 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 513 through 515
      removed outlier: 5.930A  pdb=" N   THR A 859 " --> pdb=" O   VAL A 877 " (cutoff:3.500A)
      removed outlier: 7.605A  pdb=" N   VAL A 879 " --> pdb=" O   THR A 859 " (cutoff:3.500A)
      removed outlier: 6.280A  pdb=" N   MET A 861 " --> pdb=" O   VAL A 879 " (cutoff:3.500A)
      removed outlier: 7.773A  pdb=" N   LEU A 881 " --> pdb=" O   MET A 861 " (cutoff:3.500A)
      removed outlier: 7.154A  pdb=" N   GLY A 863 " --> pdb=" O   LEU A 881 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   CYS A 530 " --> pdb=" O   VAL A 744 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ILE A 746 " --> pdb=" O   CYS A 530 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   PHE A 532 " --> pdb=" O   ILE A 746 " (cutoff:3.500A)
      removed outlier: 8.529A  pdb=" N   PHE A 837 " --> pdb=" O   VAL A 743 " (cutoff:3.500A)
      removed outlier: 6.604A  pdb=" N   MET A 745 " --> pdb=" O   PHE A 837 " (cutoff:3.500A)
      removed outlier: 6.881A  pdb=" N   LEU A 809 " --> pdb=" O   VAL A 836 " (cutoff:3.500A)
      removed outlier: 7.872A  pdb=" N   ALA A 838 " --> pdb=" O   LEU A 809 " (cutoff:3.500A)
      removed outlier: 6.326A  pdb=" N   LEU A 811 " --> pdb=" O   ALA A 838 " (cutoff:3.500A)
      removed outlier: 4.189A  pdb=" N   THR A 812 " --> pdb=" O   LEU A 772 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLN A 773 " --> pdb=" O   GLU A 783 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   GLU A 783 " --> pdb=" O   GLN A 773 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 544 through 549
      removed outlier: 5.699A  pdb=" N   VAL A 545 " --> pdb=" O   SER A 722 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   SER A 722 " --> pdb=" O   VAL A 545 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLY A 547 " --> pdb=" O   VAL A 720 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG A 684 " --> pdb=" O   VAL A 721 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   SER A 634 " --> pdb=" O   ARG A 623 " (cutoff:3.500A)
      removed outlier: 5.461A  pdb=" N   ARG A 623 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   LEU A 636 " --> pdb=" O   HIS A 621 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU A 618 " --> pdb=" O   VAL A 608 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   VAL A 608 " --> pdb=" O   LEU A 618 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 664 through 666

    399 hydrogen bonds defined for protein.
    1152 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: 2.64

  Time building geometry restraints manager: 2.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2516
        1.34 -     1.46: 1437
        1.46 -     1.58: 4054
        1.58 -     1.69: 0
        1.69 -     1.81: 69
  Bond restraints: 8076
  Sorted by residual:
  bond pdb=" CB  MET A1110 "
       pdb=" CG  MET A1110 "
    ideal  model  delta    sigma   weight residual
    1.520  1.462  0.058 3.00e-02 1.11e+03 3.71e+00
  bond pdb=" CG1 ILE A 620 "
       pdb=" CD1 ILE A 620 "
    ideal  model  delta    sigma   weight residual
    1.513  1.451  0.062 3.90e-02 6.57e+02 2.56e+00
  bond pdb=" CG  MET A 513 "
       pdb=" SD  MET A 513 "
    ideal  model  delta    sigma   weight residual
    1.803  1.765  0.038 2.50e-02 1.60e+03 2.30e+00
  bond pdb=" CB  MET A1112 "
       pdb=" CG  MET A1112 "
    ideal  model  delta    sigma   weight residual
    1.520  1.475  0.045 3.00e-02 1.11e+03 2.21e+00
  bond pdb=" CG  LEU A 451 "
       pdb=" CD2 LEU A 451 "
    ideal  model  delta    sigma   weight residual
    1.521  1.474  0.047 3.30e-02 9.18e+02 2.06e+00
  ... (remaining 8071 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.70: 10547
        1.70 -     3.40: 347
        3.40 -     5.10: 47
        5.10 -     6.80: 12
        6.80 -     8.50: 5
  Bond angle restraints: 10958
  Sorted by residual:
  angle pdb=" N   VAL A 489 "
        pdb=" CA  VAL A 489 "
        pdb=" C   VAL A 489 "
      ideal   model   delta    sigma   weight residual
     108.88  116.92   -8.04 2.16e+00 2.14e-01 1.38e+01
  angle pdb=" C   ILE A 831 "
        pdb=" CA  ILE A 831 "
        pdb=" CB  ILE A 831 "
      ideal   model   delta    sigma   weight residual
     114.35  110.81    3.54 1.06e+00 8.90e-01 1.12e+01
  angle pdb=" N   PRO A 490 "
        pdb=" CA  PRO A 490 "
        pdb=" C   PRO A 490 "
      ideal   model   delta    sigma   weight residual
     110.70  114.50   -3.80 1.22e+00 6.72e-01 9.69e+00
  angle pdb=" C   VAL A 877 "
        pdb=" N   GLY A 878 "
        pdb=" CA  GLY A 878 "
      ideal   model   delta    sigma   weight residual
     121.65  119.94    1.71 6.80e-01 2.16e+00 6.30e+00
  angle pdb=" C   GLU A 692 "
        pdb=" N   LEU A 693 "
        pdb=" CA  LEU A 693 "
      ideal   model   delta    sigma   weight residual
     121.54  126.22   -4.68 1.91e+00 2.74e-01 6.01e+00
  ... (remaining 10953 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.25: 4418
       16.25 -    32.50: 361
       32.50 -    48.74: 85
       48.74 -    64.99: 10
       64.99 -    81.24: 4
  Dihedral angle restraints: 4878
    sinusoidal: 1935
      harmonic: 2943
  Sorted by residual:
  dihedral pdb=" CA  PRO A 490 "
           pdb=" C   PRO A 490 "
           pdb=" N   PRO A 491 "
           pdb=" CA  PRO A 491 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.63  -31.37     0      5.00e+00 4.00e-02 3.94e+01
  dihedral pdb=" CA  ILE A 495 "
           pdb=" C   ILE A 495 "
           pdb=" N   GLU A 496 "
           pdb=" CA  GLU A 496 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.98  -23.02     0      5.00e+00 4.00e-02 2.12e+01
  dihedral pdb=" CA  VAL A 488 "
           pdb=" C   VAL A 488 "
           pdb=" N   VAL A 489 "
           pdb=" CA  VAL A 489 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.67  -21.33     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 4875 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 828
       0.040 -    0.081: 314
       0.081 -    0.121: 99
       0.121 -    0.161: 28
       0.161 -    0.201: 3
  Chirality restraints: 1272
  Sorted by residual:
  chirality pdb=" CG  LEU A 333 "
            pdb=" CB  LEU A 333 "
            pdb=" CD1 LEU A 333 "
            pdb=" CD2 LEU A 333 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 1.01e+00
  chirality pdb=" CB  ILE A 956 "
            pdb=" CA  ILE A 956 "
            pdb=" CG1 ILE A 956 "
            pdb=" CG2 ILE A 956 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.31e-01
  chirality pdb=" CA  THR A1114 "
            pdb=" N   THR A1114 "
            pdb=" C   THR A1114 "
            pdb=" CB  THR A1114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 6.96e-01
  ... (remaining 1269 not shown)

  Planarity restraints: 1389
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 490 "   -0.060 5.00e-02 4.00e+02   9.21e-02 1.36e+01
        pdb=" N   PRO A 491 "    0.159 5.00e-02 4.00e+02
        pdb=" CA  PRO A 491 "   -0.049 5.00e-02 4.00e+02
        pdb=" CD  PRO A 491 "   -0.051 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 131 "    0.036 5.00e-02 4.00e+02   5.48e-02 4.81e+00
        pdb=" N   PRO A 132 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 132 "    0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 132 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 517 "    0.028 5.00e-02 4.00e+02   4.21e-02 2.83e+00
        pdb=" N   PRO A 518 "   -0.073 5.00e-02 4.00e+02
        pdb=" CA  PRO A 518 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 518 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1386 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.68: 135
        2.68 -     3.23: 7968
        3.23 -     3.79: 12200
        3.79 -     4.34: 15203
        4.34 -     4.90: 25237
  Nonbonded interactions: 60743
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 299 "
            pdb=" OG  SER A 314 "
     model   vdw
     2.120 3.040
  nonbonded pdb=" OG  SER A1153 "
            pdb=" OD1 ASP A1155 "
     model   vdw
     2.182 3.040
  nonbonded pdb=" OG1 THR A 697 "
            pdb=" NE2 GLN A 700 "
     model   vdw
     2.190 3.120
  nonbonded pdb=" NH2 ARG A 680 "
            pdb=" OD1 ASP A 788 "
     model   vdw
     2.191 3.120
  nonbonded pdb=" NZ  LYS A 845 "
            pdb=" OD1 ASP A 868 "
     model   vdw
     2.223 3.120
  ... (remaining 60738 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.830
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.350
  Check model and map are aligned:         0.050
  Set scattering table:                    0.080
  Process input model:                     21.780
  Find NCS groups from input model:        0.070
  Set up NCS constraints:                  0.030
  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:2.830
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6372
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      :  0.006   0.062   8076  Z= 0.274
  Angle     :  0.729   8.505  10958  Z= 0.383
  Chirality :  0.048   0.201   1272
  Planarity :  0.005   0.092   1389
  Dihedral  : 12.730  81.238   2970
  Min Nonbonded Distance : 2.120

Molprobity Statistics.
  All-atom Clashscore : 15.73
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.98 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.34 %
    Favored  : 99.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.07 (0.25), residues: 1005
  helix:  0.42 (0.23), residues: 446
  sheet: -0.19 (0.54), residues: 103
  loop : -0.11 (0.28), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 600 
 HIS   0.009   0.002   HIS A 874 
 PHE   0.020   0.002   PHE A 664 
 TYR   0.018   0.002   TYR A1071 
 ARG   0.010   0.001   ARG A 216 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.16172 (  399)
  hydrogen bonds       : angle       6.96589 ( 1152)
  covalent geometry    : bond        0.00606 ( 8076)
  covalent geometry    : angle       0.72912 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 GLU cc_start: 0.8339 (tt0) cc_final: 0.8071 (tt0)
REVERT: A  339 LEU cc_start: 0.8284 (tp) cc_final: 0.8037 (tp)
REVERT: A  425 LYS cc_start: 0.7542 (ttmm) cc_final: 0.7268 (ttmm)
REVERT: A  750 ASN cc_start: 0.7759 (t0) cc_final: 0.7520 (t0)
REVERT: A 1056 LEU cc_start: 0.7814 (tp) cc_final: 0.7476 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.2047
  time to fit residues: 46.8567
Evaluate side-chains
  155 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 84 optimal weight:    2.9990
   chunk 75 optimal weight:    3.9990
   chunk 42 optimal weight:    1.9990
   chunk 25 optimal weight:    5.9990
   chunk 51 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9980
   chunk 58 optimal weight:    0.7980
   chunk 90 optimal weight:    0.1980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A1061 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.177716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.153356 restraints weight = 11731.050|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 3.19
r_work: 0.3938 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6693
moved from start:          0.1224

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8076  Z= 0.145
  Angle     :  0.618   8.095  10958  Z= 0.315
  Chirality :  0.044   0.164   1272
  Planarity :  0.005   0.098   1389
  Dihedral  :  4.584  31.195   1079
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 10.47
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.59 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.28 %
    Favored  : 89.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    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:  0.51 (0.25), residues: 1005
  helix:  1.02 (0.24), residues: 438
  sheet: -0.28 (0.51), residues: 104
  loop : -0.04 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 257 
 HIS   0.005   0.001   HIS A1065 
 PHE   0.020   0.001   PHE A 664 
 TYR   0.015   0.001   TYR A 413 
 ARG   0.008   0.001   ARG A 310 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04809 (  399)
  hydrogen bonds       : angle       5.32690 ( 1152)
  covalent geometry    : bond        0.00318 ( 8076)
  covalent geometry    : angle       0.61769 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 161
  time to evaluate  : 0.875 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  158 LEU cc_start: 0.8132 (mt) cc_final: 0.7929 (mt)
REVERT: A  214 GLU cc_start: 0.7447 (pm20) cc_final: 0.7027 (pm20)
REVERT: A  219 GLU cc_start: 0.8377 (tt0) cc_final: 0.7037 (mt-10)
REVERT: A  237 LEU cc_start: 0.8814 (OUTLIER) cc_final: 0.8598 (tt)
REVERT: A  425 LYS cc_start: 0.7579 (ttmm) cc_final: 0.7364 (ttmm)
REVERT: A  511 LEU cc_start: 0.6980 (mp) cc_final: 0.6645 (mt)
REVERT: A 1056 LEU cc_start: 0.7787 (tp) cc_final: 0.7540 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 163
  average time/residue: 0.2119
  time to fit residues: 46.3116
Evaluate side-chains
  166 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 159
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1069 LEU
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 98 optimal weight:    0.3980
   chunk 7 optimal weight:    0.0020
   chunk 1 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 66 optimal weight:    0.3980
   chunk 50 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    0.5590

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 579 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4375 r_free = 0.4375 target = 0.179333 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.154897 restraints weight = 11996.061|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 3.26
r_work: 0.3943 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3943
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6667
moved from start:          0.1620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8076  Z= 0.121
  Angle     :  0.570   7.087  10958  Z= 0.286
  Chirality :  0.042   0.153   1272
  Planarity :  0.005   0.098   1389
  Dihedral  :  4.275  28.806   1079
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.39 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 12.83 %
    Favored  : 85.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 1005
  helix:  1.35 (0.24), residues: 440
  sheet: -0.52 (0.52), residues: 98
  loop :  0.03 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 784 
 HIS   0.006   0.001   HIS A1065 
 PHE   0.025   0.001   PHE A 249 
 TYR   0.012   0.001   TYR A 690 
 ARG   0.003   0.000   ARG A 632 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04164 (  399)
  hydrogen bonds       : angle       4.86538 ( 1152)
  covalent geometry    : bond        0.00269 ( 8076)
  covalent geometry    : angle       0.57015 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.784 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7391 (pm20) cc_final: 0.7099 (pm20)
REVERT: A  219 GLU cc_start: 0.8351 (tt0) cc_final: 0.7067 (mt-10)
REVERT: A  237 LEU cc_start: 0.8744 (mt) cc_final: 0.8515 (tt)
REVERT: A  416 ARG cc_start: 0.7442 (mtm-85) cc_final: 0.7197 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7546 (ttmm) cc_final: 0.7335 (ttmm)
REVERT: A  480 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6780 (mm-30)
REVERT: A  653 VAL cc_start: 0.7968 (OUTLIER) cc_final: 0.7588 (p)
REVERT: A  987 MET cc_start: 0.6908 (tpp) cc_final: 0.6656 (mpp)
  outliers start: 13
  outliers final: 6
  residues processed: 175
  average time/residue: 0.2175
  time to fit residues: 50.9502
Evaluate side-chains
  169 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 162
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 13 optimal weight:    0.9980
   chunk 14 optimal weight:    2.9990
   chunk 10 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 58 optimal weight:    0.9980
   chunk 1 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** A 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.178186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.153841 restraints weight = 11817.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 3.18
r_work: 0.3933 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6699
moved from start:          0.1739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8076  Z= 0.148
  Angle     :  0.580   7.640  10958  Z= 0.290
  Chirality :  0.043   0.149   1272
  Planarity :  0.005   0.097   1389
  Dihedral  :  4.277  29.674   1079
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.99 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 14.55 %
    Favored  : 83.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.77 (0.26), residues: 1005
  helix:  1.33 (0.24), residues: 440
  sheet: -0.54 (0.53), residues: 98
  loop :  0.07 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A 874 
 PHE   0.024   0.001   PHE A 249 
 TYR   0.015   0.001   TYR A 807 
 ARG   0.003   0.000   ARG A 632 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04236 (  399)
  hydrogen bonds       : angle       4.71480 ( 1152)
  covalent geometry    : bond        0.00336 ( 8076)
  covalent geometry    : angle       0.57984 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 168
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7385 (pm20) cc_final: 0.6723 (pm20)
REVERT: A  219 GLU cc_start: 0.8366 (tt0) cc_final: 0.6985 (mt-10)
REVERT: A  237 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8516 (tt)
REVERT: A  336 CYS cc_start: 0.8194 (p) cc_final: 0.7994 (p)
REVERT: A  416 ARG cc_start: 0.7490 (mtm-85) cc_final: 0.7221 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7599 (ttmm) cc_final: 0.7379 (ttmm)
REVERT: A  480 GLU cc_start: 0.6924 (mm-30) cc_final: 0.6710 (mm-30)
REVERT: A  511 LEU cc_start: 0.6945 (mp) cc_final: 0.6598 (mt)
REVERT: A  653 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7645 (p)
REVERT: A  740 SER cc_start: 0.8062 (t) cc_final: 0.7796 (t)
  outliers start: 19
  outliers final: 9
  residues processed: 178
  average time/residue: 0.2027
  time to fit residues: 48.6817
Evaluate side-chains
  177 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 166
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  488 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 90 optimal weight:    0.7980
   chunk 81 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0030
   chunk 91 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 63 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 359 GLN
A 533 ASN
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 625 HIS
A 986 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.178716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.154209 restraints weight = 11811.629|
|-----------------------------------------------------------------------------|
r_work (start): 0.4077 rms_B_bonded: 3.18
r_work: 0.3944 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3944
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6664
moved from start:          0.1923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   8076  Z= 0.124
  Angle     :  0.578   8.809  10958  Z= 0.283
  Chirality :  0.042   0.144   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.173  28.217   1079
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.79 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.69 %
    Favored  : 81.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.84 (0.26), residues: 1005
  helix:  1.46 (0.24), residues: 439
  sheet: -0.58 (0.53), residues: 93
  loop :  0.04 (0.29), residues: 473

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 784 
 HIS   0.004   0.001   HIS A 874 
 PHE   0.025   0.001   PHE A 249 
 TYR   0.017   0.001   TYR A 807 
 ARG   0.003   0.000   ARG A 632 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03950 (  399)
  hydrogen bonds       : angle       4.57661 ( 1152)
  covalent geometry    : bond        0.00279 ( 8076)
  covalent geometry    : angle       0.57826 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  193 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 169
  time to evaluate  : 0.819 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7307 (pm20) cc_final: 0.7024 (pm20)
REVERT: A  219 GLU cc_start: 0.8334 (tt0) cc_final: 0.7258 (mt-10)
REVERT: A  283 GLN cc_start: 0.6817 (tp40) cc_final: 0.6474 (tp40)
REVERT: A  302 GLN cc_start: 0.6337 (OUTLIER) cc_final: 0.5895 (tt0)
REVERT: A  336 CYS cc_start: 0.8205 (p) cc_final: 0.7996 (p)
REVERT: A  391 VAL cc_start: 0.6484 (m) cc_final: 0.5998 (p)
REVERT: A  416 ARG cc_start: 0.7445 (mtm-85) cc_final: 0.7181 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7574 (ttmm) cc_final: 0.7359 (ttmm)
REVERT: A  480 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6518 (mm-30)
REVERT: A  653 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7652 (p)
REVERT: A  740 SER cc_start: 0.8101 (t) cc_final: 0.7827 (t)
REVERT: A  826 GLN cc_start: 0.7283 (tp40) cc_final: 0.7027 (tp40)
REVERT: A 1008 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6882 (mm-30)
  outliers start: 24
  outliers final: 12
  residues processed: 184
  average time/residue: 0.2072
  time to fit residues: 51.2659
Evaluate side-chains
  180 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 165
  time to evaluate  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  533 ASN
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 25 optimal weight:    0.9980
   chunk 57 optimal weight:    2.9990
   chunk 40 optimal weight:    0.9980
   chunk 3 optimal weight:    8.9990
   chunk 13 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 94 optimal weight:    2.9990
   chunk 34 optimal weight:    0.7980
   chunk 44 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
A1065 HIS
A1131 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4338 r_free = 0.4338 target = 0.176059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4060 r_free = 0.4060 target = 0.151656 restraints weight = 11883.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.4048 rms_B_bonded: 3.16
r_work: 0.3911 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3911
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6729
moved from start:          0.1938

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   8076  Z= 0.198
  Angle     :  0.627   8.732  10958  Z= 0.309
  Chirality :  0.044   0.152   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.348  30.191   1079
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.99 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.27 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    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:  0.62 (0.26), residues: 1005
  helix:  1.19 (0.24), residues: 440
  sheet: -0.55 (0.53), residues: 98
  loop : -0.00 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 784 
 HIS   0.006   0.001   HIS A 833 
 PHE   0.025   0.002   PHE A 249 
 TYR   0.017   0.002   TYR A 807 
 ARG   0.006   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04452 (  399)
  hydrogen bonds       : angle       4.62496 ( 1152)
  covalent geometry    : bond        0.00447 ( 8076)
  covalent geometry    : angle       0.62715 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 168
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 GLU cc_start: 0.8352 (tt0) cc_final: 0.7140 (mt-10)
REVERT: A  237 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8535 (tt)
REVERT: A  264 TYR cc_start: 0.6877 (m-80) cc_final: 0.6587 (m-80)
REVERT: A  300 MET cc_start: 0.6661 (tpt) cc_final: 0.6403 (tpt)
REVERT: A  302 GLN cc_start: 0.6248 (OUTLIER) cc_final: 0.5830 (tt0)
REVERT: A  336 CYS cc_start: 0.8239 (p) cc_final: 0.8016 (p)
REVERT: A  391 VAL cc_start: 0.6464 (m) cc_final: 0.5967 (p)
REVERT: A  416 ARG cc_start: 0.7459 (mtm-85) cc_final: 0.7188 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7640 (ttmm) cc_final: 0.7420 (ttmm)
REVERT: A  480 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6559 (mm-30)
REVERT: A  511 LEU cc_start: 0.6909 (mp) cc_final: 0.6641 (mt)
REVERT: A  634 SER cc_start: 0.7316 (p) cc_final: 0.7038 (m)
REVERT: A  653 VAL cc_start: 0.8007 (OUTLIER) cc_final: 0.7661 (p)
REVERT: A  740 SER cc_start: 0.8054 (t) cc_final: 0.7699 (t)
REVERT: A  826 GLN cc_start: 0.7300 (tp40) cc_final: 0.7035 (tp40)
REVERT: A 1000 TYR cc_start: 0.8307 (m-80) cc_final: 0.7979 (m-80)
REVERT: A 1110 MET cc_start: 0.7961 (tpp) cc_final: 0.7267 (ttm)
  outliers start: 30
  outliers final: 17
  residues processed: 184
  average time/residue: 0.2130
  time to fit residues: 53.1195
Evaluate side-chains
  183 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 163
  time to evaluate  : 0.791 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 LEU
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  339 LEU
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  477 LEU
Chi-restraints excluded: chain A residue  481 CYS
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1131 ASN
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 31 optimal weight:    0.0870
   chunk 58 optimal weight:    0.9980
   chunk 89 optimal weight:    4.9990
   chunk 18 optimal weight:    7.9990
   chunk 83 optimal weight:    0.9990
   chunk 7 optimal weight:    0.8980
   chunk 94 optimal weight:    2.9990
   chunk 37 optimal weight:    0.0970
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    6.9990
   overall best weight:    0.5956

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

Flipped N/Q/H residues before XYZ refinement:
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
A1002 GLN
A1065 HIS
A1131 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.178227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4084 r_free = 0.4084 target = 0.153766 restraints weight = 11951.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.4073 rms_B_bonded: 3.20
r_work: 0.3937 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3937
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6674
moved from start:          0.2151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8076  Z= 0.123
  Angle     :  0.593   8.085  10958  Z= 0.290
  Chirality :  0.042   0.185   1272
  Planarity :  0.005   0.097   1389
  Dihedral  :  4.197  28.475   1079
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.89 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.27 %
    Favored  : 80.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1005
  helix:  1.52 (0.24), residues: 433
  sheet: -0.66 (0.53), residues: 93
  loop :  0.02 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A1065 
 PHE   0.025   0.001   PHE A 249 
 TYR   0.015   0.001   TYR A 807 
 ARG   0.002   0.000   ARG A 552 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03945 (  399)
  hydrogen bonds       : angle       4.51713 ( 1152)
  covalent geometry    : bond        0.00281 ( 8076)
  covalent geometry    : angle       0.59256 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 167
  time to evaluate  : 0.774 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 TYR cc_start: 0.6829 (m-80) cc_final: 0.6550 (m-80)
REVERT: A  302 GLN cc_start: 0.6316 (OUTLIER) cc_final: 0.5865 (tt0)
REVERT: A  336 CYS cc_start: 0.8165 (p) cc_final: 0.7951 (p)
REVERT: A  391 VAL cc_start: 0.6305 (m) cc_final: 0.4918 (t)
REVERT: A  416 ARG cc_start: 0.7446 (mtm-85) cc_final: 0.7191 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7556 (ttmm) cc_final: 0.7345 (ttmm)
REVERT: A  480 GLU cc_start: 0.6861 (mm-30) cc_final: 0.6560 (mm-30)
REVERT: A  634 SER cc_start: 0.7255 (p) cc_final: 0.7034 (m)
REVERT: A  653 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7675 (p)
REVERT: A  740 SER cc_start: 0.8030 (t) cc_final: 0.7739 (t)
REVERT: A  826 GLN cc_start: 0.7267 (tp40) cc_final: 0.6998 (tp40)
REVERT: A  987 MET cc_start: 0.6906 (tpp) cc_final: 0.6630 (mpp)
REVERT: A 1110 MET cc_start: 0.7816 (tpp) cc_final: 0.7288 (ttm)
  outliers start: 30
  outliers final: 19
  residues processed: 183
  average time/residue: 0.2022
  time to fit residues: 50.0536
Evaluate side-chains
  181 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 160
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  557 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  705 LYS
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1131 ASN
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 76 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 25 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 52 optimal weight:    5.9990
   chunk 18 optimal weight:    7.9990
   chunk 71 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9990
   chunk 42 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
A1065 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.178242 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.153668 restraints weight = 11987.504|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 3.21
r_work: 0.3927 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6694
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8076  Z= 0.138
  Angle     :  0.609   8.921  10958  Z= 0.297
  Chirality :  0.044   0.214   1272
  Planarity :  0.005   0.097   1389
  Dihedral  :  4.191  28.889   1079
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.79 %
    Favored  : 97.11 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.53 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.26), residues: 1005
  helix:  1.49 (0.24), residues: 433
  sheet: -0.74 (0.52), residues: 93
  loop : -0.02 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A1065 
 PHE   0.012   0.001   PHE A1012 
 TYR   0.025   0.001   TYR A 807 
 ARG   0.007   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03989 (  399)
  hydrogen bonds       : angle       4.49405 ( 1152)
  covalent geometry    : bond        0.00314 ( 8076)
  covalent geometry    : angle       0.60888 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 165
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 TYR cc_start: 0.6876 (m-80) cc_final: 0.6592 (m-80)
REVERT: A  283 GLN cc_start: 0.6860 (tp40) cc_final: 0.6522 (tp40)
REVERT: A  300 MET cc_start: 0.6474 (OUTLIER) cc_final: 0.5994 (tpt)
REVERT: A  302 GLN cc_start: 0.6226 (OUTLIER) cc_final: 0.5801 (tt0)
REVERT: A  336 CYS cc_start: 0.8202 (p) cc_final: 0.7969 (p)
REVERT: A  391 VAL cc_start: 0.6278 (m) cc_final: 0.4951 (t)
REVERT: A  416 ARG cc_start: 0.7450 (mtm-85) cc_final: 0.7192 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7594 (ttmm) cc_final: 0.7382 (ttmm)
REVERT: A  469 ASP cc_start: 0.7550 (t0) cc_final: 0.7345 (t0)
REVERT: A  480 GLU cc_start: 0.6842 (mm-30) cc_final: 0.6516 (mm-30)
REVERT: A  700 GLN cc_start: 0.7370 (OUTLIER) cc_final: 0.6930 (tp40)
REVERT: A  740 SER cc_start: 0.8011 (t) cc_final: 0.7723 (t)
REVERT: A  826 GLN cc_start: 0.7313 (tp40) cc_final: 0.7046 (tp40)
REVERT: A  987 MET cc_start: 0.6908 (tpp) cc_final: 0.6625 (mpp)
REVERT: A 1110 MET cc_start: 0.7771 (tpp) cc_final: 0.7412 (ttm)
  outliers start: 25
  outliers final: 16
  residues processed: 178
  average time/residue: 0.2119
  time to fit residues: 51.0197
Evaluate side-chains
  180 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 161
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  383 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  700 GLN
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 89 optimal weight:    6.9990
   chunk 97 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 74 optimal weight:    2.9990
   chunk 63 optimal weight:    0.9980
   chunk 45 optimal weight:    6.9990
   chunk 83 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 24 optimal weight:    5.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1065 HIS
A1131 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.178283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4078 r_free = 0.4078 target = 0.153665 restraints weight = 12059.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 3.23
r_work: 0.3929 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3929
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6690
moved from start:          0.2307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8076  Z= 0.136
  Angle     :  0.611   9.737  10958  Z= 0.298
  Chirality :  0.043   0.193   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.173  28.185   1079
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.69 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.75 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.26), residues: 1005
  helix:  1.53 (0.24), residues: 433
  sheet: -0.74 (0.53), residues: 93
  loop : -0.05 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 784 
 HIS   0.006   0.001   HIS A1065 
 PHE   0.023   0.001   PHE A 249 
 TYR   0.020   0.001   TYR A 807 
 ARG   0.010   0.000   ARG A1042 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03965 (  399)
  hydrogen bonds       : angle       4.46678 ( 1152)
  covalent geometry    : bond        0.00308 ( 8076)
  covalent geometry    : angle       0.61079 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 163
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 TYR cc_start: 0.6900 (m-80) cc_final: 0.6606 (m-80)
REVERT: A  283 GLN cc_start: 0.6857 (tp40) cc_final: 0.6506 (tp40)
REVERT: A  300 MET cc_start: 0.6553 (OUTLIER) cc_final: 0.6114 (tpt)
REVERT: A  302 GLN cc_start: 0.6210 (OUTLIER) cc_final: 0.5798 (tt0)
REVERT: A  336 CYS cc_start: 0.8197 (p) cc_final: 0.7972 (p)
REVERT: A  391 VAL cc_start: 0.6303 (m) cc_final: 0.5761 (p)
REVERT: A  416 ARG cc_start: 0.7446 (mtm-85) cc_final: 0.7186 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7603 (ttmm) cc_final: 0.7389 (ttmm)
REVERT: A  469 ASP cc_start: 0.7552 (t0) cc_final: 0.7336 (t0)
REVERT: A  480 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6564 (mm-30)
REVERT: A  700 GLN cc_start: 0.7375 (OUTLIER) cc_final: 0.6968 (tp40)
REVERT: A  740 SER cc_start: 0.8005 (t) cc_final: 0.7737 (t)
REVERT: A  826 GLN cc_start: 0.7309 (tp40) cc_final: 0.7042 (tp40)
REVERT: A  987 MET cc_start: 0.6916 (tpp) cc_final: 0.6617 (mpp)
REVERT: A 1110 MET cc_start: 0.7721 (tpp) cc_final: 0.7411 (ttm)
  outliers start: 25
  outliers final: 19
  residues processed: 176
  average time/residue: 0.2052
  time to fit residues: 48.7908
Evaluate side-chains
  179 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.800 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  700 GLN
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1131 ASN
Chi-restraints excluded: chain A residue 1162 LEU
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 97 optimal weight:    8.9990
   chunk 50 optimal weight:    5.9990
   chunk 74 optimal weight:    0.9980
   chunk 27 optimal weight:    3.9990
   chunk 6 optimal weight:    6.9990
   chunk 93 optimal weight:    0.2980
   chunk 69 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 19 optimal weight:   10.0000
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 986 GLN
A1065 HIS
A1131 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4357 r_free = 0.4357 target = 0.177182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.152785 restraints weight = 11886.992|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 3.17
r_work: 0.3934 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6685
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8076  Z= 0.138
  Angle     :  0.626  11.136  10958  Z= 0.304
  Chirality :  0.043   0.175   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.189  28.685   1079
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 17.30 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.79 (0.26), residues: 1005
  helix:  1.52 (0.24), residues: 433
  sheet: -0.75 (0.53), residues: 93
  loop : -0.05 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 784 
 HIS   0.007   0.001   HIS A 874 
 PHE   0.014   0.001   PHE A 450 
 TYR   0.020   0.001   TYR A 807 
 ARG   0.012   0.000   ARG A1042 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03997 (  399)
  hydrogen bonds       : angle       4.48517 ( 1152)
  covalent geometry    : bond        0.00313 ( 8076)
  covalent geometry    : angle       0.62638 (10958)

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

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

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2010 Ramachandran restraints generated.
    1005 Oldfield, 0 Emsley, 1005 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 156
  time to evaluate  : 0.820 
Fit side-chains
REVERT: A  264 TYR cc_start: 0.6882 (m-80) cc_final: 0.6591 (m-80)
REVERT: A  300 MET cc_start: 0.6544 (OUTLIER) cc_final: 0.6115 (tpt)
REVERT: A  302 GLN cc_start: 0.6207 (OUTLIER) cc_final: 0.5796 (tt0)
REVERT: A  336 CYS cc_start: 0.8196 (p) cc_final: 0.7967 (p)
REVERT: A  360 MET cc_start: 0.4923 (mmp) cc_final: 0.4159 (mmp)
REVERT: A  391 VAL cc_start: 0.6260 (m) cc_final: 0.5710 (p)
REVERT: A  416 ARG cc_start: 0.7429 (mtm-85) cc_final: 0.7169 (mtm-85)
REVERT: A  425 LYS cc_start: 0.7595 (ttmm) cc_final: 0.7381 (ttmm)
REVERT: A  469 ASP cc_start: 0.7560 (t0) cc_final: 0.7346 (t0)
REVERT: A  480 GLU cc_start: 0.6872 (mm-30) cc_final: 0.6565 (mm-30)
REVERT: A  592 LYS cc_start: 0.8285 (mmmt) cc_final: 0.7840 (mmmt)
REVERT: A  700 GLN cc_start: 0.7416 (OUTLIER) cc_final: 0.7002 (tp40)
REVERT: A  740 SER cc_start: 0.7991 (t) cc_final: 0.7718 (t)
REVERT: A  826 GLN cc_start: 0.7295 (tp40) cc_final: 0.7032 (tp40)
REVERT: A  987 MET cc_start: 0.6922 (tpp) cc_final: 0.6647 (mpp)
  outliers start: 27
  outliers final: 22
  residues processed: 169
  average time/residue: 0.2066
  time to fit residues: 47.6591
Evaluate side-chains
  180 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 155
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  253 CYS
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  300 MET
Chi-restraints excluded: chain A residue  302 GLN
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
Chi-restraints excluded: chain A residue  545 VAL
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  598 VAL
Chi-restraints excluded: chain A residue  653 VAL
Chi-restraints excluded: chain A residue  700 GLN
Chi-restraints excluded: chain A residue  721 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  807 TYR
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue  955 SER
Chi-restraints excluded: chain A residue 1007 LEU
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain A residue 1010 VAL
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1067 LEU
Chi-restraints excluded: chain A residue 1131 ASN
Chi-restraints excluded: chain A residue 1162 LEU
Chi-restraints excluded: chain A residue 1165 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 4 optimal weight:   10.0000
   chunk 32 optimal weight:    0.9980
   chunk 93 optimal weight:    0.0980
   chunk 20 optimal weight:    0.0010
   chunk 71 optimal weight:    0.0770
   chunk 96 optimal weight:    2.9990
   chunk 13 optimal weight:    0.9990
   chunk 54 optimal weight:    4.9990
   chunk 56 optimal weight:    0.4980
   chunk 67 optimal weight:    0.0040
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.1356

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

Flipped N/Q/H residues before XYZ refinement:
** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 533 ASN
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 818 HIS
A1065 HIS
A1131 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.180871 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.156202 restraints weight = 12013.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.4099 rms_B_bonded: 3.25
r_work: 0.3965 rms_B_bonded: 3.77 restraints_weight: 0.5000
r_work (final): 0.3965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.2626

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   8076  Z= 0.112
  Angle     :  0.620  10.892  10958  Z= 0.303
  Chirality :  0.043   0.162   1272
  Planarity :  0.005   0.097   1389
  Dihedral  :  4.045  26.641   1079
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.09 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 17.75 %
    Favored  : 79.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.85 (0.26), residues: 1005
  helix:  1.69 (0.24), residues: 433
  sheet: -0.89 (0.49), residues: 103
  loop : -0.07 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 600 
 HIS   0.009   0.001   HIS A1065 
 PHE   0.021   0.001   PHE A 249 
 TYR   0.018   0.001   TYR A 807 
 ARG   0.004   0.000   ARG A 702 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03650 (  399)
  hydrogen bonds       : angle       4.45976 ( 1152)
  covalent geometry    : bond        0.00242 ( 8076)
  covalent geometry    : angle       0.61967 (10958)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3664.30 seconds
wall clock time: 63 minutes 39.96 seconds (3819.96 seconds total)