Starting phenix.real_space_refine
on Wed Sep 17 09:50:26 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbr_61323/09_2025/9jbr_61323.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbr_61323/09_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_61323/09_2025/9jbr_61323.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbr_61323/09_2025/9jbr_61323.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbr_61323/09_2025/9jbr_61323.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbr_61323/09_2025/9jbr_61323.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.08, per 1000 atoms: 0.26
  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: 0.58
  Conformation dependent library (CDL) restraints added in 465.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.56
  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: 1.53

  Time building geometry restraints manager: 0.85 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:             1.230
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     9.810
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.500
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.010   0.001   ARG A 216 
 TYR   0.018   0.002   TYR A1071 
 PHE   0.020   0.002   PHE A 664 
 TRP   0.016   0.002   TRP A 600 
 HIS   0.009   0.002   HIS A 874 

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

*********************** 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  : 0.328 
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: 0.0940
  time to fit residues: 21.5647
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  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 49 optimal weight:    0.1980
   chunk 97 optimal weight:    0.0670
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.5980
   chunk 65 optimal weight:    6.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.6980
   overall best weight:    0.4518

-------------------------------------------------------------------------------
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**
** 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 = 0.4372 r_free = 0.4372 target = 0.178588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.154210 restraints weight = 11933.795|
|-----------------------------------------------------------------------------|
r_work (start): 0.4090 rms_B_bonded: 3.21
r_work: 0.3949 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3949
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6670
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   8076  Z= 0.138
  Angle     :  0.608   7.954  10958  Z= 0.311
  Chirality :  0.043   0.162   1272
  Planarity :  0.005   0.098   1389
  Dihedral  :  4.528  30.964   1079
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.29 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  9.16 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.89 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.60 (0.25), residues: 1005
  helix:  1.11 (0.24), residues: 438
  sheet: -0.26 (0.51), residues: 104
  loop : -0.02 (0.28), residues: 463

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 310 
 TYR   0.013   0.001   TYR A 413 
 PHE   0.020   0.001   PHE A 664 
 TRP   0.009   0.001   TRP A 257 
 HIS   0.005   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00292 ( 8076)
  covalent geometry    : angle       0.60824 (10958)
  hydrogen bonds       : bond        0.04712 (  399)
  hydrogen bonds       : angle       5.28253 ( 1152)

*********************** 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
  174 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 164
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7454 (pm20) cc_final: 0.7236 (pm20)
REVERT: A  219 GLU cc_start: 0.8365 (tt0) cc_final: 0.7029 (mt-10)
REVERT: A  237 LEU cc_start: 0.8802 (mt) cc_final: 0.8569 (tt)
REVERT: A  425 LYS cc_start: 0.7561 (ttmm) cc_final: 0.7353 (ttmm)
REVERT: A  480 GLU cc_start: 0.7089 (mm-30) cc_final: 0.6670 (mm-30)
REVERT: A  511 LEU cc_start: 0.6864 (mp) cc_final: 0.6593 (mt)
REVERT: A  658 GLU cc_start: 0.7431 (tp30) cc_final: 0.7205 (tp30)
REVERT: A 1056 LEU cc_start: 0.7793 (tp) cc_final: 0.7555 (tp)
  outliers start: 10
  outliers final: 6
  residues processed: 166
  average time/residue: 0.0953
  time to fit residues: 21.2817
Evaluate side-chains
  167 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 161
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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 91 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 45 optimal weight:    0.1980
   chunk 28 optimal weight:    0.1980
   chunk 79 optimal weight:    2.9990
   chunk 63 optimal weight:    0.5980
   chunk 81 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 99 optimal weight:    0.7980
   chunk 52 optimal weight:    8.9990
   chunk 77 optimal weight:    3.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4370 r_free = 0.4370 target = 0.178631 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.154449 restraints weight = 11823.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.4081 rms_B_bonded: 3.19
r_work: 0.3947 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6658
moved from start:          0.1603

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= 0.122
  Angle     :  0.571   7.176  10958  Z= 0.286
  Chirality :  0.042   0.157   1272
  Planarity :  0.005   0.098   1389
  Dihedral  :  4.276  29.198   1079
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.69 %
    Favored  : 97.21 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.60 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.26), residues: 1005
  helix:  1.37 (0.24), residues: 440
  sheet: -0.49 (0.52), residues: 98
  loop :  0.05 (0.28), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 632 
 TYR   0.012   0.001   TYR A 413 
 PHE   0.023   0.001   PHE A 249 
 TRP   0.006   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 8076)
  covalent geometry    : angle       0.57092 (10958)
  hydrogen bonds       : bond        0.04210 (  399)
  hydrogen bonds       : angle       4.91775 ( 1152)

*********************** 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
  181 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 171
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 GLU cc_start: 0.8365 (tt0) cc_final: 0.7116 (mt-10)
REVERT: A  237 LEU cc_start: 0.8740 (mt) cc_final: 0.8505 (tt)
REVERT: A  425 LYS cc_start: 0.7578 (ttmm) cc_final: 0.7362 (ttmm)
REVERT: A  480 GLU cc_start: 0.6970 (mm-30) cc_final: 0.6727 (mm-30)
REVERT: A  577 LEU cc_start: 0.8503 (mt) cc_final: 0.8223 (mt)
REVERT: A  592 LYS cc_start: 0.8458 (mmmt) cc_final: 0.8089 (mmmt)
REVERT: A  653 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7626 (p)
REVERT: A  658 GLU cc_start: 0.7347 (tp30) cc_final: 0.7071 (tp30)
REVERT: A  725 LEU cc_start: 0.7905 (mp) cc_final: 0.7692 (mp)
REVERT: A  987 MET cc_start: 0.6843 (tpp) cc_final: 0.6623 (mpp)
REVERT: A 1056 LEU cc_start: 0.7861 (tp) cc_final: 0.7646 (tp)
REVERT: A 1110 MET cc_start: 0.7914 (tpp) cc_final: 0.7467 (mtt)
  outliers start: 10
  outliers final: 5
  residues processed: 175
  average time/residue: 0.1001
  time to fit residues: 23.4418
Evaluate side-chains
  169 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 163
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  578 MET
Chi-restraints excluded: chain A residue  653 VAL
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 60 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 39 optimal weight:    0.2980
   chunk 79 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 5 optimal weight:    2.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4370 r_free = 0.4370 target = 0.178811 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.154090 restraints weight = 11969.154|
|-----------------------------------------------------------------------------|
r_work (start): 0.4070 rms_B_bonded: 3.23
r_work: 0.3934 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3934
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6684
moved from start:          0.1749

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= 0.137
  Angle     :  0.581   7.828  10958  Z= 0.288
  Chirality :  0.042   0.178   1272
  Planarity :  0.005   0.097   1389
  Dihedral  :  4.222  29.437   1079
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 9.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.89 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 13.86 %
    Favored  : 83.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.81 (0.26), residues: 1005
  helix:  1.41 (0.24), residues: 439
  sheet: -0.62 (0.53), residues: 98
  loop :  0.07 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 632 
 TYR   0.019   0.001   TYR A 807 
 PHE   0.025   0.001   PHE A 249 
 TRP   0.006   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 8076)
  covalent geometry    : angle       0.58137 (10958)
  hydrogen bonds       : bond        0.04158 (  399)
  hydrogen bonds       : angle       4.71284 ( 1152)

*********************** 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
  181 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 162
  time to evaluate  : 0.321 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7461 (pm20) cc_final: 0.7130 (pm20)
REVERT: A  219 GLU cc_start: 0.8358 (tt0) cc_final: 0.6996 (mt-10)
REVERT: A  425 LYS cc_start: 0.7590 (ttmm) cc_final: 0.7372 (ttmm)
REVERT: A  480 GLU cc_start: 0.6936 (mm-30) cc_final: 0.6586 (mm-30)
REVERT: A  653 VAL cc_start: 0.7997 (OUTLIER) cc_final: 0.7628 (p)
REVERT: A  725 LEU cc_start: 0.7944 (mp) cc_final: 0.7717 (mp)
REVERT: A  740 SER cc_start: 0.8045 (t) cc_final: 0.7775 (t)
  outliers start: 19
  outliers final: 12
  residues processed: 172
  average time/residue: 0.0962
  time to fit residues: 22.4401
Evaluate side-chains
  174 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 161
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
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  721 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 1023 LEU
Chi-restraints excluded: chain A residue 1069 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 14 optimal weight:    2.9990
   chunk 59 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 50 optimal weight:    3.9990
   chunk 66 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   chunk 35 optimal weight:    0.0470
   chunk 99 optimal weight:    5.9990
   chunk 17 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.1082

-------------------------------------------------------------------------------
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 = 0.4356 r_free = 0.4356 target = 0.177745 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4080 r_free = 0.4080 target = 0.153330 restraints weight = 11850.639|
|-----------------------------------------------------------------------------|
r_work (start): 0.4063 rms_B_bonded: 3.20
r_work: 0.3921 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3921
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6710
moved from start:          0.1817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8076  Z= 0.156
  Angle     :  0.588   8.887  10958  Z= 0.291
  Chirality :  0.042   0.146   1272
  Planarity :  0.005   0.095   1389
  Dihedral  :  4.258  28.912   1079
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 10.59
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.08 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 15.81 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.76 (0.26), residues: 1005
  helix:  1.36 (0.24), residues: 439
  sheet: -0.67 (0.53), residues: 98
  loop :  0.06 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 416 
 TYR   0.018   0.001   TYR A 807 
 PHE   0.025   0.001   PHE A 249 
 TRP   0.007   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A 874 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 ( 8076)
  covalent geometry    : angle       0.58793 (10958)
  hydrogen bonds       : bond        0.04233 (  399)
  hydrogen bonds       : angle       4.62817 ( 1152)

*********************** 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
  192 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 168
  time to evaluate  : 0.341 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 GLU cc_start: 0.8360 (tt0) cc_final: 0.7007 (mt-10)
REVERT: A  237 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8518 (tt)
REVERT: A  302 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5903 (tt0)
REVERT: A  391 VAL cc_start: 0.6477 (m) cc_final: 0.5981 (p)
REVERT: A  425 LYS cc_start: 0.7606 (ttmm) cc_final: 0.7384 (ttmm)
REVERT: A  480 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6565 (mm-30)
REVERT: A  634 SER cc_start: 0.7163 (p) cc_final: 0.6912 (m)
REVERT: A  653 VAL cc_start: 0.8021 (OUTLIER) cc_final: 0.7672 (p)
REVERT: A  725 LEU cc_start: 0.7903 (mp) cc_final: 0.7630 (mp)
REVERT: A  740 SER cc_start: 0.8071 (t) cc_final: 0.7804 (t)
REVERT: A  826 GLN cc_start: 0.7337 (tp40) cc_final: 0.7075 (tp40)
  outliers start: 24
  outliers final: 13
  residues processed: 181
  average time/residue: 0.0960
  time to fit residues: 23.4723
Evaluate side-chains
  180 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 164
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
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  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
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 1023 LEU
Chi-restraints excluded: chain A residue 1069 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 78 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9990
   chunk 9 optimal weight:   10.0000
   chunk 6 optimal weight:    5.9990
   chunk 83 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.4347 r_free = 0.4347 target = 0.176776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.152197 restraints weight = 11924.871|
|-----------------------------------------------------------------------------|
r_work (start): 0.4051 rms_B_bonded: 3.19
r_work: 0.3914 rms_B_bonded: 3.67 restraints_weight: 0.5000
r_work (final): 0.3914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6720
moved from start:          0.1876

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   8076  Z= 0.175
  Angle     :  0.616   8.751  10958  Z= 0.303
  Chirality :  0.043   0.148   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.354  30.194   1079
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.89 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 16.15 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.65 (0.26), residues: 1005
  helix:  1.25 (0.24), residues: 440
  sheet: -0.73 (0.53), residues: 98
  loop :  0.03 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 702 
 TYR   0.016   0.001   TYR A 807 
 PHE   0.026   0.002   PHE A 249 
 TRP   0.007   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A 741 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 8076)
  covalent geometry    : angle       0.61589 (10958)
  hydrogen bonds       : bond        0.04336 (  399)
  hydrogen bonds       : angle       4.62984 ( 1152)

*********************** 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
  193 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 162
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7325 (pm20) cc_final: 0.7044 (pm20)
REVERT: A  219 GLU cc_start: 0.8340 (tt0) cc_final: 0.6988 (mt-10)
REVERT: A  237 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8520 (tt)
REVERT: A  300 MET cc_start: 0.6591 (tpt) cc_final: 0.6278 (tpt)
REVERT: A  302 GLN cc_start: 0.6265 (OUTLIER) cc_final: 0.5844 (tt0)
REVERT: A  391 VAL cc_start: 0.6459 (m) cc_final: 0.5951 (p)
REVERT: A  425 LYS cc_start: 0.7615 (ttmm) cc_final: 0.7404 (ttmm)
REVERT: A  480 GLU cc_start: 0.6918 (mm-30) cc_final: 0.6592 (mm-30)
REVERT: A  511 LEU cc_start: 0.6911 (mp) cc_final: 0.6648 (mt)
REVERT: A  634 SER cc_start: 0.7298 (p) cc_final: 0.7041 (m)
REVERT: A  653 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7700 (p)
REVERT: A  740 SER cc_start: 0.8090 (t) cc_final: 0.7735 (t)
REVERT: A  826 GLN cc_start: 0.7297 (tp40) cc_final: 0.7044 (tp40)
REVERT: A 1106 MET cc_start: 0.7023 (tmm) cc_final: 0.6707 (tmm)
REVERT: A 1110 MET cc_start: 0.7972 (tpp) cc_final: 0.7265 (ttm)
  outliers start: 31
  outliers final: 19
  residues processed: 178
  average time/residue: 0.0994
  time to fit residues: 23.7843
Evaluate side-chains
  184 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 162
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
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  294 MET
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 1008 GLU
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1069 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 10 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 76 optimal weight:    0.9980
   chunk 1 optimal weight:    0.3980
   chunk 44 optimal weight:    3.9990
   chunk 71 optimal weight:    2.9990
   chunk 38 optimal weight:    1.9990
   chunk 77 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 98 optimal weight:    0.3980
   chunk 24 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A 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 = 0.4362 r_free = 0.4362 target = 0.178223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.153807 restraints weight = 11961.185|
|-----------------------------------------------------------------------------|
r_work (start): 0.4072 rms_B_bonded: 3.21
r_work: 0.3936 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.2064

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= 0.124
  Angle     :  0.580   8.712  10958  Z= 0.285
  Chirality :  0.042   0.177   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.193  28.451   1079
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  3.32 %
    Allowed  : 16.61 %
    Favored  : 80.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.86 (0.26), residues: 1005
  helix:  1.54 (0.24), residues: 433
  sheet: -0.81 (0.53), residues: 93
  loop :  0.06 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 416 
 TYR   0.015   0.001   TYR A 807 
 PHE   0.024   0.001   PHE A 249 
 TRP   0.007   0.001   TRP A 784 
 HIS   0.006   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 8076)
  covalent geometry    : angle       0.57956 (10958)
  hydrogen bonds       : bond        0.03906 (  399)
  hydrogen bonds       : angle       4.51499 ( 1152)

*********************** 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
  194 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 165
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 TYR cc_start: 0.6815 (m-80) cc_final: 0.6549 (m-80)
REVERT: A  300 MET cc_start: 0.6592 (tpt) cc_final: 0.6373 (tpt)
REVERT: A  302 GLN cc_start: 0.6258 (OUTLIER) cc_final: 0.5835 (tt0)
REVERT: A  391 VAL cc_start: 0.6375 (m) cc_final: 0.5037 (t)
REVERT: A  425 LYS cc_start: 0.7524 (ttmm) cc_final: 0.7318 (ttmm)
REVERT: A  480 GLU cc_start: 0.6873 (mm-30) cc_final: 0.6590 (mm-30)
REVERT: A  633 MET cc_start: 0.7446 (tmm) cc_final: 0.6610 (tmm)
REVERT: A  653 VAL cc_start: 0.8033 (OUTLIER) cc_final: 0.7702 (p)
REVERT: A  740 SER cc_start: 0.8045 (t) cc_final: 0.7755 (t)
REVERT: A  826 GLN cc_start: 0.7281 (tp40) cc_final: 0.7009 (tp40)
REVERT: A  987 MET cc_start: 0.6892 (tpp) cc_final: 0.6619 (mpp)
  outliers start: 29
  outliers final: 16
  residues processed: 179
  average time/residue: 0.0958
  time to fit residues: 23.1744
Evaluate side-chains
  177 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 159
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  294 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  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  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 1069 LEU
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 36 optimal weight:    0.9980
   chunk 89 optimal weight:    7.9990
   chunk 43 optimal weight:    4.9990
   chunk 79 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 58 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 78 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 97 optimal weight:    0.4980
   chunk 91 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 533 ASN
A 986 GLN
A1002 GLN
A1065 HIS
A1131 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.178365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.154026 restraints weight = 11862.739|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 3.17
r_work: 0.3939 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.3939
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6677
moved from start:          0.2237

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= 0.130
  Angle     :  0.592   9.453  10958  Z= 0.291
  Chirality :  0.043   0.209   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.160  28.770   1079
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.30 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.88 (0.26), residues: 1005
  helix:  1.59 (0.24), residues: 433
  sheet: -0.81 (0.52), residues: 93
  loop :  0.04 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 702 
 TYR   0.023   0.001   TYR A 807 
 PHE   0.024   0.001   PHE A 249 
 TRP   0.013   0.001   TRP A 257 
 HIS   0.004   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00296 ( 8076)
  covalent geometry    : angle       0.59169 (10958)
  hydrogen bonds       : bond        0.03902 (  399)
  hydrogen bonds       : angle       4.45047 ( 1152)

*********************** 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
  189 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 164
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 TYR cc_start: 0.6838 (m-80) cc_final: 0.6555 (m-80)
REVERT: A  283 GLN cc_start: 0.6859 (tp40) cc_final: 0.6512 (tp40)
REVERT: A  302 GLN cc_start: 0.6329 (OUTLIER) cc_final: 0.5866 (tt0)
REVERT: A  391 VAL cc_start: 0.6251 (m) cc_final: 0.4879 (t)
REVERT: A  480 GLU cc_start: 0.6863 (mm-30) cc_final: 0.6535 (mm-30)
REVERT: A  566 GLU cc_start: 0.7034 (mp0) cc_final: 0.6833 (mp0)
REVERT: A  653 VAL cc_start: 0.8067 (OUTLIER) cc_final: 0.7701 (p)
REVERT: A  740 SER cc_start: 0.8025 (t) cc_final: 0.7745 (t)
REVERT: A  826 GLN cc_start: 0.7259 (tp40) cc_final: 0.6996 (tp40)
REVERT: A  987 MET cc_start: 0.6902 (tpp) cc_final: 0.6629 (mpp)
REVERT: A 1106 MET cc_start: 0.6913 (tmm) cc_final: 0.6563 (tmm)
REVERT: A 1110 MET cc_start: 0.7887 (tpp) cc_final: 0.7196 (ttm)
  outliers start: 25
  outliers final: 16
  residues processed: 178
  average time/residue: 0.0835
  time to fit residues: 20.3414
Evaluate side-chains
  178 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 160
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
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  383 VAL
Chi-restraints excluded: chain A residue  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
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  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 1069 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 28 optimal weight:    0.0050
   chunk 66 optimal weight:    0.8980
   chunk 62 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0170
   chunk 53 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 4 optimal weight:   10.0000
   chunk 43 optimal weight:    0.0170
   chunk 51 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   chunk 73 optimal weight:    0.6980
   overall best weight:    0.2870

-------------------------------------------------------------------------------
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 986 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4393 r_free = 0.4393 target = 0.180820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4108 r_free = 0.4108 target = 0.155985 restraints weight = 11929.252|
|-----------------------------------------------------------------------------|
r_work (start): 0.4089 rms_B_bonded: 3.24
r_work: 0.3954 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6641
moved from start:          0.2413

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= 0.113
  Angle     :  0.604  10.557  10958  Z= 0.294
  Chirality :  0.042   0.171   1272
  Planarity :  0.005   0.096   1389
  Dihedral  :  4.060  27.403   1079
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 9.21
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.29 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.87 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.26), residues: 1005
  helix:  1.75 (0.24), residues: 434
  sheet: -1.00 (0.48), residues: 103
  loop : -0.01 (0.28), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A1042 
 TYR   0.017   0.001   TYR A 807 
 PHE   0.024   0.001   PHE A 249 
 TRP   0.008   0.001   TRP A 257 
 HIS   0.006   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 8076)
  covalent geometry    : angle       0.60428 (10958)
  hydrogen bonds       : bond        0.03630 (  399)
  hydrogen bonds       : angle       4.39904 ( 1152)

*********************** 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
  184 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 164
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 TYR cc_start: 0.6870 (m-80) cc_final: 0.6588 (m-80)
REVERT: A  283 GLN cc_start: 0.6845 (tp40) cc_final: 0.6498 (tp40)
REVERT: A  300 MET cc_start: 0.6340 (OUTLIER) cc_final: 0.5768 (tpt)
REVERT: A  302 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5782 (tt0)
REVERT: A  360 MET cc_start: 0.4999 (mmp) cc_final: 0.4208 (mmp)
REVERT: A  391 VAL cc_start: 0.6025 (m) cc_final: 0.4605 (t)
REVERT: A  480 GLU cc_start: 0.6807 (mm-30) cc_final: 0.6510 (mm-30)
REVERT: A  653 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7695 (p)
REVERT: A  740 SER cc_start: 0.8076 (t) cc_final: 0.7816 (t)
REVERT: A  826 GLN cc_start: 0.7265 (tp40) cc_final: 0.6995 (tp40)
REVERT: A  874 HIS cc_start: 0.6019 (t70) cc_final: 0.5775 (t-90)
REVERT: A  987 MET cc_start: 0.6915 (tpp) cc_final: 0.6621 (mpp)
REVERT: A 1106 MET cc_start: 0.6917 (tmm) cc_final: 0.6566 (tmm)
REVERT: A 1110 MET cc_start: 0.7838 (tpp) cc_final: 0.7133 (ttm)
  outliers start: 20
  outliers final: 14
  residues processed: 175
  average time/residue: 0.0917
  time to fit residues: 21.9819
Evaluate side-chains
  175 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 158
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
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  448 ILE
Chi-restraints excluded: chain A residue  481 CYS
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  743 VAL
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1069 LEU
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 83 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   chunk 96 optimal weight:    1.9990
   chunk 77 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 85 optimal weight:    0.6980
   chunk 19 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4371 r_free = 0.4371 target = 0.178779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.153925 restraints weight = 11925.106|
|-----------------------------------------------------------------------------|
r_work (start): 0.4068 rms_B_bonded: 3.22
r_work: 0.3933 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6681
moved from start:          0.2405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   8076  Z= 0.144
  Angle     :  0.628  10.620  10958  Z= 0.306
  Chirality :  0.044   0.178   1272
  Planarity :  0.005   0.095   1389
  Dihedral  :  4.126  28.667   1079
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 18.56 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.26), residues: 1005
  helix:  1.64 (0.24), residues: 433
  sheet: -0.94 (0.48), residues: 103
  loop : -0.02 (0.28), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A1042 
 TYR   0.019   0.001   TYR A 807 
 PHE   0.023   0.001   PHE A 249 
 TRP   0.007   0.001   TRP A 784 
 HIS   0.005   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 8076)
  covalent geometry    : angle       0.62778 (10958)
  hydrogen bonds       : bond        0.03928 (  399)
  hydrogen bonds       : angle       4.46285 ( 1152)

********************** 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
  174 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A  214 GLU cc_start: 0.7583 (pm20) cc_final: 0.7274 (pm20)
REVERT: A  264 TYR cc_start: 0.6858 (m-80) cc_final: 0.6572 (m-80)
REVERT: A  283 GLN cc_start: 0.6834 (tp40) cc_final: 0.6471 (tp40)
REVERT: A  300 MET cc_start: 0.6297 (OUTLIER) cc_final: 0.5685 (tpt)
REVERT: A  302 GLN cc_start: 0.6208 (OUTLIER) cc_final: 0.5809 (tt0)
REVERT: A  360 MET cc_start: 0.4977 (mmp) cc_final: 0.4268 (mmp)
REVERT: A  391 VAL cc_start: 0.6213 (m) cc_final: 0.4833 (t)
REVERT: A  480 GLU cc_start: 0.6822 (mm-30) cc_final: 0.6529 (mm-30)
REVERT: A  658 GLU cc_start: 0.7453 (tp30) cc_final: 0.7200 (tp30)
REVERT: A  740 SER cc_start: 0.8028 (t) cc_final: 0.7768 (t)
REVERT: A  826 GLN cc_start: 0.7288 (tp40) cc_final: 0.7027 (tp40)
REVERT: A  987 MET cc_start: 0.6883 (tpp) cc_final: 0.6577 (mpp)
REVERT: A 1106 MET cc_start: 0.6990 (tmm) cc_final: 0.6644 (tmm)
REVERT: A 1110 MET cc_start: 0.7881 (tpp) cc_final: 0.7253 (ttm)
  outliers start: 18
  outliers final: 14
  residues processed: 165
  average time/residue: 0.0875
  time to fit residues: 19.9817
Evaluate side-chains
  172 residues out of total 873 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 156
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
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  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  721 VAL
Chi-restraints excluded: chain A residue  743 VAL
Chi-restraints excluded: chain A residue  867 ASN
Chi-restraints excluded: chain A residue 1008 GLU
Chi-restraints excluded: chain A residue 1023 LEU
Chi-restraints excluded: chain A residue 1069 LEU
Chi-restraints excluded: chain A residue 1162 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 100
   random chunks:
   chunk 0 optimal weight:    9.9990
   chunk 42 optimal weight:    0.0000
   chunk 8 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0470
   chunk 20 optimal weight:    0.6980
   chunk 73 optimal weight:    0.7980
   chunk 97 optimal weight:    1.9990
   chunk 23 optimal weight:    9.9990
   chunk 24 optimal weight:    0.9990
   chunk 96 optimal weight:    0.6980
   overall best weight:    0.3682

-------------------------------------------------------------------------------
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 568 HIS
** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 818 HIS
A 986 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.180382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.155559 restraints weight = 11990.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.4093 rms_B_bonded: 3.23
r_work: 0.3961 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6622
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   8076  Z= 0.112
  Angle     :  0.599  10.528  10958  Z= 0.291
  Chirality :  0.042   0.155   1272
  Planarity :  0.005   0.095   1389
  Dihedral  :  3.978  27.062   1079
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  2.29 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 18.33 %
    Favored  : 79.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.26), residues: 1005
  helix:  1.82 (0.24), residues: 433
  sheet: -0.88 (0.45), residues: 120
  loop : -0.03 (0.29), residues: 452

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 702 
 TYR   0.016   0.001   TYR A 807 
 PHE   0.015   0.001   PHE A 450 
 TRP   0.007   0.001   TRP A 257 
 HIS   0.006   0.001   HIS A1065 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8076)
  covalent geometry    : angle       0.59945 (10958)
  hydrogen bonds       : bond        0.03507 (  399)
  hydrogen bonds       : angle       4.35623 ( 1152)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1831.09 seconds
wall clock time: 32 minutes 15.24 seconds (1935.24 seconds total)